Using deleterious mutations to cross fitness valleys - as misunderstood by ID creationists

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:
“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.”

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.

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.

Stenger's physics of atheism

Gotta love Victor Stenger.

As a biologist, I have frequently been irritated to no end with creationists who say that what I believe (yes*) and do for a living - evolution - is a hoax. Though I deal with these people less often nowadays (but in the past...**), it is always somehow in the back of my mind. Geologists, too, have a problem (see, for example, PZ's post on that), though geology claiming that the Earth is million and billions years old vex creationists less than the idea that humans evolved from monkeys (yes***). And physicists even less so, even though one of the hardest arguments to refute is that of fine-tuning. But enter Stenger:

Yet for Stenger, fine-tuning is a fallacy and so there is no case for atheists to answer. They simply do not need to resort to Multiverses or to cyclical universes. His book discusses each of the usual examples of fine-tuning that Christian apologetics raise. He applies well-established physics, seeking to demonstrate that in each case, “the parameters of physics and cosmology are not particularly fine-tuned for life, especially human life.”

For example, Stenger agrees that the ratio of protons and electrons in the universe is sufficiently precise as to enable life to ultimately form. However that does not mean that there was the need for a divine being to intervene to ensure that the ratio was correct. He writes, “The number of electrons in the universe should exactly equal the number of protons because of charge conservation, on the reasonable assumption that the total electric charge of the universe is neutral—as it should be if the universe came from ‘nothing’ and charge is conserved.”

Similarly, it is true that the universe would have collapsed before it reached its present size if its expansion rate at one second after the Big Bang had been lower by as little as one part in many billions. However he explains that the expansion rate was automatically very close to the critical rate due to the energy density of the universe.

You can read the rest on eSkeptic.

* I believe it based on the evidence. 'Believe' does not only mean 'on faith', and I do not care to let creationists (or atheists) dictate how I use the word.

** For some past posts dealing with creationists, also in the comments:
Watching multicellularity evolve before our eyes
The Rzeppa game show
My own pet creationist

*** Surely, given the diversity of animals that we call 'monkeys', the last common ancestor of all primates looked like a monkey (though not necessarily like any extant monkey).

In Oklahoma for Evolution 2011

I've arrived in Norman, Oklahoma for the 2011 Evolution conference. You can follow tweets here: #evolution2011.

Tomorrow, Saturday, I'm giving a talk on evolutionary metagenomics, which you can also read about on BEACON's blog.

And if you're here yourself, come and say hi (good luck finding me).

Evolutionary metagenomics

We would like to know how soil bacteria evolve. They are important for humans and other living things, as they are involved in chemical processes that are both beneficial and harmful to us. They emit and absorb greenhouse gases: carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O), and they are part of the nitrogen cycle, which is important for agriculture. Which you care about even if you don’t eat your veggies.

There is a reason why soil bacteria are not model organisms in biology. They are hard to study because they are difficult to grow in the laboratory. Also, there are many different species of soil bacteria, so even if we did mange to grow a couple in the lab, we would not likely learn much about the overall function of the bacterial communities in soil. So what to do?

You take a handful of soil and you sequence that – after removing earthworms. Simple. It’s called metagenomics.

Read the rest on BEACON's blog.

Homophobes are turned on by homosexuality

Unfortunately I can't access the full length article of this one: Is homophobia associated with homosexual arousal?

But it is obviously too good to miss. The abstract reads:

The authors investigated the role of homosexual arousal in exclusively heterosexual men who admitted negative affect toward homosexual individuals. Participants consisted of a group of homophobic men (n = 35 ) and a group of nonhomophobic men (n = 29); they were assigned to groups on the basis of their scores on the Index of Homophobia (W. W. Hudson & W. A. Ricketts, 1980). The men were exposed to sexually explicit erotic stimuli consisting of heterosexual, male homosexual, and lesbian videotapes, and changes in penile circumference were monitored. They also completed an Aggression Questionnaire (A. H. Buss & M. Perry, 1992). Both groups exhibited increases in penile circumference to the heterosexual and female homosexual videos. Only the homophobic men showed an increase in penile erection to male homosexual stimuli. The groups did not differ in aggression. Homophobia is apparently associated with homosexual arousal that the homophobic individual is either unaware of or denies.

So, homophobic men are aroused by homosexual porn, and either they don't know it (hmmm), or they deny it (looking at you, Fred Phelps).

Reference:
Adams, H., Wright, L., & Lohr, B. (1996). Is homophobia associated with homosexual arousal? Journal of Abnormal Psychology, 105 (3), 440-445 DOI: 10.1037/0021-843X.105.3.440

CoE 36 is up

At Greg Laden's blog.

This month there are several posts by researchers at BEACON, which is the place that I work at myself at Michigan State. One of those is by a postdoc, Kevin Theis, who works on the microbial communities in the anal pouch of spotted hyenas. The bacteria in those pouches produce scents that the hyenas use for communication. Kevin is investigating if the bacteria and the hyena are coevolving.


Kevin Theis with an anesthetized adult male hyena named Detroit.