Evolution 101

The Problem of Species

2007-01-11T05:15:00.000-08:00

Part 1

Part 2

Part 3

The Female Orgasm

2006-10-29T18:51:00.000-08:00

Well, the first attempt at the Evolution 101 live broadcast was kind of a bust. I only had one person tune in to ask me a question, Scott Burger, who asked about the potential for human speciation in the context of space exploration. I don’t know if I was sufficiently able to answer his question because his internet connection kept dying on him, but the gist of my response was this: given humanity’s capability for technological adaptation, our genetic adaptation is probably going to be minimal, even once we begin to explore different planets. I would imagine that we would use our capacity for technology to replicated as best as possible Earth’s environment wherever we go, so the necessity for adaptation will probably be pretty low. There’s a more pressing distinction, however- the founder effect. If our understanding of the laws of physics don’t change dramatically before then, we’ll be faced with the very real prospect of population separation once we do begin to colonize other planets. It just isn’t physically feasible, unless something like Star Trek’s warp drive or Star Wars’ hyperdrive is invented, that allows for the travel form one planet to another in a reasonable timeframe. Otherwise, once you decide to visit a new planet, that’s it- you live there and die there, and likely you children and children’s children too. The only way to avoid that multi-generational aspect of space travel is suspended animation, like is used in 2001: A Space Odyssey. But even then, the sheer distances required to travel mean that a crew of any significant size will maintain a particular genetic sample which is for all intents distinct from the population back home on Earth. Because remember, evolution really works on populations, so once you’ve removed one population from another, so that the exchange of genetic information is stopped, there is the potential for speciation, especially if there are significant forces affecting adaptation from the environment. But this would take a long time, much longer than the 10 generations that Scott was guessing it would take.

So, anyway, that was it for the live show. Not really enough to save and podcast on it’s own, so I just reiterated my answer here. But I am going to try again next Saturday at 4:00 PM CST, so send me an email if you’re planning on showing up, otherwise I won’t waste my time.

As it happens, there’s a few good questions that I received this week that I really wanted to address here, so I’m just going to go ahead with the regular format. Also, since it’s so close to Halloween, I thought I might talk about something truly frightening- the female sexual response and evolution! But first, the questions.

Garrett and Leslie both wrote to ask about the relationship between evolution and morality. I’ve just finished reading “The God Delusion” by Richard Dawkins, and he devotes an entire chapter in that book on the subject of morality, so I would recommend that highly to anyone who finds this topic as fascinating as I do. Garrett asked if a sense of inherent morality existed in humans, and why did it arise?

I think that an inherent sense of morality does, in fact, exist within humans, and to lesser extents within other animals as well. Experiments have been performed in primates, for example, that establish a clear sense of “fairness”- if two chimpanzees are given treats separately, and one is given a banana but the other is given a carrot, but they can’t see each other, both chimps are quite content with their respective prizes. But if both chimps are in full view of the other, and the same treats are given, the chimp which is given a carrot reacts negatively to the observed inequality (obviously, a carrot is an inferior treat to a banana). In fact, the chimp who receives the carrot will, if he knows that his comrade has been given something better, refuse to eat the carrot until he is given a banana as well. So I think that this points to a genuine sense of fairness, which isn’t unremarkable if you think about it, because chimpanzees are very social creatures, and some kind of ingrained rule system would be adapatively useful to preserve the social order.

You can make the same kind of argument about humans, but since we can verbally communicate, there is the ability to discover even more subtleties about our moral convictions. And given the scientific method, you can even measure them. In his book, Dawkins relates the results of several psychological studies on morality, in which specific questions are asked in the context of hypothetical situations. For example, let’s say a train is speeding down a track, and there happen to be five people standing on the track ahead, about to be hit by the train, and with no way to save themselves. Then let’s say that you are standing at the track switcher, and can move the train from its present track to a side-track, avoiding the five people ahead. But there also happens to be a man standing on the side track, who will be assuredly killed if the tracks are switched. What is the moral course of action?

And the vast majority of people will say that it is moral to switch the tracks, because it is better to save the five people even if the one man is accidentally killed. Simple enough, but there are many different permutations of this example, each one affecting the morality of a particular choice. I won’t get into those details here, but I will say that the morality of these situations seems to be, upon asking large groups of people, under general agreement. If you want more information, then check out Dawkins’ book. But my point is not that what is right is decided based on what the majority of people think. But if there were some inherent moral sense, then we should expect to see most people coming to the same conclusions given any moral situation. And in fact the same moral responses are found whether you’re asking college psychology students, or isolated tribesmen in the Amazon- what is moral seems to be pretty well-known, even if it’s difficult for people to articulate why. This is similar to the sense of lust- an equally universal, evolutionarily-selected sense. You may not be able to explain why exactly you find a man or a woman so appealing, but you know that you do, and evolution explains it perfectly.

Ravi asked about the genetic basis for the variety of human faces. Yes, our facial features are genetically based, as are pretty much all of our physical features, like height, hair color, eye color, etc. The fact that our facial features are remarkably individualized, with similar-looking people extremely rare, (although occasionally some Dopplegangers do meet, it’s primarily a dramatic device used in movies) is likely the result of our being such visually-oriented creatures, and also highly social. But this may be just a psychological illusion- there is the clichéd phrase, “you all look alike to me” which is used commonly when a person of one race is referring to another race, whether it be a black person talking about white people, a white person talking about Asian people, or an Asian person talking about black people. Certainly other species exist, such as chimpanzees, which are highly social, but whether a chimpanzee’s face is as distinctive to a chimpanzee as a human’s face is distinctive to a human, I don’t know. There are other species, such as whales, which use sound as their primary means of identification, and we do know that different groups of whales have different “languages” when they communicate- I wouldn’t be at all surprised if a whale’s “voice” is distinctive at the individual basis as well.

Julian asked about the video game Metal Gear Solid. Yes, I have played (and beaten!) that game, and am familiar with the premise of the genetic development of “Super Soldiers.” This is a new play on the significantly older theme of eugenics, which of course we can thank the Nazis for giving such a bad reputation to. There have been other popular media incarnations that used the idea of genetically breeding super soldiers, like the X-Files and Dark Angel, to name a couple recent television shows. First of all, there’s no compelling scientific reason why a concerted effort couldn’t be put into place to breed soldier-humans. It would be no different from breeding dogs for characteristics that make them good fighters. But doing it the old-fashioned way would take hundreds, if not thousands of years, assuming a minimum generation time of twenty years. We could maybe speed things up if we knew precisely which genes conferred the desired traits, but we’re not quite there yet. It’s going to be quite a long time before we can do justice to the human genome, and as far as I know, the alleviation of human disease is much more pressing than the generation of any super soldier. One thing about Dark Angel I found amusing is the idea of transferring genes from animals into humans, based on the idea that cat DNA could make someone be able to jump as high as a cat. Sorry- the reason a cat can do what it can physically is because of the entire development of its body, not just a few choice genes. To be able to get a human to function like a cat in terms of agility, you would have to change its anatomy to a sufficient degree that it probably wouldn’t look like a human anymore, much less Jessica Alba.

And while we’re on the subject of genetics, evolution, and popular television, I want to just point out really quickly that the new show “Heroes,” while it may be a compelling drama, is about a wacky as you can possibly get in terms of understanding evolution. There’s the book that is central to the plot thus far which is called, “Activating Evolution.” Sorry- no such thing. It makes about as much sense as “Activating Gravity-“ which, given the ability of one of the characters to fly, would have a lot more to do with the plot than evolution. Simply put, this is not science fiction, this is pure fantasy- closer to the X-Men than to anything that has to do with science. If you want to see a movie that really deals with the human issues involved in the control of evolution, go see Gattaca.

And finally, something really frightening- the female orgasm. What does this have to do with Halloween? Nothing, really. But I am a little afraid of what my female listeners will say after I talk about it. I recently listened to a lecture by Dr. Elisabeth Lloyd, author of “The Case of the Female Orgasm.” She talks about the evolutionary explanation for the female orgasm, and why she thinks that male-influenced science has distorted the way that the female orgasm has been regarded by science. There is, as should be obvious, a great deal of political baggage associated with this topic. Prior to the sexual revolution, the female sexual response was barely regarded by science- any kind of sexual anomaly was regarded as simply female hysteria. Strangely enough, the first dildo (in modern times) was invented as, surprise, surprise, a remedy for this hysteria, because it seemed that troubled women became much more relaxed when, well, diddled (assuming that word has scientific merit). At that point, the only orgasm that mattered was the male orgasm, because that is what made babies, and anything else experienced by women was just unnecessary. But during the sexual revolution, the rise of feminism prompted women to claim their sexuality for themselves, at which point the female orgasm was regarded as just as important as that of the male. At this point science followed politics, as many scientists, such as Desmond Morris, began to submit evolutionary rationales for the existence of the female orgasm. But for there to be some evolutionary explanation, there had to be some kind of adaptive function that the female orgasm played that made it essential to reproduction. And therefore it was proposed that female orgasm existed to cement the pair-bond that was formed when a couple had intercourse. That in order to better care for children, a couple needed to have a strong bond, and mutual orgasms cemented this relationship. This was tempting, but unfortunately was not born out by the numbers. Most women do not have orgasms by intercourse alone, although they can induce orgasms quite easily by masturbation. So this seems to contradict the idea that female orgasms play a huge role in the psychological benefits of intercourse. Then there was the “sperm upsuck” theory, in which is was postulated that the female orgasm caused more sperm to be retained in the vagina after intercourse, and so promoted reproduction in that way. This theory actually gained some wide acclaim, but Dr. Lloyd points out that the actual experiments behind this theory were performed so unscientifically as to be completely ruled out. But the psychological damage had already been done- giving female orgasms a strong functional role to play meant that they were important, and thus not only women were concerned about them, but men too.

Dr. Lloyd suggests that female orgasms aren’t functionally important. There just isn’t any evidence to suggest that they reinforce the pair-bond, nor that they enhance sperm retention. Her conclusion is that female orgasms are just like male nipples- a shared, but inessential characteristic in one sex because in the other, they do serve a very obvious adaptive purpose. As I’ve talked before about male nipples, they occur because the development of humans follows a common path in utero before certain hormones cause males to diverge from the standard female development path. Likewise, our genitalia are based on a common form which in males becomes the penis and testicles, but in the female becomes the clitoris and ovaries. It is essential for the male orgasm to take place- otherwise, there would be no fertilization. And since the female genitals are related developmentally to the male gentials, the potential for orgasm also exists (and is tied to the clitoris, not the vagina), but exists, as Dr. Lloyd concludes, as a “happy bonus,” but not as an essential function.

The criticism that Dr. Lloyd gets is primarily from women who feel entitled to their orgasms, and feel that the dismissal of any functional purpose makes their orgasms less important, even to suggest that they shouldn’t be having them. But this is not the case- she does call it a “happy bonus,” after all. The fact that female orgasms exist because of male orgasms should be a chance for reconciliation between the sexes. After all, women wouldn’t have orgasms if it weren’t for the need of men to have them too. If you want to learn more about this, check out Dr. Lloyd’s book, “The Case of the Female Orgasm.”

Icons of Evolution

2006-09-24T19:38:00.000-07:00

Today, instead of answering your questions, I’m going to give a review of the DVD “Icons of Evolution,” which was actually produced a couple of years ago, but a friend of mine gave me a copy a while ago and so I finally got a chance to see it. This will be long enough to take up the whole podcast, so I’ll get to your questions next time.

The documentary “Icons of Evolution” is a good representative of the current argument from those who have, in the past, argued against the teaching of evolutionary theory in public schools. Although it was produced three years before the Dover trial, it’s argument amounts to essentially the “Teach the Controversy” approach which so many Evolution deniers have resorted to since that trial.

Without a doubt, it’s an effective way to frame the issue. And the documentary goes right for that from the beginning, by setting some common anti-evolutionary arguments in the context of an educator’s fight to teach “all the facts” about evolution to his students. Those of you from outside America may not be fully aware of how persuasive such an argument actually is- Americans take great pride in their freedom of speech, and the idea that any person should be able to voice their opinions on a subject, no matter what they are. They strongly believe in the concept of a marketplace of ideas, in which all points of view are, if not equally valid, at least given equal time. It’s this same mentality that, in my home city of Cincinnati, resulted in the display of a cross on Fountain Square at Christmas time, sponsored by the Ku Klux Klan. And I think, personally, that this is a mentality which should be supported- after all, what is the value of freedom if some voices are being silenced?

But this issue is not about silencing the voices of evolution deniers. There is no law that explicitly says that creationism cannot be taught in public schools- although the documentary tries its best to imply it. The educator in question whose struggle is the framing device for the documentary is Roger DeHart, who taught Biology and Earth Science at Burlington-Edison High School in Burlington, Washington. He got in trouble because, as the documentary says, he cared so much about his students that he wanted to teach them the truth about evolution. But Roger DeHart is no John Scopes. The documentary pushes very hard to cast him as the mirror image of the Tennessee teacher who was taken to trial for teaching evolutionary theory in the face of a law specifically prohibiting it. To quote from that law, the Butler Act: “that it shall be unlawful for any teacher in any of the Universities, Normals and all other public schools of the State which are supported in whole or in part by the public school funds of the State, to teach any theory that denies the story of the Divine Creation of man as taught in the Bible, and to teach instead that man has descended from a lower order of animals.” I’m sure you can see that for the argument to be made that Roger DeHart is the modern-day mirror image of John Scopes is exactly what the evolution denial position does not want to admit. You see, this law was written with an explicit Christian bias, against which the teaching of science was an infraction. But if DeHart is mirroring John Scopes, then it follows that he is against the teaching of science, and instead seeks to teach his explicit Christian bias. Of course, this would never be admitted to by either Mr. DeHart or the evolution denial groups which have sponsored this documentary. And rightly so, because I don’t think DeHart is a modern juxtaposition of John Scopes in the slightest. DeHart was not charged with any crime. He was not taken to trial. He was, however, criticized by his community for teaching a deviation of the prescribed curriculum which was recognized at that time, and has been recognized officially and legally after the fact in Dover, Pennsylvania, as a specifically religious deviation. In fact, DeHart was examined as part of the Dover proceedings, and admitted that a significant part of his evolution lesson plan was derived from the book, “Of Pandas and People,” which was found to be a clear piece of educational propaganda of the evolution denial movement, and part of the evidence which sealed the decision at Dover against evolution denial. As a matter of fact, Mr. DeHart has admitted to evolution denial, belief in a young earth of less than 100,000 years old, and instead claims that a better explanation of the facts comes from the belief in a designer. That’s right- Intelligent Design raises its head.

Suddenly this issue seems a lot less like a lone science teacher wanting to take a stand to teach the honest truth about his subject, and more like someone with an ideological axe to grind. I don’t intend here to use ad hominem criticisms of Mr. DeHart or anyone else who is involved in this issue, but it strikes me as telling that the central player in this drama just happens to be teaching a curriculum that just happens to be aligned closer to his theological position than to accepted science. And ultimately his community found that telling as well- and criticized him for preaching his theological beliefs as science in the classroom to the point where he resigned (was not fired, but resigned) from his position and eventually ended up moving to California and teaching at Oaks Christian High School, where presumably, his desire to teach Intelligent Design is not a problem.

After setting up a sympathetic context to get the audience in the mindset to favor a “teach the controversy” approach, the documentary moves on to the meat of the issue, which is essentially attempting to trash evolutionary theory. The arguments that follow are from a book by Jonathan Wells, not coincidentally titled “Icons of Evolution.” Before I address those arguments, I think something needs to be said about Wells also. Again, I don’t want to engage in ad hominem criticisms, but it can be informative to know the biases of those to whom you’re listening. For example, you should know that my sources of bias are: I am a molecular biologist, taught that evolution is a fact of reality. I’m also an atheist, and so I have no compelling theological reason to reject evolutionary theory (or any other scientific theory, for that matter, but evolution is the subject here). So that’s my bias, and you have to, as the listener, take that for what it’s worth. I don’t believe that either my scientific training nor my lack of god-belief give me a particular axe to grind in regards to evolutionary theory- in fact, I’ve said before that even when I was a Christian and before I entered college, I didn’t think twice about accepting evolutionary theory. But I think it’s significant when a person not only has potential sources of bias, but admits them as responsible for his positions outright. Jonathan Wells is a theist, and a member of the Unification Church. For those of you that aren’t familiar with this denomination, they’re frequently called the “Moonies,” because they believe that their leader, Sun Myung Moon, is the Second Coming of Jesus Christ, called by the Moonies themselves as “Father.” From Wells’ own words: At the end of the Washington Monument rally in September, 1976, I was admitted to the second entering class at Unification Theological Seminary. During the next two years, I took a long prayer walk every evening. I asked God what He wanted me to do with my life, and the answer came not only through my prayers, but also through Father's many talks to us, and through my studies. Father encouraged us to set our sights high and accomplish great things. He also spoke out against the evils in the world; among them, he frequently criticized Darwin's theory that living things originated without God's purposeful, creative activity. My studies included modern theologians who took Darwinism for granted and thus saw no room for God's involvement in nature or history; in the process, they re- interpreted the fall, the incarnation, and even God as products of human imagination. Father's words, my studies, and my prayers convinced me that I should devote my life to destroying Darwinism, just as many of my fellow Unificationists had already devoted their lives to destroying Marxism. When Father chose me (along with about a dozen other seminary graduates) to enter a Ph.D. program in 1978, I welcomed the opportunity to prepare myself for battle.”

Thus, Jonathan Wells sought out and earned a Ph.D. in molecular and cell biology at Berkeley specifically to earn the credentials he felt were necessary to attack evolutionary theory from “within.” He did, in fact, publish two peer-reviewed papers as a graduate student on the subject of frog embryo development, but nothing else. After graduating, he was placed briefly in an unpaid postdoc position by his mentor Philip Johnson of the Discovery Institute, and then moved directly into a position there. He published the book “Icons of Evolution” in 2000. And as I mentioned, it is the arguments from this book which form the bulk of the documentary. I’ll go through them now, and explain what mistakes are made in the presentation of these arguments, and what the scientific evidence actually shows.

The arguments against evolutionary theory in the documentary, as in the book, attempt to undermine certain evidences that support evolutionary theory which are considered key, or defining evidences. Wells argues that these evidences are treated as icons, hence the title of the documentary and book. The implication is that if these icons can be undermined in some way, evolutionary theory as a whole is called into question. Even if this task was achieved, of course, this wouldn’t threaten evolutionary theory in the slightest- I’ve spoken at length about the molecular evidence for evolution, which is not considered by this documentary. Given just the molecular evidence, a substantial case could be made for evolutionary theory by itself.
The first icon is Haeckel’s embryos. I won’t go into detail about this argument, because I’ve already debunked it months ago, in podcast 107. If you remember that episode, you recall that Haeckel had advanced the hypothesis that “ontogeny recapitulates phylogeny.” Evolutionary biologists have since then rejected that hypothesis, although it is worth nothing that ontogeny does organize according to phylogeny- human embryos do have “gill slits” as Haeckel drew, it’s just that they don’t turn into actual gills. Incidentally, none of my biology textbooks from college have this image in them, although they did dedicate entire sections to explaining evolution. I find it somewhat odd that these embryo drawings could be honestly considered to be an “icon” of evolution when they didn’t even factor into my biological or evolutionary education in the slightest. In fact, the first that I had ever heard about them was through being exposed to attacks on evolution from people such as Jonathan Wells. It seems that the science has long since moved past the need for Haeckel’s embryos, but the evolution deniers have not.

The second icon is Darwin’s finches. As I’ve mentioned in a previous podcast, Charles Darwin visited the Galapagos islands as part of his voyage on the H.M.S. Beagle, and although he wasn’t particularly interested in the different finch species while he was there, they did influence the development of his theory of natural selection when he had returned to England. Of particular note to Darwin was the size of the beaks of the various species, and how they correlated to the availability and size of seeds as a food source. According to Darwin, these species of finch were evidence for adaptive radiation, meaning that one finch species had been introduced to the islands at some point in the past, and the forces of natural selection among the different islands had caused speciation from that original population. What’s curious to me is that, in the documentary, no criticism is directly made against the finches themselves, the fact that their beak size changes in response to environmental changes, or even that this process can be observed. What happens is that Wells makes the argument that these changes cannot be extrapolated into actual speciation- instead, he says, it represents a kind of cyclic variation within the different populations of finches. Specifically, that since beak size changes in a way which correlates to changes in the environment, a population with a larger beak during drought reverts back to a population with a smaller beak during good rainfall. In other words, he’s making the argument that Darwin’s finches represent microevolution, and not macroevolution. Again, this is a subject that I’ve covered before, in podcast 102. There is no mechanistic difference between micro and macroevolution, just differences in scale. Beside the fact that there is a clearly observed mechanism for physiological change in the finches, morphological comparisons demonstrate that macroevolution has indeed occurred.

The documentary then moves on to the fruit fly. Fruit flies have long been used in studies of genetics because they are small, grow very fast, reproduce in large numbers, and have a small number of chromosomes. Also, the techniques for manipulating fruit fly genes have been around for a long time and are well established, so there’s a pragmatic aspect to using them as a model. In addition, they’re not vertebrates, so there’s not as much bureaucratic red tape associated with growing them in a laboratory compared to, say, mice and rats. In the documentary, the argument is made that although genetic change can be induced in the laboratory, the phenotypic results of these changes are not the kind which confer any kind of selective advantage. For example, fruit flies can be induced to grow an extra set of wings. In the documentary, these four-winged flies are shown buzzing around ineffectively, hampered by the extra, non-functional wings, and unable to survive normally, without being in the laboratory. The argument is then made that since this mutation actually makes the fruit fly’s life more difficult, then it is not a selective advantage and is not evidence for evolution. This kind of argument is typically referred to as a “straw man,” because it addresses a position not claimed by its opponent, which is roughly equivalent to picking a fight with someone, but instead of fighting them directly, building a straw dummy of that person, and then beating up the straw man. No geneticist has ever claimed to my knowledge that the mutations induced in the fruit fly in a laboratory setting have ever been an example of a speciation. That’s not why fruit flies are important, and this really troubles me about the documentary that it could take such an incorrect view of a basic model organism like the fruit fly. Fruit fly mutations aren’t important in and of themselves as an example of speciation- they’re nothing more than phenotypic markers, visible signals that show when a gene has been altered in some way. What the fruit fly has contributed is the basic understanding of genetics- by observing the frequency and heritability of the mutations that are induced, geneticists have been able to learn a great deal about how genes function in all organisms. I don’t think any geneticist actually set out to “evolve” a new species from fruit flies. That might be interesting, but not nearly as interesting as learning how genes function within organisms. So this “icon” really doesn’t support the overall argument of the documentary. Of course a four-winged fruit fly would be selected against in the wild- this explains why fruit flies have not evolved with four wings.

The documentary then moves on to the concept of antibiotic resistance in bacteria. This “icon” is kind of a mix between Darwin’s finches and the fruit fly in concept. Just as with the finches, the argument is made that selective changes revert back to a preexisting population genotype, and just as with the fruit flies, these changes are charged with not being examples of speciation. And as you would expect, the rebuttal to both these points remains the same as before, so I won’t belabor it. But briefly, the selection of bacteria by environmental condition (presence or absence of an antibiotic) is absolutely the mechanism of change that is posited by evolutionary theory- so I’m not sure what the problem is here. The fact that the bacteria lose antibiotic resistance when the antibiotic is removed from their environment isn’t an argument against evolution- it completely supports it. When any selective pressure is removed from a population, evolution is going to favor those members of the population which can reproduce best in the absence of that pressure. And when antibiotics are concerned, those bacteria which are not resistant reproduce much better, because antibiotic resistance comes at a metabolic price. And no microbiologist has ever claimed to be interested in creating new species of bacteria simply by adding or removing an antibiotic. So again, this is a straw man.

The next attack is on the concept of homology as evidence for common descent. Not homology per se, it’s pretty tough to refute the actual homology that exists between different organisms, even for a documentary as obtuse as this one. Instead, they make the argument that structures that share homology between different organisms should also share a genetic basis for that homology, if common descent is correct. They then look at the fruit fly again, and compare it to the wasp. The body segments, they say, are considered to be homologous, but instead of being controlled by the same gene, they are controlled by different genes. Thus, biologists cannot explain homologous structures that are caused by different genes. First of all, yes biologist can explain them- it’s called convergent evolution. This is the idea that selective forces experienced by different organisms are similar enough that, in certain situations, different organisms can “come up with” the same evolutionary solution to a selective problem. For example, the wings of birds and bats are an example of convergent evolution- bats did not evolve from birds, and in fact, if you go back to the nearest shared common ancestor between bats and birds, you find no wings at all. So both birds and bats evolved wings independently, as separate but very similar solutions to the problem of how to achieve powered flight. Going back to the fruit fly and wasp- this really isn’t an example of convergent evolution in my mind, but it’s awfully hard to tell, because the documentary doesn’t even give the name of the gene that supposedly is different between the two species. So there’s no way to verify if what they’re claiming is true. What I do know is that there have been several mutant genes identified in wasps which affect the development of body segmentation which are different from the mutations characterized in fruit flies, but this is no problem either, since fruit flies diverged from wasps over 200 million years ago, and we would expect some divergent evolution during that time. So once again, a straw man.

The final so-called “icon” of evolution is the “tree of life”, which is a metaphorical concept used by evolution to explain the relationships between all organisms. The argument that is used in the documentary is one that is based on a fundamental misconception of evolution that is actually pretty common among evolution deniers. The tree of life is not some kind of teleological necessity- in other words, the relationships between different organisms are not necessarily a reflection of the progression of time. That is, as time marches on, the number of species in existence does not necessarily increase. In fact, if anything, the number of species in total existence has decreased- millions upon millions of species have gone extinct over time, and species are constantly going extinct even today. So the idea that the tree of life is one which is small on one end and large on the other isn’t really an evolutionary necessity. Certainly, at some point in the history of life, the number of species was very very small. But once life was able to diversify, it did so without question, and the rest of biological history has been a refinement of that diversity, as different species compete for resources. The documentary focuses on the so-called Cambrian “explosion,” as a contradiction of its own assumptions about evolutionary history. Yes, you guessed it, another straw man. The argument says that since there were so many species in existence during the Cambrian period, and since this happened so quickly, it contradicts evolutionary theory. Well, first of all the Cambrian explosion did not happen overnight. Nor did it happen over seven days. It occurred over a range of time between 490 and 550 million years ago. And there are many explanations for the wide diversity of animal groups found within Cambrian rock, all of which are consistent with evolutionary theory. One explanation is that, it was only during the Cambrian period that organisms had evolved which contained body parts that lent themselves well to fossilization. Imagine, for example, if newspapers started to be printed on plastic sheets, instead of paper sheets. The plastic newspapers would be thrown away at about the same rate as the paper newspapers, but they wouldn’t degrade as readily. Thousands of years in the future, I could imagine a team of archaeologists unearthing a garbage dump from the early 21st century and wondering how strange it was that people suddenly started reading newspapers after the turn of the millennium. Another possibility is that environmental oxygen levels had not yet become high enough to promote the evolution of animals into any degree of complexity or diversity. Another explanation is that severe environmental and weather changes on the Earth at that time affected the chemistry of the oceans, promoting wide diversity and evolution of the organisms there. And a recent explanation involves the genes that have been characterized by Evo-Devo (which I’ve mentioned before) such as the Hox genes, which may represent the minimum requirement genetically for the development of wide diversity. It’s possible that these genes or prototype versions of these genes had developed by the Cambrian period allowing for a genetic basis of the kind of diversity seen in Cambrian fossils today.

The documentary is capped off again by an appeal to the audience’s sense of fairness, and an appeal to do the best thing for our students by teaching them the “full story” of evolution. Again, this is a strategy which has a lot of sympathy with the average person, especially here in America, but it just doesn’t hold up. I have shown here and others have shown elsewhere and much more detailed than myself that the so-called “rest of the story” that the evolution deniers want to be taught does not represent an accurate scientific argument. Are we really doing our children any favors by teaching them material in the science classroom that is demonstrably not science? Should we teach astrology to our children, to give them the “full story” about astronomy? Should we teach alchemy, to give the “full story” about chemistry? The power of science lies not just in the information that it adds to our body of knowledge, but in the information that it removes from it. Make no mistake, evolutionary theory is a scientific theory, like it or not. The only controversy that needs to be taught is the public controversy that should serve as a warning to everyone that science can and will be threatened by those who place ideology above reality.

Are There Significant Differences Between Human and Chimp Genes?

2006-09-10T21:26:00.000-07:00

Kyle- What is the evolutionary explanation for humor? Humans and other animals find things funny, sometimes debilitating so, but I have trouble seeing why and to what end.

Humor is a tricky thing to even define colloquially, let alone technically. But one such definition that I’ve heard that I think is appropriate in both contexts is that humor equals tragedy plus time, or tragedy averted. Take, for example, the classic gag of a person slipping on a banana peel. The person comes walking along, slips, and falls on their behind. The tragedy would be if that in falling, that person broke his neck and died, but this is never part of the gag. The person suffers no more than a bruised ego, and so we regard it as funny. Or you could think of it in less of a “gag” setting, and somewhat more personal. Let’s say that you’re walking down the street with some friends, and you slip on something and fall to the ground. Immediately, you’d probably expect your friends to show concern for your well-being- they are anticipating some tragedy. But you get up again, dust yourself off, and appear to be fine- at which point they start to laugh at that same specific thing that threatened you just a few seconds before, and even point out your facial expression as the thing most hilarious. So how does this make sense in evolutionary theory? Well, there has actually been a good bit of research on the origins of laughter, and there are some reasonable hypotheses out there. There is a highly detailed, but worthwhile review paper published in the December 2005 Quarterly Review of Biology, authored by Matthew Gervais and David Sloan Wilson from Binghamton University. They define classical laughter as a response a sudden unexpected change in events that is perceived to be at once not serious and in a social context. The actual physical act of laughing is homologous to the play-panting seen in other primates, and thus would be considered a pre-adaptation for the development of laughter in humans. Laughter would have become a ritualized way to spread positive emotional states within a social group in early hominids, as far back as 4 million years ago. Thus, laughter evolved as a kind of social glue in our ancestors to promote social interactions during those times in which they were not being threatened by predators, famine, or other environmental stressors. And in fact, this is still how laughter is used today- it’s still a powerful social tool, and can even be taken advantage of to lift our emotional states during times which are actually tragic.

Elias- My main problem is with how information can come to together to actually create lifeforms. How is it that DNA came to be? I know evolution doesn't deal with the origins of life, but sooner or later something has to. It all seems way too complicated to have happened by chance.

Well, first of all, there are two words here that should signal alarm bells for those of you who have been listening to this podcast from the beginning. The first is “information.” I’ll refer you to the excellent discussion of information theory in the context of evolution which was given by my good friend Ryan just a couple podcasts ago. Secondly, the word “chance.” I’ll refer you back to the “Random or nonrandom” podcast for that. Briefly, information doesn’t “create” lifeforms, and life doesn’t happen by “chance.” And, you’re right- the origins of life, or abiogenesis, are not part of evolutionary theory. However, there are several hypotheses of abiogenesis, and the one which I find most plausible is the one put forth by Richard Dawkins, in his book “The Selfish Gene.” Basically, it hinges on the concept of replication. Of all the prebiotic organic molecules which could have existed prior to the origin of life, only a few could have been able to replicate themselves. But all that is needed is for one species of molecule to be able to replicate, and then by definition it will outcompete everything else. DNA was likely a later adaptation of RNA, or something similar to RNA, since it is a more stable replication template, but RNA is still used as the sole replication medium for many kinds of viruses.

Jack- are advances in modern science slowing human evolution by enabling people who would normally be unable to reproduce, to pass on their genes; and if so, are humans going to keep evolving?

The question is: do humans need to keep evolving? If we have developed the capability to control our environment to the point where people who otherwise would be unable to live and reproduce are doing so, then there’s very little that evolution needs to do. Think for a moment- the only goal of your genes is to replicate themselves. If modern science allows for more genes to replicate, then from the perspective of evolution, that’s just fine and dandy. I think the unstated part of your question is: are we damaging ourselves, or are we precluding ourselves from becoming something better by enabling more people to pass on their genes? I think the first part of that is a serious consideration, but bear in mind that science has to be able to ameliorate that damage, or else we wouldn’t be having so many more people survive. From a moral standpoint, it’s possible that certain recessive genes are being increased in frequency which cause painful genetic diseases, but it remains the individual moral choice of the individuals who have those recessive genes to procreate. Many people, due to genetic counseling, choose not to pass on their recessive genes in the hope that they will prevent the suffering of their children. But that’s not a decision that science can force on them- it can only inform. The second part- are we preventing ourselves from becoming something better? I think this is just an X-Men fantasy. We can’t predict what the next evolutionary step will be in human development, because we can’t be sure what environmental changes will take place. Remember, evolution is driven by the adaptation to the environment. It’s quite possible that the next evolutionary step would be to lose traits- this happens in many species. Evolution is not necessarily a teleological process- there’s no evolutionary ladder. And there may be no next step at all- it could be extinction.

Steve- I am wondering why so much of the furor over evolution is dedicated to Animals and (I think mostly) Humans. Is there ever a controversy over plant life? And, I am wondering how complete the fossil record is for plants, can we see more transitional species in plant fossils? Also, do you have a suggested reading list? Maybe non-techincal books?

Humans are egotistical. We like to think of ourselves most of all, and we like to think of those animals which are more similar to us next, on and on in due order. Plants tend to be taken for granted most of the time, or at the least they don’t get as much time in the spotlight. But they have been, and are being studied. Paleobotany is the field of research which studies prehistoric plant life. There are plenty of plant fossils showing the progression of plant evolution onto land- and the molecular evidence shows that the earliest of these would have been liverworts, which are very similar to mosses in many ways, and in fact used to be classified with mosses. After these, we find plants with a true vascular structure, of which the earliest are ferns. And finally, we find seed-bearing plants, with the flowering plants being the most recently evolved of this group. As far as a suggested reading list, I think P.Z. Myers has come up with an excellent list, which you can find at his blog “Pharyngula,” but I’ll highlight some of my favorites. “Finding Darwin’s God” by Ken Miller is a great non-technical book in general, and is especially good for those who have, for whatever reason, a theological predisposition against evolution. Matt Ridley’s book “Genome” is also a pretty good read, as is anything by Richard Dawkins, particularly his most recent, “The Ancestor’s Tale.” If you’re feeling particularly intrepid, I can’t help but recommend reading Charles Darwin himself. Very few people do, but I think it adds a good perspective to read the man’s own words.

Tom- Wouldn't a genetic designer (of any kind) tend to use the same proteins/DNA sequences over and over if he or she were to modify an organism or build one from scratch? I think your argument left a hole open for the Intelligent Design crowd to walk into. Repetitive protein functionality between species could be viewed as the act of a logical and efficient "designer", be it human, God or extraterrestrial, one who repeatedly uses genetic sequences that are known to work well. -- You might comment on this perspective and also about how human genetic engineers are tinkering with evolution.

This is a tricky argument, because you’re presuming to know what intentions such a designer would have had when designing organisms. The problem is that, given the existence of such a designer, we can determine empirically what options would have been available. If you’re familiar with my series on the molecular evidence for evolution, you already know that all options would have been available. So there is no compelling reason why conserved genes would have shown similar sequences between different species. It would have been entirely possible for each species to have a completely different sequence. But the opposite is true, also. As I’ve shown before, the yeast cytochrome C gene can be replaced by the human cytochrome C gene, even though the sequences are very different. So… if a designer really wanted to be logical and efficient, it would have made all species with genes that are coded by the same sequences, since clearly they’re interchangeable. What is actually the case, however, is that species which share physiological homology also share molecular homology, and at the same amount. That is, a human shares more physiological homology with a mouse than with yeast, and it also shares more molecular homology with a mouse, even though it’s been shown that there is no molecular need for this to be. So the conclusion has to be that, if there is a designer, it has designed the genes of all organisms to indicate that they have not been designed at all.

Jase- I'm curious about how blood types came to be. I keep hearing about a 'blood type' diet and I was wondering if there is any real evolutionary support that people with different blood types should have diets that include the foods that were available in the areas that each blood type developed. Is it important enough to be considered advantageous to consume these foods for health benefits?

Although the data is not completely clear, recent research seems to suggest that blood types arose as part of the immune system. Blood type is conferred by molecules that bind to the outside of your erythrocytes, or red blood cells. These molecules are essentially made up of sugar chains that are attached to the outer membrane of the red blood cell, and are immunologically reactive. Because of this, they are considered to be antigenic, which means that the can bind to specific antibodies which will recognize their particular three-dimensional structure. The only chance they’ll have to come in contact with these antibodies is if they’re placed into a person’s body who does not have the specific blood type molecules already. For example, a person with A type molecules on their red blood cells will have antibodies against B type, but not A. And a person with B type molecules will have antibodies against A type, but not B. So if a person with B type blood receives A type blood as a donation, the anti-A antibodies will bind to the A-type blood, and do what antibodies are supposed to do, and essentially blow them up. And this is why it’s important to receive only blood that is your type. Unless you’re type AB, which means that you have neither A nor B antibodies, and can receive anybody’s blood. The opposite of this would be type O, which means that since you have neither A nor B molecules on your red blood cells, you have antibodies against each, and so you can only receive type O blood.

The reason why these specific molecules seem to have arisen through evolution is suggested in the fact that people who have either A or B molecules on their blood cells seem to be better at fighting off bacterial infections, while those who have neither seem to be better at fighting off viral infections. Because populations are burdened with bacterial and viral infections at different times, neither genotype has become the most popular, and we have a pretty good mix of the different blood types in the population today, although type A is pretty popular in most populations except among Bengalis, who favor type B. What doesn’t seem to have any weight is the notion that someone’s blood type determines what kind of diet one should eat. This is a fallacious way of thinking about genetics- there are many factors which influence how one is able to metabolize certain foods, and there is no reason to think that all of the genetic factors would associate with the gene that assigns blood type. In addition to diet, according to this blood type diet book, people with different blood types are also supposed to have specific personality traits. That just adds more complexity to the whole mess- now we’re supposed to believe that the many genetic and environmental factors that lead to the development of our personality are determined simply by the single gene that determines our blood type? This sounds like so much hogwash to me. This is classic pseudoscience- it plays on people’s general knowledge of blood type as a scientific reality, and then adds on fantastical claims that run counter to what we know about genetics, all while playing on people’s desire to have an easy solution to the problem of being too fat. My advice- eat well-balanced meals, get plenty of exercise, get advice from your physician, and try not to pay attention to the media-driven beauty ideals.

Lenny- My Brother’s local public school started to post these stickers on textbooks, what is the best organization to contact with this that would want to overturn it?

Well, the same thing happened in Georgia, as you probably know, and a federal district judge ruled that unconstitutional last year. That case was brought by the ACLU- if you want to contact them about this, they’d probably be the best bet, although I would imagine that they’re either already aware of it, or their efforts are already underway. But certainly give them a call- and write me back to let me know what progress is made.

Bonnie- I love debating science controversies with my colleagues, but one particularly religious one didn't deny evolution, but had a few reservations about it. His argument referred to why scientists can't put survival pressures on organisms in the lab to make them evolve. I know that this happens with quickly reproducing organisms like bacteria, but has anyone tried it with higher organisms? Such as making a frog fly? I'd imagine getting the funding for this sort of thing might be difficult, and take a long time. :) Do you think it's possible? And if so why hasn't it been done (or has it)?

Scientists do put survival pressures on organisms in the lab to make them evolve all the time. And in fact, there are frogs that fly already- or glide, actually. Many species of Asian tree frogs can glide from branch to branch using the extended webbing between their toes to cushion their fall, just like flying squirrels or lizards or snakes do. But if it’s real powered flight you’re after- given the reproduction rate of frogs, it’s just not something that’s feasible within even the career of one scientist. Just look at dogs- we’ve been breeding them for thousands of years, and while we’ve been able to get them to change in amazing ways, we just don’t have enough time to turn them into separate species. Not that we’ve been trying to make new species, necessarily. But that gives you some idea of the amount of time required for such large changes. But I don’t really see why you need to reproduce in the laboratory what can be verified already in nature. Frogs (or, frog-like amphibians) did evolve to fly- they’re called birds. Birds evolved from saurid reptiles, which evolved from diapsid reptiles, which evolved from early amniotic tetrapods, which split from amphibians. We don’t need to replicate this in the laboratory because we can use the fossil and molecular evidence to demonstrate that it’s already happened.

Brian- In your Molecular Evidence for Evolution #2 you said that no human and chimp gene differ by more than 3%. Please see the HAR1 gene, which is one of several HARs that differ by as much as 20%!

This was a great email, and I really wish I had some kind of prize to hand out, but I don’t, so let me just say, kudos to you, Brian! Really, well done. Yes, it’s true- I said, “Since the average primate generation is 20 years, the predicted difference between a chimpanzee gene and a human gene is less than 3%. And this is true for most other genes too- every gene that I’ve looked at, no less. In fact, I’d like to challenge anyone who’d like to disprove this evidence to find a gene that shows more than 3% difference- I’ll even do the work for you, even thought it’s easy to do by yourself.”

And HAR1 does indeed show a great deal of difference between humans and chimpanzees, in fact. I was wondering if anyone would mention this to me, since I’m pretty sure that the same article Brian read also came across my desk, although for a slightly different reason- one of the genes that interacts with HAR1 is relevant to my research. It was a recent publication- in the August 18th issue of Nature, no less, a very prestigious journal. So, in my defense, when I issued the challenge earlier this year, these genes had not yet been discovered. Also, in my defense, the difference isn’t quite so much as Brian says, but it’s a really interesting discovery anyway, and relevant to evolution, so I’ll go into it here.

As you know, human and chimpanzee genomes are incredibly similar, and in fact are more similar to each other than to any other organism, indicating that the two species split from a common ancestor. Well, it’s no big surprise to anyone listening, I hope, that despite the close similarities in our genes, humans and chimpanzees have a lot of differences. I’ve mentioned many here before, such as our conspicuous lack of body hair, but another obvious difference is our advanced intellectual capacity. It would seem to be a reasonable prediction of evolution that of the genetic differences that exist between humans and chimpanzees, a significant number of them should be in some way related to our neurological development.

Now, ten years ago, it would have been a very difficult task to find these differences. Sure, you could compare each gene one by one, but we have a lot or genes, so that would take a very long time. Now, however, the entire genome of both humans and chimpanzees has been published and is available electronically, so comparing differences is now just a matter of using the right algorithms and utilizing enough processing power. And this is exactly what was done by a collaborative effort out of UC Santa Cruz, UC Davis, and Cornell University in the United States, the University of Brussels in Belgium, and the Universite Claude Bernard in France. They went looking for regions of the human and chimpanzee genomes that showed a significant difference, and they found some. Forty-nine, to be exact. The name given to these regions is “human accelerated regions,” or HARs, which pretty much tells you that they’re different right in the name. One region stood out as much more different than the rest, and since they were numbered as ranked by difference, it is, in fact, HAR1. And yes, within a 118-base pair region, there are 18 substitutions in the human sequence as compared to the chimpanzee sequence, which is actually a 15% difference, not 20%, but it’s still a big difference compared to most other regions.

However, HAR1 is not in itself a gene, it’s a region in a gene. Two genes, actually. HAR1F and HAR1R, which both utilize the HAR1 region as part of their transcript, but are transcribed in different directions. Now, I went ahead and compared the full-length HAR1F genes in humans and chimps, and when you compare the entire gene, the difference drops down to 6.3%. But that’s still double the difference in most other genes- as it happens, most of the difference is confined to one section of the gene transcript, which gives some insight into why that large difference is meaningful. As it happens, this gene does not appear to result in the synthesis of a protein product. As you probably remember from my molecular biology primer, a protein is the ultimate result of a gene… most of the time. Remember, DNA is transcribed to RNA, which is translated into protein. If there’s no protein being made, but the gene is being transcribed, then… there has to be something being done by the RNA transcript. And the analysis of the RNA transcript shows that, in fact, there is a predicted structure formed from the RNA transcript itself, and most of the differences between the human and chimpanzee genes seem to be within this structure. It seems to be likely that this RNA structure is providing some kind of functional difference between humans and chimpanzees, and the scientists examined the expression pattern of this transcript to determine if they could find anything relevant about gene by looking at where and when it is turned on.

What they found was that this gene is activated during brain development, and is actively expressed by specific neurons crucial to cortical growth and organization. This strongly suggests that it has played an important role in the evolution of the human brain, and is one of the major genetic distinctions between humans and chimpanzees. Not surprisingly, close to a quarter of the other HAR regions were found in the noncoding regions adjacent to genes important to neurodevelopment, suggesting that they play a role in the regulation of those genes, and thus also contribute to our enhanced brains.

So, although for most of our genes, we differ only slightly from chimpanzees, the few places that do show a significant difference, not surprisingly, are places that contribute to the physiological characteristics which we already know are significantly different between our two species. This is a really cool utilization of genomics, molecular biology, and evolutionary biology, and I’m all too happy to have my challenge met.

Is Evolution Racist?

2006-08-27T16:32:00.000-07:00

Let's start with some listener email...

Christopher asked if the imperfection of the fossil record is a serious problem for evolutionary theory. In other words, since these evidences are not capable of reproduction in a laboratory setting, don’t they fall outside the aegis of actual science? Not really. You see, the scientific process is one in which observations of the natural world are necessary for the investigatory process. Experiments, especially those conducted in a laboratory setting, are used to remove as many variables as possible. But this does not mean that observations made outside the laboratory are worthless. Paleontology, which is the branch of scientific inquiry that studies prehistoric animals by examining their fossil evidence, is unable to perform variable-controlled experiments in the classical sense, but that doesn’t matter. The scientific method isn’t just observation-hypothesis-experiment-conclusion, like you probably learned in school. The purpose of the experimental component is to generate data. If your observations are about living animals, such as mice, well, then you probably can set up an experiment in the laboratory that will provide you data about that animal. But if your observations are about long-extinct animals, then the only source of data lies in the fossils that you can discover. This is why paleontologists spend so much time out in the field, whereas molecular biologists spend so much time on the laboratory bench. We’re both in search of data, but because of the differences in our focus of study, we have to find that data in different ways.

Daniel asked if much of the information about Darwin that appears in science textbooks and popular literature, such as his being hired as the naturalist on the Beagle, and his observing the finches on the Galapagos are actually apocryphal. Well, technically, Darwin was not hired as the naturalist on the Beagle. After graduation from seminary, Darwin had intended to visit the tropics with a friend in order to indulge his interest as a naturalist, but these plans fell through when his friend died. He found a berth on the Beagle because of the recommendation of his mentor, the Reverend John Henslow, but his position was not paid and it was not as a naturalist. He was the gentleman’s companion of the captain of the Beagle, and just indulged his interest in naturalism in a purely amateur capacity. This was not a typical arrangement, however, the previous captain of the Beagle had committed suicide on its preceding voyage. The new captain, FitzRoy, was worried about the loneliness of life as a captain, and requested that a companion be found for him. He had suggested finding a naturalist, since they frequently were members of voyages as passengers, in the interest of furthering their discoveries. Darwin happened to be one of the ones suggested, and the only one who agreed to them arrangement. The captain had someone interesting to talk to during dinner, and Darwin got to explore South America, the Galapogos, and Australia. Win-freaking-win. While visiting the Galapogos, it is true that Darwin didn’t really pay much attention to the finches there- he was more interested in the different species of mockingbirds on the island. However, once he had returned to England and began to formulate his theory, he realized that the finches there were an important piece of evidence, and got more information on them including better-labeled specimens from others who were on the Beagle. But the finches themselves exist, and have been studied in depth since Darwin, confirming his theory.

Gary asked about chromosomes- what makes a chromosome, how can species with different chromosome numbers interbreed? Well, if you can envision your genome, that is- the entire collection of genetic information in each cell of your body- as a library, then a chromosome would be one book in that library. We number them by size- the largest chromosome is number 1, the second-largest is number 2, and so on. Humans have 22 regular chromosomes, or autosomes, and two sex chromosomes, X and Y. In order for sexual reproduction, we carry two copies of each chromosome, with a total number of 46, except for those cells that are used in reproduction, spermatocytes or oocytes, which only have 23. Hybridization between species with different chromosome numbers is only possible for species which are closely related enough to have very similar chromosome numbers. For example, horses have 64 chromosomes, and donkeys have 62. The hybrid of the two species, the mule, has as a result 63. The reason for this, if you recall what I said about the sex cells, is that the horse contributes 32 chromosomes, and the donkey only contributes 31. 32 and 31 is 63. Since this is an odd number of chromosomes, any attempt to form sex cells in a mule will fail, because there has to be an even pairing of chromosomes for successful meiosis, and the mule will always have one extra. Other hybrids with an even number of chromosomes may be fertile, but it’s usually the female that is, according to Haldane’s Rule. This rule comes from the evolutionary biologist J.B.S. Haldane, who observed that the heterogametic sex (usually the male) is likely to be sterile or rare in a hybrid cross. The reason for this is that, certain genes which are necessary for fertility or viability will be found on the sex chromosome of one species but not another, and so when the two are mixed, the correct configurations of genes are not present. This is less of a problem for females, since they carry two copies of their sex chromosome, and thus have a built-in backup.

Jay asked about the scientific refutation of creationism. He noted that in the final installment of my series on the molecular evidence for evolution, I pointed out that the creationist response amounts to an argument from ignorance, or a “God of the Gaps” approach. However, since the creationist position itself is not a scientific claim, he wondered how I as a scientist could refute it. Well, Jay, that’s an accurate observation, and I’m in total agreement with you. Creationism is a theological position, not a scientific position, and the only basis which I use to interact with it is on those grounds. The only thing I’m interested in doing is refuting those creationists that claim either that creationism is science, or that evolutionary theory is not science. In regards to the molecular evidence, I want to make it very clear that the creationist response does not have scientific merit, and that’s it.

Steven asked about a connection between evolutionary theory and racism. This is an important question, and I want to spend the rest of the time for this podcast on the subject, particularly because a new program has been produced by Coral Ridge Ministries, called “Darwin’s Deadly Legacy.” This program is hosted by Dr. James Kennedy (a theologian, not a scientist) and features Michael Behe as the only scientist, specifically for his views on irreducible complexity, which I’ve gone over in this podcast already. The rest of the experts interviewed are those who are already famous for their rejection of evolution, such as Ann Coulter, Ken Ham, Jonathan Wells, and others.

I want to avoid any theological criticism of this program, but I’ll just point out that it seems to me that this kind of attack on evolution only seems to come from those with a theological bent against it, which I’ve mentioned before.

But what about the question at hand? Is evolution racist? Well, quite frankly, no. Racism is the position that certain races are “better” than others. This is a moral and proscriptive position, whereas evolution is a scientific and descriptive position. Evolutionary theory doesn’t make any kind of claim concerning which species are “good” or “bad.” It simply predicts that, as I’ve said many times, gene frequencies will change within a population over time. Science is a wonderful tool for explaining reality, and it can be used to inform our moral values, but it cannot generate them for us. To claim that one can do so is to invoke the naturalistic fallacy- that is, to claim that because something is natural, it is right to do. Or in other words, to transition from an “is” to an “ought.” Any person who uses scientific facts to derive their moral position in this way is thus violating logic.

That being said, there have been many instances throughout history of people committing this fallacy in regards to evolution. Firstly, it’s important to bring up the point that racism existed long before Darwin was even born. It may seem somewhat strange to realize, but racism was really more like the default position for everyone throughout the world. It just so happens, due to the circumstances of history, that Europeans have, at least in the past several hundred years, been in a unique position of power to institute their racism to a scale which was previously not possible. The rise of colonialism meant that European power extended all over the globe, whereas before each group of people were confined, more or less, to their own small geographical patch of earth.

Darwin himself would be considered racist by today’s standards, but then again, so would pretty much everyone in his society. In fact, by his own society’s standards, Darwin was less racist than most, because he believed that all humans were members of the same species, whereas many others believed that the different races were actually different species. Of course, science now demonstrates clearly that racial differences are very minor in terms of overall genetics- there is more total genetic variability among members of a particular “race” than there are between two average members of different races. The examination of gene flow among the races by comparing genetic sequences shows that there has been an incredible amount of mixing all throughout history- the pattern of descent looks less like a simple tree-branching pattern, and more like a back-and-forth ivy vine.

A pretty good analogy for the concept of race can be seen in the different breeds of domesticated animals. Humans have amplified certain traits through artificial selection to generate different breeds of dogs, for example. But is a rottweilier a “better” dog than a cocker spaniel? Is a Siamese cat “better” than a Manx? Is an Arabian horse “better” than a Thoroughbred? It makes no sense to talk this way, just as it makes no sense to talk about “races” of humans as “better” than others, especially scientifically.

But there have been people in history who have made such claims, despite the lack of scientific justification. Interestingly, the beginning of this in modern history begins not with Darwin, but precedes him in an essay written by Joseph de Gobineau titled, “On the Inequality of the Human Races.” In this essay, he divided humanity into three main races, claiming the “Aryan” race as the most powerful. This idea influenced later racist theories. Later, when evolution was gaining acceptance, it was incorporated into these racist theories to posit that some races were “more evolved” than others. This idea is obviously incorrect, and I’ve talked before on this podcast about why the idea of certain species being “more evolved” is not supported by evolutionary theory at all.

This combination of evolution with pre-existing racist social theories came to be known as “social Darwinism,” although it’s not something that was advocated for by Darwin himself, or supported by his scientific theory. As applied, social Darwinism gave rise to the practice of “eugenics,” which is a directed and artificial selective process analogous to selective breeding in animals. Not surprisingly, those in power decreed that those groups which were not in political favor were “unsuitable” genetically, and had to be removed from the breeding population. Forced sterilizations were common all over the world, actually, during this time, including here in America. It was only after the practices of eugenics by the Nazis were publicized that public support for it dried up.

Eugenics actually runs counter to evolution, as you should be able to realize by now. Evolutionary theory shows that the genetic makeup of any given population is based on the selective pressures of its environment. This is a process that is in constant flux, but one thing is certain- every organism alive today is the ultimate descendent of a very long line of winners. You, and I, and everyone listening to this podcast are the product of an ancestry of only those people who were able to successfully survive and procreate. The results of evolution then speak for themselves. As long as you survive long enough to reproduce, evolution considers you a success, no matter what color your skin may be.

But what if evolution really was racist? What if Darwin was a racist? What if Hitler really did believe he was acting in accord with evolution? This has no bearing on the truth of evolutionary theory. Those people like Dr. Kennedy who attack evolution as racist are committing a different logical fallacy- the genetic fallacy. People who commit this fallacy make the argument that the truth of an idea is based on the source of that idea. This is a well-known logical fallacy, and is usually pretty obvious because Hitler is commonly used to condemn many other things beside evolution. However, if everything Hitler advocated was a bad thing, we have to take everything else he believed in as wrong. For example, in addition to being in favor of eugenics, he supported capital punishment, gun control, and vegetarianism. Among the things he opposed were atheism, capitalism, homosexuality, and pornography. Quite a grab-bag.

All right, so let’s review. Evolution is claimed, primarily by its creationist detractors, to be racist. However, as a scientific theory, evolution makes no proscriptive moral statement. In addition, the historical promotion of racism predates evolution, and those individuals who tried to combine racism with science were doing so in defiance of what science teaches. And finally, those who attempt to condemn evolution for the evils committed by individuals throughout history are committing the genetic fallacy. So no, evolution is not racist- but I have to wonder at those people who seek to characterize it as such- isn’t there any good scientific criticism they can use? I guess not.

What is Information Theory?

2006-08-13T21:42:00.000-07:00

I received some feedback from David regarding the discussion of human nudity from last week that I thought was relevant. In addition to the explanations which I gave regarding the presence of pubic hair, he mentioned that it also functions to retain the body odors produced by the apocrine glands located in and around our genitals. These odors are relevant to sexual signaling even today, it has been reported that men can tell by sense of smell when women are the most fertile. So an additional selective pressure to retain pubic hair even as humans lost hair over the rest of our bodies, was to preserve this sex-related scent, since the presence of hair prevents secretions from evaporating quickly.

Frank writes to ask:

Can human inventions, such as the car, influence evolution? For example, if enough deer get hit by cars, and there is a tiny percentage that run away from headlights, (instead of staring into them), is it possible that some day very few deer would ever be hit by cars?

It certainly is possible for humans to influence evolutionary development, since evolution is dependent on the selective pressures of a populations’ environment, and humans are a part of the environment. This is especially evident when you look at the development of domesticated animals and plants- almost always vastly different from their closest-related wild relatives. But domestication is a kind of an accelerated evolutionary adaptation, since intentional breeding patterns are set up in just about every generation. For organisms that are still outside of direct human control, like deer, changes would be much longer in development, if at all. In the example you gave, I doubt that there would be much of a trend away from being hit by cars, since the genetic causes of that behavior are very complex. In addition, you want to look at the specific behavior in question. If there is enough of an advantage to that behavior to offset any disadvantage, then it’s unlikely that you would see a dramatic reduction. Here, the tendency of deer to cross large swaths of territory in search of food and shelter necessitates their crossing of roads. It’s conceivable that if there was a large enough disparity in the number of deer hit and killed versus those deer that successfully crossed roads, there might be enough environmental pressure to select for the best crossers, but the deer population is large enough and the percentage killed this way is small enough that I doubt this would happen.

Jason writes in to tell us,

“Apparently, there has been some research of homosexuality being potentially created by Neanderthals, who then engaged with homo erectus in sex and spread this gay disease to current man. Honestly, I've read conflicted interest on whether or not Neanderthals could have sex or even breed with homo erectus. But in the event this was true, could the changes even last this long, or affected enough people to make it a modern day problem? Fox News recently had an article of the US Government arguing how homosexuality is a mental condition, a "disease" that can be cured someday.”

First of all, homosexuality is not an infectious disease. You can’t “catch” homosexuality. Homo neanderthalensis was a prehistoric hominid, but was not a direct ancestor of modern humans. It is possible that some sexual contact between our ancestors and Neanderthals took place, but if it was it was infrequent enough not to make any impact on our genetics. Certainly homosexual contact between the two would have had no impact on our genetics whatsoever. I am aware of the classification by the United States Department of Defense citing homosexuality as an example of a mental disorder, but this seems to be just a holdover from decades ago, when this was actually the majority view. Whatever their reason for doing so, I can guarantee this has nothing to do with Neanderthal gay sex.

Brad asks:

“is the wide range of intelligence in the human species similar to what you would find in other higher mammals? I realize that intelligence levels often are reflected in the social aspects of a person...are some monkeys clearly smarter than others...do some monkeys "live" in higher-class places?”

Well, although this is a really interesting question, I don’t think that there’s much in the way of “higher-class” accommodations in the jungle. But in recent years there has been growing support for something called the Machiavellian Intelligence Hypothesis, which suggests that intelligence evolved in our ancestors as a way to better adapt to the complexities of the social order. That is, in order to keep track of social relationships and how to make the most advantage of them, essentially “playing politics,” higher intelligence was selected for. In primates of nearly all species, excluding non-social species like the orangutan, we would expect the most “intelligent” members of their population to also be the most socially cunning, and would likely be the ones with the most social power. This phenomenon is also seen quite often in the human species, as embodied by the phrase, “It’s not what you know, it’s who you know.”

Jordan asks:

“A friend of mine is wondering about mimics (in biology). I explained the basic natural selection process to him - how, if a certain physical characteristic proved reproductively beneficial that it would become more frequent, etc. But he's stuck on the "what are the odds" question, and I'm not sure how to get past that. In his example, there's an island with poisonous snakes on it that are black with yellow stripes. There's also a worm that has developed the same coloration in order to avoid becoming prey. How does this happen?”

Just think about the selective forces at work here. A classic example of mimicry is the Monarch and Viceroy butterflies. The monarch caterpillar feeds on milkweed and thus the later butterfly is bitter-tasting. The viceroy does not feed on milkweed, and thus tastes quite normal. However, both butterflies appear very similar in terms of coloration and marking. Consider this: predators experience the bitter taste of the monarch, remember its coloration, and avoid killing further monarch butterflies. Since the avoidance is based on that particular visual imagery, any other butterflies that happen to look similar to it (like the viceroy) would also be avoided by the predator, since they evoke the same visual imagery. Any members of the viceroy population that happen to look significantly different from the monarch would not evoke this avoidance, and would be eaten at the same rate as other non-bitter butterflies. Thus, the only viceroys that remain to breed are those that look more like monarchs. Over time, this mimicry was amplified, to the point where it is today. This is classic natural selection in action- and a phenomenon that is predicted by evolutionary theory.

And finally, some criticism from Susan:

“Hey, I just thought that I would say that I really thought that I would like this podcast, I believe in evolution and am very well read in evolution. But after listening too quite a few podcasts, I couldn't stand it anymore, I had to delete it. You see I believe in evolution, but I am also a Christian and couldn't take the bashing every minute in the podcast, I loved the information, but I couldn't take the slamming anymore. You see, I find no problem with believing in evolution and believing in God. I know that there are creationists that may be very outspoken with their beliefs or rather disbelief in evolution, but to say that everyone that believes in God does not believe in evolution and is uneducated in the area of evolution is a very ignorant statement. Also the conclusion that was made of the correlation between creationists and intelligent design is not true, I do not believe in intelligent design because you cannot rationalize God, because God is not science, God is a belief, so to try and put God in boundaries of science would not be true. Listening to the podcast did not teach me anything about evolution, but did teach me about how someone who is so smart in one area can be so ignorant and uninformed on another. Take for example Francis Collins, the director of the Human Genome Project, he is a Christian, but also is a Christian. You slam creationists, believing that creationism is all wrong, but what you don't mention is that evolution also has things that have been changed and holes that are still present in evolutionary theory. For a well educated person, you are very narrow minded.”

Well Susan, I’m sorry that you feel I’m bashing you, but I have never said that “everyone that believes in God does not believe in evolution.” In fact, I’ve tried to make it very clear that there are many Christians that do! Ken Miller, as I’ve mentioned before on this podcast, is a Catholic and evolutionary biologist who has written the excellent book “Finding Darwin’s God,” which is an excellent resource for anyone seeking to learn more about evolution, and especially for those who want to resolve evolution and the Christian faith. If you didn’t learn anything about evolution from this podcast, you might want to check out this book, written by a fellow Christian who believes that creationism is wrong and evolutionary theory is the only scientific explanation.

Today I want to get back to one of the questions that was posted on the old site. Grelnixar asked,

“What exactly are “information” in a pure biological sense? When speaking to creationists I often encounter analogies to digital information (which always require a designer(s)) but how accurate are these analogies? Can you give an example of observed positive genetic-information increase.”

This is an excellent question, and it’s getting at one of the common objections to evolutionary theory, which goes something like this: For evolution to take place, the genome of a species must become more complex. An increase in complexity requires an increase in information, and according to information theory, random mutations cannot increase information. Therefore, evolutionary theory cannot be true. This objection is frequently made by those who are advocates of “intelligent design,” and particularly one William Dembski, who considers himself one of the front-line experts of information theory as it relates to evolution.

Any time you see one of these objections which refer to “information,” genetic or not, especially in reference to this “information” either increasing or decreasing, there’s a good bit of underlying assumption behind it, which is usually unknown to the objector. This underlying assumption is that information theory directly interacts with evolutionary theory. The short answer is that information theory is relevant to evolutionary theory, but not in the way that is intended by the objection. Unfortunately, that’s the best answer that my expertise can provide, because information theory is well beyond my training and understanding. To get to the long answer, I’ve asked a good friend of mine and mathematical expert to explain what “information theory” is in the first place, and how it relates to evolution. I’ll yield the floor to him.

Why Are Humans Naked?

2006-08-06T19:06:00.000-07:00

I’d like to thank those of you who have donated to Evolution 101- I’ve received several donations over the past couple weeks, and while they are not necessary, they are appreciated. If you’re so inclined, you can find buttons both at my website and at the Freethought Media website to do so.

Now on to listener questions! I do appreciate all your questions, but this podcast is getting just too popular for me to answer them all. Keep sending them in, though, and I’ll do my best to answer as many as I can, both in direct replies and also here.

The first question is from Danny, who asks: “A friend was offering some counters to evolution (though he admits there aren't any other scientific theories to replace evolution). One specific case he mentioned was the development of the human eye (or even eyes in general). He seemed to be making an argument of irreducible complexity for vision, which I talked about a little bit. However it did make me curious, how did vision evolve?”

First of all, Danny, if you remember from the podcast on irreducible complexity, this kind of argument is an argument from personal incredulity. That is to say, since your friend cannot conceive of a method by which the eye could have evolved, such a development was impossible. This is logically fallacious- just because your friend isn’t aware of such a method or doesn’t posess sufficient imagination, it does not follow that evolution of the eye was impossible.

This problem was actually singled out by Charles Darwin himself, who is often quoted by evolution deniers as saying that the evolution of the eye is “absurd to the highest degree.” This is another example of a dirty rhetorical trick- quoting out of context. Darwin did say this, but out of sheer scientific integrity, and as I’ve mentioned before, acting as his own worst critic. Darwin concedes that for such a complex organ to evolve seems counterintuitive, but much in science is counterintuitive. What most evolution deniers don’t mention is that after saying this, Darwin goes on to lay out a perfectly reasonable method for the evolution of the eye as predicted by his theory. First, there would be photosensitive cells, followed by clusters of pigmented cells, then an innervated cell cluster covered by a translucent membrane, then the formation of a small depression, followed by a deeper depression, then lens-like skin covering the depression, and finally the development of muscles allowing this lens to move. There are organisms in existence today which are known to have each one of these structures as a viable method to detect light. In addition, certain genes which are found in organisms that are known to be essential for the formation of a lens are also found in organisms which do not have lenses, suggesting that these non-lens genes have been co-opted from structures lacking a lens. Unfortunately, eyes are structures that do not readily fossilize, so we cannot compare this evidence to the fossil record, but this is certainly a plausible evolutionary explanation.

Jeffrey asks: “If we never treat a virus like HIV would the body eventually become immune to it through generations? Or are some things too lethal to become immune to? In other words, would it be quicker to let the human body build up its own resistance to it by letting HIV infected people reproduce over and over with other HIV infected people until they had an offspring that was immune to HIV and then synthesize the chemical resistance made from that offspring for the masses, instead of introducing drugs into the human body that try to resist HIV but can never hold it off fully or cure it? Making HIV and AIDS adapt and become that much stronger...”

This is a tricky question, in that it has obvious ethical repercussions. But let me address the most obvious mistake first- failure to treat an individual for HIV would not make the body immune to it over generations. This is what is known as Lamarckian evolution, the inheritance of acquired characteristics. This is not evolutionary theory as we understand it today- Darwinian evolution posits the mechanism of natural selection as the adaptive mechanism. How this would work is, if you had a population of humans, infected them all with HIV, only the ones which were already more resistant to it would survive, and the rest would die. After many successive generations of this process, eventually those individuals which had the highest genetic resistance to HIV would contribute the most DNA to the population genome, and eventually the bulk of the human population would be, more or less, “immune” to HIV.

This would not necessarily be a “chemical” resistance, but more likely a genetic resistance, as we can see with those individuals who are already resistance to HIV, by virtue of the fact that they lack expression of the chemokines receptor 5, which is a co-receptor for the HIV virus. Current drug development efforts are being made to exploit this fact, but the natural resistance is in fact genetic, not chemical.

There are often criticisms of the currently available HIV treatment drugs, since they often have unpleasant side effects and can potentially be unsuccessful. But I would point out that even the genetic resistance that I mentioned isn’t perfect. The co-receptor deficiency may work for one strain of the virus, but it’s possible that the virus could mutate and use a different co-receptor to enter host cells, in which case the intitial mutation is worthless. Evolution is almost like a competition between organisms, each competing to replicate its genes more than the other, and when the relationship between those organisms is as parasitical as a virus to a host, that competition is deadly-serious. The virus cannot exist without a host, and the host cannot exist with the virus. There will always be mutation and adaption on both sides- that’s just the way evolution works.

Sean asks: “Why do people have pubic hair and underarm hair?”

The more interesting question is not, “why do people have hair in these weird places,” but “why don’t they have hair anywhere else?” Or in other words, “why are we naked?”

The standard answer to Sean’s question is that pubic hair and underarm hair are visual sexual cues- hair begins to grow in these locations during puberty (hence, pubic hair), signaling to others in the population that individuals with pubic hair are sexually mature and ready to procreate. Now, modern humans have adopted the use of clothing, and so the impact of this particular visual cue is less relevant today. But that’s an interesting development on it’s own- the only reason we wear clothes is because we’re naked- so why are we naked?

All other primates are well-covered with a thick complement of hair. In actuality, we have just as much hair as the others in terms of hair follicles- look closely at your skin and you’ll see them, thin and tiny, but definitely there. But our hair tends to be a lot more thin and tiny than the hair on, say, a chimpanzee. So much so that on a rough inspection, the zoologist Desmond Morris has no qualms in classifying humans as “the naked ape.”

The mammalian clade is distinguished by its hair, and by far most mammals have hair aplenty. Hair can be extremely useful- it warms and insulates those mammals which have to deal with cold temperatures, and it shields from the sun those mammals which live closer to the equator. Only a few groups of mammals have given up their hair- burrowing mammals, like the aardvark, or the naked mole rat, and aquatic animals, like the cetaceans or the hippopotamus. In both those cases it’s clear that hair would be more trouble than it is worth- trapping dirt in the former case and slowing down swimming speed in the latter. Even competitive swimmer knows to shave off their hair before getting in the pool.

But how did this happen? Unfortunately, hair and skin does not readily fossilize, and so there is very little in the fossil record that exists to help us answer this question, but there are some very likely hypotheses that take into account what is known about our evolutionary origins. The best one, in my opinion, is that which suggests that neoteny is the reason for our nudity. Neoteny is the retention of juvenile characteristics into adulthood. One classic example of this phenomenon is seen in the salamander Axolotl, which unlike other salamanders, does not metamorphosis into a terrestrial form and stays aquatic, retaining the external gills that would be lost during this process. Interestingly, the axolotl can be induced into metamorphosis if given the proper hormones, or if their environment is properly manipulated. If this happens, they lose their gills, and turn from pink into dark mottled terrestrial form similar to a Tiger salamander, to which they are likely related.

As it happens, there are several aspects of juvenile chimpanzees which are also found in humans, supporting the idea that humans are a neotenic species of great ape. At birth, a chimpanzee is almost completely hairless except for on the top of their head. This would explain our nudity, but it also explains a number of other human aspects- especially our ability to learn. Young chimpanzees have an incredible capacity to learn that is turned off upon entering maturity- but in humans, this capacity continues throughout adulthood. Proportionally, the chimpanzee head is much larger in relation to the rest of its body as a juvenile, similar to the proportions of the human head to the human body. It’s in fact quite possible that neoteny may have been selected for the intellectual benefits, and nudity simply followed as part of that process.

But it is reasonable to think that if our nudity is a result of being neotenic apes, there could have been some compelling selective reason for this change. There are many explanations for this to have been the case. One is that, as you remember from the previous podcast on human origins, our ancestors distinguished themselves from their fellow apes by the ability to hunt. Upon abandoning a nomadic existence, their homes would have been infested with insects and parasites, which would have been a problem for those with hair. However, many other hairy organisms deal with skin and hair parasites without much problem, so this seems unlikely to have been of much importance. Another suggestion is that the transition to hunting would have exposed our ancestors to blood and guts and other detritus in the butchering process, which would have been a liability if they had a hairy coat to become matted and sticky with the meaty muck. For example, vultures have lost the feathers around their head and neck due to the fact that they’re always sticking them is sticky and nasty places. But certainly if our ancestors had the intelligence to develop the tools necessary to bring down prey, they also would have been able to use those tools to skin and process their prey without making a disgusting mess. Others make the suggestion that, upon the discovery and management of fire, the need for warm insulation at night was no longer a selective pressure to maintain a full body of hair.

There is another interesting idea called the “Aquatic Ape” theory, which suggests that during human evolution, our ancestors left the trees which they were accustomed to and moved to an aquatic environment of some sort, either by the ocean or near some marshland. Other mammals which have returned to an aquatic existence have also lost their hair- cetaceans, as I mentioned before, and hippos. This theory also explains several other aspects of human physiology that differ from the other apes. For example, humans tend to be fairly agile in the water even at a very young age, unlike chimpanzees, which are very poor swimmers and easily drown. It may explain why our bodies are more streamlined than other apes, and even why we have vertical posture, presumably from having to hold our bodies upright in deep water. In addition, the hairs on our backs are angled diagonally toward the center of our spine, which is different from other apes and is seemingly perfectly adapted to the flow of water across the back. This also explains a particularly notorious difference between humans and other apes- thick deposits of subcutaneous fat. No other apes have this characteristic, but it is argued that fat deposits are particularly useful for other marine mammals, in that they aid in flotation. However interesting this theory may be, there is unfortunately no good fossil evidence to support it, although there has not been much investigation of human ancestor fossils in areas which would have been aquatic in the past, but it remains a minority view.

Another beneficial aspect of nudity was the impact on body cooling. As hunters, our ancestors had to exert themselves to an extent which their evolutionary heritage had not prepared them as efficiently as it had for other hunters like lions or wolves. In order to pursue their prey, our ancestors would have experienced severe overheating, to the extent to which the lack of body hair would have been a great benefit. This loss of protection during the day could have been offset by the gain of protection from the cold afforded by the subcutaneous layer of fat that I mentioned before.

Getting back to what I initially answered about the existence of pubic hair, nudity may have been selected for as a sexual signal. Male humans are distinctively hairier than females, and it’s entirely possible that the lack of hair on a female would have been a attractive signal for males. Carried out over many generations, this would have resulted in an overall lack of body hair in both sexes, with more pronounced nudity continually seen on the female. This would also be consistent with the retention of pubic hair, as I mentioned before that this hair is a distinctive sexual cue.

So, we see that the reason for human nudity is most likely because of neoteny, which is the retention of juvenile traits throughout adulthood. Like young chimpanzees, we lack thick hair all over our bodies except for our heads. This may also have been tied in with our brain development. The selective reasons for this change could be from a number of explanations, including parasite infestation, the domestication of fire, an aquatic existence, the demands of a hunting lifestyle, and sexual cues.

Why Do Men Have Nipples?

2006-07-30T20:46:00.000-07:00

Let’s start off with some listener questions.

From Elias: We humans are different since we have control over our environment not much change occurs, so survival of the fittest is no longer true. At the beginning of life was it just a big mess of a puzzle that fell into place over time? For example were there animals who had no reaction to predators hence they died off since they didn’t react to danger.

What I believe he’s trying to ask here is a question about the mechanism of natural selection. Does natural selection mean that you start off with a large group of random organisms, and then end up with only the few that are well-adapted to the environment? Well, sort of, but not exactly. This would make sense if one assumed that the environment was static- it never changed. But the environment is always changing, and so populations that are well-adapted today may be incredibly poorly adapted to it fifty years from now. A predator species that restricts the adaption of another species may go extinct, and allow the prey species to evolve into something different. Or predator species may be introduced to new species, which are not adapted at all to them. This was the situation with the dodo bird, which had adapted to easy island life by growing large and flightless. But when humans arrived, they were easy pickings for food from both humans and the other animals that were introduced by humans to their environment. Survival of the fittest still happens with humans, of course, and even though we do have incredible control over our environment compared to other species, we are not omnipotent.

From Richard: hey, just curious why you didn't mention the arguments against carbon dating in the podcast 122 - what is the evidence against evolution. I have heard this argument from many creationists.

I actually had a separate podcast on radiometric dating methods- the episode just prior to that, 121, titled “How Are Fossils Dated?” But yes, very often evolution deniers will criticize radiometric dating methods as a way of criticizing evolutionary theory. Usually, however, they don’t know what they’re talking about, and one easy way to tell is if they talk about “carbon dating” and “fossils” in the same breath. Radiocarbon dating is really not useful for most fossils, since it can’t be effectively used for artifacts older than about 60,000 years. What evolution deniers are trying to do with this kind of attack is, not to address evolutionary theory on its own merits, or even to question the principles of radiometric dating, but just to try to inject as much uncertainty into the evidence from radiometric dating as possible. Usually they try to make the claim that radiometric dates are made in such a wide range that they can’t possibly be used accurately, or that they have been used in the past to make blatant mistakes. I’ve run into the bulk of these claims made by Kent Hovind and a lot of them are just outright lies or misrepresentations of the actual dating methodology. He makes a claim that living snails were tested by radiocarbon dating and shown to be 2300 years old. What he doesn’t say is that a lot of the carbon in the snails’ shells was derived from dissolved limestone, which was very old, and screwed up the ratio of radioactive to nonradioactive carbon in the water.

From Lee: I just heard and enjoyed your interview on the biota.org podcast, and I thought that you and/or your audience might be interested in an OpEd that I published on evolutionary computation and intelligent design in the Boston Globe last year (August 29, 2005). It's a short, easy read and I've received a lot of feedback from non-scientists saying that the case that it makes is particularly compelling to them because it requires no familiarity with molecular biology, or with the fossil record, or with other areas of science. It is available directly from the Globe here. Alternatively, I have a local copy here.

Thanks, Lee, I had a great time on the Biota.org podcast, and I understand from Tom that it was very well received on his end as well. Digital evolution tools are already and will continue to be great tools both for discovery and education, so anyone who’s interested in that subject can go check out your op-ed.

From Mike: My question is about mammals. How did mammals evolve from Reptiles? Are there transitional fossils of egg laying / lactating species? Reptiles with nipples? I’m sure such a leap had to take thousands if generations. Have any such fossils ever been found to your knowledge?

The short answer is, mammals are distinguished from reptiles partially because of their ability to lactate. So, no, simply by definition, there are no reptiles with nipples, at least no extant species. By looking at the mammal clade as it exists today, it would seem to indicate that the whole nipple-mammary gland structure as it generally understood among mammals today wouldn’t have existed at all in reptiles, although it’s not known precisely when this trait evolved in mammal evolution. Let me just go through the basic steps of mammalian evolution quickly. Mammals and reptiles are both part of the larger clade, the amniotes. Of these, there is a further division into the reptilians, which would include turtles, lizards, snakes, and birds. Yes, that’s right- birds are cladistically reptiles, even though they used to be thought of as similar to mammals, since they’re warm blooded. But the bird singing on your fence is more closely related to the lizard sunning itself on a rock in your garden than to the cat watching both of them at your window. The other division in the amniote clade is the synapsids, which as a group is also very reptilian, but are different from all the other reptiles we know today. The characteristic that made these animals different is primarily the presence of an opening in their skulls just behind their eye. This may seem like a trivial distinction, but it allowed for stronger jaw muscles to develop, and much of an organism’s evolutionary fitness is tied directly to how well it’s able to eat. What makes this especially hard to conceptualize, is that of most of the synapsids, we would recognize nearly all of them as indistinguishable from reptiles, but we would be more closely related to them than we would be to a snapping turtle. However, among this group of synapsid reptiles, a subgroup evolved which we call the therapsids, and it is this group which eventually gave rise to modern mammals. The therapsids are often referred to as “mammal-like” reptiles. It’s within this group that warm-bloodedness evolved, the bones of the reptilian jaw moved into the mammalian ear, scales were lost, and fur eventually began to grow on some of the later therapsids. Eventually, an even further subgroup of the therapsids, the cynodonts, which were small, shrew-like organisms. Finally, from these small organisms, have evolved all living mammals, from whales to elephants to lions and tigers and bears, and humans. So yes, mammals did evolve from reptiles, and we can still see some hints of that in living mammals today- the monotremes. These include the duck-billed platypus and the echidna, both of which lay eggs instead of giving birth to live young, which the other two mammal groups, the marsupials and the eutherians, do today.

Interestingly, and to get back to the nipple question, monotremes do provide milk for their young, but they don’t have nipples. Instead, the milk is secreted sort of non-specifically from their skin, and their young lap it up off of their fur. So nipples as a physiological structure would seem to be a relatively recent evolutionary development in the history of mammals, and not even one that is necessary to be designated as a mammal.

But this brings me to another interesting nipple topic, and one that is commonly brought up in evolutionary discussions- why do men have nipples? It seems pretty obvious that for females, these structures are of obvious utility, both to mother and child. But wouldn’t it be just as useful for the child to have access to milk from both parents? In many species, food is provided for offspring by both male and female parents, to the obvious advantage of the young. This is a common behavior in birds, for example. Why, then, are male mammals so selfish? Why is there no such thing as the milk of male kindness?

As above, I’ll give a short answer and a long answer. The short answer is, men don’t nurse because we don’t have to. It’s not in our interest, evolutionarily speaking. The long answer is there is absolutely no physiological reason why men couldn’t nurse babies- all the equipment is there. The development of mammary glands in embryonic development happens independently of sex- for all intents and purposes, these glands remain indistinguishable between the sexes until puberty, during which exposure to hormones from the ovaries, adrenal glands, and pituitary gland. Pregnancy further enhances the development of these glands, especially the hormone prolactin. But exposure to the same kinds of hormones at the same times would give the same results for men, or, more specifically, removing the masculinizing hormones like testosterone. Mutations of the testosterone pathway can cause males to be born without recognizable masculine genitalia, and they develop usually into extremely beautiful “women”, with long legs and full breasts, simply because they’ve had their masculinization progress impaired. Genetically and genitally they’re still male- they have internal testes, not ovaries, but they sport breasts that could grace a magazine pictorial.

But, even without the full-on breast development that is caused by hormones, men can still lactate. Even human women who have never gone through pregnancy can induce lactation by mechanical manipulation of their nipples, since the nerve stimulation causes expression of the same hormones that induce lactation after pregnancy. These same hormones can be induced in males, making it the case that, if a man really wanted to breastfeed his child, all he’d really have to do is… well, practice.

So, we can see clearly that there’s no big physiological barrier standing between men and the ability to lactate. So what’s the reason why they don’t, especially because they do have nipples, after all? The reason is not physiological, but evolutionary. In the vast majority of mammalian species, offspring are born and raised solely by the female- the male plays no parental role at all. His evolutionary interests are best served by having children with as many females as possible, and so he doesn’t gain any advantage to sticking around to help raise one or two of them. According to the rules of evolutionary selection, whichever organisms pass on the most copies of their DNA are the most successful. I hesitate to use the word “rules,” because that makes it seem as if evolution was a game being played by all creatures, but that’s sort of how it works out.

But what about those species for whom males do play some role in the parenting of their offspring? This would include humans, of course. Well, we see that the male contributions in these species include things like bringing back food for the female, chasing off potential competitors within its species, and looking out for predators from other species. These alternatives to lactation are well-adapted traits for the species in which they’re found, and offset any benefit which male lactation would provide evolutionarily. But this doesn’t preclude the existence of any species for which male lactation would be an evolutionary benefit, and in fact one has been recently discovered, the Dyak fruit bat found in Malaysia. Males of this species were discovered with functioning mammary glands, both full and drained, indicating that they were providing milk to their young. This species hasn’t been studied enough to determine why male lactation was advantageous for development, but as you should know already, the physiological requirements would already have been in place. As bats are closely related to humans (just outside of the primates), this seems to suggest that male lactation in humans is only a few environmental variables away from becoming commonplace. Certainly it’s not outside of the range of personal choice, although cultural pressures may discourage this behavior.

So, to review, males have nipples because the development of mammary glands is independent of sexual development, at least until puberty. And the reason why men don’t use those nipples is because, at least so far, it hasn’t been evolutionarily advantageous for us to do so, although physiologically, we have essentially the same equipment as females and can produce a comparable product.

What is Punctuated Equilibrium?

2006-07-23T20:34:00.000-07:00

I received a message from a listener, DH, that I wanted to pass along to all of you. In the popular culture, oftentimes the idea is propagated that evolutionary theory is a controversial theory within science itself. This could not be further from the truth, and an international organization of science academies, the IAP, has released a statement that clarifies their official scientific position in regards to evolutionary theory. I’d like to read that statement to you now:

We, the undersigned Academies of Sciences, have learned that in various parts of the world, within science courses taught in certain public systems of education, scientific evidence, data, and testable theories about the origins and evolution of life on Earth are being concealed, denied, or confused with theories not testable by science. We urge decision makers, teachers, and parents to educate all children about the methods and discoveries of science and to foster an understanding of the science of nature. Knowledge of the natural world in which they live empowers people to meet human needs and protect the planet. We agree that the following evidence-based facts about the origins and evolution of the Earth and of life on this planet have been established by numerous observations and independently derived experimental results from a multitude of scientific disciplines. Even if there are still many open questions about the precise details of evolutionary change, scientific evidence has never contradicted these results:

1. In a universe that has evolved towards its present configuration for some 11 to 15 billion years, our Earth formed approximately 4.5 billion years ago.

2. Since its formation, the Earth – its geology and its environments – has changed under the effect of numerous physical and chemical forces and continues to do so.

3. Life appeared on Earth at least 2.5 billion years ago. The evolution, soon after, of photosynthetic organisms enabled, from at least 2 billion years ago, the slow transformation of the atmosphere to one containing substantial quantities of oxygen. In addition to the release of the oxygen that we breathe, the process of photosynthesis is the ultimate source of fixed energy and food upon which human life on the planet depends.

4. Since its first appearance on Earth, life has taken many forms, all of which continue to evolve, in ways which palaeontology and the modern biological and biochemical sciences are describing and independently confirming with increasing precision. Commonalities in the structure of the genetic code of all organisms living today, including humans, clearly indicate their common primordial origin.

We also subscribe to the following statement regarding the nature of science in relation to the teaching of evolution and, more generally, of any field of scientific knowledge: Scientific knowledge derives from a mode of inquiry into the nature of the universe that has been successful and of great consequence. Science focuses on (i) observing the natural world and (ii) formulating testable and refutable hypotheses to derive deeper explanations for observable phenomena. When evidence is sufficiently compelling, scientific theories are developed that account for and explain that evidence, and predict the likely structure or process of still unobserved phenomena. Human understanding of value and purpose are outside of natural science’s scope. However, a number of components – scientific, social, philosophical, religious, cultural and political contribute to it. These different fields owe each other mutual consideration, while being fully aware of their own areas of action and their limitations. While acknowledging current limitations, science is open-ended, and subject to correction and expansion as new theoretical and empirical understanding emerges.

Signed to this statement are the national academies of sciences from 66 countries, including the United States, the United Kingdom, Poland, Ireland, Italy, Greece, Hungary, Japan, Lithuania, Germany, Austria, Australia, and interestingly enough, Iran. It’s great to see such clear international support for science, and I think that everyone will eventually take notice of it.

On a similar note, I received a question from JM asking me about the beliefs of the current Pope about evolutionary theory. Pope John Paul II, as some of you are probably aware, was fairly well-educated about science, and accepted evolution explicitly in a 1996 speech, although he warned against the acceptance of any material explanation for the existence of the human soul. The current Pope Benedict XVI, before he was elected, made statements accepting of evolutionary theory as well. Recently, the Vatican’s chief astronomer explicitly endorsed evolutionary theory and rejected intelligent design as unscientific. However, other statements made by Catholic officials support the idea that the evolutionary process is guided by the divine, although the specific details of this are never made clear. This seems to be essentially the position that’s promoted by Dr. Kenneth Miller, the author of “Finding Darwin’s God.” In that book, as I’ve mentioned before, Dr. Miller explains evolutionary theory in very basic language, dismisses the claims of intelligent design proponents, and provides room for his faith. I would recommend that book to anyone interested in evolution just in a general sense, but especially to those who consider their faith as an obstacle to the acceptance of evolutionary theory.

Today I’d like to talk about punctuated equilibrium. This concept was coined by the famous paleontologist Stephen Jay Gould, and it has become somewhat of a controversy within evolutionary theory. This fact is, predictably, seized upon by various evolution deniers as a way to challenge evolutionary theory as a scientific theory, as if to say, “Aha! The scientists disagree about evolution! Therefore, it is wrong.” But this is unfounded. Scientists disagree all the time- by that logic, all scientific theories are null and void, because there’s always some controversy going on at some point in time about some aspect of just about every theory.

What is meant by the term, “punctuated equilibrium” is that, throughout evolutionary history, the evolution of one species to another has not been a constant process, but has instead been one of population stability followed by rapid speciation, followed by long periods of stability. You might be wondering, “Why is this controversial?” but in the definitive paper on punctuated equilibrium, published by Gould and Niles Eldredge in 1972, they made the case for their concept as an alternative to what they called, “phyletic gradualism.” This would be the opposite to what they proposed of the stability-speciation-stability model of evolution, and would describe the situation of whole populations speciating slowly, and constantly over time.

To give you a better idea of the distinction between the two, just imagine a child growing. When it is born to just prior to puberty, the average child grows pretty gradually and steadily. This is roughly the kind of change that is thought of with phyletic gradualism. Now imagine that same child going through puberty, and experiencing growth spurts. It could go one or two years without growing much at all, and then over a three month period shoot up several inches. Then maintain that height for another year, and then experience another growth spurt. This is roughly the kind of change that is thought of with punctuated equilibrium. There are long periods of little to no change, or equilibrium, which are punctuated by short periods of rapid change.

This does not imply in any way that new species spring into existence instantly and magically. Just like a growing child doesn’t snap its fingers and shoot up three inches, new species don’t just “appear” out of nowhere. This is called “saltation,” and it’s associated with ideas like creationism, not evolutionary theory.

So, why did Gould and Eldredge even come up with this concept anyway? Were they just sitting around, trying to come up with ways to pick fights with other scientists?

The reason for the theory comes from the natural evidence, actually the fossil evidence. Throughout the course of paleontological investigation, fossils of any given species were found, more or less with the same basic anatomy, throughout the range of their presence in the fossil record. As one moved along the geological column closer to present day, one would find descendent species that were obviously related by their anatomy, but were different enough to be classified as different species. And so on and so forth, with daughter species continuing to be found in more recent strata, but again, with very little gradation among the species population. If you recall from the podcast on transitional species, this same phenomenon is latched onto by evolution deniers as being “gaps” in the fossil record, and is seen as a refutation of evolutionary theory.

The common objection is that, if evolution is true as Darwin described it, then we should be able to dig into the ground, find the fossil of a species, dig a little farther, find the fossil of its parent that looks slightly different, dig again and find its grandparents that look even more different, and dig once again to find its great-grandparents that look different enough to be classified as a different species altogether. That’s somewhat of a simplified account of that objection, but it encompasses the intended spirit. Essentially, deniers of evolution claim that we should have an unbroken chain of fossils that demonstrate the minute evolutionary changes over time. That is, we should not only have fossils that demonstrate separate species, but we should also have the fossils of the organisms that are in between those species.

If you remember from the podcast about the concept of a species, you’ll of course realize how silly a request that is. Fossil species are defined retroactively- there isn’t some kind of label that switches from one species name to another as populations change.

In addition, consider that the geological record is not perfect. It’s not a filing cabinet where fossils are neatly ordered, ready for discovery by paleotologists. It is incredibly unlikely that the remains of an organism will become fossilized instead of decomposed, and even for those that become fossilized, their continued preservation is not certain. Fossils are destroyed all the time, by seismic activity, volcanic activity, and erosion.

However, even given that consideration, what punctuated equilibrium does is explain the pattern of the fossil record in a way that is consistent with evolutionary theory. Namely, that speciation involves a small group of organisms with the parental population, this group is typically isolated geographically from the parental population, and this genetic isolation promotes rapid morphological change in the daughter species population. Because of this, fossil records of the parent and daughter populations will appear to be geographically and chronologically distinct in the geological column. This concept really isn’t anything that revolutionary when you think about it- the famous evolutionary biologist Ernst Mayr had conceived of both of those mechanisms long before Gould and Eldredge came around. In trying to figure out mechanistically how species develop, he came up with peripatric speciation, in which a small subset of a population forms into a new species population, and allopatric speciation, in which geographically isolated members of a population form a new species population. If that sounds exactly like what happens in punctuated equilibrium, you’re basically right- and this is what the real controversy is about.

Within the scientific community, it’s never been a question of whether evolution was right or wrong, or whether punctuated equilibrium was right or wrong. For the most part, punctuated equilibrium was accepted by the scientific community almost immediately. What is in dispute, rather, is to what extent punctuated equilibrium was in agreement with Darwin, and to what extent it differed from evolutionary theory prior to the Gould and Eldredge’s introduction of the concept. It’s true that Darwin wrote extensively about the concept of gradualism in his work, but he seems to have anticipated an idea like punctuated equilibrium, as he suggested that the period of time in which a species doesn’t change is likely much longer than the period of time in which it does. You’ll remember that previously I mentioned that Gould and Eldredge had introduced the concept of phyletic gradualism as a counter to their own concept. Many scientists see this as a strawman, in that they made the case that Darwinism implied phyletic gradualism, to which they were proposing their own scientific alternative. This is simply not true of Darwin himself, and I’ve already mentioned that he anticipated the concept of punctuated equilibrium himself. Why Gould and Eldredge would have painted Darwin with such an inaccurate brush is a question I can’t answer, although it should be noted that Gould was known for speaking about his discoveries in a manner which some would consider overemphasizing their revolutionary nature, to the extent to which many people thought he was criticizing the existing tenets of evolutionary theory.

Essentially, punctuated equilibrium is an accepted part of evolutionary theory, and not only that, it’s a clear concept that follows clearly from the original theory as first conceived of by Charles Darwin all the way to present-day. It’s a very useful concept for understanding the patterns within the fossil record, and the only controversy that still exists is in regards to how revolutionary of an idea it actually was within evolution.

Miscellanea

2006-07-16T06:42:00.000-07:00

I was interviewed this week for the Biota.org podcast, which focuses on the development of artificial life models. This field is of interest to evolution, because these models can be wonderful experimental tools to test out specific components of evolutionary theory without having to wait for hundreds of thousands of years, and they can also be great educational tools. One fun artificial life program that I’d recommend for you to check out is called, “Gene Pool,” and it can be found at www.ventrella.com. At any rate, check out the Biota.org podcast if you’d like to hear that interview.

This podcast is growing in popularity, and I’m getting more and more questions emailed to me. This is great, and I would encourage anyone who has a question to send it in, and I might even answer it on this podcast! This week, I’m not going to have a specific topic, and instead I’m going to respond to as many emailed questions as I can.

The first question is from Mark, although I received several similar emails from other people asking about a comment I made in response to an email that I answered last week. He writes:

You mentioned in the podcast that, although you are an atheist, you spend your Sundays in church. That was a little surprising, though not a lot. I continued to attend church for a few years after rejecting religion, I suppose out of habbit and for socialization. I was just curious as to why you continue to do so and whether you find yourself in situations where your scientific knowledge is in direct conflict with church lessons or issues.

Well, I’m sure that the idea of an atheist attending church seems a little strange to some people, but it’s a unique situation. I visit with a specific group at the church that examines issues that most people regard as being in opposition to religion, such as evolution. I go there every week, partially because I like interacting with the people there, and also so that I can provide accurate information about things like evolution that people there wouldn’t be aware of. You might think of it like an Evolution 101 house call, or church call, more accurately.

The next question is from Eddy, who writes:

macro and micro evolution When using terms like these it is hard to say that there is no difference between the two.... Dr. Raoul A. Robinson defines a difference between macro and micro evolution. Two distinctions he makes are: - timescale, some changes can occur in relatively short period of time (decades to millenia) - persistence, some change occur, but can be changed back... Does this makes sense?

Well, Eddy, I touched on micro and macro evolution back in podcast 102, where I looked at examples of what evolution is not. Dr. Robinson is correct in that, typically we think of microevolution occurring over a short period of time. However, the best distinction that could be made is that microevolution is that which does not change one species into another, and macroevolution is that which changes one species into another. But the only difference here is timescale, not mechanism. The same mechanism that causes an organism to gain a single trait is the same mechanism that causes a new population to speciate from another. We’re only talking in difference of scale. As a comparison, think of a garden hose- turn the water on high, point it at the ground, and within a few minutes you’ve cleared out a good-sized rut in the dirt. Nothing too special- that’s the force of erosion at work. But instead of running it for ten minutes, what if you run it for ten years. How big a rut do you think it would be then? What about ten thousand years? Now you’re getting a sense of the difference in timescale between micro and macroevolution. Or you can think about economics. Do you think that the five dollars you spend at Wendy’s to buy a chicken sandwich affects the amount of money the store makes in a day? Of course it does. What about the millions of customers ordering chicken sandwiches around the world- does that affect the multimillion dollar deal they make with an advertising company? Of course it does- same mechanism (people buying chicken sandwiches), just an increase in scale. Remember that the next time anyone tries to use micro and macroevolution as a way to deny evolutionary theory.

The next question is from James. He writes:

All my life (almost 54 years now), I have heard statements regarding the evolution (in humans) of a larger brain being significant; that evolving a larger brain is what made us more intelligent (whatever that is) than other animals. So, my thoughts are: Elephants have larger brains than humans. Why aren't they more intelligent than us? I believe some whales also have brains larger than humans. The average man has a bigger head than the average woman, but women and men seem to be equal in intelligence; some people have tiny heads, but are very smart, while others have large heads, and are quite stupid. My hypothesis is that brain size is insignificant (beyond a certain point). It must be how the brain is organized that really matters. Brain structure, along with proper wiring or programming (a.k.a. experience), is what makes the difference, not the size. Am I right? And if I am, why do scientists and teachers (including yourself) constantly refer to brain size instead of brain structure? I hope the question is not stupid. If it is, perhaps my brain is too small.

Well James, you’re right- brain structure is important, but so it brain size. But it’s not just brain size as a single measurement- what seems to be most important is the ratio of brain size to body size. That is, the higher the ratio, the more brain per body weight, and the more intelligent the animal. This is called the Encephilization Quotient, or EQ. Primates have some of the highest EQs of all mammals, with humans obviously at the top of that list. Dolphins also have a very high EQ, which shouldn’t be any big surprise, since they’re widely known to be relatively intelligent also. Interestingly, octopi have the highest EQ of any invertebrate animal, which means they may be spineless, but they’re pretty smart. But EQ isn’t a perfect measurement- because of their small size, shrews have the highest EQ, and they don’t seem to be particularly intelligent. So absolute brain size is also important. Curiously, Homo neandethalensis, or Neanderthal Man, had a larger brain than modern humans, but there is no indication that they were particularly intelligent, or at least more intelligent than the human ancestors that lived at that time. This may have been because they lacked language, since their throat structure wasn’t likely condusive to the development of language. The development of structures within the brain, specifically the neocortex, is what sets humans apart from other organisms. This region of the brain is where the intellectual and reasoning capacity exists, and differences in this region are likely more important among humans for determining intelligence than absolute brain size.

The next question is from DR, who writes:

In your last podcast, #123, you gave examples of homosexuality in other animals. But all the examples seem to show 'homosexual behavior' but overall the animal was bisexual. Are there any examples that we know of where the animal is purely homosexual. For example, I have friends who are homosexual who do not mate with women--they are not attracted to women at all--there is no sometimes. That is homosexuality. In the examples you gave all the animals were bisexual. So are there any animals that are homosexual (besides human animals of course) ?

This is true- the examples that I gave were of various species pursuing homosexual interactions part of the time, while also pursuing heterosexual interactions for the other part. The purpose for doing so was to show that homosexual behavior is not fatal to evolutionary theory, and in fact can provide reproductive fitness to the population. But there are many examples of individuals in populations seeking out exclusively homosexual interactions- I’m sure many of you have heard of the “gay penguins” that refuse the attraction of females, and studies have seen that some male bighorn sheep actually prefer males to females. It’s just as tricky defining this as strictly homosexual in terms of orientation, because we can’t actually ask the animals which they prefer, and even in humans, many heterosexuals engage in some homosexual interactions at some point, and many homosexuals engage in some heterosexual interactions at some point as well. So, remember that I said sex isn’t black or white? This is why.

The next email is from Eddie, who writes:

I debate often with creationists in an internet chat room and the issue of random vs. nonrandom comes up often. I enjoyed your podcast on the subject but had one comment. At the end of the podcast, after making a great case that causality/environment is essentially the determining factor in mutation and which mutations survive, you end by saying evolution is both a random *and* a nonrandom process. This i thought re-opened the door on the very debate you were trying to close. As true randomness is theoretically impossible (it would be an effect with no precedent) in a causal system. No computer model of true randomness has ever been created. And there is nothing at all random about evolution. However the extreme complexity of the systems are so far beyond what we can calculate that it just appears random to us.

You’re right- in a deterministic universe, nothing is truly random, but from our perspective, mutations are generally unpredictable events, or at least the specific mutations are unpredictable- we know pretty well that if you expose DNA to UV radiation, you’ll get thymine dimerization, but we can’t predict which bases will and which will not dimerize. We know that mutation rates can change, and that some regions of a genome are more likely to mutate than others, but it’s still a generally unpredictable process. What’s more causally apparent to us are the environmental factors which affect reproduction fitness and mortality- these are obviously nonrandom. So that’s really what I mean by evolution being both nonrandom and random- I hope that clarifies my position.

This next email is from D.B.

Why is it that humans can hear there own thoughts in our heads with out speaking the words that come out of the mouth?

We can hear our own thoughts because all our senses are processed in our brain. So, we don’t technically need our ears to “listen” to something, just as we don’t need our eyes to “see” something. What is an interesting question to consider is whether or not other animals have that same ability. No other creature has such an audible language as humans, but do they represent their thoughts symbolically in their minds as they’re thinking them? It’s something fun to ponder.

Jeff asks:

I was listening to a creationist poodcast the other day when one of the speakers said that Stephen Hawking is a deist.

Supposedly Stephen Hawking said that the universe is so extremely complex, and the probability of the universe and life coming into existence is so small that there must have been an intelligent creator who created the universe.

I would like to know how you would respond to Stephen Hawking's statement from an atheistic point of view.

That quote sounds bogus to me, especially since Hawking just gave an interview in China recently where he said, “There is no evidence for intelligent design. The laws of physics and chemistry, and Darwinian evolution, are sufficient to account for everything in the universe.” But, if you want me to respond to that statement in general, regardless of who actually said it, I would say that it sounds like a combination of an argument from incredulity, and also a misunderstanding of statistics. For example, it is incredibly improbable that I will win the lottery today. But it is incredibly probable that somebody will win the lottery today. Thus, it may have been improbable for life to arise in one specific place, but very probable that it did arise somewhere.

And finally, one last email from John:

Recently, an anti-evolution friend of mine, whose studying computational biology, asserts the following to me contra Darwin:

"the fact that no random polypeptide chain ever folds into a stable native state at all, let alone into a nontoxic one, let alone into a specifically useful one, let alone into a specifically useful one which is preserved through natural selection."

Not being a biochemist or biologist, I couldn't immediately respond. Is this true to your knowledge?

This is a similar problem to the statistical improbability I mentioned in the previous email. It’s true that any given random polypeptide chain won’t fold into a stable conformation, but would likely just flop around with one or two interactions between different residues in the chain. Most proteins are combinations of two different types of conformation structures- a helix, like a DNA spiral, or a back-and-forth folded sheet. What this problem ignores is the fact of selection- if you have a large number of different proteins, most of them will be useless, but one will be useful. It’s just like with the lottery example- it’s improbable that any one person will win, but it’s certain that somebody will win. Just like this, although any random protein won’t fold into a useful structure, the genome doesn’t encode for random proteins, and neither does evolution conserve random proteins. Small random changes are made to individual proteins, and those changes are selected for their relative effect on reproductive fitness, after which the changes are increased or decreased in a population. That’s evolution in a nutshell. You might say, evolution 101. That’s all for this week, take care.

Why Did Homosexuality Evolve?

2006-07-09T11:58:00.000-07:00

All right, now to start things off with some listener email. I’m very pleased to have received my first critical email. You might think that podcasting on a topic that is so controversial in the popular culture would get me lots of criticism, but I’ve only received positive comments so far. That is, unless you check out the reviews on the iTunes page- there have been a number of 1-star reviews. But this email, although it’s critical, is so polite I just have to share it with you right off the bat.

Dear Dr. Zach,

I hope you are well and your weekend is running smoothly.

The Infidel Guy recently turned me onto your podcast, apparently he holds you in high esteem.

I was excited to hear the gospel of evolution from an educated person, as most of the times I hear it spouted are from high-schoolers and fellow workers, who are innocent in the fact that they believe in evolution simply because it has been crammed down their throats.

I expected your podcast to at least acknowledge the number of evolutionary frauds that have been presented(all of them) and the number of evolutionary evidences that stand before science(none of them).

I was dissapointed to hear your podcast sounds like someone reading a public school text-book. I was hoping to at least hear about microbial evolution or evidences that may be true that I haven't heard of, instead I hear things like, "We Suppose" "The evidence suggests" "The Fossil Record" and I wonder exactly which evidences have solidified your understanding of evolution, because it is all clearly a religion, and the most boring fairy tale ever told, to those of us who understand the theory.

The main evidence that it seems you are relying on for the foundation of your religion is the occurence of variation within a species. The correct term is variation, evolutionists such as yourself have misnomered it to be "Micro-Evolution" so you can piggy back upon something that has actually happened. Micro-evolution(I'll use your word) will NEVER lead to a new improvement of a species or the formation of a new species.

I hope you have a good Sunday, please consider spending it in Church.

Yours,
C.S.

Well, C.S., as it happens I do spend my Sundays in church. Although, I can’t see what that has to do with evolutionary theory. I’m glad to hear that you connected to this podcast through the Infidel Guy- as my long-time listeners know, he was the one who first conceived of Evolution 101. I certainly haven’t had evolution “crammed down my throat” as you say, I’ve been learning as much as I can on my own, since it is so scientifically compelling. Hopefully, I can communicate enough of what I know to creationists who have had nothing but pseudoscience crammed down their throats, instead of real science. I’m not sure which evolution “frauds” that you’re talking about- although I can hazard a guess. Nebraska Man? Piltdown Man? The thing is, these just aren’t scientifically relevant anymore- who do you think recognized them as frauds? Scientists! The only people who are interested in them anymore are creationists, because they think that bringing them up can poke holes in evolutionary theory now. That’s just not the case- if you’ll check out my podcast on human evolution, you’ll see that they’re not even part of the equation. Also, I’m not quite sure why you think I haven’t presented any evidence for evolution. I did a whole series on the molecular evidence for evolution which I’m quite proud of. Evolution is decidedly not a religion- it makes no claims about a deity, its advocates don’t get together once a week to sing songs about how wonderful evolution is, and I don’t pray to Charles Darwin. Regarding “micro-evolution,” actually it is creationists who use this term much more often than those who accept science. I’ve already discussed the reason why there isn’t a difference mechanistically between micro-and macro-evolution, any more than the difference between micro- and macro-economics.

All right, well, thanks from C.S., and now for a more inquisitive question:

The environmental pressures that lead to the reproductive selection of certain changes or mutations seem to be at a very gross level, such as at the level of reproductive success or survival.

How, then, does evolution effect something like eye color, skin color, size, cholesterol production in the liver, the presence or absence of a pinky toe, intellect, etc. that don't seem to directly effect reproductive success or survival? How does/did our body/species select for subtle changes that are effectively invisible to natural selection?

From H.G.

The reproductive success of a population isn't just one trait- instead, fitness is a comprehensive quality that takes into account lots and lots of traits. Any individual trait that gives any reproductive advantage, no matter how small, will be increased in a population over many generations.

For any given trait, we can arrive at conclusions based on what we presently know about the relative fitness associated with the presence or absence of that trait. For example, eye color (essentially the presence or absence of pigment in the iris) has historically been segregated geographically. The lack of pigment (blue eyes) occurs with the greatest frequency in Northern European populations. We know that this region tends to experience less direct sunlight, especially at the higher latitudes. We also know that other organisms that are exposed to very little light also lose pigment over time. This is either because the selective pressure to keep pigment drops (it does cost energy to make pigment molecules, after all) or because there is a selective advantage to have little pigment. Skin color is likely due to the latter- Northern Europeans also lack much pigment in their skin. There may be an advantage to their ability to synthesize Vitamin D in these environments, but I'm not sure if this has been established empirically.

There are some traits that are obviously of no bearing to reproductive success whatsoever. For example, the ability to roll your tongue. I can do it, others can't, and unless it's linked to some other important trait, it seems to be just a weird genetic coincidence. It might be left over from some earlier period in human evolution, perhaps from our smaller, fruit-eating primate ancestors. For now, though, it's a trait that just randomly shuffles through the generations, until some change in our environment makes it imperative for reproductive success.

All right- well that’s enough questions for this week, on to the main topic: why did homosexuality evolve? I realize that, just as with evolution, homosexuality is still somewhat of a controversial issue in pop culture (well, at least in American culture, for my international listeners). But nothing’s more interesting then sex, and what could be better than sex and evolution?

The common argument goes like this: if evolution is true, then only those individuals who are able to reproduce will contribute offspring to the next generation. Thus, individuals who are homosexuals will not be able to reproduce, their genes will not be passed on to the next generation, and so if there is some genetic or biological reason for homosexuality, evolution should have removed it a long time ago.

First of all, is homosexuality a specifically human behavior? If it is a fundamentally biological behavior, there should be some other species which share it. And, in fact, there are close to 500 known species which are known to engage in homosexual behavior, including elephants, dolphins, sheep, bears, deer, rats, cats, dogs, cows, rabbits, kangaroos, squirrels, whales, bats, pigs, mice, goats, as well as just about every other primate. And that’s just the mammals! There are many more birds, fish, reptiles, and even insects which have also engaged in homosexual behavior.

So it really doesn’t seem as if homosexuality is really all that uncommon. But so what? Why should homosexuality be a trait found in so many organisms if it’s so fatal to the evolution of the species.

Well, the answer is, as with most things I discuss here, that sex really isn’t black and white. And homosexuality isn’t fatal to the evolution of species. Remember the definition I gave for evolution way back in the first podcast- “change in allele frequency in a given population over time.” There’s a reason why I specified “population,” and not “individual.” Individual organisms don’t “evolve” any more than a single pixel makes up a picture on your computer screen. What is necessary for evolution to take place is for there to be a group of individuals, a population, within which genes can change and flow.

Now, it certainly is the case that, for most organisms which utilize sex, heterosexual sex is required for propagation. But consider- not all species employ strictly monogamous sexual strategies. For many species, males compete for control of several females, meaning that there are many males who are left out in the cold, so to speak, with nothing but each other and raging libidos. One hypothesis fits this scenario- homosexuality occurs in these organisms to placate the male aggression that is left over after competition for females.

But that doesn’t mean that homosexuality is always a consolation prize. Among the American Bison, male-male intercourse accounts for almost half of all mating, and not just among the losers. Both parties seem to enjoy themselves, with the subordinate male even accommodating the advances of the dominant male. The same phenomenon can be seen in bighorn sheep, where the male being mounted even adopts the arched-back posture called “lordosis,” which is typically associated with the female sexual response. Clearly, these animals seem to be enjoying what they’re doing.

But the males don’t get to have all the fun. Female homosexuality is also common, with female antelope mounting each other in simulation of heterosexual courtship behavior when males are not present. In bonobo chimpanzees, the female-dominated social network is composed of close bonds which are shown by frequent homosexual interactions between female members of the group. In fact, more than half of an adult female bonobo’s sexual interactions will be homosexual in nature.

So how, you’re probably wondering, do these populations ever manage to reproduce with so much homosexuality? Well, the reason is because, as I said before, it’s not that black and white. Sure, individuals engage in homosexuality some of the time, or even a lot of the time, depending on the species. But not all of the time- they still find time to mate heterosexually. Sex seems to be a very fluid trait in many animals- pretty much any sexual configuration that can be performed within anatomical limits is done by some kind of animal. Sorry to say, but although humans can be kinky, we’re just not that original.

Now, you remember that I said that evolution takes place in populations, not individuals? Well, consider the social benefits of a population in which all members can share the close bonds of a sexual relationship, not just males and females. Clearly, in the case of bonobo chimpanzees, the bonds formed between females by homosexual relations are socially stabilizing. A stable society is much more likely to promote successful reproduction of young. Thus, homosexuality would be an evolutionarily beneficial behavior.

But what about some molecular evidence? Well, if you’re hoping that a “gay gene” has been found you’re not in luck. One hasn’t been found, although more and more scientists are starting to look at the genetics of homosexuality. Most likely, homosexuality as a behavior is a more complex phenomenon than just blue or brown eyes- a number of factors are considered- including the number of older male siblings a person has. Scientific research out of Toronto has shown that the more older male siblings a man has, the more likely he is to be a homosexual. The hypothesis is that the mothers becomes immunologically sensitized to the successive male fetuses within her, since they contain male proteins that she is not used to. According to this hypothesis, by the time the youngest male child is being carried in utero, she has developed anti-male antibodies which effectively diminish the normal masculinization process, resulting in a tendency towards homosexuality. But there may be some other benefits to the mother- a recent study from Italy showed that the maternal relatives of homosexual men have more children than the maternal relatives of heterosexual men. If this is repeated, it would suggest that there is a reproductive benefit to women whose DNA tends to result in homosexual male children- they have more children overall, meaning that their evolutionary fitness is actually increased because of the fact that they have homosexual sons. This is a fascinating possibility, especially because a better understanding of the genes involved in this phenomenon could have a major influence on our understanding of reproduction in general, and could point towards some better therapeutic targets for women who have problems with fertility.

All right- well, that was a lot to chew on for this week. To review- homosexuality is not a strictly human trait- it is practiced commonly throughout the animal kingdom. It has a clear evolutionary benefit in that it fosters better socialization among members of both genders. In humans, the evidence strongly suggests some kind of genetic component in the development of homosexuality, although the specific genes have not yet been discovered.

Before I sign off, I do want to make it crystal clear that the discussion here is in no way establishing a moral position in favor of, or against homosexuality. To do either would be to commit a clear naturalistic fallacy- to say that because something is natural, it is either right or wrong is clearly illogical. The moral discussion of homosexuality is reserved for other, non-scientific settings. Thanks for listening, and have a great week. I’ll see you next time.

What is the Evidence Against Evolution?

2006-07-02T15:11:00.000-07:00

I’d like to welcome any new listeners this week. The listenership here is growing steadily, and I have to say I’m very happy that so many have such interest in evolutionary theory. I’m certainly glad to have you all on board, and I welcome any questions you may have- remember, your questions are what drive this podcast.

Speaking of which, here’s the listener e-mail for this week, from Cameron, who asks: “We know that monkey babies are soon thrown on the mothers back after birth and have to hang on, and have that ability in them at birth. If a monkey was slowly evolving to human and evolution was taking place the offspring would not likely survive considering survival of the fittest and all. While the human eventually would become superior intellectually, they at birth they are quite helpless. If it was a survival of the fittest situation the more human a monkey became the less likely they would be to survive. If I was forming a theory to find the common cause I would say that monkeys would more likely have evolved from humans based on what is known on the care of babies. The humans would care for the child the same and eventually they would evolve to the point that they did not need all the care. Can you follow the logic on this? But of course we have to deal with the fossil record and that seems to say a different story. What do you think?“

Well, Cameron, I think I follow what you’re saying. You're saying that although you accept the evolution of the species, you're having trouble accepting that natural selection can account for it all?

Well, you're right- it's not as simple as "survival of the fittest." Ultimately, of course, what it comes down to is which members of a population are able to reproduce the most efficiently- but that doesn't always mean that the strongest or fastest is the one that fits the bill.

Sexual selection, for example, is a component of natural selection that very often runs counter to what we would anticipate in terms of the selection of certain traits. Take the peacock, for example. The male of that species sports a tail that is nonfunctional (although attractive), and costs him much in terms of energy to produce. Yet we also observe that females are most attracted to males which have the largest and most impressive tails- hence the selection. I should probably do a podcast on this subject soon.

Also, remember that the "selection" component of natural selection is a composite of all the environmental factors that affect any group of organisms- or lack thereof. For example, you mention the fact that monkeys cling to their mothers, and yet humans do not. What we also know is that humans differ in a number of significant ways from monkeys, including the amount of body hair. There are a number of hypotheses to explain why humans lost body hair (neoteny is one, which I feel is pretty strong), but consider that without body hair, it was impossible for babies to grab onto their mothers. Thus, natural selection kicks in. Any mother which treated her child like a monkey would have lost it, and would not have passed on any genes. Only those mothers who slowed down to carry their babies were successful in raising them to adulthood, and thus the genes which encouraged this behavior were passed on. Or it could have been the other way around- mothers stopped carrying babies on their bodies, and thus there was no selective pressure to keep full body hair.

Whatever the reason, the molecular evidence clearly shows that humans and primates are descended from a common ancestor. Common heredity is the ONLY phenomenon that has been observed which can explain two different organisms having the same genetic information.

All right, on to this week’s topic. The intended audience of this podcast is, as I’ve made clear many times before, those with no formal scientific training- laypeople, if you will. One of the confusing things about being a layperson in regards to some esoteric topic, is that there are always “experts” on both sides of the issue that are trotted out to voice the opinions of both sides, and it’s very hard to decide which experts are the most believable. Believe me, this is true for me in a lot of subjects- I may know my way around evolution pretty well, but there are a lot of things in science of which I find myself at a complete loss.

For those people that are inexperienced with the evidence for evolutionary theory, the arguments from those promoting the position of creationism can be just as confusing, especially when the creationist scientists are trotted out to make their arguments against evolution. So- who do you listen to? Ken Miller advocates for evolutionary theory, and Michael Behe advocates for intelligent design. Both men have Ph.Ds, both men are college professors, both men have published primary scientific literature, and both men have written popular books on the topic. Both men were even called to testify at the Kitzmiller v Dover trial. So… who’s right? And, more importantly, what can we look at to see?

Well, I’ve already done a podcast on Behe’s argument for Irredicble Complexity. Essentially, he argues that certain biological systems are so complex that they could not have evolved from simpler systems, and thus he posits the existence of an intelligent designer to explain their existence. I already explained why, logically, this is fallacious, because it is an appeal to ignorance, and regardless, evolutionary theory aptly provides an explanation for the evolution of the few examples he gives. So, logically, Behe’s argument falls pretty flat. But what about scientifically?

If, as Behe hypothesizes, biological systems are, in fact, irreducibly complex, then we should be able to see overwhelming evidence from scientific investigation. This is where the rubber meets the road, basically. Anyone can have an idea, but without rigorous, scientific investigation, peer-reviewed and published, that idea is just an idea- and can not be treated with any scientific respect. So sure, Michael Behe has the same academic credentials as Ken Miller, but has he been able to put his grant money where his mouth is? In other words, what scientific papers have been published that support Irreducible Complexity? Or, for that matter, Intelligent Design or Creationism in general?

Let’s just take a brief sample- on PubMed, one of the most popular biomedical search engines, a search for “evolution” turns up 178,160 papers. A search for “creationism” on the other hand, yields only 48 articles. Most of those are editorial articles by scientists expressing the concern over the creation vs evolution debate in popular culture. There is one interesting scientific paper that comes up, published in the journal “Laterality,” which concludes that people with a strong preference for one hand versus the other are more likely to believe in creationism, whereas people who are ambidextrous, or those who can use both their right or left hand, are more likely to accept evolutionary theory. A search for intelligent design brings up the same small numbers. But aside from that, there is no published data that can be easily found, no primary data that leads to the conclusion: creationism is the accepted hypothesis.

Fortunately, the Discovery Institute (the most scientifically rigorous Creationist organization of which I'm aware) has helped to resolve this issue by publishing a list of peer-reviewed literature supporting ID. I should, before I proceed further, explain what “peer-review” means. Essentially, this means that once a paper has been written containing new hypotheses, data, and conclusions, it has to be given to one or more “peers”, i.e., other scientists who are also publishing data, preferably in a field close to the one that the paper in question deals with. According to the Discovery Institute, the reason for highlighting a “peer-reviewed” list of articles is due to the fact that “critics of intelligent design often claim that design advocates don’t publish their work in appropriate scientific literature. For example, Barbara Forrest, a philosophy professor at Southeastern Louisiana University, was quoted in USA Today (March 25, 2005) that design theorists ‘aren’t published because they don’t have scientific data.’”

Well, let’s see the data!

They begin by showing seven "featured" articles. However, all of them are reviews, or position papers. None of them contain any basic research, and I'm unsure why they would want to "feature" them. Most of them are published in "Proceedings of" journals, which have a slightly different peer review process than other journals. Basically, as long as you can get a member of that particular society to sponsor your paper, it'll be published. The one contribution by Jonathan Wells would seem to be interesting, in that it proposes an experiment, but doesn't actually carry it out. I can't find any follow up papers, and it appears that it was just an abstract that was presented at a conference.

They likely realize that seven articles, none of which present any basic research, seems kind of weak, so they fill out the list categorically, starting with four "peer-reviewed" books. I'm not completely sure how these University presses work, but I very much doubt its anything similar to the review process for scientific articles. There's also three books that are "supportive" of ID, although not peer-reviewed (again, what does that mean?)

And finally we're down to the real meat, articles published in peer-reviewed scientific journals. Here we're down to six, only two of which were "featured" above. The first is in the journal "Chaos, Solitons, and Fractals." The second is in a "Proceedings" journal, and actually caused quite a stink from that society towards the editor who allowed its publication. The third is actually by Behe and is from a respectable journal, Protein Science, although it received a lengthy rebuttal in that same journal which basically showed that they had made several mistakes in assumptions for their calculations (Behe had tried to use mathematical modeling to show that mutations couldn't accrue fast enough to result in modification).The fourth is a review that questions the relevance of transposons to evolution (but not supportive of ID).The fifth is published in the "International Journal of Fuzzy Systems." And the last is in the "Journal of Theoretical Biology," postulating that the limited and predictive arrangement of protein folds represents a manifestation of "Natural Law," as opposed to "natural selection." This is not contary to evolutionary theory, however, since evolution does not predict that chemical interactions between amino acids change over time, just the arrangements of amino acids in a peptide chain, in response to varying levels of environmental selection.

Following these is a list of seven articles published in "peer reviewed" anthology books, five of which were published by members of the Discovery Institute. And then they have another seven "peer-edited" articles, four of which were also written by DI members. And they round it off with five philosophical papers, (with the guarantee of no basic research) one by Behe and the rest by William Lane Craig.

So that's it. The most the Discovery Institute can muster is 26 articles (none with a single experiment) and four books. As a point of contrast, remember there are 178,160 articles (25,672 of which are reviews) on PubMed which involve evolution (and that only goes back to 1916).

I want to repeat- not a single experiment has been published to test a hypothesis advanced by creationism or intelligent design. Not a single one. So sure, there are definitely scientists with real degrees out there, talking about intelligent design, but they can’t perform a single experiment to back up their arguments. Remember that next time you find yourself torn between two “experts” in the creationism/evolution debate. Firstly, there is no scientific debate on the subject- we can see that in the constant and overwhelming asymmetry of papers published in support of evolution versus those published in support of creationism. When less than 0.01% of the papers published on a topic are in support of an alternative explanation, you can pretty much guarantee that there’s no debate. And secondly, there’s just no evidence to support any other hypothesis but evolution. Not a single experiment. Which makes complete sense, of course- how can you hope to conduct an experiment to test a phenomenon which is, ultimately, supernatural? Those who would deny the fact of evolution know this, which is why the only arguments they can hope to get away with are those that attempt to discredit evolutionary theory. Remember- if an “expert” has no direct evidence in support of his own position, but can only attempt to tear down the opposing position, you can reasonably conclude that he doesn’t have anything meaningful to offer.

So, in conclusion, evolutionary theory is the only explanation for the data that is available to us, and no alternative hypothesis (creationism, intelligent design, etc) even has the power to propose a single experiment which could support it. I think it should be pretty clear now that, for those inexperienced with evolutionary theory, choosing the experts to listen to should be a no-brainer. Thanks for listening, and take care.

How Are Fossils Dated?

2006-06-24T08:26:00.000-07:00

I’m going to try something slightly new here this week. As some of you know, I answer questions that you ask me through email, but I thought that instead of keeping those questions just one-to-one, there might be others listening with the same questions, who just aren’t as driven to email me. So, I’m going to be adding a listener email section to the beginning of the podcast, so keep those questions coming!

The premier listener email is from Roger, who writes: “Any time I talk with my Christian family about evolution, I am teamed up against for even questioning anything, which I find humorous, because I can hold my own when it comes to reason, but I’d like to ask a question about the evolution of humans. i listened to one of your podcasts dealing exactly with the transitions in to Homo sapiens and I learned a great deal, but I was still wondering that when I argue that humans and chimpanzees split at some point in time, how I can get it across to those arguing against me, when they make comments like "why aren't chimps still evolving in to humans!" i usually try to explain it that at some point they split off, but i feel like I’m missing that one big nail to close the coffin on that subject for good. i have also been questioned about why humans aren’t evolving further, and I suggested that in fact we are because of our increasing knowledge that has grown significantly in recent times and other small aspects, but anyway, that is a constant argument with family and friends back home, and if you could help with the "why aren't chimps still evolving in to humans" question better than I can, I’d be very appreciative. Thank you, and keep up the good work!”

This is, as many of you are no doubt aware, a common objection. Given the fact that Roger’s friends and family are Christians, I would suggest making an analogy which they can understand from their religious perspective. According to Christianity, all humans alive today are descended from Adam and Eve. It's also an easily observable fact that different groups of humans have very distinctive physical features (Africans, Asians, Caucasians, etc.) In the same way that we wouldn't expect an African person to give birth to an Asian baby, we also wouldn't expect a chimpanzee to give birth to a human baby. Instead, just like Africans, Asians, and Caucasians all have a common ancestor, chimpanzees and humans have a common ancestor. So asking why "chimps aren't still evolving into humans" makes as much sense as asking why "Africans aren't still evolving into Asians."

Now, this will be a tricky analogy for two reasons. The first is that I’m analogizing different human races with different species. This DOESN'T mean that the different races are in actuality different species. Many creationists have jumped to this conclusion for the purpose of denouncing evolution as racist. Be sure you make it clear that you're not arguing that the different races are actually different species- just that you're using them as an analogy. The second reason is that I’m using a Biblical concept (Adam and Eve) in my analogy, which may make them think that you accept their existence as part of evolution. Again, this is only to illustrate the analogy- if you're familiar with the concept of the Mitochondrial Eve, you might want to bring it up at that point.

Regarding the second objection, humans are indeed continuing to evolve. All species do, it's just that the rate of change depends on the selective pressures of our environment. For the past several millennia, humans have been able to control their environment significantly, and so few physical changes have been necessary. However, a new study has shown that there are several genes which are continuing to evolve, all of which are related to brain function. This makes sense, because the most crucial human organ that's tied into our reproductive success is our brain.

Okay, well I hope that’s helpful, and again, I’ll be looking for your questions. On to this week’s topic.

I’ve also received several emails asking about how scientists are able to accurately date fossils to the millions and millions of years old they often are claimed to be. I’ve been avoiding answering this question because it’s not really a biological issue, but since it is of close interest to evolutionary theory, I figured that it might be a good idea to do an episode on this topic anyway.

We’re going to have to start with some very basic nuclear physics. All matter is made up of atoms. An atom is essentially the smallest unit of matter which can be described as still having unique physical and chemical properties. Imagine that each kind of atom is a different kind of car. So, a hydrogen atom would be like a Mini Cooper, a carbon atom would be like a Toyota Camry, and an iron atom would be like a Chevy Suburban. Now, even though each type of atom is different in terms of size and capabilities, each has the same basic components. In fact, the particles that are smaller than atoms are basically interchangeable. That is, you could take a particle from a carbon atom and trade it with the same particle from an iron atom, and you wouldn’t be able to tell the difference. Just like you could take a steering wheel from a Chevy Suburban and get it to work in a Toyota Camry. I’m not too much of an mechanical expert, but I know that it’s not exactly the same, but it’s close enough for this analogy.

Well, these subcomponents in atoms are three basic types. They’re called electrons, protons, and neutrons. Protons and Neutrons have the same mass, but protons are positively charged, whereas neutrons don’t have any charge at all. Both protons and neutrons clump together, and form what is called the nucleus of the atom. Electrons are much smaller than either protons or neutrons, are negatively charged, and exist in a kind of an orbit around the nucleus. The number of protons determines the basic physical properties of that substance, and defines that atom as one element of matter or another. For example, all atoms with one proton are considered hydrogen atoms, all atoms with six protons are considered carbon atoms, and all atoms with 26 protons are considered iron atoms. Electrons give atoms specific chemical properties, and the number of electrons can be fairly fluid, but it’s not really relevant to the point I’m making, so I’m just going to move on.

Neutrons give atoms stability. Usually, there are about as many neutrons as protons in an atomic nucleus, although the larger the nucleus, you tend to find slightly more neutrons. The number of neutrons added to the number of protons gives the atomic weight, which is essentially the measure of mass for the atom, since electrons don’t really have much mass to them at all. As I said, usually there are the same number of neutrons as there are protons, so in the average atom of carbon, there are six protons, as I mentioned before, and there are also six neutrons. This gives the carbon atom the atomic weight of twelve. But not all atoms of carbon will have six neutrons. A few will have eight instead. This gives some carbon atoms the atomic weight of fourteen. Now, since the both have six protons, they’re both defined as carbon, but since they have different atomic weights, we classify them differently. Different atoms of one particular element that differ in terms of atomic weight are called “isotopes.” We can differentiate between them by referring to them as “Carbon-12” and “Carbon-14” based on their respective atomic weights.

Now, you remember that I told you that nuclei prefer to be stable, which means that they keep about the same number of protons and neutrons. So, since Carbon-14 has more neutrons than protons, it’s unstable- which means that something interesting happens. One of the extra neutrons ejects an electron, which means that it loses a negatively charged particle. Thus, the neutron becomes a proton. This changes the atomic number of the atom, raising it from six to seven, which means that the atom itself changes from carbon to nitrogen. The electron that’s ejected is thrown out of the atom, and is a form of radiation called beta-radiation. What’s particularly interesting about this process is that this change occurs at a measurable rate. We can determine empirically the amount of time it takes for one-half of an unstable isotope to decay into a stable isotope. This amount of time is called the “half-life,” and is unique to every different isotope.

As you may have guessed, we can use the known half-life of a particular isotope to calculate backwards in time, assuming we know the ratio of unstable to stable isotope to expect. And as it happens, there are several isotopes for which we do have this information- and carbon-14, which I already mentioned, is one of them. Carbon-14 makes up a small fraction of all the carbon in the environment, but it is basically a steady fraction. And since all living organisms take up carbon in any number of organic molecules, each living organism- including you- has the same ratio of carbon-14 in its body to carbon-12 as can be found in the environment. Now, of course this carbon-14 is being decayed to carbon-12 according to its half-life, but as long as an organism is taking in carbon from the environment, that carbon-14 is being replaced. The only time that the ratio stops being maintained is at death. Once an organism dies, the amount of carbon-14 in its body slowly but steadily becomes converted to nitrogen, leaving only the regular carbon-12. The half-life of carbon-14 is 5730 years, which means that 5730 years after an organism has died, there is only half as much carbon-14 left in its body as when it was living. After another 5730 years, there will only be a quarter as much, and then only an eighth as much, and then a sixteenth as much, and so on. Because the amount is halved every time, it never drops to nothing, but after about 60,000 years, it’s dropped too low to measure. This means that anything organic which was alive prior to then can be dated with reasonable accuracy according to the amount of carbon-14, what is called “radiocarbon dating.”

Now, you may be thinking at this point, “60,000 years is a long time, but most fossils are much older than this. How do you measure farther back in time without carbon?” Well, carbon is only one of several useful isotopes. You may have heard of uranium, the element that is usually used in nuclear reactors- well, no surprise, but it’s radioactive, and decays into lead at a very slow rate. Two rates, actually- two different isotopes of uranium decay into two different isotopes of lead, one with a half-life of 700 million years, and the other with a half-life of 4.5 billion years. That’s right- billion. In addition, potassium decays to argon with a half-life of 1.3 billion years, and rubidium decays to strontium with a half-life of 50 billion years. Now, obviously, this is far older than any existing fossil- but these dating techniques are used on the rocks which surround the fossils. Fossils exist in very specific and discrete layers of rock strata, and so all a geologist has to do is date the strata layer using one of these radiometric methods, and then any fossils found within that layer are placed roughly within that time frame.

But, are there any problems with these methods? Well, they’re not perfect, of course- no measurement is. But when scientists make measurements, they use the power of statistics- that is, if a measurement accurately reflects a particular phenomenon, then multiple, independent measurements of that same phenomenon should distribute around a clear average, with proportionally little variation. And that’s what happens- many measurements are made when dating a particular strata, or organic sample, and only if those measurements show a clear consensus is the date accepted. In addition, depending on the phenomenon, radiometric dates can be cross-checked with other observable dating methods- dendrochronology, for example- the counting of tree rings.

So, to review- certain radioactive and naturally occurring isotopes of various elements are known to decay into other elements at measurable rates, and by analyzing the ratios of the starting isotope and its product, scientists are able to reliably date organic objects only a few hundred years old, as well as inorganic objects more than a billion years old. These methods are independently verifiable, and can also be compared with other empirical dating methods for calibration.

What are the Practical Applications of Evolution?

2006-06-17T13:10:00.000-07:00

If this humble podcast isn’t enough Dr. Zach to fill your week, please go and check out the podcast produced by the New England Skeptical Society called the “Skeptic’s Guide to the Universe.” I was interviewed this week for their podcast, and had an absolutely excellent time. I know that most of you who subscribe to my via iTunes already know how excellent their show is, so I’m really just telling everyone else- if you like evolution, there are so many other topics germane to skepticism, and they do an excellent job of covering them.

Now, some of you may be thinking, “Here we’ve come 20 weeks, and I’ve never heard a single practical use of evolution.” In fact, this is a pretty common criticism of evolutionary theory, but it’s a criticism that doesn’t really take into account what science is.

Science is an exploratory, explanatory process. Science affords us the opportunity to ask questions about the way the world works, and be reasonably sure that the answers we find actually correspond with reality. This makes the knowledge associated with scientific inquiry significantly different from the knowledge associated with, say, superstition. While superstition will explain reality according to seemingly unrelated phenomena, such as one’s success in life and the color of cats that happen to walk in front of you, science will actually test those phenomena, substituting one for another as variables to determine if changing those variables actually does make a difference. Science, for example, would have a large group of individuals from all different backgrounds, divide them up into random groups, and then assign different color cats to walk in front of them, then follow up with a number of success criteria. If there is a significant difference imparted by a black cat, it’ll be shown in the numbers.

That’s what the intrinsic value of science is- it dispels superstitions and gives us real, accurate knowledge about the world around us. So evolution does the same thing- as a scientific theory, it explains the vast panoply of phenomena seen throughout the biological sciences- as the Russian geneticist Theodosius Dobzhansky noted, “Nothing in biology makes sense except in the light of evolution.” Evolution has tremendous explanatory power- it’s often referred to as the central framework of biological science, and rightly so. In a way, evolutionary theory was an inevitable scientific occurrence, because all the evidence points so strongly to common descent among all organisms. As I mentioned in the Darwin Day podcast, Alfred Wallace was another scientist working at the time who had come to the same conclusions as Darwin. And if neither of them had lived, there would have undoubtedly been another scientist who would have come to the same conclusions. That’s kind of the remarkable thing about Science- the conclusions are eventually inevitable, since they’re based on the facts of reality. At some point in history, Darwin or no, the evidence in Science would have screamed evolution to someone, and now that it has, our knowledge is all the more complete for it.

Now, that being said, I don’t want to leave you with the impression that Science is just about esoteric knowledge about the secrets of this world that are only of interest to ivory-tower scientists who cackle with glee about discoveries about which the average person could care less. Far from it- the explanatory power of evolutionary theory has innumerable practical benefits to each and every one of you, and I’ll try to explain a few today.

First a foremost, evolution helps us to understand a problem that is a growing concern in the field of health-care today. Namely, antibiotic-resistant bacteria. Now, antibiotics have been one of the greatest advances in health care in all of human history. The first, and still the most well-known antibiotic is penicillin. Penicillin works by inhibiting a process in the bacterial cell wall that is necessary to keep the bacteria alive. Essentially, bacteria are always springing leaks as a normal part of their life process, and they’re constantly patching those leaks. With penicillin, those leaks can’t be patched, water pours in, and the bacteria bursts and dies. It’s pretty awesome, actually. And in a perfect world, penicillin would mean that mankind would never have anything to fear from any bacterial infection, ever. But, this is not a perfect world, it’s a world that contains clear biological principles, and evolutionary theory is part of that. What would evolution predict in this situation? The antibiotics introduce a new element to the environment of the bacteria- one that makes it impossible to reproduce. In evolutionary terms, penicillin introduces a selective pressure. That is, all bacteria whose biology is interrupted by penicillin will no longer be able to reproduce, and won’t contribute anything to the species. However, evolution also predicts that due to random variation brought on by mutations and recombination (the latter not so much of a factor in bacteria), some members of a population can respond with greater fitness to any given selective pressure. That is, most bacteria will be killed, but a very few will have a genetic resistance to the antibiotic, and will either reproduce normally, or be able to reproduce at a higher rate than most other bacteria in the population.

So, given these predictions, what should we expect to see? The use of penicillin to kill bacteria will positively select those individual bacteria who are resistant to its mode of action, and they will be able to reproduce at a faster rate than those bacteria which are susceptible to penicillin. Over many generations, the majority of the bacterial population will consist of individuals which are resistant to penicillin, and it will be essentially useless.

And that’s precisely what has happened. Especially in situations where people are prescribed a course of antibiotics, but don’t finish the entire course, bacteria have been selected for throughout the human population which are resistant to many kinds of antibiotics. This means that biomedical research has to work hard to stay one step ahead of resistant pathogens like staphylococcus aureus, or “staph”, which can have deadly consequences if not controlled. And this evolution of resistance isn’t just relevant to health care- in agriculture, insects are becoming resistant to pesticides, also through natural selection.

But the selective pressures can also be used to our advantage. Take, for example, nearly every domesticate animal and plant in use today. Each one was, at one point, an organism very different from what we know today. Take the banana for example- you might think that the banana is a happy coincidence of nature- not so. The banana we eat today is a world apart from the wild banana which was originally domesticated and modified through selection by humans. The original wild banana was a small, tough, starchy fruit with large seeds. Through applied evolution, we now have a large, soft, sweet fruit with no seeds to speak of- even though our ancestors didn’t know what evolution was, they knew how it worked. And the same can be said about dogs, cats, cattle, fowl, corn, blackberries, apples, wheat, and just about everything you put on your table. If it wasn’t for evolution, we’d still be eating, quite literally, twigs and leaves.

Applied evolution is also a potent force in my own field, biomedical research. When investigating new genes, the selection of bacteria is used as a tool to help characterize and understand them. New drugs are discovered through an evolutionary process, in which millions of chemical compounds are sent through a rigorous selective process to see which molecule has the best properties with the least number of side effects. And all results are verified first in non-human animal models, on the evolutionary assumption that mice, rats, and other animals share our biochemical properties because of common ancestry.

The application of evolution even jumps beyond biology. In computer science, genetic algorithms, that is, a programming technique that allows the program to consider a range of possible alternatives and then evaluate them all based on their relative fitness to the problem at hand, is becoming more and more relevant. Evolutionary computing has been used to solve problems in mathematics, molecular biology, robotics, chemistry, and astrophysics.

So, to review, evolutionary theory is a Science, and like the other sciences, exists to examine the nature of reality. That’s its only intrinsic goal and purpose. However, as with all the other sciences, the discoveries of evolution have led to a number of incredibly useful and immensely practical applications that help us to live safer and better lives.

Who Was The Mitochondrial Eve?

2006-06-10T12:47:00.000-07:00

You may have heard, at some point in time, about the “Mitochondrial Eve.” This title refers to the most recent common female ancestor of all humans currently in existence. That is, a woman who lived in the past of whom all modern humans are descendents. Some of you may be wondering- did such a woman really exist? And the answer is yes, but- she wasn’t who most people think of when they think of someone named, “Eve.” The mitochondrial Eve was someone quite different.

Before searching her out, let’s first go over the word, “mitochondrial.” A “mitochondrion” is an important part of every animal and plant cell in existence. You can think of a cell like a large machine with a number of different systems within it that contribute in an interconnected way to the overall function of the cell, much in the same way that a car is a large machine with a number of different systems that all work basically together to make the car go. You can also think of your body- it’s composed of a number of subsystems, which contribute different functions to the overall performance of the body. Each system is composed of a separate structure, called an organ, which houses that particular function. In the same way, the separate subsystems of a cell are also made of individual structures, and biologist call them organelles, because they’re like organs, except they’re, to use a technical phrase, very very tiny.

One of these organelles is the mitochondrion. The mitochondrion is a small, oval-shaped structure that provides the cell with the energy that it needs to carry out all its other functions. You might remember from way back in high school biology class, the basic formula for the generation of energy. Sugar, or glucose, plus oxygen becomes carbon dioxide, water, and energy. Seems basic enough, sure, but there’s a lot of details that are sort of glossed over in the word, “becomes.” I’m not going to do much better either- I don’t really have time for an overview of the Krebs cycle, but I do want to point out that the “becomes” part takes place (mostly) in the mitochondrion. The mitochondrion contains a lot of really cool proteins that play a kind of chemical shell game with the electrons that are found in the carbon bonds of sugar, with the eventual result being the formation of a molecule called “adenosine triphosphate,” or simply, “ATP.” This molecule is the basic energy currency for all the important chemical processes that take place in the cell- if something exciting is happening, it’s using ATP.

So the mitochondrion is an absolutely essential part of the cell- it seems nearly impossible that plants or animals could have evolved without them. And the story of how we got them is an interesting little aside, but it’s also relevant to the subject of Mitochondrial Eve, I promise. Mitochondria don’t really seem as if they belong in cells- they chug along, virtually self-sufficient, really only relying on the rest of the cell to supply it with sugar and oxygen, and remove the waste products. In fact, it almost seems like a kind of parasite. But not really a parasite- parasites don’t give anything back to their host. Mitochondria are more like a symbiote, that is, they’re in a symbiotic relationship with the cell around them in which they provide things that the cell needs (ATP), and the cell provides things that the mitochondrion needs (sugar and oxygen). But if the mitochondria in your cells are part of a symbiotic relationship, when did that relationship start? Very likely, a long, long time ago. Probably before there were even multicellular organisms. Mitochondria actually resemble bacteria in a number of ways, and it’s likely that at some point in our evolutionary history, a species of bacteria that was very good at converting organic carbon to a simpler kind of energy currency was engulfed by a larger cell, that perhaps was pretty good at collecting organic carbon, but not so good at breaking it down. Since this pairing was of selective benefit to both species, they continued to associate, and since the selective pressure for the bacteria to function outside the larger cell was reduced, it lost that ability, and became stuck. Not that it cared, of course- all it cared to do was convert energy and replicate.

One strong piece of evidence for this scenario is mitochondrial DNA. That’s right- mitochondria have their own DNA, completely separate from what we typically consider as the center of DNA in the cell- the nucleus. Mitochondrial DNA contains most of the genes that mitochondria need to make their proteins and replicate (some have migrated to the nuclear genome, actually), and it replicates itself completely separately from the rest of the genome. Mitochondrial DNA even uses a slightly different genetic code from nuclear DNA- you’ll remember from the molecular biology primer that DNA is read in three-nucleotide segments called, “codons,” each of which correspond to an amino acid for the synthesis of proteins. In mitochondria, a DNA codon that would correspond to some particular amino acid in the nuclear genome would instead corresponds to a completely different amino acid.

So what do mitochondria, fascinating as they are, have to do with our mothers, and our mothers’ mothers, all the way back to the most recent common mother? Well, that has to do with two significant aspects of biology. One, as I’ve already mentioned, is that mitochondrial DNA replicates only in mitochondria, and doesn’t interact with the rest of the genome. This means that not only are mutations occur completely separately, but they also won’t be covered over by recombination with genomic DNA. The other thing is that sexual reproductions involves two gametes, or sex cells. One, the female, is very very large. The other, the male cell, is very very small. So small, in fact, that it really doesn’t contribute anything to the next generation other than its DNA. So what does that mean? That’s right- mitochondria are only present and passed down in the female gamete, which means that every mitochondria in your body right now is shared with your mother only, and not your father.

Now, this presents a very interesting opportunity. Your genomic DNA is composed equally of DNA from your mother and your father, so it’s not always that easy to figure out genetic ancestry, especially if you go back many generations. However, if you use mitochondrial DNA, you’re guaranteed a source of DNA that is only passed down from mother to child, and that is not complicated by recombination with genomic DNA. Now comes the fun part. The idea of an “Eve,” or a most recent common female ancestor, isn’t really that hard to grasp, nor is it dependent on genetics. It’s just common sense. Think about it- family trees tend to get wider and wider as they progress down the generations, so it stands to reason that they will also get narrower and narrower as you go back in time. If you go back enough generations, eventually every single human living today will have the same female name in their family tree. That’s just logical deduction. The same is true of all organisms, not just humans- there’s a bear “Eve,” a sparrow “Eve,” and an aardvark “Eve.”

The trick, then, is to take a look at the mitochondrial DNA from a wide sample of humans, and upon calculating the mutation rate, work backwards until you figure out when the most recent female ancestor would have lived. And to spare you the trouble of going over the calculations, I’ll just give you what’s been discovered- the mitochondrial Eve lived about 150,000 years ago. That’s quite a bit older than most people associate with the name “Eve,” but that isn’t the only difference. The mitochondrial Eve wasn’t the only human woman alive at the time- if she had been, then it’s likely humans would have gone extinct soon after. In actuality, the mitochondrial Eve was one of many women alive at the time, and the only thing that makes her distinctive is the fact that there is an unbroken chain of female descendents going from her to each and every one of you listening to this podcast today. Other women living at the same time may have had only sons, which means that their mitochondria wouldn’t have been passed on, even though their genomic DNA would have. Still other women would have had daughters, but their daughters might have had only sons, with the same result to the flow of mitochondrial DNA. For many years, in fact, the honor of mitochondrial Eve would have switched from one woman to the other, as different lineages either died out or produced only males.

Speaking of males, we men have something to offer to the study of gender-specific heredity- our Y chromosomes. Since Y chromosomes are only inherited from father to son, and since the Y chromosome doesn’t travel in pairs, it’s also an excellent source of information for paternal inheritance in human history- a marker of the Y-chromosome Adam. Interestingly, the data so far seem to indicate that the male who would have been the Y-chromosome Adam would have lived many years after the mitochondrial Eve, so there was virtually no chance they would have even lived in the same time, let alone known each other. And with that, the last of the comparisons to the mythical Eves and Adams dies.

So, to review, the concept of the “mitochondrial Eve” refers to the woman in human history whose mitochondria have been inherited by all humans living today. This is due to the fact that mitochondria remain somewhat separate from the rest of the cell, and carry their own DNA separately from the nuclear genome. Comparison of mutations in mitochondrial DNA from modern humans indicates that the mitochondrial Eve lived about 150,000 years ago, although her male genetic counterpart, the Y-chromosome Adam, lived much later.

Why did Sex Evolve?

2006-06-03T13:59:00.000-07:00

What is sex? Why did sex evolve? If you think about it, the time and energy invested by organisms in pursuit of sexual reproduction is pretty significant- wouldn’t it be a more efficient use of resources if all organisms reproduced asexually? Bacteria, by far the most abundant type of life on this planet, reproduce by binary fission- each bacterium simply splits in half, and where once there was one, there are now two. Doesn’t it seem as if existence would be a lot more simple if we could just split into two, instead of spending time searching for a mate, risking injury or death competing for that mate, and allocating resources to birthing babies? Why sex?

In order for populations of any organism to survive, they have to be compatible with the selective forces of their environment. But environments are not static- the study of geology is partially the study of changing environments. Over millions of years, continents move around, seas and lakes dry up and fill again, forests turn to grasslands and back again, and tropics can turn into frozen wastelands. So to be able to adapt to an environment constantly in a state of flux, populations have to change their makeup, and that means changing their genes.

Let’s look at an example of how populations change without sex. Bacteria, as I mentioned before, reproduce asexually- one becomes two, becomes four, becomes, eight, becomes sixteen, etc. The only mechanism for genetic change in bacteria is simple mutation. Mutations occur randomly in a population, and only affect one bacterium at a time, which means that unless some overwhelming environmental pressure is present, that mutation might appear and disappear just as quickly when that bacterium dies. If, however, some change in the environment makes that mutation extremely advantageous, so much so that death is the alternative, then the entire population crashes down to a handful of bacterium which have that mutation. So the life of a bacterial culture is very chaotic- it can be fine an dandy one day, and then the next the entire population is reduced to one or two lucky cells, which just happen to have protective mutations. Now, obviously, this strategy has worked out reasonably well for bacteria- as I mentioned, they’re the most populous type of organism on the planet. But it’s only efficient for them because they’re so small, they don’t need large sources of energy to survive, and they reproduce very, very quickly. In the evolutionary past, organisms which began to expand larger than bacteria found that asexual reproduction wasn’t as efficient or effective anymore.

First of all, sex didn’t evolve out of nothing. At its very essence, the purpose of sex is the horizontal exchange of genetic material between members of a population. Now, although bacteria are technically asexual, they have been observed to exchange bits of DNA with each other. This is a very rudimentary kind of genetic exchange, and it’s not considered sex, but I mention it only to let you know that it’s the same kind of exchange that characterizes what we would truly consider as sex. Also, sex is not all or nothing. That is, an organism doesn’t have to choose between only sexual or only asexual reproduction. Take yeast, for example- ordinary baker’s yeast. Yeast is actually both asexual and sexual- depending on the environment. If the environment is favorable, then yeast are happy to reproduce just like bacteria. But if the environment becomes difficult, then yeast undergo sexual reproduction. And how in the world does a single-celled organism like yeast have sex? Well, remember, the purpose of sex is exchange of genes. So this is basically all that’s happening- genes are being exchanged. But to grasp how this is accomplished, I’ll have to explain another concept: chromosomes.

Chromosomes are long chains of DNA that operate, more or less, as discrete units of an organism’s genome. If an organism’s genome is like an encyclopedia, then you can think of them as the individual volumes. You don’t find chromosomes in bacteria- their genomes are just one long strand of DNA. But in all the organisms from yeast all the way to humans, chromosomes are used. Chromosomes help to organize an organism’s genome for the purpose of a process essential to sexual reproduction- called meiosis. Meiosis is a lot like the binary fission that bacteria use- the cell simply splits in half. But instead of reproducing the entire genome and passing it on, meiosis begins with two copies of the genome, and produces cells which only have one. But why start out with two copies? Well, having two copies of a gene is like having two copies of a book. If something happens to one copy, you have the second as a backup. In the case of genes, mutations are the primary threat, and so having another copy in the cell allows for it to have a pretty good chance at fixing whatever mutations crop up. It also allows for efficient gene shuffling. For bacteria, the genome is one long strand of DNA, so it can be tricky to figure out where to add or subtract DNA in the even of a horizontal transfer. But if you split up the genome into discrete units, as in chromosomes, and then you make sure to have two copies of each, all you have to do is swap chromosomes back and forth to get a pretty efficient shuffling of the genes. Just think of shuffling playing cards- each suit represents a different organism’s genome, and each card is a different chromosome. If you shuffle the cards together, there are many possible groups of cards that could result. For bacteria, it’s like the cards are taped together in a long chain- not so easy to shuffle.

And that’s essentially what sexual reproduction does, all the way from yeast to humans. A single copy of each chromosome from both parental cells is combined to make a new cell that has two copies of each chromosome, one from each parent. The upshot of this is that mutations have a higher penetrance in the population, but without much risk, because if they’re unhelpful, then the second copy of the gene usually makes up for it, and if they’re helpful, they tend to increase in the population. This effect of gene shuffling allows for greater adaptability, as compared to asexual reproduction where all members of a population are essentially clones of each other. If the environment becomes unfavorable for one organism of an asexual population, then it’s unfavorable for all the organisms, because they’re essentially identical clones. But for a sexual population, gene shuffling makes more variation among the population itself, meaning that on average, a greater percentage of the population will be able to adapt to a changing environment that becomes unfavorable for many of the population.

One specific explanation of this advantage of sex is called the “Red Queen Hypothesis.” The name of this hypothesis comes from the character of the “Red Queen” in Lewis Carroll’s story, “Through the Looking Glass,” which is a sequel of sorts to the more widely-known “Alice in Wonderland.” In the story, Alice meets characters from a chess game playing a very abstract game of chess, and the character of the Red Queen tells her that in order to stay even with the other players, it’s necessary to run as fast as you can. This idea, of strenuous competition simply to maintain the status quo, is at the heart of the Red Queen hypothesis. Now, organisms, and even populations, don’t exist in a vacuum- they interact with all manner of other species all the time. So if two species are inter-dependent- let’s say, wolves which prey on rabbits- then a mutation in one species affects the environment of the other, in that the environment also includes all organism populations. So let’s say that a mutation appears in rabbits which makes them twice as fast. This mutation will be highly selected for in the rabbit population, and so within a short amount of time, the population of rabbits will be able to outrun all the wolves. Now, obviously, the selective pressure is now on the wolf population. All the slowest wolves will be unable to catch any of the faster rabbits, and will be selected against. Only the very fastest wolves, perhaps those with mutations that make them faster than the rest of the population, will be able to catch rabbits and pass on their own genes.

In addition to predator-prey relationships, there are also parasite-host relationships. Parasites tend to have shorter lifespans than their hosts, and thus reproduce much more quickly. So the potential for mutational change is much greater in a parasite, which means that for a host organism to successfully resist any particular parasite, it has to have the right combination of genes. The most effective and efficient way to maintain a population with the right combination of genes, while at the same time maintaining genes which are not necessary now but may be necessary in the future, is sexual reproduction.

To review, sex is the horizontal exchange of genetic information between members of the same population. The purpose is to increase the amount of genetic variability within a population, especially for those organisms which have a slow reproductive rate, such as vertebrates. The evolutionary benefit of this increased genetic variability is the enhanced ability to adapt to changing environments, which include interdependent organisms, as well as avoiding dependent organisms such as parasites. I know this hasn’t been quite as titillating as some of you might have hoped, but there’s much more evolution that goes into the naughty aspects of sex, and we’ll get to those eventually.

What is Irreducible Complexity?

2006-05-28T05:41:00.000-07:00

I received an email from a fellow podcaster, Emery Wang, who wrote to ask me about the arguments from scientists who deny evolutionary theory to be scientific. To be blunt, there really aren’t that many. The best place to find them, to the best of my knowledge, is the Discovery Institute, which is a creationist organization that tries its very best to portray itself as scientific. You can find them online at www.discovery.org. They do actually have a few scientists in their ranks, but only a couple with the necessary biological credentials to speak authoritatively about evolution from a scientific standpoint. Their shining star, so to speak, is a man named Michael Behe, although most of the other well-known names in the Intelligent Design movement, such as William Dembski and Jonathan Wells, are also affiliated with this group. Behe is a legitimate scientist, a biochemist actually, and a professor at Lehigh University in Pennsylvania. If you know Behe at all, you know him primarily as the author of the book, “Darwin’s Black Box: The Biochemical Challenge to Evolution.” It’s the book that has the old man and the chimpanzee sitting next to each other, facing in different directions. It’s in this book that Behe first put forth the idea of “irreducible complexity.”

Irreducible complexity was an incredible success for the Intelligent Design movement, because at its core it’s very intuitive- unfortunately, however, it’s also unscientific. But since the scientific theory of evolution is counter-intuitive, it was widely accepted by the public, while scientists who knew better were grinding their teeth in frustration.

Irreducible complexity works like this: Suppose that you have a mechanism of some sort, perhaps a mousetrap. This mousetrap is composed of several different parts, each of which is essential to the operation of the mousetrap. You’ve got the flat wooden base, the spring, the horizontal bar, the catch bar, the catch, and the staples that keep all the metal parts attached to the wood base. Now, if you have all the parts together and assembled properly, the mousetrap works like it’s supposed to- pulling back on the horizontal bar causes the spring to wind back, and the catch bar holds the horizontal bar in place as long as it’s jammed in place by the catch. Once the catch is disturbed, the catch bar is free to swing out of the way, and the spring winds shut slamming the horizontal bar down hard on whatever disturbed the catch. Makes sense. But let’s say that you remove one part of the mousetrap- the catch. Well, in that case, you can never set the trap because you can’t keep the catch bar still. Or let’s say that you remove the spring. Well, in that case, the trap will never close because there’s no force to move the horizontal bar. Or if you remove the horizontal bar itself, there’s nothing for the spring to move. You get the idea, I’m sure- if you remove one part of the mechanism, the whole thing can’t work. Thus, the design of the mousetrap is described by Behe to be irreducibly complex- in other words, the complexity of the design requires that it can’t be reduced any farther without losing functionality.

Now, you’re thinking, “So what’s the problem with irreducible complexity? Obviously a mousetrap won’t work if you remove the spring, that’s just common sense.” And so it is. And I don’t think there’d be any problem if Behe had stuck to talking about mousetraps. But he doesn’t- he’s a biochemist, and so he applies this concept of irreducible complexity to something much smaller than a mousetrap, something so small it’s invisible to the naked eye- a bacterial flagellum. A flagellum is a long, whiplike structure that is used by cells to move around. Think of the tail on a sperm cell, and you’re basically there. Bacteria use flagella too, and the structure is of a long, hollow cord attached to the wall of the bacterium where it hooks into a molecular rotor that spins in response to an ion gradient, as much as 1000 rpm. When the rotor spins, the flagellum spins, and the bacterium moves forward. It’s a little bit like an outboard motor on a boat, and like a motor, it’s composed of a lot of different parts, in this case proteins, each of which is essential for the proper functioning on the flagellum. Well, you can probably see where I’m going with this: if the mousetrap is irreducibly complex since removing one part means that the whole thing doesn’t work, then a flagellum is irreducibly complex for the same reason, right?

Wrong. And hopefully once I explain why, you’ll understand that it’s necessary to assume design in order to come up with a concept like irreducible complexity in the first place. Let’s go back to the mousetrap. Let’s say that I remove the catch- mousetrap doesn’t work, right? Well, not exactly. It may not work the way that the manufacturer intended for it to work, that’s true, but is it absolutely good for nothing? I would say no- I can set the trap by pulling the horizontal bar into place, setting the catch bar over it, and then carefully laying the trap upside down so that its own weight holds the catch bar in place. I can still bait the trap, and the jostling of the upside-down trap by an eager mouse can still move the catch bar out of position and cause the trap to release. It’s not the best way for the trap to function, of course. But even though it’s not as effective, it still does function to some extent. And even if you removed the spring, you could still use it as a paperweight- it’s still good for something.

Likewise, the incomplete flagellum is also good for something. Recent research on bacterial flagella have shown that very similar proteins functioning in a very similar way, but without the flagellar whip structure, have another kind of function in bacteria- they form the basis of a secretory apparatus- a mechanism that allows bacteria to inject toxins into other cells. So half a flagellum is still useful to the bacteria, even if it’s not functioning in the same way that the full flagellum does. Thus, the flagellum is not irreducibly complex. You see, evolutionary theory doesn’t have a particular goal in mind- that’s why Behe’s analogy of the mousetrap doesn’t make any sense. Someone who sets out to build a mousetrap has an idea in mind of what he wants that trap to be capable of, but this is not the case for evolution. Structures and systems are only useful to an organism if they confer some kind of selective advantage- it doesn’t matter how that advantage operates.

Think of a fighter jet- that’s a pretty complex system, right? Every component in that fighter jet is absolutely essential for its operation, otherwise it wouldn’t be built into it. If you were looking at the jet from Behe’s point of view, you would say, wow, this jet is incredibly complex. This must have been engineered from a blank diagram specifically to work this way. But we know better. Airplanes themselves have been constantly evolving, since even before the Wright brothers flew their machine in North Carolina. Before that, there were all sorts of variations on gliders. Each component was added gradually, but each airplane that was built started with the blueprint of the one that went before it, and then added new things. If those additions made a better airplane, then everyone copied it. If those additions made it worse, then it was scrapped. This is how evolution works- variations are made on existing organisms, and if they confer an advantage, they are selected for. Just as we know that an airplane motor evolved from a more simple model, we can also show that a bacterial motor, a flagellum, evolved from a more simple structure.

And in fact, after looking at it in both simple mechanical and biomechanical examples, what does the concept of irreducible complexity really give us? Not really anything useful at all. Because the critical component here is complexity- this is something which is dependent on the proposed function. A mousetrap is a reasonably complex way to kill a mouse, but it’s a simple enough paperweight at the same time. And a bacterial flagellum is a reasonably complex way to move a cell around in a fluid medium, but it’s also a reasonably good way to inject proteins into other cells, if you take a few parts away. And complexity is also dependent on the point in time which you examine a system. If you look at a stone arch, it seems irreducibly complex- if you remove a single stone from the archway the whole thing comes tumbling down. But we know that a common architectural technique is called scaffolding- that is, the archway is built under support from a wooden scaffold that allows the stones to be put in place without falling apart- and it’s only after all the stones are secure that the scaffold isn’t needed anymore. Biological systems can evolve using scaffolds also- with less selective pressure, new proteins and enzymes can evolve unique functions which may become essential if other scaffolding enzymes are lost to the dustbin of evolutionary change.

So, in the end, we’ve seen that irreducible complexity is neither- biological structures are, in fact, reducible to states which give rise to other functions, and these functions are only as complex as their context requires of them. It’s an attractive concept to people that aren’t familiar with evolutionary theory, but it’s just not born out by science.

How Did Humans Evolve?

2006-05-20T16:20:00.000-07:00

You’ve no doubt noticed the opening music that I’ve added. It’s the “Sunrise” piece by Richard Strauss, of the work, “Thus Sprach Zarathustra.” It’s more popularly known as the theme to the movie, “2001: A Space Odyssey,” and it’s from that usage that I take my inspiration. The opening scenes of the movie are subtitled, “The Evolution of Man,” and show a group of ape-like creatures learning how to use tools, and thus, become human. This aspect of evolutionary theory- the treatment of humans by evolution- is one of the central interests of the theory, because let’s face it- we humans are continuously preoccupied with ourselves. You’ve also seen this in the logo for the podcast- a variation of the classic, “March of Progress” imagery that shows hominids walking in a line at side profile, beginning with an ape-like creature and ending with a modern human.

So I thought that this week I would talk about the evolution of humans. I think we’ve tackled enough relevant topics so far to begin investigating the subject. The molecular evidence showed very clearly that chimpanzees are our closest living relatives, and so, logically, we must share an ancestor in common at some point in the past. This common ancestor, or concestor, wasn’t necessarily identical to modern chimpanzees- remember, all populations are in a state of evolutionary flux, it’s just that some are required by their environments to evolve faster than others. So although the human-chimpanzee concestor wasn’t a chimpanzee, we’d probably recognize it as being more chimpanzee than human if it were alive today.

So, humans and chimpanzees are both descended from an ape-like concestor. When did the lines split into human-only and chimpanzee-only lines? The answer may not be as cut and dry as you might think. The best theories based on the fossil evidence indicate that our concestor lived between 5 to 7 million years ago, at which point evolutionary forces caused one population to evolve human-like characteristics while the other line evolved more chimpanzee-like characteristics. However, new evidence has just been made available that shows by examining the human and chimpanzee genomes that human and chimpanzee ancestors diverged and then converged, before diverging for a final time less than 5 million years ago. Genetic analysis suggests that humans and chimpanzees evolved into separate species which then interbred, forming a hybrid species which then bred back into one of the parent populations. It’s not clear whether this human-chimpanzee hybrid returned to the human or the chimpanzee population, but the molecular evidence is clear that the hybridization did happen- the X chromosome has a particularly recent connection to the chimpanzee genome. This means that human-chimpanzee hybrid males would have been infertile, but the females were not, and thus returned back to the parental population, mixing chimpanzee and human genes each time. This new study by the Broad Institute in Massachusetts is scheduled to be published in Nature later this year, but the results have been made available on the Internet, so I’m sharing the scientific cutting edge with all of you.

But regardless of the human-chimpanzee hybrids, eventually the two lines did split for good. And gradually, our ancestors changed from being something that was willing to mate with a chimpanzee, into something that would rather hunt them for food, train them for entertainment, or sequence their DNA. What was the first step? The first step, as it seems, is literally a step. A bipedal step, to be precise- the first thing to distinguish our ancestors from chimpanzee ancestors is the ability to walk upright. But being able to walk upright doesn’t earn the scientific, phylogenetic designation of human- we designate all human species by the genus “Homo” as in our binomial, “Homo sapiens.” But these first human ancestors weren’t human enough to be considered part of our genus, and instead are called, “Australopithecus.” One species of this genus in particular is thought to have been ancestral to humans- Australopithecus afarensis, one specimen of which has been nicknamed, “Lucy.” Like most of the Australopithecines, Lucy lived in Africa.
Lucy, and the rest of her species, resembled chimpanzees in a lot of ways, but one difference is obvious- she walked upright, like a human. And not just sometimes, the bone structure of her pelvis indicates that she was upright most of the time.

The next big change in human evolution was the expansion of the brain. This was different than a lot of scientists had expected- they had assumed that a larger brain would have been the first change in the human-chimpanzee divergence, followed by other human traits such as bipedalism and tool use. This turned out not to be the case- walking upright evolved first. But the expanding brain followed soon after, and in fact it’s how we classify human species- that is, species that belong to the genus “Homo.” The first human, or at least the first recognizable human species to which we’re willing to give the designation, is the Handyman, Homo habilis. The Handyman lived between 1.5 and 2.5 million years ago, and he gets his name because rudimentary tools have been found with fossils of this species. These tools weren’t anything spectacular- just flakes of stone used as rudimentary knives, for the cutting of meat off dead animals. It’s unlikely that the Handyman was a hunter- more likely, he would have taken meat from already dead animals like a scavenger.

After Homo habilis, we find the next major step in human evolution. Homo erectus, or the Upright Man arose in Africa about 1.5 to 1.8 million years ago. Homo erectus had a larger brain than Homo habilis, and its anatomy was more similar to modern humans. But the most interesting thing about Homo erectus was its incredible success- it was the first human species to engage in actual hunting, and this had the effect of expanding its territory. Because its diet became more reliant on animals than plants, Homo erectus began to migrate- and thus spread out of Africa, and colonized southeast Asia, even going up farther north into Eurasia. There is also evidence that Homo erectus was able to control fire. There is some controversy about whether Homo erectus evolved into a separate species once it migrated out of Africa and into Asia, but even if this happened, the two species are so similar to make it almost impossible to tell today.

Homo erectus is the last major evolutionary transition before we get to modern humans, Homo sapiens. But how did this transition take place? There are a couple hypotheses- the “Out of Africa” hypothesis suggests that Homo sapiens evolved from the Homo erectus population back in Africa, and migrated out again, following the path that Homo erectus had taken earlier. The multiregional hypothesis suggests that Homo sapiens evolved in different geographical locations independently from different Homo erectus populations. This would suggest that European Homo sapiens evolved from a European population of Homo erectus, and the same is true of Asians, Africans, and Indonesians. This latter hypothesis is looking weaker and weaker as the genetic evidence piles up- any given human isn’t that significantly different from another, whatever the geographical origin. Richard Dawkins has come out in support of an “Out of Africa again and again” hypothesis, which suggests that Homo sapiens migrated out of and back into Africa several times before finally spreading out over all the continents. This hypothesis is backed up by genetic evidence tracing the genetic similarity of various genes among different human populations, and it looks the most promising. One of the major differences setting Homo sapiens aside from the other homonids is our use of language. This development is likely what allowed modern human society to expand and become as complex as it is now.

But what about the Neandethals? I haven’t forgotten them. Homo neandethalensis doesn’t figure in human ancestry- they aren’t direct ancestors. Analysis of mitochondrial DNA found in Neandethal fossils has confirmed this. What is most likely is that Neanderthals evolved from European populations of Homo erectus, and were either hunted or out-competed by the our ancestors, the Homo sapiens that had migrated into Europe from Africa. So you can think of them as our evolutionary cousins, if you like.

So that’s the basics of human evolution. The transitions aren’t really as simple as I’ve made them seem, and there are several subspecies that are transitional between the major species, but by and large, this is what you should know. After diverging with the other great apes, bipedalism evolved in the Australopithecines, but they weren’t human quite yet. Once a large enough brain evolved, rudimentary tools began to be used, as seen in Homo habilis, the Handyman. These then became migratory hunter/gatherers, as seen in Homo erectus. Modern humans evolved the use of language, and migrated out of Africa and all over the world, to where we are today.

What are Transitional Species?

2006-05-14T12:16:00.000-07:00

This week I’d like to take a look at an important concept to evolutionary theory- that of the transitional species. This concept is also often referred to by a less-meaningful term, “missing link.” This concept is packed with mistaken assumptions and used unscientifically far too often, which is partially the fault of uninformed journalists and partially the fault of creationists.

The problem is that there is really no such thing as a transitional species. The reason for this is that all species are transitional species. Now, obviously that sounds like I just contradicted myself, but let me explain. Dedicated listeners will remember from the episode about species that I never really defined what a species is. I gave a number of different methods that can be used to describe a species, but I also said that there’s no clear-cut definition, because every system has exceptions. So, if there’s no way to absolutely define species, then there’s no way to absolutely define transitional species. However, our brains don’t like ambiguity. Humans like to classify things, and so we come up with systems of organization and classification, such as the Linnean taxonomy that I’ve mentioned already. And usually classification makes sense- dogs are different species from cats, for example, by any objective measurement. But what about the ring species that I mentioned before, like the salamanders of which all subspecies but two can interbreed? There, the concept of species is not so clear.

In the same way that the concept of species can be provisionally meaningful to describe organisms at a single point in time, the concept of transitional species can be provisionally meaningful to describe organisms over a length of time, usually quite a long time, like hundreds of thousands or millions of years.

The concept, in essence, is fairly straightforward. Let’s say that you have a Species A that existed some time in the past, say, 10 million years ago. Currently, we observe Species C that exists now and shares a lot of the anatomical characters that are seen in fossils of Species A, but which also has several characters that are not seen in Species A. Evolutionary theory predicts that if Species C is descended from Species A, then there is likely a Species B which has more characteristics in common with Species C than Species A. We refer to Species B as a transitional species, but this is only in the context of the difference between Species A and C. These transitional species are often referred to as “missing links” because they are hypothesized to exist, given the fact that fossils are not found one after the other in a continuous line into the past, but are found corresponding to various points in prehistory, which is the reason that gaps exist in the fossil record.

The fact that these gaps exist is not a failing of evolutionary theory, however- it is a limitation of human investigation. We have no way of knowing where fossils are going to be exactly (although we can make some pretty good guesses), and we don’t know what specific fossils are going to be found (although we have some pretty good guesses on those too).

I also want to point out again that the concept of a species being “transitional” is only relative to the species that existed before and after it. And the concept of “species” is a classification that is made by humans strictly for organizational purposes. So a “transitional species” is a contextual classification, nothing more. This is what I meant when I said that there’s really no such thing as a transitional species. But since, given evolutionary theory, all species are in the process of evolutionary change (assuming they don’t become extinct), all species are themselves giving rise to new species eventually, and thus we can say equally that all species are “transitional.”

Now, since I’ve just gone to the trouble of confusing you at length by telling you that transitional species don’t really exist, let me confuse you further by giving you some examples of some. What I mean here is that, since the concept of a transitional species is contextual and relative to a specific classification, it can be meaningful if we view it in that restricted way- that is, if we assume a specific context relative to specific classifications.

For example, if you assume the classifications Fish and Amphibians, there are a number of excellent transitional species, including one amazing species discovered in the past year, called Tiktaalik. Tiktaalik lived about 375 million years ago, and belonged to the group of fish called “lobe-finned,” which are ancestral to all tetrapods, that is, all animals with four limbs. Tiktaalik had characteristics of both fish and tetrapods, including the scales and gills of a fish, limbs that are intermediate between fish and tetrapods, and the mobile neck and lungs of a tetrapod. That’s right- it had both gills and lungs. You can learn more about Tiktaalik at its very own website, http://tiktaalik.uchicago.edu/.

If, however, you assume the classifications Reptiles and Birds, there are also a number of transitional species, most notably Archaeopteryx. Archaeopteryx lived about 150 million years ago, and would technically be classified among dinosaurs, which are a subset of the reptile group. Archaeopteryx had characteristics of both reptiles and birds, including a long bony tail, and a bones structure that is very similar to a reptile. It also had fully-formed, flight-capable feathers, which makes it distinctly similar to birds. It’s unknown whether Archaeopteryx was able to fly the same way that modern birds do- it may have only been able to glide, or perhaps to take wing-powered hops, but the feathers are there, and they show it to be distinctly transitional between reptiles and birds.

There are also a couple well-characterized transitional species in the mammal lineage, especially in the evolution of the whale and the evolution of the horse. Ambulocetus was an amphibious mammal and ancestral to modern whales- it lived about 50 million years ago and has many characteristics of modern whales and many characteristics of the artiodactyla family, the cloven-hoofed mammals, which it is transitional between. In the evolution of the horse, clear transitions can be seen between Eohippus, which is recognized as the first horse, and all the later species such as Mesohippus, Parahippus, Merychippus, all of which used fewer and fewer digits on the foot until our modern horses, which use only one.

More recently, and of more personal interest, is the evolution of humans. Although the specific relationships between fossil species are still somewhat controversial, it is clear that transitional species exist between Australopithecus and modern Homo sapiens, including Homo habilis, and Homo erectus. Homo neanderthalensis, also known as Neandethal Man, is not our direct ancestor, as has been shown by mitochondrial DNA analysis, but is a related ancestral human species, sort of like an uncle.

To review- a transitional species is a classification based on a specific context- a species that exhibits characteristics of species that existed prior to and following it. Gaps in our knowledge of specific transitional species is a function of limited detection, not a failing of evolutionary theory. And many excellent examples of transitional species exist between any number of biological classifications, and more are being discovered every year.

Molecular Evidence 6: Objections to Molecular Evidence

2006-05-04T06:54:00.000-07:00

All right, this is the final podcast in a series of six that I’ve planned on the molecular evidence for evolution. I’ve been using Dr. Douglas Theobald’s resource on Talk.Origins.org pretty heavily, so you can use that to follow along with the previous five episodes if you like.

To get to this point, I’ve introduced you to the basics of molecular biology, I’ve explained why function follows from structure, why structure follows from sequence, and why sequences are functionally redundant, both with amino acids and with nucleic acids. I’ve shown you sequence homology between different species, verifying the evolutionary hypothesis. I’ve also taken you through noncoding DNA sequences, analyzing three different kinds of molecular artifacts which also verify the evolutionary hypothesis. Every last bit of genetic information that’s contained in your genome indicates that you share a common ancestor with chimpanzees and other primates, by any conceivable measurement.

Genetic information has an advantage over other kinds of evidence, such as fossils. Fossils are the result of genes that existed in the past, but the genetic information we analyze in living organisms is very much a part of the here and now. It’s a living, breathing (literally) piece of evidence. We can measure it, find out how it works. If you compare the fossils of two different kinds of dinosaurs, for example, which both have the same kinds of foot structure, we can hypothesize that they were related phylogenetically, but that’s all we can do. If we were to take two different kinds of organisms today, we can do the same thing, but we can go one step further- we can compare their DNA. Every physical structure that exists as a part of their body is the result of their particular genes- their genotype. The physical manifestation of that genotype is called a phenotype. So, a gene which codes for a protein which regulates beak shape in a bird is part of its genotype, and the shape of the beak is the phenotype. For living organisms, we can correlate genotype with phenotype, and since heredity is the only known mechanism for shared genotype, it’s so much more powerful than just comparing the way animals look.

Despite the power of genetic evidence, there are still detractors, people who don’t accept the conclusion that the molecular evidence supports the evolutionary hypothesis. This is just one of those things that happens in Science- not everybody is going to accept your conclusions. That’s okay, and it happens with just about everything. There are people who don’t accept the HIV hypothesis of AIDS- they don’t believe that the Human Immunodeficiency virus is what causes AIDS. There are also people that don’t accept the cholesterol hypothesis of cardiovascular disease- they think that you can eat as much cholesterol as you want and you won’t get a heart attack. Some of these criticisms come from scientists- the scientific community in general isn’t monolithic and dogmatic, at least it’s not supposed to be. There are always conflicting hypotheses in Science, and it often takes a long time before there’s sufficient experimental evidence to show that one hypothesis is right and the other is wrong. Whatever the case, when the evidence piles up, scientists generally all get behind the hypothesis that the evidence supports, and the conclusion is, for all practical purposes, a closed issue.

This is the case for evolution. The evidence supporting evolutionary theory has been piling up for a couple centuries now, and it’s basically a closed issue in the scientific community. It’s like the HIV hypothesis of AIDS or the cholesterol hypothesis of cardiovascular disease- there’s just no debate among scientists; the evidence is overwhelming.

The reason why I’m making this point is because I want to make it clear that the objections raised against evolutionary theory don’t come from scientists. They come from people with an ideological and theological presupposition that demands a rejection of evolution- of course, I’m talking about creationists. If you have noticed, there’s a critique of Dr. Theobald’s reference at Talk.Origins that is written not by another scientist, but by a lawyer, named Ashby Camp. Why would a lawyer be interested in critiquing scientific evidence for evolution? Well, it just so happens that Mr. Camp is not just a lawyer, he’s a Church of Christ minister and avowed creationist who wrote his critique for the website TrueOrigin.org, which is subtitled, “exposing the myth of evolution.” Clearly, Mr. Camp has a theological interest in portraying evolution as false- he views evolutionary theory as incompatible with his own theology, and therefore must choose one or the other. Obviously, he’s chosen to assert his theology- but this is not always the case. Dr. Kenneth Miller is an evolutionary biologist who finds the science of evolutionary theory compatible with theology, and he writes about this in his book, “Finding Darwin’s God,” which I can recommend highly as a popular introduction to evolutionary theory, especially for those who are under the same assumptions as Mr. Camp.

Since arguments against scientific theories from theology can’t offer competing scientific evidence, they almost always employ a type of argument commonly referred to as an “argument from ignorance.” These are very attractive, but are also logically fallacious. They’re easy to spot, too- all you have to do is listen or watch for someone to start talking about something that Science “doesn’t know,” or talk about something which “may be possible,” even though there’s no evidence to support the conclusion now. The implication is that since something is not known to be the case, it is not the case, or vice versa. Since these arguments against Science often come from a theological perspective, they’re also known as “God of the Gaps” arguments, because the idea is that there is some gap in scientific knowledge that is explained only by assuming that a deity is responsible for that phenomenon. Coming from a theological perspective makes these kinds of arguments no less fallacious, however, and if you run across any kind of criticism of this sort, be sure to pay attention for the arguments from ignorance, or the “God of the Gaps.”

This kind of argument is precisely what we see from Ashby Camp. When confronted with the evidence from protein functional redundancy, he says, “how could one be sure that God would not conserve amino acid sequences (or the underlying codons) when creating cytochrome c in separate species? After creating cytochrome c in the first organism, it certainly is conceivable that he would make changes to that blueprint only when necessary for his purpose. In other words, the default in this instance may be similarity rather than dissimilarity. There is no basis for demanding that God introduce novelty for novelty’s sake.” In other words, since we don’t know that God did not create cytochrome c functionally redundant in different species, he must have done so. Did you catch the argument from ignorance? When confronting the evidence from DNA functional redundancy, he says basically the same thing, “how could one be sure that God would not conserve codon sequences when creating cytochrome c gene in separate species? After creating the cytochrome c gene in the first organism, it certainly is conceivable that he would make changes to that blueprint only when necessary for his purpose. In other words, the default in this instance may be similarity rather than dissimilarity. Again, there is no basis for demanding that God introduce novelty for novelty’s sake.” Same argument from ignorance, and it’s just as fallacious the second time around.

The same mistake is repeated for the rest of the evidences. Regarding transposon, he says, “God may have had a functional reason for initially placing them at the same chromosomal location in separately created species. He also may have had a functional reason for designing certain transposons with an insertion bias for certain loci.” Regarding redundant pseudogenes, he says, “maybe lateral gene transfers occurred in the past through a mechanism that targeted a specific location in recipient cell DNA and that did not leave viral sequences near the inserted pseudogenes. Perhaps this mechanism is no longer operating, as a result progressive degeneration, and the viral action we see today is a distorted remnant of that originally designed process.” Regarding endogenous retroviruses, he says, “God may have had a functional reason for initially placing them at the same chromosomal location in separately created species. He also may have had a functional reason for designing a system to favor the insertion of certain ERV sequences at certain loci.” Did you catch all those “maybes” and “perhaps?” That’s right, obvious giveaways that he’s arguing from ignorance.

And it’s also the special case of the argument from ignorance, the God of the Gaps. For every piece of evidence, Mr. Camp makes the statement, “God may have a purpose for doing so that is beyond our present understanding.” In other words, Mr. Camp is making the claim that there is some kind of gap in our scientific knowledge about molecular biology in which some yet unknown purpose may have been intended by God.

This should be pretty easy for you now. When it comes to criticisms of the evidence for evolution, keep your ears open for arguments from ignorance, and that special case, the God of the Gaps. If you do that, it should be pretty easy for you to shut down critics who use logical fallacies as their only weapons. Well, this is it for the Molecular Evidence for Evolution. I hope this has been interesting and instructive, and more than that, I hope I’ve motivated some of you to check out the evidence for yourselves. Next week, I’ll be back to answering questions. Take care.

Molecular Evidence 5: Endogenous Retroviruses

2006-04-21T21:24:00.000-07:00

All right, this is the fifth podcast in a series of six that I’ve planned on the molecular evidence for evolution. I’ll be using Dr. Douglas Theobald’s resource on Talk.Origins.org pretty heavily, so you can follow along with me there if you like.

The fifth and final piece of evidence is from endogenous retroviruses.

First, I want to get something straight- I know that the plural of virus is virii. But I’ve heard plenty of scientists use the word viruses, so I’m going to use it here. If I was writing a paper, I’d use virii, but this is just a podcast, targeted toward non-science people, so I think viruses is fine. If any of you want to try to talk about this subject with your friends or family, you’ll look a lot less crazy if you don’t insist on calling them virii, at any rate.

I’m sure most of you have experienced some kind of illness from a virus, but what is it, exactly? A virus is about as low as you can go on the complexity scale of life and still have people arguing about whether is actually qualifies as something that’s actually alive. If you remember me talking about transposons from two weeks ago, you remember that a transposon is basically just mobile DNA that has to stay within a cell. Well, a virus is just a little more complex than that- it’s mobile DNA that can leave a cell. Structurally, a virus is a shell made of protein or membrane filled with genetic information. That’s it. A virus can’t reproduce on its own, doesn’t take in energy, doesn’t have a metabolism, doesn’t grow, doesn’t respond to stimuli, and isn’t made out of cells. It violates almost all criteria for life, and yet… it is organized, it is composed of the same macromolecules that all other life forms are composed of, and it can reproduce. It might be a little disconcerting to think that you’ve suffered through an infection by something that isn’t technically alive- at least with a bacterial infection, the little bugs are growing, eating, and reproducing- if they’re alive, they can be killed, and that’s what antibiotics are for. You can’t technically kill a virus, since it’s technically not alive.

Depending on the type of virus, they can be spread in different ways and affect different cells in your body. Some viruses don’t last if they’re exposed to air, some do very well as airborne particles. Some viruses target liver cells, like hepatitis C, and some viruses target immune cells, like HIV. All viruses follow the same basic infection cycle. First, they attach somehow to a host cell. Then, either the viral genome itself or the entire virion moves into the host cell. Once the genome is exposed to the host genetic replication machinery, it begins to transcribe viral genes that code for proteins which are necessary to make more virus particles. The viral genome is also replicated during this time, and these copies are packaged into full virus particles, and this process continues until the cell explodes or until it dies from metabolic drain. At this point, the newly replicated virus particles are free to infect more cells, move around the body, and even venture outside the body where they can come in contact with other potential hosts.

Viruses carry their genome either as DNA or as RNA. For the viruses that use DNA, it’s treated just as the DNA from the host cell. The DNA is transcribed into RNA, which is then translated into protein. Some of the viruses use RNA sequences to store their genetic information, however. These viruses use RNA as their template and make more RNA copies from that template, which are then translated into protein. But there’s another variety of RNA viruses that is a little more complicated. It uses the same proteins that I told you were used by retrotransposons to replicate- reverse transcriptase and integrase. These viruses use reverse transcriptase to reverse transcribe their RNA genome into a DNA sequence, which is then integrated into the host genome. Because of this process, these viruses are called retroviruses. The most well-known retrovirus is human immunodeficiency virus, or HIV, which is the virus that causes AIDS by targeting specific immune cells. Any of you that have cats are probably aware of the Feline Leukemia virus, which is also a retrovirus.

Some of you may be thinking- hey, these retroviruses sound awfully similar to the retrotransposons you talked about before- and they are, certainly. It seems very likely that that retroviruses and retrotransposons share common ancestry way back in the past, but trying to establish which one came first is more than a little difficult at this point.

So, now everyone knows what a retrovirus is, I hope, but what is an endogenous retrovirus? Well, you know that a retrovirus functions by inserting its DNA into the genome of its host cell. Once that happens, the DNA is there for the entire life of the cell. But what if that cell has an exceptionally long life? What if it’s, for lack of a better word, immortal? Germ cells are kind of immortal- the cells that are passed on to descendents during procreation. In males, these would be spermatocytes, and in females, these would be oocytes. Let’s say that a retrovirus infected a germ cell which produced spermatocytes that fertilized and egg and resulted in a new organism. What would happen? Well, since that germ cell has a copy of the viral DNA, and all the cells in the progeny were derived from that germ cell, every single cell in the body of the progeny would also have the viral DNA. At this point, the virus is endogenous- that is, it exists natively in the organisms own’s genome from birth because of an infection that occurred one or more generations previous to it. The virus can still be actively transcribed, and continue to be infectious, but it will continue to be passed on to further progeny. Since the endogenous retrovirus, or ERV, is not necessary for reproduction, there is no selective pressure to keep it free from mutations, and so ERVs will acquire mutations at about the same rate as other non-essential non-coding DNA. Eventually, ERVs are rendered inactive because of these mutations, and they sit quietly in the host genome, a testament to an infection that occurred generations in the past.

The evolutionary hypothesis would posit that for any two given organisms, finding common ERV sequences in their respective genomes would be a confirmation of common heredity between them, since the only mechanism to explain common ERV sequences would be a shared ancestry. There is no conceivable reason, outside of common descent, why any two unrelated organisms would have the same ERV insertions. So let’s look at the evidence.

ERVs make up as much as 8% of the human genome, comprising close to 30,000 separate insertions. There have been seven common insertions characterized so far between humans and chimpanzees, with more expected as the published genomes of both are analyzed more closely. A Russian study looked at the insertions of the Human Endogernous Retrovirus, or HERV-K, and compared insertions of HERV among different primates to see which insertions are held in common by which species of primate. Figure 4.4.1 at the Talk.Origins website that I’ve been referencing comes from this study- I’ve included it also in the mp3 that you’re listening to- if you open it in iTunes, you should be able to see it as attached artwork just after the logo. This figure shows all of the HERV insertions that were found, and a cladogram was constructed to indicate phylogenetic relationships. Individual arrows mark specific insertions, and all branch points to the right of an arrow have that insertion in common. The cladistic relationship predicted by ERV evidence is exactly what is predicted by evolutionary theory- humans and chimpanzees are more closely related, with gorillas as the next most related species, followed by orangutans, gibbons, Old World monkeys, and New World monkeys. This takes into account evidence from 14 separate insertions. Again, there is no reason for insertions to be held in common without common ancestry. The evidence from ERVs is devasating to the null hypothesis, and exceptionally strongly supports evolutionary theory.

Molecular Evidence 4: Redundant Pseudogenes

2006-04-15T08:00:00.000-07:00

All right, this is the fourth podcast in a series of six that I’ve planned on the molecular evidence for evolution. I’ll be using Dr. Douglas Theobald’s resource on Talk.Origins.org pretty heavily, so you can follow along with me there if you like.

The fourth piece of evidence is from redundant pseudogenes.

A pseudogene is very similar to a regular gene at the DNA level, but with one crucial difference- it never gets transcribed. You can think of a pseudogene as a vestigial molecular structure- sort of like how the appendix is a vestigial organ in humans. Vestigial means that a structure is in degenerate, or atrophied, or somehow imperfect state. For example, the human appendix is basically a degenerate cecum, which is an essential digestive organ in mammals which eat lots of plant matter. You can get along fine without your appendix, but we still have them as an evolutionary carryover from a more herbivorous ancestor.

In the same way, pseudogenes are evolutionary carryovers from our ancestors, and we have them for a few different reasons. The first kind of pseudogenes are called “processed” pseudogenes. You’ll remember from last week’s episode that there are important enzymes used by retrotransposons, which allow them to copy and paste themselves throughout the genome. These enzymes, reverse transcriptase, and integrase, function by taking an RNA transcript, which is a copy of the original gene, and copying it back into a DNA form, which is then integrated back into the genome. This process is beneficial to retrotransposons, since it’s the only way that they can proliferate. But the same enzymes that work on retrotransposon RNA transcripts can work on other RNA transcripts as well. Since all genes are transcribed from the genome into RNA transcripts, there is the potential for reverse transcriptase and integrase to take a random RNA transcript, turn it back into DNA, and stick it back in the genome somewhere. Now, you might think, great, extra copies of a gene! That’s got to be a good thing, right? Well, not really. You’ll remember from the Junk DNA episode that I talked about regulatory sequences that exist in the noncoding DNA surrounding a gene. These regulatory sequences are actually quite important, and without them, you don’t get proper expression of a gene. Since integrase is fairly random in the way that it inserts DNA into the genome, what you end up with is a copy of the original gene stuck in a place that is of absolutely no value- it can’t be expressed there, since there aren’t the proper regulatory sequences.

The second way that pseudogenes can form is through gene duplication. This process occurs through improper recombination of chromosomes during the reproductive process called “meiosis,” which is necessary for sexual reproduction. Most organisms are considered “diploid,” which means that they have two copies of each chromosome. For sexual reproduction, the number of chromosomes in a germ cell has to be reduced to one copy for each chromosome, and meiosis accomplishes this through a mechanism that I won’t detail just yet. One of the stages in meiosis involves recombination between both copies of a chromosome before they’re separated, during which each can swap DNA sequences with the other. Picture two identical twin girls, one wearing a blue headband and one wearing a red headband. If they were to exchange headbands, they’d look basically the same, except for that one small change. That’s similar to what happens with chromosomes, in which sister chromatids exchange DNA. But sometimes mistakes can happen, and the exchange isn’t completely equal. Imagine the twin girls again, exchanging headbands, but only one girl is able to make the exchange. What you’d end up with is one girl with no headbands, and the other girl with two. For chromatids, this means that sometimes one can end up with two copies of a gene, which can get passed on to future generations. In addition to chromosomal recombination errors, sometimes whole chromosomes can be doubled, again due to a problem with the meiosis mechanism. This kind of thing rarely happens in animals, and is usually very detrimental. Down Syndrome is also known as Trisomy 21, which means that an extra copy of Chromosome 21 is present and causes developmental problems. Chromosome duplication, also known as polyloidy, is more common in plants. Recently, evidence has been found that long segments of the human genome exist as replications, although the mechanism for this process is unknown. Whatever the case, be it recombination or segmental duplication, these duplicate genes represent a pretty significant portion of the genome- over 15,000 duplicate genes according to a recent review out of the University of Michigan, which is close to 2/5 of all genes.

The final way that a pseudogene can arise is through evolutionary forces. Just like the ancestral cecum shrank down into an appendix because the evolutionary necessity of having a way to digest a large volume of plant matter was no longer present in human evolution, the lack of selective pressure for a particular gene can make it more likely that mutations and other changes can occur without sacrificing evolutionary vigor. To borrow from the cliché, “if you don’t use it, you lose it.” For an essential gene, a mutation that causes it not to work is likely fatal, or at least decreases the ability of that organism to procreate. Either way, mutations in essential genes have a hard time staying in a population. But if a gene isn’t necessary- let’s say, a gene that synthesizes an essential molecule in a population where that same molecule is available in abundance in the common food sources. In that case, mutations that disable that gene aren’t any more likely to occur on an individual basis, but they are more likely to increase in frequency within the population because there’s no selective pressure to maintain a fully-functioning gene. You’ve probably already guessed this, but this is the reason why duplicated genes often become pseudogenes- if you have two copies of an essential gene, there’s no selective pressure to keep both of them free from mutations- you only need the one. This is why many pseudogenes are found in close proximity to fully functional copies of the normal gene- there’s no pressure to keep both copies functional.

So why is this relevant? Well, for one thing, the formation of pseudogenes is controlled by random processes, whether by retropositioning or duplication. So there’s no good reason why two completely different organisms would have the same pseudogenes in the same genomic locations… other than common heredity. But wait, there’s more! Because of the fact that pseudogenes are largely nonfunctional, they pick up mutations at about the same rate as other noncoding DNA. And as you already know, the acquisition of individual mutations is itself a random process, so there would be even less reason for different organisms to have identical pseudogenes in the same locations with the same mutations… other than common heredity. So let’s look at the evidence.

There are, in fact, many shared pseudogenes between humans and primates, including the enolase pseudogene, hemoglobin pseudogene, sulfatase pseudogene, and the steroid 21-hydroxylase pseudogene. In this last pseudogene, an 8-nucleotide deletion has been found in both the human and the chimpanzee versions of the pseudogene, which in both is responsible for deactivating the gene function. Outside of common ancestry, there is no reason why humans and chimpanzees would share the same pseudogenes, and especially no reason why they would share the same inactivating mutations. This evidence strongly supports evolutionary theory.

Molecular Evidence 3: Transposons

2006-04-08T06:58:00.000-07:00

All right, this is the third podcast in a series of six that I’ve planned on the molecular evidence for evolution. I’ll be using Dr. Douglas Theobald’s resource on Talk.Origins.org pretty heavily, so you can follow along with me there if you like.

The third piece of evidence is from transposons.

Now, you’ll remember that back in episode 106, we looked at junk DNA, and what it meant. Well, for the past two weeks we’ve been looking at the coding part of the genome, essentially the genes themselves and the products of their transcription, that is, proteins. For the next three weeks we’re going to leave those evidences behind in the coding part of the genome, and we’re going to look at the noncoding part, which some people call “junk.” That’s right- one man’s junk is another man’s treasure, and so-called junk DNA is a treasure of evidence, very powerful evidence in support of evolutionary theory.

Well, what is a transposon? A transposon is a mobile section of DNA. What I mean by saying that it’s “mobile” is that it can literally change its position within the genome. I’m afraid that there really aren’t any good analogies for this, so I’ll just have to resort to some bad ones. You remember that before I said that the genome is kinda like a magazine, where the genes are articles which are separated by pages and pages of advertisements. Well, you know those annoying advertisements that, instead of being printed in the pagestock, are printed on little cards and just kinda stuck in the magazine, near the spine? Or maybe one side of the card is glued to the page with that flimsy, rubbery glue that you have to peel and pull off at the same time? That’s basically what a transposon is. In the same way that those little cards are mobile advertisements, a transposon is mobile DNA.

Let’s say that you’ve got one of those annoying sticky cards in your magazine, and you pull it out. But then you accidentally drop both the card and the magazine, and they both land together. The card is going to be restuck in the magazine, but probably not in the same place. It might be stuck to the front cover. It might be stuck on another advertisement page that had nothing to do with where it came from. Or, it might be stuck on the story that you were reading, obstructing a couple paragraphs and preventing you from finishing the article. Well, that’s also what happens with transposons. A transposon can be cut out of the genome and then reinserted someplace else. The genome is a pretty big sequence, so there’s lots of places a transposon can reinsert. Sometimes a transposon will reinsert at another noncoding region. Actually, this is usually what happens, since there’s so much more noncoding DNA than there is coding DNA. But sometimes a transposon can reinsert in a coding region, and disrupt a gene. Now, in the same way that the stuck card in your magazine prevents you from reading the story, the inserted transposon prevents the gene from being transcribed, effectively turning it off. You might also think of a transposon like a pop-up ad on a website that pops up out of nowhere and obscures the content that you’re trying to see on the page.

Now, one of the obvious questions at this point is: why in the world do transposons exist? They seem pretty annoying, from a strictly genetic perspective, and they also seem dangerous, since by inserting into a gene a transposon could cause a debilitating mutation or disease. And indeed, this is the case- transposons are mutagenic, and are associated with a number of diseases, including hemophilia, severe immunodeficiency, and cancer. So why do transposons exist in genomes at all? Well, you can think of a transposon as existing as a separate selective entity to its host genome- almost like a DNA parasite. Now, admittedly, this is a hard concept to grasp, since we’re talking about a chunk of DNA and not something typically associated the word “parasite,” like a mosquito or a tick. But remember that even though it’s easier for us to think of concepts in black and white terms, science isn’t quite so discrete. Transposons come in two basic types: class I transposons, which are also called “retrotransposons,” and class II, which are simply DNA transposons. Retrotransposons function by allowing their sequence to be transcribed into RNA. It’s at this point that a retrotransposon does something odd- it reverse-transcribes the RNA sequence back into DNA, and this DNA copy of the original retrotransposon sequence is then integrated back into the original genome, but at a different location. Both of these functions are carried out by enzymes whose genes are encoded for within the retrotransposon sequence itself- pretty clever. In fact, this is the same way that retroviruses like HIV work- except that a retrotransposon never leaves the cell in a virus particle. You can almost think of a retrotransposon as a virus that made itself comfortable within an organism and decided never to leave. DNA transposons use a different enzyme called transposase, which actually cuts out the genomic transposon sequence and puts it back into the genome in a different location. This skips the whole process of reverse transcription of RNA that retrotransposons use, but you get the same basic effect.

Retrotransposons themselves come in two basic types- long and short. The longer ones are called “long interspersed elements,” or “LINEs.” The shorter ones are called “short interspersed elements,” or “SINEs.” LINEs contain the two enzymes necessary for the reverse transcription and integration that I already mentioned- called, predictably, “reverse transcriptase” and “integrase.” SINEs, on the other hand, don’t carry these genes, and so are dependent on LINEs for their propagation. You can think of the enzymes used by the retrotransposons as a “copy and paste” function, just like in a word processor. The transposase used by the DNA transposons is more like the “cut and paste” function, however. And I’m sure you know that if you cut and paste words in a document, you may screw up the meaning of the text, but you’re not going to significantly add or subtract to the length of the text. If you copy and paste, though, you’ll find that not only have you screwed up the meaning of the text, but you’ve also added overall length to it, and depending on how many times you paste, you may have added a lot of length to it. And that’s what we see with retrotransposons- both LINEs and SINEs are found all throughout the human genome, for example, and are responsible for nearly 30% of the total size of the genome. 30%! That’s a lot of space wasted on DNA parasites.

But it’s not all for naught. Because so much of the genome is made up of these predictable sequences, and because these sequences occur randomly in different places in the genome, transposons offer an excellent way to identify individuals genetically. I’m sure you’ve heard of technology like “DNA fingerprinting,” or something similar, that is used to establish paternity using a genetic test. These tests take advantage of the fact that two different individuals in a population having the transposon sequences in the exact same location is extremely rare, so much so that you can conclude genetic relation based on similar patterns of genomic transposons. Well, I’m sure you’re all astute enough to realize that if transposons can be used to establish a hereditary relationship between a father and his offspring, it can also be used to establish a hereditary relationship between two organisms from different species! Remember, the only observed mechanism for two organisms to have similar genomic sequence is through heredity, and so if two different species can be shown to have similar genomic sequences, then we can conclude that they share a common ancestry. So we hypothesize that if evolutionary theory is correct, and different species share common ancestry, then closely related species will share common transposon insertions. So let’s look at the evidence.

We’ll look at one of the common SINE retrotransposons, called the Alu element. This is a sequence only about 300 nucleotides long, and it found in all mammal species, and particularly in humans, where it composes close to 10% of the entire genome. In alpha-globin gene cluster, 7 separate Alu elements are known to exist, and all seven are found in the exact same location in the corresponding chimpanzee gene. According to our hypothesis, corresponding transposon sequences imply shared ancestry, and thus this evidence supports evolutionary theory.

So, to review, transposons are mobile DNA sequences that create distinct insertion patterns that allow us to distinguish hereditary links between individuals of the same species, as well as to establish common ancestry between organisms of different species. Once again, the evidence of common transposon insertions in humans and chimpanzees strongly supports the evolutionary hypothesis. Next week, we’ll look at pseudogenes, and how these broken genes also support evolutionary theory. Take care!

Molecular Evidence 2: DNA Functional Redundancy

2006-04-01T08:00:00.000-08:00

All right, this is the second podcast in a series of six that I’ve planned on the molecular evidence for evolution. I’ll be using Dr. Douglas Theobald’s resource on Talk.Origins.org pretty heavily, so you can follow along with me there if you like.

The second piece of evidence is DNA functional redundancy.

The basic concept behind this piece of evidence is very similar to that which I discussed last week, which should be pretty obvious since they both have very similar names. They’re so similar that I’ll go ahead and review the basic argument behind last week’s evidence, since it has relevance here. All organisms share a number of proteins which are universally necessary for basic life processes; these proteins are called “ubiquitous proteins.” Because of the functional redundancy implicit in the structure/function relationship of amino acid sequences, there are a vast number of potential sequences for any given ubiquitous protein. Since the only mechanism for sequence similarity between organisms is common ancestry, similar amino acid sequences imply a phylogenetic relationship. As a specific example, I pointed out the ubiquitous protein cytochrome C, which has the exact same amino acid sequence in humans and chimpanzees, which strongly indicates common ancestry between the two species. The sequence similarity of cytochrome C between humans and just about every other species is higher than would be predicted if evolution is not a valid hypothesis. Thus, protein functional redundancy is strong evidence supporting evolutionary theory.

DNA functional redundancy is basically the same phenomenon, but instead of comparing amino acid sequences of protein, the underlying DNA sequences are compared. Now, you’ll remember from the Molecular Biology Primer two weeks ago that the amino acid sequence of a protein is determined by the nucleic acid (that is, DNA) sequence found in the corresponding gene. The nucleotide sequence of a gene is transcribed into an RNA message, which is then translated into an amino acid sequence, forming a functional protein. All right, and I’m sure you also remember that the genetic code which translates nucleotides to amino acids also reads the nucleotide sequence in groups of three, called codons. Since there is a 1:1 relationship between codons and amino acids, that means that there’s a 3:1 relationship between nucleotides and amino acids. If you haven’t already guessed it by now, the short answer to the question of DNA functional redundancy is that you take the strength of the evidence for protein functional redundancy and raise it to the power of 3.

I’ll try to explain a few of the details of this before getting into specific examples again. You’ll remember from the Molecular Biology Primer that I said that there are 64 different codons. You get this by raising the number of different nucleotides, 4, to the power of 3, which is the number of individual nucleotides in a codon. You’ll also remember that I said that there were only 20 different amino acids that are used to make proteins. Obviously, this means that you have 44 more codons than you actually need, if you were trying to be as efficient as possible. Theoretically, codons could be assigned completely at random, and the genetic code could be different for different organisms. If it were true, it would be an excellent refutation of evolutionary theory, but this is not what we observe. Interestingly, we find that for any three-nucleotide codon, the identity of the third nucleotide is less important for determining the corresponding amino acid than the first two. This phenomenon is referred to as codon degeneracy. Degeneracy means that for just about any codon, the third nucleotide can be changed to something different without affecting the corresponding amino acid that will result from translation. For example, the amino acid alanine has a four-fold degenerate codon, since any codon starting with guanine and cytosine will result in the translation of alanine. That is, you can find GCT, GCC, GCA, or GCG in the sequence of a gene, and all four will be eventually translated as an alanine. Other amino acids are less degenerate-tyrosine, for example, is only translated by codons beginning with thymine and adenine and ending with thymine or cytosine. The other two degenerate codons, the ones ending in adenine or guanine, are reserved as signals telling the transcription machinery to stop- they’re basically called “stop codons.”

So what does all this coding redundancy imply? Well, when all is said and done, it basically means that there are an astronomical number of ways that one could encode just about any given gene, without changing a single amino acid of the final protein sequence. Thus, there is no reason to assume, a priori, that any two organisms would have the same nucleotide sequence for any particular gene, even if they had the exact same amino acid sequence. Let me stress that again. Two different species with the exact same amino acid sequence for a protein have no biological reason, outside of common ancestry, to have high similarity between their corresponding nucleotide sequences. There isn’t even a name (I think) for the number of different possible nucleotide sequences. You just have to use exponents and powers of 10.

Well, let’s go back to the same example I used last week- cytochrome C. This, again, is a ubiquitous gene- it’s found in all living organisms. For this gene, the number of possible nucleotide sequences for any given amino acid sequence is higher than 10^49. That’s quite a lot. And remember, the human and chimpanzee cytochrome C sequences are exactly the same. So, there’s 10^49 different nucleotide sequences that could exist for the human and chimpanzee genes. Now, what happens when we compare the human and chimp sequences? We find they’re only different by 4 nucleotides. That’s only 1.2% different between them. The chance of this happening without common ancestry is infinitesimally small. And this evidence supports the existing fossil evidence. Most fossil evidence estimates that humans and chimpanzees separated from a common lineage somewhere around 10 million years ago, maybe sooner. We can measure the background mutation rate in humans (and other mammals), and we’ve shown it to be about 1-5 every 100 million nucleotides per generation. Since the average primate generation is 20 years, the predicted difference between a chimpanzee gene and a human gene is less than 3%. For cytochrome C, this prediction is undoubtedly fulfilled. And this is true for most other genes too- every gene that I’ve looked at, no less. In fact, I’d like to challenge anyone who’d like to disprove this evidence to find a gene that shows more than 3% difference- I’ll even do the work for you, even thought it’s easy to do by yourself.

Fortunately, the good people at the American National Center for Biotechnology Information (which can be found at the difficult to remember address of “ncbi.nlm.nih.gov”- I’d recommend just typing in “NCBI” to your Google search) have done everyone the service of publishing the entire human genome and the entire chimpanzee genome online. You can, if you like, download the entire human genome right to your computer. Burn it on a CD. Upload it to your iPod. Whatever. But the great thing is that you can use tools that they provide on their site to directly compare the sequences for yourself. You don’t need to take my word for it. But there’s not enough time now for me to tell you exactly how to use the website, so you can either spend some time fooling around with it on your own, or you can see what I’ve done with it. There’s a new resource website that I’ve started that has some gene comparisons including cytochrome C that you can look at for yourself. Just go to: http://www.drzach.net/evolution101/. I know, I know- another website to remember. I’ve tried to keep links reasonably redundant between the Freethought Media site, the blog, and this resource site- you can decide which one you want to bookmark. I’ll be updating the resource page with more information eventually, including a tutorial on how to use NCBI’s tools to analyze sequence similarity on your own. I’ve also tried to compare genes between as many organisms as are available, including orangutan, gorilla, cow, pig, dog, zebrafish, mouse, rat, etc. Comparing all these different organisms allows me to construct a genetic cladogram, and the predictions based on genetic similarity reinforce the phylogenetic relationships predicted by anatomy.

So, to review, DNA functional redundancy shows that the extra layer of redundancy implicit in the coding of DNA reinforces the evidence from protein functional redundancy, and makes it even less likely that organisms share similar DNA sequences for any reason other than common ancestry. This one-two punch of protein and DNA evidence has hopefully been convincing- next week we’re going to leave the strong evidence within the coding part of the genome and look at some equally strong, if not stronger evidence within the noncoding part of the genome.

Molecular Evidence 1: Protein Functional Redundancy

2006-03-25T09:21:00.000-08:00

All right, this is the first podcast in a series of six that I’ve planned on the molecular evidence for evolution. I’ll be using Dr. Douglas Theobald’s resource on Talk.Origins.org pretty heavily, so you can follow along with me there if you like.

The first piece of evidence is protein functional redundancy.

Proteins are, as a group, completely essential for life’s function, but there are some proteins that are more essential than others. These proteins perform very basic but essential tasks that all organisms require for life. We can call these proteins, “Ubiquitous Proteins.” These ubiquitous proteins are completely independent of an organism’s specific function or ecological niche- all organisms from bacteria to humans have these proteins, and they do the same thing no matter where they’re found.

Now, if you remember the previous podcast, the Molecular Biology Primer, you remember me talking about the relationship between protein structure and function. I didn’t get into much detail last time, but I’ll expand on it a bit more here, because it’s a pretty crucial concept for this piece of evidence. The function of a protein is determined by its structure. Imagine that we have an enzyme, which is a chemically active protein, that has the function of cutting other proteins in half. To create a conceptual model in your mind, imagine that the protein is basically like a pair of scissors. The function of a pair of scissors, to cut things, is determined by its structure, which is essentially two blades and a fulcrum, or pivot point. A pair of scissors has a pretty basic structure AND function, and so it’s not too hard to make different variations on the basic structure without changing the function too much. For example, you can make the scissors out of steel, iron, brass, or even plastic. You can make the handles longer, or shorter. You can make the blade longer or shorter. You can even have left-handed, versus right-handed scissors. So it’s pretty safe to say, if you want to cut something, you have a pretty wide variety of choices if you need a pair of scissors.

In the same way that you can vary the way you make a pair of scissors without giving up its basic function, you can vary the way you make a protein without giving up its basic function. Remember, a protein is made by constructing a long chain of amino acids, and each amino acid is distinguished from the others because of its unique side chain. That makes each amino acid slightly different from all the others both chemically and physically. Some amino acids are large, some are small, some are electrically charged, some are not, some attract water, and some repel water. Depending on specific interactions between different amino acids in the chain, the protein will twist around itself and fold up in a very specific structure. Now comes the tricky part- you can get two very similar structures from two very different chains of amino acids. To help you follow along with me, try out another conceptual model- imagine that a protein, instead of being constructed from amino acids, is constructed from Legos. (I hope I’m not violating any copyright here) Maybe I should say “small plastic construction blocks that are similar to Legos.” Whatever. Anyway, let’s say that you have a huge box of Legos, but the whole box only containes 20 different pieces. If I ask you to build me a pair of scissors out of Legos, how many ways do you think you could put the pieces together to get a decent Lego model of scissors? I haven’t actually tried this, but you could probably get pretty many, right? Probably a whole bunch. OK, well, in the same way that you can use many different combinations of Legos to give the same endproduct, you can use many different combinations of amino acids to give the same basic protein function. A more technical way of saying this is that for any given protein, there are many different amino acid sequences that are functionally redundant.

OK, this is all well and good, but what does it mean in terms of evidence for evolution? Well, you remember that I started by talking about Ubiquitous Proteins. These are proteins that are so essential to the basic functions of life that they can be found in every living organism. That is to say, their function is absolutely necessary, and what did we just learn about function? It can be produced from many different combinations of amino acids. So ubiquitous proteins are also functionally redundant in terms of amino acid sequence.

Now, before we look at the evidence, it behooves us to come up with hypotheses. This is part of the scientific method, and very essential. Without a hypothesis, we can’t draw meaningful conclusions- we’re just making observations. Now, we need to have two hypotheses- an evolutionary hypothesis and a null hypothesis. If the data support the evolutionary hypothesis, then we can conclude that evolution is the best explanation for the data. However, if the data support the null hypothesis, then we can conclude that evolution is not the best explanation for the data.

The null hypothesis posits that the evidence will show that amino acid sequences of ubiquitous genes will not be highly similar between any two given organisms. We know that the null hypothesis is possible because of the nature of protein function to be caused by many, many different variant amino acid sequences- that for any given protein, there are many amino acid sequences that are functionally redundant. Thus, since there are so many possible amino acid sequences for any given ubiquitous protein, there is no reason why each organism could not have a completely different amino acid sequence for any given ubiquitous protein. But, let’s say that the null hypothesis isn’t true- what other phenomenon could the evidence show? Well, if the evolutionary hypothesis is true, then different organisms are related to each other by heredity. Since, as I’ve mentioned before, the only mechanism which has been shown to result in similar sequences between organisms is heredity, the evolutionary hypothesis posits that the evidence will show that amino acid sequences of ubiquitous genes will be highly similar between different organisms.

So, let me just go over those two hypotheses one more time before we look at the evidence. If evolution is not true, then we would expect to see that the amino acid sequence of a ubiquitous protein would be completely different in different organisms. If evolution is true, however, then we would expect to see that the amino acid sequence of an ubiquitous protein would be more similar between organisms that are closely related. And the more similar the sequence, the closer the hereditary relationship. OK, let’s look at the data.

Cytochrome C is a ubiquitous gene that is found in all organisms, including animals, plants, and bacteria. It’s an essential gene for cellular metabolism, and helps to provide energy for all life processes. Cytochrome C fulfills the prediction of ubiquitous proteins- that is, it is extremely functionally redundant. Many different amino acid sequences have been shown to fold up into the basic structure required for Cytochrome C function, and in fact among bacterial strains, completely different amino acid sequences are redundantly functional. Experiments in yeast show that if you remove the yeast’s own Cytochrome C protein, you can replace it with Cytochrome C from humans, rats, pigeons, or even fruit flies, and it works fine. A study was published that shows there are, in fact, over 10^93 different possible amino acid sequences for Cytochrome C. That’s more possible sequences then there are atoms in the Universe. So, Cytochrome C is very functionally redundant, and it would be possible for every single different organism to have a completely different amino acid sequence, if evolution is not true.

So what do the sequence comparisons show? Let’s compare humans and chimpanzees. If evolution is true, then chimpanzees are our closest relative, but if evolution is not true, we’re no more related to chimps then we are to crickets. But if you compare the amino acid sequence of humans and chimpanzees, you see that they are exactly the same. Exactly the same. And when you compare human Cytochrome C to that of other mammals, you find that there is only about 10 amino acids difference between them. The chance of this happening without shared heredity is about 1 in 10^29. If you compare human Cytochrome C with the organism the least related to us, outside of bacteria, you find that there’s only about 51 amino acids difference between us. The chance of this happening without shared heredity is about 1 in 10^25.

To review, protein functional redundancy is the phenomenon by which many different amino acid sequences can give the same function in any particular protein. This phenomenon means that closely similar amino acid sequences between organisms implies shared heredity. Examination of the amino acid sequence of a ubiquitous protein shows that different organisms have a greater sequence similarity than would be expected by chance, and thus supports the evolutionary hypothesis.