Evolution 2013 Greatest Hits

Tags

biology, David Sloan Wilson, evolution, Fairfield University, Gene duplication, human evolution, Joan Roughgarden, publishing, Salt Lake City, science

This past week I attend the annual “Evolution conference,” which is a joint meeting of The Society for the Study of Evolution, the American Society of Naturalists and the Society of Systematic Biologists. Evolution 2013 was held in Snowbird, Utah, a ski resort and conference center that feels isolated despite being right up the road from Salt Lake City. I also attended a special workshop for undergraduate educators (there was also a workshop for K-12 educators). This workshop was so popular that they expanded the attendance from thirty participants to fifty. The focus on education was just one trend I noticed at this year’s meeting, where I saw many changes from when I first started attending meetings fifteen years ago.

View of Salt Lake valley from 11,000 foot summit of Hidden Peak, reached via Snowbird tram. (Photo credit: Wikipedia)

For those of you that haven’t attended one of these meetings, here’s a brief run-down of how it goes: during the day scientists present their research in twelve-minute talks. These are arranged in fifteen-minute blocks so that people have time to take questions and go from one room to another: there are up to ten of these sessions going on at the same time, hence they are called “concurrent sessions.” This is analogous to what people used to call “reading a paper” or “giving a paper,” but we call it “giving a talk” or “doing a talk.” In the evening there’s a long talk by a society president or someone getting a major award, and then people gather for a social event, usually a poster session. A poster session is when researchers present their data literally on a poster tacked to a wall, and stand beside it while people drinking wine and munching hors d’oeuvres walk by and receive five-minute mini-talks on the data in the poster. I presented a poster on my sexual selection research.

Interesting Talks and Posters

I found many of the talks and posters at the meeting very interesting. Going to scientific meetings is where we see the real communication in the scientific community. At a symposium entitled “Evolution out of bounds,” several speakers examined the promise and failings of evolution when applied to human problems.

David Sloan Wilson

David Sloan Wilson presented his collaborations with economists and the results of a project to help academically failing high-school students using the principles of evolution of cooperation. Joan Roughgarden presented an organismically based model of the evolution of physical intimacy. She had previously announced her talk as “Evolution of human sexuality,” but opened by apologizing and saying we can’t discuss the evolution of something we haven’t described completely. Roughgarden put forth the radical idea that we could consider immediate organismal causes for certain behaviors (i.e. something she called “fun”) before considering evolutionary consequences.

In regular paper sessions Michael Sheehan of Arizona University presented evidence that there is selection for diversity of human faces to aid in individual recognition. Corlett Wood of University of Virginia showed what might happen when the environment induces a correlation between response to selection and heritability. And one of many presentations on archaic hominins showed that the epigenetic changes between modern humans and Neanderthals lead to broadening of knees and other Neanderthal features. A packed room listened to Michael Turelli admit (in his own special way) that he had completely screwed up the statistical analyses in a talk that he had already been giving as an invited speaker — and submitted for publication! Opposite my own poster at the Sunday night poster session was one of a few studies of the development of feathers in pigeons and doves: the authors narrowed down the cause of curly feathers in certain dove breeds to a single biochemical factor, due to a single nucleotide change.

I missed a talk that had people talking by Adi Livnat of Virginia Tech. Based on one of my colleagues’ descriptions, Livnat is dissatisfied with adaptive explanations of the origin of new genes. Whenever anyone questions the gospel of adaptationism, people definitely start talking. Livnat was going further than questioning however, so a lot of people were talking. I actually overheard someone saying “Did you hear that? Wow…”

A new form of neofunctionalization

The talk that excited me most was the last talk of the meeting, about two hours before the banquet. I’ll admit that I was only there because I had dinner with the speaker after striking up a random conversation in the hotel lobby. Myself, Ashley Byun of Fairfield University and her former student and colleague Russ Meister of UConn were looking for a place to eat dinner the night before the education workshop. At the time of Ashley’s talk there were fewer than twelve people in the room, backing up our concensus from dinner that most people would be off showering for the banquet or hiking. Despite all this, for very important reasons I liked the last talk of the meeting the best.

Mutation by gene duplication (Photo credit: Ethan Hein)

Dr. Byun presented a new idea for the neofunctionalization of duplicated genes: protein subcellular relocalization. For many reasons in eukaryotic organisms (for example, animals, plants, fungi) genes can become duplicated so that for a while there are two copies of a gene doing the same thing. Theory suggests that while two copies is better than one for some genes, as long as they produce the same product, they are relatively redundant, and one of the copies may acquire mutations that cripple its function over evolutionary time. It may then degrade into junk (“die”). However, the theory goes, the duplicate gene may acquire a new function. The most common explanation (i.e. the one we tell students in basic science courses) is that the duplicate would mutate into a gene producing a new protein.

Duplicate genes acquiring new functions by producing new proteins is incredibly unlikely. If we assume that crippling mutations are more common than “beneficial” mutations (that enhance the function of a protein), then there’s probably no way getting a new function would happen before the duplicate gene turns into biochemical sewage. Despite this problem, we commonly teach undergrads that this exact process is what made the Cambrian Explosion possible.

A nifty function of eukaryotic cells is how they package proteins and tell them where to go in the cell (or out of the cell). When proteins leave the site of protein synthesis, they are tagged with a sequence of amino acids (the “signal peptide”) that tells them where to go in the cell, e.g. to mitochondria, endoplasmic reticulum or a chloroplast. Normally the signal peptide is just a signal and when the gene reaches its destination, it is cleaved off and does not do anything else. If this sequence mutates, the protein product could get sent to a new part of the cell, where Byun points out it could perform a new function.

Apoptosis Network (Photo credit: sjcockell)

Now I don’t want to get too excited, but this is the first positive hypothesis I’ve seen for neofunctionalization, which could explain two of the most puzzling (for me) features of eukaryotes: the complexity of body plans and the dazzling, bewildering, uber-complicatedness of eukaryotic epistatic gene networks. As I mentioned above, we commonly teach that gene duplication, especially in homeobox genes, was the key to the diversification of animal body plans, but we don’t point out the exceedingly unlikely events that would make gene duplication and neofunctionalization actually work. Over the past year I taught cellular and developmental biology, and then genetics and molecular biology. As one example of eukaryotic complexity I learned that between the already complicated steps of apoptosis in Caenorhabditis elegans and the same process in Homo sapiens there’s about a gazillion things making it more complicated. An answer for this based on adaptation is that humans are more complex than worms, and therefore need more complex signaling pathways. This hypothesis ignores the fact that humans didn’t exist before the pathway got more complex, or why such complex organisms exist in the first place. We often assume it’s adaptation. An answer that I find more likely is that these biochemical networks are built by patching together steps that are slight modifications of completely unrelated functions. Eukaryotic cells are like Rube Goldberg machines built by a team of six-year-olds all working on only one piece at the same time. At the end they all get together and link things up.

Dr. Byun’s talk showed compelling evidence that duplicated genes that acquire mutations in the signal peptide are more likely to stay alive over evolutionary time instead of degrading into junk. In other words, acquiring a new cellular destination appears to keep duplicate genes from acquiring mutations that would cripple their biochemical function. Let’s be clear: she did not show that these mutations actually do send duplicate gene products to new organelles. However, she looked over a huge diversity of taxa and a huge number of genes, and almost all the data was significantly in favor her hypothesis.

I found Byun’s talk compelling for another reason: her speaking style. First of all she went slowly and explained her hypothesis clearly enough that a guy with minimal experience with cell biology could understand it. Secondly, she prepared the audience in two ways: by explaining which numerical values would support her hypothesis, and by showing snippets of data before blowing away the audience with a huge array of results. She walked slowly through what a hazard ratio is, then explained “If this ratio is greater than 1…less than 1…equal to one…then…” Then she showed a slide that had results for about five genes (as I recall). On this she explained a color code that showed supportive, not supportive, and inconclusive results, and walked the audience through why each cell in the table was coded the way it was. Then she flipped the slide and showed a huge table with many species and it was clear from the predominance of green color that most of the results supported her hypothesis. She did all that without saying “This is really complicated so I’m going to walk you through it…” (For non-initiates, that is a phrase that some speakers use, but many have advised me not to, because it may sound condescending to the audience).

Trends

I noticed several trends developing at this meeting:

1. Focus on education: not only did I attend a workshop for educators, but the meeting was interspersed with papers and discussions of how to better teach evolution, not just of how to convince basic science students against creationism
2. Experimental evolution: Rich Lenski and his academic offspring have shown that experimental evolution directly tests the hypotheses of evolutionary theory. I saw many talks using artificial selection, and not just in microbes.
3. Applying evolution to non-biological systems: two symposia were devoted to applying evolutionary biology to problems outside the typical realm of discourse. This used to be unpopular, but is now gaining momentum.
4. Multilevel science: some people might derisively call it reductionism, but what I saw was a lot of researchers testing behavioral, anatomical and systematic hypotheses, and then going to the very lowest levels of biological organization to find data. Now that gene sequencing is becoming less expensive, technology is enabling scientists to find support for their predictions at all levels of biological organization, from genes up to global geographic data, quite often in the same study (e.g. Michael Sheehan’s work on faces).

The importance of scientific meetings

Attending the Evolution 2013 meeting reinforced to me that scientific meetings are where the most important scientific communication takes place. I find this quite important, especially considering all the discussion of publishing lately. If we consider that what you hear at meetings is mostly new, very little of it published, and that scientists at meetings are face-to-face where they can discuss ideas spontaneously, then publication appears in its proper place: as a public record, a way of preserving research for posterity, not as the end-all goal of scientific exploration. Much of what is presented at meetings is preliminary, some of it is just new ideas people have. Very little of it is so polished that it isn’t open to amendment or suggestion. And most scientists are open to new ideas at the stage where they are: once a paper is published, the work has been done for almost a year, sometimes five years. At that point, all that is left is to deposit something for archaeologists to dig up. In other words, going to meetings like this reminds me that publications are not science, nor are they even the best way of communicating science. The best way to communicate science, or anything, is face-to-face.

Related articles

• New research suggests complex animals evolved more than once (sciencenews.org)
• Two mutations triggered an evolutionary leap 500 million years ago (sciencedaily.com)
• Mutation-Driven Evolution (sandwalk.blogspot.com)

Advertisements

New Journal Publishing Models

Tags

open access, publishing, research, science

Really interesting stuff is happening this week in the world of scientific publication. Scientists and editors are trying out new publication models that will change science. This is important because science publication is science. Scientists rely on citing printed works to give credibility to their arguments, their data, and basic knowledge. Everything that scientists put in a new article has to be attributed to an already-printed article, be a new result, or be generally accepted by the community. This last provision doesn’t stop most papers I see from citing Charles Darwin within the first paragraph. Even when we all know who he was and what he said, citing a printed work still lends the most weight to any point a scientist makes.

Why is this true? Because there’s an ironically Darwinian process behind publication called peer review. Once an article has been accepted for publication by a journal, it has been reviewed thoroughly and revised significantly. If it’s published, then several knowledgeable people agreed that it was important and well-done. Here’s a basic run-down of the process: I do some research and I want to tell people about it; I submit that paper to a scientific journal’s editor; the editor gives it to an associate editor who chooses (usually) three reviewers who prepare detailed comments on everything from spelling to the validity and the overall scientific significance of the results; the editor then looks over those comments and decides whether the paper is right for the journal, is well-done, etc. Then he can make one of several decisions (there are many variations, but these are the most common): reject the paper, give the authors a chance to revise and then start the process again, accept it given that the authors do what the reviewers suggest, or accept it outright. The last option is unheard of — except that it happened to me once; that was crazy — but it’s important for understanding new developments in publishing.

The last part of the process is that if the author gets the chance to publish the article, he has to pay to publish it. This is the weird part of scientific publishing that I think many people are unaware of, or might have thought they misheard. Yes, scientists pay to have their work published.

Ideally the process of peer review should live up to the ideals that I outlined above, but there are a lot of people who think it is outdated, unnecessary or evil. There are other problems in the process, such as authors paying for work, and then there is the cost of disseminating the research, i.e. actually getting it to its readers. As of this week, scientists are now toying with every part of this process along with the help of the internet.

The biggest development over the past ten years has been Open Access publishing, which takes care of the last part of the process, the dissemination of research. Open Access articles are reviewed just like other articles, but they are offered free of charge over the internet to anyone who wants to read them. This is unlike most journals that are only available to people with a subscription, for example students at a university where the library subscribes. The biggest argument in favor of Open Access has been that citizens are being made to pay for research twice: federal grants (that originate from tax dollars) pay to do the research and publish it, and then taxpayers have to pay to read the work once it’s published. There are now thousands of Open Access journals and you can read them as easily as you are reading this blog. This is a good thing.

Moving back through the process, a new sort of non-journal is experimenting with publication costs. PeerJ is not really a journal, but promises peer-reviewed publication on the internet for a one-time fee for the authors: you pay only $99 for one publication a year, instead of up to $1000 for one publication at a time. PeerJ also promises to publish articles on the basis of scientific merit rather than impact. Most journals, including my favorites, will only accept paper if the editor and the reviewers can agree that it’s significant to the scientific community. PLoS ONE changed that by accepting papers only based on whether the science was well-done, and PeerJ plans to do the same thing. As you can imagine PLoS ONE publishes a lot of papers: there are over 2,000 a month these days, which makes it really hard to find interesting papers to read. If I publish a paper in PLoS ONE, I will definitely blog about it.

Dealing with the problems of peer review is the goal of Peerage of Science, which is a network of scientists that distribute their work and get it reviewed before submission to a journal. I think the idea here is that you can then submit your paper saying that it’s already been reviewed. I like the idea of forming a community of peers where we can review each others’ work without things becoming competitive. This is one of the biggest complaints about peer review. I’ve never experienced competition during the review process, but I know people who have thought that was going on. Reviews are typically anonymous, but Peerage of Science encourages the breaking of anonymity.

A new microbiology journal called mBio plans on dealing with the editor’s decision-making process. Instead of all the variants, and the reviewers getting whatever they want (“we kindly thank the reviewers for making us do additional experiments that had nothing to do with our hypothesis, but that seem to fit the research program of another biologist we know very well”), mBio promises to either reject a paper or accept it with minor revisions. A minor revision is something like the decision to not include a figure, or to add one or two additional citations. This means that the editor can make a faster decision, but it also means that reviewers are given less (more?) power. Sounds like if a paper needs significant revisions, mBio will just reject it, saving the authors some time.

I think what all these experiments are going for is making scientific publication a lot more like a wiki: a place where people can easily access each others’ work and data, easily share their work and data, and review is still there. Review, with all its problems, is still incredibly important. Lots of people have suggested alternatives, and there are some good ones, but I still appreciate the review process, even if I don’t like it all the time while I’m in the middle of it. I recently had a paper rejected because the reviewers just didn’t get what I was saying, but that is my problem, not theirs, so they did their jobs. Moving scientific publication in the direction of openness, through any of these ideas, is a huge step forward.

We should be a long way from the days when scientists would deliberately obfuscate their results from their peers — Galileo disseminated his results to other astronomers written in a cipher. The biggest thing holding us back is the idea that scientists own their research: I don’t believe I own my ideas, but there are people who want to keep their ideas to themselves as long as possible (i.e. until after it’s been through peer review). And of course there are people who profit from keeping scientific results hard to get at. However, as the free software movement shows, today’s technology (incidentally, built out of free software) makes sharing incredibly easy for those of us who want to share. The people who created arXiv understood this even when it wasn’t so easy.

Thanks for reading.