Category Archives: evolution

biology, Darwin Eats Cake, evolution, genomic imprinting, journal club, science

Mitochondria and Hypertension

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So, here’s a new thing.

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This is based on a recent paper (citation below) where they identify a point mutation in the mitochondrial DNA that appears to result in hypertension.

So why is this interesting? Well, for me, as an evolutionary theorist who works on intragenomic conflict, it is interesting because the mitochondrial DNA is, in principle, subject to selection pressures different from the rest of the genome. For instance, mitochondrial genes present in a female would, in principle, benefit from skewing the sex ratio of the offspring of that female, since those genes can only be passed on to grandchildren through daughters. Furthermore, since mitochondria are maternally inherited, the intragenomic conflicts over inclusive fitness effects that underlie the phenomenon of genomic imprinting could potentially shape the evolution of mitochondrial genes as well.

Sadly (from the theory perspective), the scope of phenomena influenced by mitochondria is fairly limited, with a lot of the effects limited to core metabolism. That’s not to say that core metabolism is not important. Obviously, core metabolism is important to the survival of the individual. In fact the importance of these genes to survival is exactly what tends to make them evolutionarily less interesting. By and large, core metabolism is unlikely to be a significant locus of intragenomic conflict because all of the genes in an individual need that individual to be able to do things like, e.g., make ATP.

From this perspective, then, this mutation is interesting in that it represents an example of a phenotype that can be quantitatively affected by the mtDNA. This particular mutation is likely best interpreted as a mildly deleterious one that happens to exist within a particular family in China. However, it opens up the possibility of mutations with subtler phenotypic effects, which could potentially be subject to divergent selective pressures for different parts of the genome. For instance, if elevated blood pressure during pregnancy results in a greater transfer of resources from mother to offspring, we would expect autosomal and mitochondrial genes to favor different optimal blood pressures.

The other thing that is interesting is the type of mutation it is. It is actually a point mutation in the gene that produces the mitochondrial Isoleucine tRNA. This mutation messes up a site that is cleaved as a part of the normal post-transcriptional processing. The result is that the steady-state level of mitochondrial Isoleucine tRNA is reduced by 46%. This, in turn, impacts the translation of other mitochondrial gene products with protein translation reduced by an average of 32%. So, basically what it does is just muck up mitochondrial function a little bit.

Wang, S., Li, R., Fettermann, A., Li, Z., Qian, Y., Liu, Y., Wang, X., Zhou, A., Mo, J., Yang, L., Jiang, P., Taschner, A., Rossmanith, W., & Guan, M. (2011). Maternally Inherited Essential Hypertension Is Associated With the Novel 4263AG Mutation in the Mitochondrial tRNAIle Gene in a Large Han Chinese Family Circulation Research, 108 (7), 862-870 DOI: 10.1161/CIRCRESAHA.110.231811

biology, evolution, Politics, science

Important Harvard Scientists Attack Kin Selection: Context

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So, a couple of days ago, I made a video dramatizing the scientific kerfuffle surrounding a paper published in Nature by Martin Nowak, Carina Tarnita, and E. O. Wilson of Harvard. My original goal had been to create something that would be entertaining to the people involved in the argument.

The original post, which contains the video, is here.

Over the past day or so, it has become clear that a lot of people are seeing the video who are maybe not familiar with the context in which the kerfuffle arose. If you’re one of those people, here’s an attempt to provide a little background.

Nowak and Wilson, two of the authors of the article, are two of the most prolific and high-profile evolutionary biologists working today. If you’re in the field, you probably own at least one of Wilson’s books. Tarnita is a postdoc working with Nowak who already has an impressive set of credentials. Last August, the three of them published a paper in the scientific journal Nature, which, for biologists, is one of the the two super-high-profile places where your papers can be published. It is incredibly difficult to get a paper into Nature, and, if you are a young scientist, a publication in Nature will go a long way towards getting you an academic job.

Modeling and eusociality

Their paper was about the evolution of eusociality, which is the thing that you sometimes find in species like bees and ants, where one individual – the queen – makes all the babies, while everyone else builds the nest or the hive, and does not reproduce themselves. These are interesting evolutionary systems, because, if you think about it naively, why should the worker ants or worker bees give up their own reproduction so that the queen can have babies? If natural selection is all about who passes on the greatest number of copies of their genes, how can you possibly get this worker behavior, where a huge number of individuals don’t reproduce, and are, in fact, willing to sacrifice their lives so that someone else (the queen) can reproduce?

[Note: this is a cartoon description. The real biology is, as always, enormously more complicated, and there is a huge amount of variation in the way in which eusociality works, in insects and elsewhere.]

Here’s the way that I like to think about it. Think about a cell in your brain. There is absolutely no chance for that cell to pass on copies of its genes to the next generation. That brain cell is an evolutionary dead end. In fact, no genes in any cell in anyone’s brain have ever been passed on.

Nevertheless, natural selection has created genes that lead to enormously complex functions in the brain. The reason is that for every gene that is present in your brain, there is an identical (probably) copy of that gene in your germ line (in your testes or ovaries) that can be passed on. So, genes that lead to brain functions that help you to survive and reproduce can be favored by selection, even if the gene copies that are physically present in the brain are not passed on themselves.

That is the basic idea behind the evolution of eusociality. Workers that don’t reproduce have evolved because they help the queen to reproduce, and, in particular, they help her to make more queens, who go off and start their own colonies. So, in a sense, the colony as a whole reproduces, and genes that facilitate that non-reproductive worker behavior are passed on, even though they are not passed on by the workers themselves.

At this verbal, qualitative level of description, everyone agrees about what is going on. But, in evolutionary biology, we are interested in developing mathematical, formal, quantitative descriptions of the process. This is where the divisions start.

There are different ways that these ideas can be formalized. Traditionally, the two major formalisms have been “kin selection” or “inclusive fitness” models on the one hand, and “group selection” models on the other. I won’t go into detail here about the differences, because I don’t personally find them interesting. The fact is, if you do your math correctly, you can accurately describe any system using either of these frameworks, as well as others. They’re not totally identical, in the sense that certain systems can be described more simply using one framework than another, or in that some questions can be more natural to ask in one framework than another, or in that the framing entailed by your choice of model can influence how you tend to interpret the results of the model. That being said, there is a deep way in which all of the different modeling frameworks are mathematically interchangeable, and this interchangeability has been demonstrated repeatedly over the past few decades.

The problem with the paper

The thing about this particular paper that roused the ire of so many evolutionary biologists was that much of the text was devoted to discrediting the kin selection approach.  The problem with the paper is that it does not actually go after any of the core ideas that underlie the kin selection approach. Nor does it criticize models of kin selection in the way that people actually use them.

Instead, the paper sets up a straw man, and then tears it down. The “kin-selection approach,” as it is described by them, would certainly be a limited, flawed modeling framework. But the limitations that they describe in the paper fall into three categories:

  1. Limitations that are not a part of kin-selection models as they are actually used by anyone.
  2. Limitations that may apply to particular models applied to particular systems, but are not limitations that are inherent in the approach.
  3. Limitations that apply to all evolutionary models, including the alternative that they are championing.

I won’t go on more here. If you’re interested, I recommend reading the original criticisms, which I have cited and linked to in my original post.

Now, one interesting thing about this paper is that many of the papers that have extended kin-selection models beyond the limitations that the paper accuses them of are actually cited in the supplementary materials. And yet, the main text of the paper (which is the only thing that most people will read) seems to be written as if none of those papers exist.

The personalities

Back in the 1970s and 1980s, E. O. Wilson was a polarizing figure in evolutionary biology, due to his role in championing the application of evolutionary reasoning to the study of behavior, particularly human behavior. (In a previous post, I recommended this article, which provides an entertaining overview of the sociobiology wars, in which Wilson was a central figure.) However, over the past couple of decades, Wilson has become one of the Grand Old Men of evolution, and is nearly universally respected.

Martin Nowak, by contrast, is a controversial and polarizing figure in evolutionary biology today. However, whereas Wilson became controversial for his ideas, Nowak is controversial for the way that he presents his ideas. In particular, many people within the evolutionary biology community feel that Nowak has a tendency to oversell the importance and originality of his own work. More specifically, many people feel that he systematically fails to give enough credit to previous work by other scientists.

So, while I believe that the criticisms leveled against this particular paper – specifically those in the published responses in Nature – are all legitimate, I can see how it might seem like a lot of controversy over a little problem. I would like to suggest what I think might be an explanation for the volume (both number of words and loudness of those words) of the response that the paper seems to have elicited. Although I know some of the letter writers personally, and know many of them professionally, I claim no privileged insight as to their motivations. So, what I am presenting here is pure speculation, and should be taken with large quantities of salt, but here it is:

My suspicion is that the response was as broad and strident as it was specifically because it was a response to Nowak. The shortcomings that they have pointed out the current paper are certainly all there. But, I think that those shortcomings perhaps seem all the more galling because they represent an extreme case of a style of argument and presentation that Nowak has used repeatedly over the years, and which has long been infuriating to many evolutionary biologists, including, I suspect, many of the authors of the letters.

The politics

I mentioned at the beginning of this post that the paper was published in Nature, and publications in Nature are worth their weight in gold in terms of a biologist’s career. But the reputation of Nature within evolutionary biology is a complicated one. Many people will routinely dismiss Nature as a “science tabloid” that is very interested in publishing flashy results, but interested enough in whether or not those results are true. At the same time, most of these same biologists would gladly trade their right gonad for a Nature publication themselves, as Nature publications open the door to future success, like getting academic jobs, getting grant money from funding agencies, and getting, well, more Nature publications. As one colleague of mine put it, it’s like how everyone wants to have their picture taken with the dictator.

So, one thing that is going on here is that there are a lot of people who have published a lot of very good work in a lot of very good journals. Then, along comes this paper, which basically dismisses that whole body of work. You could say (as a different colleague of mine did), “Well, if the arguments in the paper are wrong, why not just let it go. No one will believe it in the long run anyway.” The problem is that the impact of this one article in Nature may outweigh the impact of all of those very good articles in all of those very good (non-Nature) journals, at least in the eyes of anyone who is not, themselves, an evolutionary biologist. So, while this paper will have little to no effect on the way that evolutionary biology is done, it may have a big impact on the way that evolutionary biology is perceived by people outside the field.

So, some of this is probably a combination of righteous indignation and sour grapes, similar to what you might feel upon seeing some celebrity interviewed on CNN as an “expert” on some topic that you feel they don’t really understand, and that you feel that you, in fact, understand much better.

Then, there is the funding issue. There are two funding sources that Nowak has that are viewed with some suspicion by many evolutionary biologists (and probably most academics, more generally): the Templeton Foundation and Jeffrey Epstein, both of which/whom are thanked in the acknowledgements of the original paper.

The Templeton Foundation funds a lot of science, but has a particular interest in science that relates to issues of religion and spirituality. This interest is, in itself, enough to make many evolutionary biologists feel that any research supported by Templeton is inherently suspect. I have no horse in that race, and my view is that as long as they are not dictating the outcome of your research, there is no problem. Then, of course, there is the fact that Nowak himself is a devout Catholic, which, I suspect, makes his relationship with Templeton seem even more problematic to your average evolutionary biologist.

Jeffrey Epstein is, of course, the hedge-fund mogul who pled guilty a couple of years ago to a charge of soliciting an under-age girl for prostitution. There is an argument to be made that his extreme wealth allowed him escape much more severe charges, such as sex trafficking. More recently he has been in the news following accusations that he “trained up” a girl who lived with him from age 14 to 18, and loaned her out to his rich friends.

Now, one can take a range of positions on this issue. One viewpoint, probably espoused by many academics (including me), is that any money from someone like Epstein is inherently dirty, and that the choice to take money from him casts doubt on one’s ability to make valid moral – and, by extension, scientific – judgments.

An alternative viewpoint would be that money is money, there’s not enough of it out there to support all the interesting research that could be done, and you’ve got to take money where you can get it. An even more extreme viewpoint would be that every dollar that you take from Epstein for science is one dollar that he won’t be spending to pay some underage girl to give him a “massage.”

As I say, I side with the first viewpoint, that Epstein’s moral violations are severe enough that there is no excuse for interacting with or taking money from him. However, I suspect that some people may feel differently without necessarily being bad people.

The point is that Nowak’s associations probably color how he is perceived by the academic community. That does not mean that those associations have affected his science. And, in fact, I believe that the scientific points of the argument can be completely understood without any reference to these other issues.

However, I think the intensity of the response to this paper was enhanced by things that form a part of the sociology of science, rather than a part of the science itself. It is in this vein that I mention Nowak’s associations, which are fairly well known to most evolutionary biologists (who, like all academics, are a gossipy bunch).

Wrap-up

So, what you have in Martin Nowak is a guy who has been enormously well funded and enormously prolific, publishing a huge number of papers in high profile journals. As a result, Nowak has become one of the best known evolutionary biologists, particularly outside the field. However, many other evolutionary biologists are suspicious (and probably resentful) of his high profile. This suspicion comes in part from a feeling that he has not really earned his reputation, that his reputation exceeds his actual accomplishments, and that he associates with unsavory characters. It is not surprising, then, that he is something of a lightning rod in the field.

I doubt that I have written anything here that will be surprising or new to anyone who actually works in evolutionary theory, or follows it closely. But, I wanted to lay this out because I know that this sort of academic dust-up always looks really bizarre and petty when viewed from the outside. And, it is clear in this case that the debate is emotionally charged. So, if you’ve stumbled upon this, and were confused, but interested enough to slog through this whole post, I hope that maybe this provided some degree of context.

Nowak, M., Tarnita, C., & Wilson, E. (2010). The evolution of eusociality Nature, 466 (7310), 1057-1062 DOI: 10.1038/nature09205

Update: PS If you came here through finding the video posted on Richard Dawkins’s site, it is shoebucket productions, not shoebox productions.

biology, evolution, science, video

Kin Selection: Nowak vs the world

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So,  if you’re an evolutionary biologist, or really if you follow the biology literature at all, you have probably heard about the paper published last fall in Nature by Martin Nowak, Corina Tarnita, and E. O. Wilson. The paper claims that all theories based on kin selection and inclusive fitness are fundamentally flawed and unsupported by any empirical evidence.

Recently, responses to the paper were published in Nature, and the original article has been criticized on a number of counts. The controversy sparked by the paper has been covered journalistically by Carl Zimmer (and others, I’m sure).

I’ll just say that I am not really sure what the authors of the original article were hoping to accomplish. From my read, the article seems to reveal a rather disturbing lack of familiarity with a huge body of scientific literature from the past few decades. Either that, or it represents a rather disturbingly disingenuous attempt to misrepresent that huge body of scientific literature. I’m sure that there are other possible explanations, but I’m not coming up with them off the top of my head.

I also don’t know what the editors at Nature were thinking when they published this paper. Or, rather, I have some personal theories as to what they were thinking, which I am afraid do not reflect well on their competence, professionalism, or honesty.

In the interests of full disclosure, I should say that I tend to side with the critics of the paper.

Anyway, there has already been a lot written about this subject, so I won’t write more. Rather, I thought that I would dramatize the situation using a few quotes and paraphrases from the debate, as well as my own opinions.

I hope that this is obvious, but just in case it is not, please keep in mind that the video is presented primarily for entertainment purposes. I have made an honest attempt to portray the spirit of the arguments accurately. However, let’s just say that it is possible that some of the nuance may have been lost.

For another thing, I have lumped together various criticisms, which has no doubt done some violence to the arguments that have been put forward. If you’re interested in the topic, I strongly encourage you to read the original article and the published responses. Citations and links are provided at the end of the post.

In the meantime, enjoy:

Like everything else on this blog, the video should be treated under creative commons. So, feel free to share this, or to embed the video into your own blog. Just don’t sell it.

Update: Now also on YouTube. That version I think will work better for embedding, if you want to share the video.

Update 2: I have added a follow-up post in which I try to provide more background context and attempt to explain why this paper generated such a large response from the evolutionary biology community.

Sources used include:

The original article:
Nowak, M., Tarnita, C., & Wilson, E. (2010). The evolution of eusociality Nature, 466 (7310), 1057-1062 DOI: 10.1038/nature09205

Responses in blog form:
Jerry Coyne
More Jerry Coyne
Richard Dawkins

Published responses in nature:

Abbot, P., Abe, J., Alcock, J., Alizon, S., Alpedrinha, J., Andersson, M., Andre, J., van Baalen, M., Balloux, F., Balshine, S., Barton, N., Beukeboom, L., Biernaskie, J., Bilde, T., Borgia, G., Breed, M., Brown, S., Bshary, R., Buckling, A., Burley, N., Burton-Chellew, M., Cant, M., Chapuisat, M., Charnov, E., Clutton-Brock, T., Cockburn, A., Cole, B., Colegrave, N., Cosmides, L., Couzin, I., Coyne, J., Creel, S., Crespi, B., Curry, R., Dall, S., Day, T., Dickinson, J., Dugatkin, L., Mouden, C., Emlen, S., Evans, J., Ferriere, R., Field, J., Foitzik, S., Foster, K., Foster, W., Fox, C., Gadau, J., Gandon, S., Gardner, A., Gardner, M., Getty, T., Goodisman, M., Grafen, A., Grosberg, R., Grozinger, C., Gouyon, P., Gwynne, D., Harvey, P., Hatchwell, B., Heinze, J., Helantera, H., Helms, K., Hill, K., Jiricny, N., Johnstone, R., Kacelnik, A., Kiers, E., Kokko, H., Komdeur, J., Korb, J., Kronauer, D., Kümmerli, R., Lehmann, L., Linksvayer, T., Lion, S., Lyon, B., Marshall, J., McElreath, R., Michalakis, Y., Michod, R., Mock, D., Monnin, T., Montgomerie, R., Moore, A., Mueller, U., Noë, R., Okasha, S., Pamilo, P., Parker, G., Pedersen, J., Pen, I., Pfennig, D., Queller, D., Rankin, D., Reece, S., Reeve, H., Reuter, M., Roberts, G., Robson, S., Roze, D., Rousset, F., Rueppell, O., Sachs, J., Santorelli, L., Schmid-Hempel, P., Schwarz, M., Scott-Phillips, T., Shellmann-Sherman, J., Sherman, P., Shuker, D., Smith, J., Spagna, J., Strassmann, B., Suarez, A., Sundström, L., Taborsky, M., Taylor, P., Thompson, G., Tooby, J., Tsutsui, N., Tsuji, K., Turillazzi, S., Úbeda, F., Vargo, E., Voelkl, B., Wenseleers, T., West, S., West-Eberhard, M., Westneat, D., Wiernasz, D., Wild, G., Wrangham, R., Young, A., Zeh, D., Zeh, J., & Zink, A. (2011). Inclusive fitness theory and eusociality Nature, 471 (7339) DOI: 10.1038/nature09831

Boomsma, J., Beekman, M., Cornwallis, C., Griffin, A., Holman, L., Hughes, W., Keller, L., Oldroyd, B., & Ratnieks, F. (2011). Only full-sibling families evolved eusociality Nature, 471 (7339) DOI: 10.1038/nature09832

Strassmann, J., Page, R., Robinson, G., & Seeley, T. (2011). Kin selection and eusociality Nature, 471 (7339) DOI: 10.1038/nature09833

Ferriere, R., & Michod, R. (2011). Inclusive fitness in evolution Nature, 471 (7339) DOI: 10.1038/nature09834

Herre, E., & Wcislo, W. (2011). In defence of inclusive fitness theory Nature, 471 (7339) DOI: 10.1038/nature09835

And the response by Nowak et al.

Nowak, M., Tarnita, C., & Wilson, E. (2011). Nowak et al. reply Nature, 471 (7339) DOI: 10.1038/nature09836

biology, Darwin Eats Cake, evolution, Politics, science

Darwin Eats Cake: Red Queen

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So, have you spend all day looking for a comic that integrates Red Queen evolutionary dynamics, commentary on the application of parsimony arguments in biology, and Newt Gingrich’s recent flip-flopping on Libya? No? Well, hopefully you’ll enjoy this anyway. For a more viewable image, see the original at Darwin Eats Cake.

URL for sharing: http://www.darwineatscake.com/?id=11
URL for hotlinking or embedding: http://www.darwineatscake.com/img/comic/11.jpg

For more on the flip-flop check out Think Progress or Weigel.

Van Valen, L (1973). A New Evolutionary Law Evolutionary Theory, 1, 1-30

biology, evolution, Politics, religion, science

Bill Zedler, champion of "academic" freedom

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So, Texas is apparently worried about losing its status as most backward state. Enter state representative Bill Zedler, who is introducing a bill that will prevent students and professors from being “discriminated against” for questioning evolution. Because apparently he believes that this is NOT the exact opposite of the problem with science education.

Texas Republican Bill Zedler has a mind that was intelligently designed with an extraordinary capacity for deliberately misinterpreting facts, and with an ability to use disingenuous arguments about academic freedom to push a religious agenda. Fortunately, millions of years of evolution have also left him with a mind that is incapable of adequately disguising his transparent attempt to violate the first amendment of the United States Constitution.

I humbly submit to Mr. Zedler that he should modify his bill, expanding it to include the following:

  1. No student shall be expected to depart any university with any knowledge that supplants or contradicts any beliefs or preconceived notions they may have had upon first enrolling.
  2. No one shall be denied employment as a doctor at any university health center as a result of their disbelief in the germ theory of disease, nor as a result of a lack of medical training.
  3. Any student accused of plagiarism or any other form of academic misconduct shall be examined by panel consisting of three members of the faculty and the university ombudsman. The student shall be held underwater for no less than twelve consecutive minutes. Should the student drown, he or she shall be deemed innocent of said misconduct.
  4. Each university shall establish a quota system for tenured faculty in each department as follows. Each Chemistry Department must have no less than four (4) practicing alchemists. No less than seven (7) members of each English Department must be functionally illiterate. Women’s Studies Departments must include at least six (6) self-identifying misogynists, including at least one (1) violent sex offender.

I look forward to seeing the revised version of the bill.

Update: New post presenting my webcomic on this subject.

biology, evolution, evolutionary psychology, homosexuality, science, sex

Re: Homophobia and Evolutionary Psychology

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So, a couple of days ago, Jesse Bering published an interesting post on his Scientific American blog, where he attempts to revive interest in a research topic that was hotly debated in the mid 1990s, but has since fallen dormant. He describes a debate between two evolutionary psychologists – Gordon Gallup and John Archer – over the evolutionary origins of negative attitudes towards homosexuality.

Bering does an excellent job describing the debate, so I will just provide the briefest synopsis here. Gallup argues that, all else being equal, natural selection would favor negative attitudes towards homosexuality. The argument is basically that people who encourage heterosexual behavior in their children will have more grandchildren. The counter-argument championed by Archer is basically, no, it’s all cultural: homosexuals are identified as “other” and are demonized in the media.

Silly girl is so unfamiliar with cultural norms, she does not even recognize that she should be vilifying anyone who looks different from her.

Bering’s stated purpose is to stir up some debate, and hopefully to prompt some new research. He takes the position – the correct one in my view – that we should not refrain from asking such questions out of fears driven by political correctness. However, the thing that caught my attention, and prompted my to write my own response, was his opening paragraph:

Consider this a warning: the theory I’m about to describe is likely to boil untold liters of blood and prompt mountains of angry fists to clench in revolt. It’s the best—the kindest—of you out there likely to get the most upset, too. I’d like to think of myself as being in that category, at least, and these are the types of visceral, illogical reactions I admittedly experienced in my initial reading of this theory. But that’s just the non-scientist in me flaring up, which, on occasion, it embarrassingly does. Otherwise, I must say upfront, the theory makes a considerable deal of sense to me.

This, in a sense, encapsulates exactly what is wrong with so much evolutionary psychology. I don’t mean that as a criticism of Bering, who writes conscientiously and consistently well about a host of tricky topics. In fact, what I am doing here is a bit unfair to him, but I want to make a lot of hay out of that last statement: “the theory makes a considerable deal of sense to me.”

Back in the late 1970s, evolutionary biology was rent by a conflict over sociobiology. The debate was perhaps at its hottest and most divisive at Harvard, where the author of the book Sociobiology, E. O. Wilson, and two of its strongest critics, Richard Lewontin and Stephen Jay Gould, were all on the faculty. The debate focused particularly on the use of adaptationist reasoning to describe the origins of human behaviors, but it had methodological implications that reverberated throughout evolutionary biology.

Like sociobiology before it, evolutionary psychology has been accused of using the veneer of objective science to promote a socially conservative agenda, reinforcing social norms. Image via imageshack.

I won’t go more into the history here, but if you’re interested in a highly entertaining historical account, which delves particularly into many of the biggest personalities involved, I highly recommend this article, published originally in the sadly now defunct Lingua Franca.

As with many such schisms, the field eventually healed, primarily through retirement and replacement. Nowadays, most practicing evolutionary biologists take a more synthetic view, one that integrates the ambitions of the sociobiology program with the demands of a more rigorous scientific foundation demanded by the critics.

Basically, the lessons of the whole sociobiology episode boil down to this: plausibility is NOT scientific proof.

In fact, it is trivially easy to come up with a plausible-sounding evolutionary argument to describe the origin of almost any trait. More importantly, it is often just as easy to come up with an equally plausible-sounding argument to describe the origin of a hypothetical scenario involving the exact opposite trait.

If you have students, you can try this little experiment, which provides a nice learning exercise for the students as well:

Divide your class into two groups. Give one group a card that describes a pattern of behavior of the form: “In species X, the females do Y, and the males do Z.” Tell them that their job is to work together to come up with an evolutionary argument for why the females do Y and the males do Z. A group of a few modestly engaged undergraduates will have little trouble constructing such an argument. The argument will likely seem plausible on its face, and the students will probably emerge from the exercise convinced of its correctness.

Give the other group the same exercise, but with the modification that their card says that the females do Z and the males do Y. You will likely find that this group also has little trouble coming up with a plausible explanation, and that they will also be convinced of its correctness. For extra fun (for you, anyway), have the two groups come back together to debate the evolutionary question, but don’t tell them at first that they were given opposite patterns to explain.

If you can create a set of journals in which you can publish evolutionary claims with no requirement that any of those claims be scientifically tested, eventually, you can generate a whole parallel literature that is self-citing, a group of researchers that are self-refereeing, and review panels that are self-funding. Congratulations! You’ve just invented an academic perpetual motion machine!

The problem with much of the early work in sociobiology was that it was based on assertions of plausible-sounding mechanisms, where not enough thought was put into consideration of alternative scenarios. One of the dangers is that the plausible-sounding mechanisms that most readily come to mind are often those that resonate with the cultural norms in which we are all immersed. This is part of the reason why molecular evolution has focused so much over the past few decades on statistical tests to look for evidence of natural selection.

While most evolutionary biologists have taken on board the cautionary tales that emerged from the sociobiology debate, most evolutionary psychologists are not evolutionary biologists. When evolutionary psychology started to become a field in the early 1990s, it basically recapitulated many of the errors of early sociobiology. It deflected criticism by claiming that politically correct academics didn’t want them to ask these questions, painting itself as a field of martyrs who were bravely trying to do science, when the actual criticism was that the science was bad.

Evolutionary biology is one of those areas, like linguistics or sociology or film, where many people have some basic understanding or exposure, and so they tend to assume that they have an expertise on the topic, and that there is nothing more to understand beyond what they know.

Evolutionary psychology is to evolutionary biology as physics is to everything.

I would not want to criticize Gallup’s methods, nor his results, insomuch as they relate to psychology. However, the leap to the evolutionary argument is complete nonsense. That is not to say that he is not right. He might be. It simply means that the studies that are the focus of the debate do not contain the information required to construct and test an evolutionary argument as a scientific question.

Gallup’s premise is that an impulse to discourage homosexuality in one’s children would be evolutionarily favored. Fine. The argument is supported by surveys about parents’ levels of discomfort with homosexuality in different scenarios, specifically that they are less comfortable having their children exposed to homosexuality at age 8 than at age 21, and that they are more comfortable with a homosexual brain surgeon than with a homosexual pediatrician. Again, Bering does a nice job of describing the studies and the arguments against them, and I won’t reproduce those here.

I will just note (as Bering does) that this interpretation hinges on the assumption that exposure to homosexuals at an early age increases the likelihood of growing up to be homosexual. Gallup has some evidence to suggest that this might be the case, although we could easily put forward, for example, the “exotic becomes erotic” theory, which might be interpreted as suggesting that early exposure to homosexuality would decrease the erotic appeal of homosexuality in later life.

Basically, the structure of Gallup’s argument is that his studies show that A * B > 0. He wants to conclude that A > 0. Therefore, he asserts that B is probably greater than zero.

The problem is that the claim that A > 0 sounds plausible. Having straight kids gives you more grandkids. Makes sense, right? Therefore, we don’t demand a real test to figure out what B is.

Let me throw out a few alternative evolutionary stories:

          1) Parents should want their own children to be straight, but they should support a culture that is broadly supportive of homosexuality, thereby reducing the number of children that other people’s children have. That would reduce the competition faced by their own grandchildren, giving them more great-grandchildren.

          2) Parents should favor sex-specific homosexuality in the general culture, facultatively based on the sex ratio among their own children. Parents with lots of sons should favor male homosexuality in the broader community, but should disfavor female homosexuality, in order to maximize the number of mates available to each of their sons.

          3) Parents should favor having their older children be homosexual during the early part of their lives, so that they stick around and help to raise the younger children, but once the younger children are old enough to fend for themselves, they should want all of their children to be straight.

Do any or all of these sound plausible to you? Maybe they do, or maybe they don’t. However, my point is that it does not matter. Whether some or all or none of these sound plausible to us depends a lot on the cultural milieu we inhabit, and almost nothing to do with the actual evolutionary origins of human sexual orientation.

It would be straightforward to construct mathematical models to support any of these verbal arguments. The key to turning this into science is to construct those models and see what other implications they have, and to look for evidence that supports or contradicts those other implications. The key is to measure what B is. The key is to uncover the genetic and neural mechanisms that underlie sexual orientation, and to subject those mechanisms to a rigorous statistical and molecular analysis. The key is to consider as broad a set of hypotheses as possible, and to be creative in identifying tests and observations capable of differentiating among those hypotheses.

I’m with Jesse Bering in hoping that there will be more research on this topic in the future. But I would add the caveat that if the research is done by psychologists in isolation, it will ultimately go nowhere, even if they are evolutionary psychologists. What is needed is a broad, transdisciplinary collaboration involving psychologists, for certain, but also evolutionary biologists, neuroscientists, anthropologists, sociologists, and who knows what else.

Gallup GG Jr, & Suarez SD (1983). Homosexuality as a by-product of selection for optimal heterosexual strategies. Perspectives in biology and medicine, 26 (2), 315-22 PMID: 6844119

biology, Books, evolution, Genetical Book Review, genetics, science

The Genetical Book Review: White Cat

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So, welcome back to the Genetical Book Review, where we use concepts from evolutionary biology and genetics to talk about novels. In this installment, we are going to talk about White Cat, written by Holly Black. This is the first book in the Curse Workers fantasy series, the second book of which is set to be published in April. Holly Black may be familiar to some readers as one of the authors of The Spiderwick Chronicles.

White Cat is, broadly speaking, the same flavor of book as the Spiderwick series. The story has a contemporary setting, but in an alternate history in which a subset of people, known as “curse workers” or just “workers,” possess special abilities. The book’s protagonist, Cassel, comes from a worker family, but has no special abilities himself. One of his brothers is a “luck worker,” who is able to give people good (or bad) luck, while his other brother is a “body worker,” meaning that he is able to hurt people. His mother is an “emotion worker” who is able to manipulate people by, for example, convincing them that they are in love with a particular person. His grandfather is a “death worker,” who is able to kill people with his touch.
In fact, all workers’ skills require that the worker touch their target. Thus, in this alternate history, everyone wears gloves, and approaching someone with bare hands represents a potential act of aggression. In this world, curse workers are subject to “blowback,” which results from a sort of conservation law. For instance, whenever Cassel’s grandfather uses his ability to kill someone, a part of his body dies, such that when we first meet him, his fingers are blackened stumps, the consequence of a lifetime of death work.
Artist imitates art. Holly Black dons eponymous gloves in an effort not to accidentally curse herself when she touches her face. Image from the Holly Black website.
In this alternate history, curse work has been outlawed, so that curse workers live somewhat in the shadows and are employed by organized crime families. Much of the book’s social commentary focuses on issues that arise from this situation. There are discussions that parallel arguments about prohibition and drug legalization. There is a political movement to require people with abilities to register with the authorities. These subjects are handled largely in subtext, providing a layer to the book that will be interesting to adult readers.
I won’t go on further here about the premise or plot, as describing more would risk revealing some of the book’s twists. In terms of summary judgment, let me just recommend the book. It is fast moving and well written, and easily the sort of book you might find yourself finishing in a single sitting. It has some dark elements that might make it inappropriate for younger independent readers, so I would not necessarily buy it for your grade-school son or daughter. On the end of the spectrum, if you are an adult who enjoys this genre of young-adult fiction (e.g., if you like the Bartimaeus trilogy by Jonathan Stroud), I suspect you’ll have a great time reading this book, which is aimed at an older age bracket than Spiderwick.
What we will focus on here is the nature of the genetic variation that underlies the ability to perform curse work. The ability clearly has a genetic basis and seems to run strongly in families. There is also an explicit discussion of the fact that there is a high frequency of workers in Australia, due to a high frequency of the trait in the founding population.
The premise of a magical ability with a genetic basis underlies many fantasy franchises, including Harry Potter, X-Men, and television’s Heroes. In each case, there is some variation in the extent of the ability among those who have it, but there is fundamentally a binary distinction between those with abilities and those without them.
The clean, binary division between wizards and muggles means that no matter how enthusiastically you grip that broom between your legs, you’re never actually going to fly. Image of the fourth annual Quidditch World Cup. A real thing that real people do. For real.
Franchises differ in how they conceive of the structure of variation among those with abilities. In Heroes and X-Men, for instance, each mutant has unique abilities. (Or, to the extent that two mutants share abilities, it is generally looked upon as a lack of creativity or lack of attention to detail on the part of the writers.) By contrast, in Harry Potter, witches and wizards have, by and large, the same set of abilities. They differ in the degree of proficiency they display in different skills, but the variation seems to be fairly continuous.
We could say the franchises differ in the extent to which the mutant phenotype is canalized. In contemporary usage, the term canalization is used to refer to mechanisms that buffer the phenotype against genetic and/or environmental variation. It is an inherently relative term, in that it makes no sense to talk in isolation about a trait being canalized or not. However, it is sometimes possible to compare the extent to which a trait is canalized in two systems. For example, if the pattern of wing veins in one species of fly is invariant in response to changes in the temperature at which the flies are raised, while the pattern in a second species changes with temperature, we could say that the patterning was more canalized (with respect to temperature) in the first species than the second. The term comes from a metaphor in which different genetic variants or environmental influences get channeled into a “canal” representing normal development.
The canalization concept is usually used in the context of stabilization of the wild-type, but we can just as easily talk about canalization of a mutant phenotype. In Heroes and X-Men, it seems that the mutant phenotype is almost completely uncanalized. These franchises employ the “Anna Karenina Principle.” To quote the most over-quoted Tolstoy passage ever, “Happy families are all alike; every unhappy family is unhappy in its own way.” Despite the fact that a specific mutation is responsible for the superpowers in Heroes and X-Men, some interaction involving the mutation (presumably with other loci in the genome) results in a wildly different phenotype in each individual.
Whenever scientists want to say that something breaks in all sorts of different ways, while at the same time establishing their credentials as cultured intellectuals, they cite the “Anna Karenina Principle,” referencing a book that they know to be important, even if they have not actually read it themselves. This mapping of a diverse array of scientific observations onto a single reference represents a kind of literary canalization.
In the Harry Potter books, the genetic basis for wizardry is less clearly articulated, but the trait appears to be more canalized than the analogous traits in Heroes and X-Men. If there were less variation in the abilities of different witches and wizards in different areas of magic, we would say that the trait was even more highly canalized.
While canalization is often currently thought of as a buffering mechanism that applies to the entire phenotype, when the idea was first introduced by C. H. Waddington, he was also interested in the idea of cell-type differentiation. He introduced the concept of the “epigenotype” to refer to distinct sets of traits that could develop from the same underlying genotype. The cells in your brain and the cells in your liver have the same set of genetic material, but the morphology and behavior of the cells is wildly different. Thus, in this original concept of canalization involved the notion of multiple, distinct canals, each of which uses some sort of buffering to produce a stereotyped outcome.
Waddington represented development as a ball following one of a set of distinct, stereotyped pathways, like the character arcs on “reality” television.
The curse-worker phenotype in White Cat is like this notion of canalization. There are a handful of very distinct types of curse work that seem to occur in fairly well defined relative frequencies. Based on Cassel’s family, the capacity to do curse work seems to be strongly genetic, but the type of curse work one is able to do may be largely stochastic. It is sort of like Plinko: the genetic mutation hurls you onto the board of being a worker, but then random processes determine which curse-work canal you wind up following.
A Plinko contestant drops a hockey-puck type thing onto a board with a bunch of pegs on it to determine which kind of curse work he will spend his life doing. Genetics works exactly like this.
There is another form of canalization that we can see in the world of White Cat, a sort of historical canalization. Like many books in this genre, White Cat takes place in a world much like our own, but with a couple of key changes. Part of the appeal of many science fiction and fantasy books of this sort is seeing how the author takes a couple of key changes and imagines how history might play out differently. What if the Roman Empire had never fallen? What if Germany had won World War II? What if Martin Sheen had only had one son? And so forth.
The characters in White Cat occupy a world that is as precisely like our own as it can be and still support the premise of the story. The forces of history are so highly canalized that you can rewind the tape hundreds of years and give a small fraction of people magical powers, and you still wind up with Facebook. Tolstoy would be proud.

WADDINGTON, C. (1942). Canalization of Development and the Inheritance of Acquired Characters Nature, 150 (3811), 563-565 DOI: 10.1038/150563a0

Update: I had originally described the book as having been written by Michael Frost and Holly Black, which is what it says on the Kindle version, where I read it. Upon further investigation, it seems that Michael Frost is responsible for the cover art, but not the writing in the book. Everywhere else, Holly Black is the only listed author, so I have corrected my review accordingly. It strikes me as odd that the only place where he would be listed as a co-author is on the Kindle, where there is no cover art, but there you have it.

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biology, evolution, genomic imprinting, primers, science

Genomic Imprinting VI: Hemimethylation

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So, last time, we discussed the fact that the expression differences associated with genomic imprinting rely on the existence of epigenetic differences, such as DNA methylation. We also mentioned that those differences are established separately in the male and female germ lines. That is, one methylation pattern is established in the female germ line during oogenesis (egg formation), while a different pattern is established in the male germ line during spermatogenesis (sperm formation).

It is straightforward to understand how such differences could be established, since oogenesis and spermatogenesis occur in physically distinct locations, where different patterns of gene expression can produce the epigenetic differences. But, after fertilization, these parent-of-origin-specific epigenetic marks are maintained across many rounds of cell division. So, a cell in, say, your liver, will exhibit different epigenetic states on maternally and paternally alleles, despite the fact that they have occupied the same cellular environment throughout development.

Alleles at an imprinted locus maintain substantial epigenetic differences, despite occupying the same environment across many cell divisions.

The allele-specific maintenance of the methylation state depends on the fact that methylation occurs at “palindromic” sequences. When we’re talking about language, a palindrome is a word or phrase that contains the same sequence of letters when read forwards or backwards, like “a man, a plan, a canal, Panama,” or “eat tea.” In genetics, a palindrome is where the nucleotide sequence on one strand of the DNA is the same as the sequence on the complementary strand (which is read in the opposite direction).

The palindrome we will be concerned with here is a really short one: CpG (where the “p” indicates the phosphate linker between the cytosine (C) and guanine (G) nucelotides).  CpG is a palindrome because C pairs with G (and G pairs with C), so that the complementary DNA strand has a CpG at the same site. Methylation occurs on the cytosines, so that if we have two alleles with different methylation states at a CpG site, they will look like this:

Here we have a schematic representation of two alleles with palindromic CpG sites that differ in their epigenetic state. In the top figure, the cytosines on both strands of the double-stranded DNA are methylated. In the bottom figure, both cytosines are unmodified.

So, how is this methylation difference maintained when the cell undergoes DNA replication and mitosis? The key lies in the fact that DNA replication is semi-conservative. That is, in order to make a copy of a double-stranded piece of DNA, what you do is pull the two strands apart and synthesize a new strand complementary to each of them.

When Watson and Crick published their paper on the structure of the DNA double helix, they noted that this structure suggested a mechanism by which the specific DNA sequence could be replicated. Crick later went on to establish a reputation for himself as a neuroscientist. Watson went on to establish a reputation for for himself as an asshole.

The newly-synthesized strands will contain normal, unmethylated cytosine, whether or not the template strand was methylated.  So, starting from unmethylated DNA, each daughter cell inherits an unmethylated copy of the allele. But, if we start from methylated DNA, each daughter cell inherits hemimethylated DNA, where one strand of the DNA double helix has a methylated cytosine, but the cytosine on the complementary strand is unmethylated.

There an enzyme, Dnmt1, that specifically targets the unmethylated cytosine at a hemimethylated CpG and methylates it. So, after the action of this enzyme, the methylated state has been restored in each of the daughter cells. The combination of the hemimethylase (or maintenance methyltransferase) activity of Dnmt1 and the semiconservative replication of DNA set up a system in which the epigenetic state of an allele can be set once, and it will be propagated across multiple cell divisions.

DNA replication of a fully methylated CpG site results in two hemimethylated copies. The hemimethylase Dnmt1 then restores these hemimethylated sites to their fully methylated form.

In the next installment, we’ll talk about another epigenetic mechanism, histone modification, and the possibility of an analogous propagation mechanism for propagating those epigenetic marks.

Yoder, J., Soman, N., Verdine, G., & Bestor, T. (1997). DNA (cytosine-5)-methyltransferases in mouse cells and tissues. Studies with a mechanism-based probe. Journal of Molecular Biology, 270 (3), 385-395 DOI: 10.1006/jmbi.1997.1125