Evolution 101

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.