Evolution 101

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.


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