Evolution 101

Thursday, January 11, 2007

The Problem of Species

Part 1

Part 2

Part 3

Sunday, October 29, 2006

The Female Orgasm

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.”

Sunday, September 24, 2006

Icons of Evolution

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.

Sunday, September 10, 2006

Are There Significant Differences Between Human and Chimp Genes?

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.

Sunday, August 27, 2006

Is Evolution Racist?

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.

Sunday, August 13, 2006

What is Information Theory?

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.

Sunday, August 06, 2006

Why Are Humans Naked?

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.