Field of Science

In which a leading geneticist makes a fool of himself

Geneticist Steve Jones claims that human evolution has grind to a halt, and that our descendants a million years hence will look just like us. John Wilkins has a nice rebuttal of this ridiculous notion, but I'd like to add that another reason why Jones is off track.

Whether a species evolves or not - change vs. stasis - depends on the environment. For a very short time in evolutionary terms the environment has been relatively stable, but once that changes - and it always does - species change with it.

There are two ways in which humans could slow down their own evolution in such an event: i) keep the effective population size large, or ii) use technology and medicine to minimize the impact of the environment. The former implies the upkeep of a global, sexually mixed society, and the latter the constant use of said technologies. Suggesting that either is certain for a million years is naïve in the extreme.

Natural Selection Fails to Optimize Mutation Rates

ResearchBlogging.orgRich Lenski's group published this paper in PLoS Computational Biology less than two weeks ago:
Clune J, Misevic D, Ofria C, Lenski RE, Elena SF, Sanjuán, R. (2008). Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes. PLoS Comput Biol 4(9). PLoS Computational Biology, 4 (9).

In the Ph.D. program I'm in we are required to give a journal club talk once per semester (the result of which is that that's exactly how many we give), and I chose to do this one for last Wednesday because it is something I worked on briefly in the NK-landscape a while back*.

Clune et al. used AVIDA to investigate if natural selection is sufficient to evolve mutation rates that are close to the static mutation rates that optimize fitness. First they do a bunch of runs with different mutation rates to find which one optimizes fitness, and find a genomic mutation rate of Uopt=4.641 (figure 1). Then they allow the value of the mutation rate to change by mutation, and compare the evolved mutation rates and resulting fitness to that of the static ones. They find that the evolved mutation rate is much lower than Uopt, and that the average population fitness is also much lower than that obtained for Uopt. In other words, a population left to evolve by natural selection does not evolve a mutation rate that benefits the population the most.


Figure 1: Population average fitness of with static mutation rates (solid black line) compared to evolving mutation rates (red and blue dots). Initial conditions were U=1 (red) and U=10-3 (blue).

Their hypothesis to explain this puzzling observation is that selection against the mutational load wins over the adaptive benefit of a high mutation rate. When a population sits on top of a local peak in the fitness landscape, it has two choices: Either evolve a low mutation rate, so that it avoids deleterious mutations, which lowers the average population fitness, or it evolves a high mutation rate, so that it can locate another higher peak somewhere not so far away in genotype space. Their result suggest that the former strategy wins. The short-term effect of minimizing the mutational load wins over the long-term benefit of adaptation.

They then went on to hypothesize that it is the topology of the fitness landscape the decides which of these alternatives wins. In AVIDA the fitness landscape is very rugged, meaning it has many fitness peaks and valleys. They therefore constructed an explicit landscape in which they could manually adjust the size of a valley that the population would need to cross in order to adapt. Since adaptation is fast, they also switched the landscape every 300 generations between two "seasons" (figure 2). This has the effect of needing more beneficial mutations to optimize fitness, resulting in a longer time of adaptation (which leads to better statistics). As can be seen in this figure, when there is no valley, the population does indeed evolve a mutation rate identical to the static optimal mutation rate. But with a valley size of 2 or 3, both the mutation rate and the resulting fitness is lower than that of a population with the optimal static mutation rate.


Figure 2: Explicit fitness landscapes. First and second column show how the fitness landscape alternate between the two "seasons". The third column is the reulting fitness as a function of the mutations rate. Solid line are static mutation rates, and red and blue points are for simulations with evolving mutation rates. The greater the valley is, the harder is is for natural selection to evolve the optimal mutation rate, and it thus fails to optimize fitness when the landscape is rugged.

What does that mean for us? For one thing is means that when using evolutionary algorithms to find solutions to human problems we need to be careful setting the mutation rate so that optimal solutions are found.

It also suggest there is a barrier preventing real populations of living organisms to optimize their reproductive output when their mutation rates can evolve. Mutation rates do vary between species and individuals. When errors are made by the DNA copying machinery during meiosis and mitosis, there are ways to correct for it. How well that is done depends on proteins that are products of genes, that themselves are prone to copying-errors. It is practically impossible to attain a 100% fidelity (i.e. zero mutation rate), but it is in principle straightforward to select for a machinery that allows more mutations to slip through uncorrected. But alas, the landscape dictates the dynamics and prevents high mutation rates.


* In the NK-landscape I found that I could only avoid fixation of a mutator-lcous with zero mutation rate by updating the environment every ten generations. This has the effect of requiring the population to continuously adapt. This was for K=3, which means there is a fair amount of epistasis - the landscape has many local peaks.

Faith begets faith

In A TEMPLETON CONVERSATION Jerome Groopman is asked by Michael Shermer why he believes at all. Here is his answer:
Why believe? I have no rational answer. The question seems to be in the domain of why do we love someone? You could reduce it to certain components, perhaps refer to neurotransmitters, but somehow the answer seems to transcend the truly knowable. This is the cognitive dissonance that people like me live with, and with which we often struggle.
He has no rational answer, no. But that is because he doesn't know enough science. One can answer that it is most likely because his was brought up to believe. The best predictor of religious faith is the faith of the parents. Faith begets faith, you might say. Another answer is that religious faith has adaptive value; it enables social cohesion and promotes altruism, both of which would have be selected for at the dawn of humanity. However, once, i.e. now, we realize this, it is no longer necessary to believe in the myth in order to appreciate the value of cooperation and altruism, etc. Additionally, as many authors have argued recently (Dawkins, Hitchens, Harris), there is a great many reasons why we should abandon faith at this point.

Why does God want us to believe in him? Yesterday Nancey Murphy started answering this question saying "because God is.." (pause), and I, to my own surprise, said "vain" out loud. Three people in front of my turned around to look at me, and I excused myself. But I really can't see any other reason why he should be so worried that we worship him, and neither can any theologians that I have ever heard of.

Education for Asperger

In Denmark the ministry of education put aside money for education for young people with Asperger-syndrome. Aspies are often quite intelligent, and can handle a narrow job with very good focus. I used to work in web development, so I know that much of the work IT is very routine. Perfect for Aspies. A story from Politiken (warning: Danish newpaper) details how to young students with Asperger was looking forward to starting an IT education, AspIT, but now the county has rejected them. That's sad, and I hope they get it all sorted out soon. But the interesting thing is the initiative. I reported a few years ago on a friend's blog (also in Danish) that a company hired several people with Autism as software testers. They were better than "normal" people at this, because of their syndrome-given attention to focus on repetitive work. And they love the work, so everybody wins. It's a great thing when a group with problems can break out and become a valued asset instead.

Perhaps we could similarly find some use for creationists? Ken Ham writing science-fiction scripts for Hollywood?

Live from 'Origins' at Caltech

So I arrived at the Beckmann auditorium at Caltech for Origins - the BIG Questions organized by the Skeptics Society. The advertised $5 book table was the table with creationist literature. The good ones were on another table (e.g. Donald Prothero's Evolution: What the Fossils Say and Why It Matters), and were no less than $25 and up to way more. Snicker. Predictable, I guess.

"No recordings or pictures of any kind is allowed."
Michael Shermer announces there is also good news in the media: Ignobel prizes awarded:
  • Coke is a spermacide.
  • Earning potential of exotic dancers: average earnings higher when the women are at their most fertile. "Science at it's best."
  • Fleas that live on a dog jump higher than fleas that live on a cat.
  • Slime molds can solve puzzles.
  • Expensive fake medicine is more effective than cheap fake medicine.
  • Plants have dignity. Would seem to be a major problem for some vegetarians.

Donald Prothero is on first. He starts out by debunking the common creationist misconception that one can calculate probabilities after the fact of an event to argue that it's improbability makes it impossible without supernatural intervention (c.f. Hoyle's Boeing 7x7 in a junkyard). Interestingly, Prothero said 707, and noted you can tell how old an argument it is. It is usually said to have been a 747, which was made in the 1960's. Hoyle died in 2001. Not sure when Hoyle made the argument.
He then goes on to talk about science: Miller-Urey, amino acids, lipid bilayers. Moves into origin-of-life questions. RNA world. Imagine a mosh pit, in which the earrings and piercing are all going to link up, as a model of how the first DNA assembled.
To my horror, he just described archaebacteria as the most primitive life form, way more primitive than (eu)bacteria. And he shows an artists rendition of the tree of life where archaea is on the left, bacteria in the middle, and eukaryotes on the right, totally ignoring the fact that archaea and eukaryotes (plants, animals, etc.) are sister groups (more related to each other), and bacteria split off first, i.e. bacteria is - at least phylogentically - more ancestral. I'm sure that gave the wrong impression on a lot of these old geezers in the audience (average age must be over 50).
Earth was a "Planet of Scum" for most of it's history, ruled by cyanobacteria (prokaryotes, not eubacteria). Then a little about Margolis' endosymbiosis, which I just see for the first time was first theorized by Russian botanist Mereschkowski in 1905. Wikipedia rules - I consider half my non-existent B.S. in biology coming from the (print version of) Natural History Magazine, and the half other from wikipedia.
Anyway, that was six weeks of lectures in forty minutes.

Leonard Susskind is next. Who starts by saying that skepticism can be very close to dismissiveness. We get "all of particle physics in 15 seconds." He fumbles with powerpoint, and it all takes way more than 15 seconds. After a minute he is still on the gluon.
The whole thing is like a Rube Goldberg machine, meaning that it's all a mess, and there doesn't seem to be much sense to it. E.g. masses of the elementary particles doesn't seem to have any logic to them. Sounds like he's going to come to fine-tuning. Yes, gravity is just right, etc. Is this an accident, having nothing to do with life, or is it something else (he implies design). Too highly fine-tuned to be an accident, he says. The constants are just right: gravitational, cosmological, etc. Finely tuned... for life, that is. Yet he is no believer in design.
He jumps into the question of design. He presents the tree of life, and notes he hates to say "bush". Laughter all around.
On to compact spaces, those rolled up dimensions which enables us to have more than three space dimensions.
During the questions, one person suggested that it might not be that the Universe is fine-tuned for life, but that we are fine-tuned for the Universe. "I don't know," was Susskind's answer.

Paul Davies... Origin of the Universe. Quite frankly, I find this cosmology stuff rather tedious. It was one of the reasons that I didn't continue doing research in it. Davies' key issues: Does the Universe have a "meaning" or "purpose", or is it ultimately arbitrary and absurd, existing without reason? I can see where this is going. Whenever people phrase questions in this way, they are almost always people of faith. For these people, life without purpose is one of the main horrors that drives them to reject cosmology and evolution.
What caused the Big Bang, and what came before it? He thinks these questions are red herrings of theology, and I agree. If you answer that it was a physical process, you can always go deeper, asking what was before, etc. Augustine said both space and time was created - the world was made with time, not in time. Crucial distinction. But a trivial one for students of cosmology. It does not make sense to ask what came before the Big Bang, because time was created at that event. Personally, I think time is an illusion, which only serves to quantify how much change goes on in the spatial dimensions.
Take home answers: Can science alone give a complete account of the Universe? Not yet, but we keep trying. Does the Universe have a purpose? The Universe is about something. The Universe is an unfolding story. That's the real mystery. Bleh.

In the break, as I was charging my computer, I was observing a group of about eight young people gathering around a seated older guy, whose name-tag I could not read. They sounded from what I could hear like "science-skeptics". It really resembled acolytes with their master. Most of the time everyone's attention was on the seated guy, and they all seemed to listen carefully to his every word. I'll try to catch his name later.

Next is Sean Carroll from Caltech (not to be confused with Sean Carroll from UW-Madison of evo-devo fame). Physics, not biology. The nature of time. Entropy increases because there are more ways to be high-entropy than low-entropy. But why was entropy low to begin with? Which lands us at the beginning of the Universe. It was low at the Big Bang. The fact that we remember the past and not the future, that there is evolution, is that we are not in thermal equilibrium. We would be the same temperature as the Sun, and there would be no life. But the receive low-entropy radiation from the Sun. The question is why the entropy was initially low. Maybe it is added on by some individual, but he will not pursue that notion further. Thank him! (In my opinion there really is nothing further to say about it anyway, if one were to go down that path. Blind alley.)
He notes about Einstein, that when talking about his theory we should not be presented with a picture of him when he was 70 years old and let it all hang loose, but one from when he actually came up with his theory, when he looked young and sharp and someone used to cut his hair.
Carroll ends by completely dismissing any notion of a designer in science as unproductive. I was glad to finally hear someone say that.
Christof Koch's up. Heavy German accent. A real scientist. Conciousness, feelings, states about zomezing. Very hard talk to summarize because covered a lot of ground, but he basically meant to explain that we still need a theory on consciousness. 4000 years of philosophy has not brought us far. We need experimentation, which is a sentiment that I very much share applied to most philosophy, as it it mostly completely uninformed by reality. Philosophy of morality is a case in point. At the end he said that while he does believe in some sort of God to create the Universe (he was brought up a Roman Catholic, but left that faith behind). However, as of yet there is no need of the God-hypothesis to explain conciousness. He also mentioned that people with different eye colors see colors different. One of my sons have heterochromia iridium, and I can't wait to ask him if it's true.

After lunch Kenneth Miller starts off what is to become a panel discussion. Kenneth was of course a prime witness in the Dover trial (something about a sticker, believe it or not). There is some applause now praising the three Dover teachers who refused to teach intelligent design, but the group of young people I am sitting among right now are solemnly quiet. Some of them were among the acolytes I mentioned above. They are also all taking notes extensively (on paper).
Kenneth refers us to a debate in print between himself and Christopher Hitchens (God Is Not Great). He recommends it for at least the entertainment value - Hitchens is his usual self, he reports. Should be a good read. His talk presented the same logic that can be found in Finding Darwin's God, which is that philosophical materialism is just as unsupported as theism, and that theism is indeed compatible with all of science. As usual he completely evades the issue of the specifics of his religion. He is a Roman Catholic, and Yahweh is certainly a very intervening god. Just think virgin birth, sainthood, and a slew of miracles.

Nancey Murphy thinks it's better to talk about materialism or naturalism, instead of atheism, which is only against something (theism). I call myself an atheist because I believe there is no supernatural anything. On the absence of evidence. Yes, I could be wrong, but so far I haven't been, and those who have claims of miracles or anything else supernatural as described in scripture have nothing to show for.

Michael Shermer recalled that he has been called an "atheist without balls" because of what he wrote for Templeton. Reminds us that words are placeholders for a deeper meaning, as when we talk about the paranormal, whereas for theists it is the answer. To Kenneth: How do you know the Universe has no purpose, you ask. But wait, those who claim there is a purpose are the ones to show some evidence. How did you get the idea that it's from God? There is purpose and design, but only from the bottom up, not from top-down. Science works: if you want to go to Mars you use science. If you have another way, go right ahead. Laughs. To Nancey: What's the difference between an invisible god and a nonexistent god? Prayer might work, but if it does, it's in a way that we can't tell the difference. Why does God hate amputees? With all that praying for wounded soldiers, not one has grown back a leg. Who is it that says we'll be able to grow new limbs soon? Everybody shouts Ray Kurtzweil. Funny!

Stuart Kauffman seems to be absent, because now were at the panel discussion, and only Kenneth, Nancey, and Michael is on stage. I'm pretty sure my deduction is accurate.

Ken says he enjoys talking with Michael, because he, unlike many other atheists, assumes that he is talking to thinking person when speaking with theists. But I think he might be wrong on that assumption. Nancey gets the word and says "What I say is a little bit relevant." She's hilarious. She's trained in philosophy, and I mention that in my defense for not really understanding what she means. It sounds so theoretical, and... scientific. But now she says she has a prayer group, in which they once prayed for a participant to become pregnant, and two weeks later it happened. She also has a prayer chair (no link on Wikipedia for that one). She sat down in it, and a few moments later she got a phone call that she got the job she wanted. Michael objects "what about all the other applicants who didn't get the job?" She says that not too many people pray for amputees. More laughter. Ken says something, but I tuned out because I am worried of running out of battery. When he's done, one person claps.
The moderator now invites people to come to the microphones with questions, and eight seconds later there are two lines of a total of over twenty eager participants. Ken answers how he thinks God can be there when biological variation is random, and natural selection is directional. The questioner should have read his book, because the second half of it answer exactly that question. Ken then argues for the historical reality of Jesus, because the gospel spread so fast. How about the fact that there is no Roman records of his crucifixion (I think that should be crucifiction)? Q: What is God made of, who made him, and why does he need amputees to be prayed for, when he should know that they would like their limbs back? Ken says something in defense of God's non-intervention, and the group I am sitting in applauds excessively. This is hilarious.
As I get up to recharge my battery, I notice one of the guys in the group applauding Ken Miller is leaning over looking at my computer. That's great. If you happen to read this, welcome! Perhaps you can tell me who you guys are?

4:15pm.
Hugh Ross: The Bible has over ten times as much cosmology as any other holy books. Biblical cosmology. He's an outright creationist, I can tell from his Bible quotes of cosmic singularity beginnings. Same tired old arguments. If space has mass, then it must be created by a causal agent. I never get what the origin of that claim is, except mere human experience. He calls on Borde, Vilenkin, and Guth to state that time is finite, and that everything must have a beginning. I'm sure he means every thing, apart from God himself, of course. Six different old testament authors talk about the expanding universe, so there. Apologetics. Zzzzz. Now he claims that currently knowledge slightly favors a closed universe. He quote-mines Lawrence Krauss about fine-tuning. It's like he wasn't here for the earlier talks on physics. He has a website. I am aware that both sides of the argument needs to be represented in order to make it a good meeting, but this guy is over the top. Enough about him.
Except to say that he now pulled out the Blount et al. paper on contingency in E. coli, which has been debated to death between Lenski and Schlafly, and many others, to surprisingly say that the non-recurrence of citrate digestion ability points to a designer.

Victor Stenger comments that he looks  forward to read Ross' paper when it comes out. Noether's theorem comes up, which leads to the statement that the laws of physics are just what they would be expected to be if they came from nothing. And then he finally says it:
  • Not everything that begins has a cause - at least according to modern quantum mechanics.
  • The Universe did not begin with a singularity, so it need not have had a beginning or a cause.
Kudos to Stenger. To answer why there is something rather than nothing: "Because nothing is unstable" (Wilczek 1980, SciAm).

"The discussion we've all been waiting for."
Ross finds more accounts of creation in the Bible than in the Quran or in the book of Mormons, which he takes to be a win for Christianity. I find many more in books of science, but I don't suppose that means anything to him. Stenger notes that Genesis 1 and 2 contradict each other, but Ross explains that 1 is chronological and 2 isn't. And that there is plenty of predictions of the future which have come true. Like "the book of Daniel, for instance", to which Stenger responds with a "what?" and sighs. Ross' answer drowns in laughter. It really is just a boring discussion about what the Bible says, now.
Last comments before questions...
Ross says his strongest argument is that the truth is revealed in the Bible and confirmed across all the sciences. Stenger thinks that God is not needed, is a meaningless concept, and that physical evidence is not better explained by a deity.
Question: What would be a pre-cambrian rabbit for your theory? Ross didn't get it. What would falsify your theory? Ross answers it would be the proof that humans are naturally made, that humanity has no spiritual dimension. That would be the end of Christianity.

Last one-sentence statements:
Murphy: "Nothing I know of science contradicts the essentials of Christianity (...)"
Ross: "Words of the apostle Paul: All things must be tested."
Carroll: "The world is not magic."
Miller: "There are two ways to look at the world: nothing is a miracle, or everything is a miracle. I choose the latter."
Stenger: "We are all frozen nothings."
Shermer: "Be skeptical."


Update 10/25:
I have finally figured out who the students I observed during the break were. They were from Azusa Pacific University, an evangelical christian college, and their professor was Michael Bruner:
Michael Bruner was born and raised in the Philippines as a child of missionary parents. He graduated from the University of Washington with a B.A. in English and received his M.Div. from Princeton Seminary. He is an ordained Presbyterian minister who currently teaches in both the English and Theology departments at AZUSA PACIFIC UNIVERSITY in southern California. He lives in Fullerton, California with his wife, Jenna, and their daughter, Belle.

Jared Diamond on Collapse

Searching for origins

I will be attending the Origins conference at Caltech this saturday, October 4th. Plan is to listen to the luminaries, sure, but also to do some networking. And to report about the whole experience here, so stay tuned.

Speakers include Donald Prothero, Leonard Susskind, Christian Koch, as well as Michael Shermer (organizer), Stuart Kauffman, and Kenneth Miller (of Finding Darwin's God) in a panel discussion on the question "Does science make belief in God obsolete?" Should be a blast.