It is fitting that an article I just got published in Proceedings of the Royal Society B [1] has been blogged about on the ID lover's Uncommon Descent: Are Fitness Valleys Too Deep?This research is part of my PhD thesis which I started in 2007, in part inspired by the creationist claim that deleterious mutations are only bad and prohibits evolution. My first objection was that they can of course exist on the line of descent as hitchhikers - deleterious mutations that go to fixation because they occur in close temporal proximity* to a beneficial mutation, so the combined effect is beneficial. Then I learned about epistasis - the interaction between mutations - which is ubiquitous and essential for non-trivial adaptation. Trivial adaptation is when evolution occurs by accumulating only beneficial mutations, as when a single fitness peak is ascended. But if the fitness landscape is rugged with many local peaks (as it necessarily always is in reality), then it is of great benefit to be able to climb down one peak and up another higher one.
The study is also highlighted in MSU Research**: Evolutionary kings of the hill use good, bad and ugly mutations to speed ahead of competition.
On Uncommon Descent, someone called PaV says
Second, here’s what the lead author had to say:The level of ignorance comes as a surprise to me, but that is of course entirely my own fault. Never underestimate these people's denseness.
“These fitness landscapes simply could not be traversed with mutations that did not interact.”
This wasn’t a ‘main conclusion’ of the study; however, I don’t know about you, but this sounds to me like any ‘single’ mutation cannot get you across any fitness valley, and, therefore, seems to rule out having a single mutation ‘sweep’ across a population to fixation.
IOW, without epistatic effects, evolution cannot move forward. This is unexpected. It makes simple neo-Darwinian evolution that more complex with more hurdles to get over. And, it is another nail in the coffin of neo-Darwinism. That is: “Another day, another bad day for Darwinism.”
That a single mutation cannot get you across a valley should rule out that a single mutation can go to fixation reveals a gaping hole in the writer's understanding of very basic population dynamics. It is a complete non-sequitur. Crossing a valley is not necessary for a mutation to go to fixation; if a mutation is beneficial it can (but doesn't always) go to fixation by selection, and whether this is one step in crossing a valley or not is besides the point.
In this study we only allowed single point mutations, which is why it is true that no single mutation can cause an organism to jump from one peak to another (this is short-hand for the parent sitting on one peak has an offspring with one mutation). In order to move from one peak to another, at least two mutations are needed - otherwise the genotypes of the two organisms would be adjacent, and so one of them would not be sitting on a fitness peak. With larger-scale mutations such as insertions, deletions, transposons, etc., it would not be impossible to go from one peak to another in a single mutational event.
Another possible misunderstanding is that evolution never occurs up one peak. It does of course, as recently reported in two papers on experimental evolution side by side in Science [2,3]. In those cases, evolution can proceed by beneficial single point mutations, until the peak has been ascended (which in non-digital evolution often takes a very long time).
Lastly, PaV says it is unexpected that evolution cannot move forward without epistasis. It isn't at all. There are cases where epistasis is not important, but overall we already knew that epistasis was required.
I picture a game of King of the Hill where the ID creationists stand atop a little hill of faulty understanding of evolutionary theory claiming victory, while the rest of us have long ago ascended an adjacent and much higher peak that the ID creationists aren't able to locate.
Apologies to Randall Munroe.
References:
[1] Østman, B., Hintze, A., & Adami, C. (2011). Impact of epistasis and pleiotropy on evolutionary adaptation Proceedings of the Royal Society B: Biological Sciences DOI: 10.1098/rspb.2011.0870
[2] Chou, H., Chiu, H., Delaney, N., Segre, D., & Marx, C. (2011). Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation Science, 332 (6034), 1190-1192 DOI: 10.1126/science.1203799
[3] Khan, A., Dinh, D., Schneider, D., Lenski, R., & Cooper, T. (2011). Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population Science, 332 (6034), 1193-1196 DOI: 10.1126/science.1203801
* I am no popular science writer, but if you don't know what I mean, feel free to ask.
** And on PhysOrg, Science Daily, Irish Weather Online, and NSF.
How does your work tie in with Gavrilets' stuff on high dimensional landscapes?
ReplyDeleteNo matter how many times it repeats itself, I still find this kind of willful misunderstanding shocking. Oh well, what can you do?
ReplyDeleteThere seems to be a pattern to a lot of the more simple-minded Creationist misquoting: A research paper on evolution sets out to say something along the lines of, "Here is a question about evolution as we understand it. Past answers to this question have been inadequate because of blah-blah-blah. Here is our answer, and why we think it is a better answer." Which is a rather natural way for a research paper to proceed, isn't it? (Far better than, "Past answers have been robust and complete and no further explanation is needed -- but just for shits and giggles I made up this other thing about it, too," eh?) But of course then the quote-mining leaves off the part about the actual answer.
Which leads to the amusing and yet utterly headdesking phenomenon of Creationists quoting a paper in order to support some idiosyncratic critique of evolution, when that very paper is itself an excellent refutation to said critique. Gotta love it..
Whoops, that was me. I was logged in under my wife's e-mail.
ReplyDeleteOkay, blah blah blah. But seriously, how do you like my figure?
ReplyDelete(Will get back to you, John, with a coherent answer, if I can.)
Hey,
ReplyDeleteI am also interested to hear your reply to John's question.
Sergey Kryazhimskiy's attempt at classifying landscapes is also very interesting - http://www.pnas.org/content/106/44/18638.full.pdf
Finally, I have not yet had the time to read your paper thoroughly, but I would appreciate if you can also comment on how you measure 'ruggedness' of a landscape.
I recall from one of Dan Hartl's talks on evolutionary analysis of malaria resistance, he mentioned, for example, that they used Aita's method to quantify the ruggedness -well, in fact, "smoothness"- of the simulated landscapes.
Aita's paper: http://www.ncbi.nlm.nih.gov/pubmed/11707608
Cheers,
ps. Those guys over at xkcd should better start looking for a job!
John, sorry for the delay. I have tried to answer your questions in a new post: More on high-dimensional fitness landscapes. Let me know if I failed to do so adequately.
ReplyDeleteAlso, note that I nicked those stick-men from xkcd by Randall Munroe, in case that wasn't clear.
Bjørn Østman: But seriously, how do you like my figure?
ReplyDeleteThe newest creation by noted artist, Bjørn Østman, will certainly raise a fuss in certain circles. The simplicity of the figures, the drama of the conflict, draws the viewer into the story. Those at the very apex of the mountain are confident, perhaps overconfident, even bored looking at the futile efforts of those stuck on the lower hill of knowledge. The vigor of the usurpers is apparent, their advance only stopped by the chasm (well, more like a short hop), separating them from the fitness slope to victory! They draw up to the very precipice, and we are left to wonder whether they dare to cross.
Might we suggest a name for the drawing, The Argument Regarding Design.
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xposted to AntiEvolution
The overwhelming majority of Christians accept some form of evolution so picking on a scant minority isnt proof of anything. I could pick Stalin or a child rapists for my atheist debate too.
ReplyDeleteThere seems to be some sense of joy in the quest for superiority as if that some how will change anything in the end. I personally dont blame a small group not trusting in people who believe something can come out of nothing, and then lop on the insurmountable odds of life forming as if it were trivial.
Carl sagan has been shown to be worse than a cartoon character in his use of logic when he said there only a few conditions a planet needed for life. You could laugh from the day he said that all the way till today and it still wouldnt do justice to its sheer stupidity--and you cant understand why some have chosen to simply plug up their ears when atheists speak?
They're too biased and its hurt education. Look how long it took them to accept a "beginning"--and now Fine tuning. Now they move to multiverses which is milk coming out of your nose type of lunacy. I think when you strip away all the quests for personal glory you left with very little but a personal opinion
John, it is simply not true that the overwhelming majority of Christians - in the US - accept evolution. Many catholics (as opposed to the Vatican), Evangelicals, Southern Baptists, many Mormons, and Seventh Day Adventists don't. There are others.
DeleteAlso, "some form of evolution" really isn't good enough. Which "forms" are you thinking about? In my book, believing only parts of current evolutionary theory (leaving out the details currently discussed and under investigation), while holding that God created part of it, is simply not enough.
No, I cannot understand why you would close your ears when "atheists speak", just because Carl Sagan may or may not have been wrong on some scientific points. That is unwarranted. I do not, similarly, close my ears to what religious people say, just because Rick Santorum talks like a deuchebag on all subjects, including evolution.
And also note, why on Earth should I ignore Christians that don't believe in evolution, when all Republican presidential candidates say they don't believe it (save for Huntsman)?