Field of Science

Seriously Tim Minchin

Shit! I love Tim Minchin with all his funny lyrics and atheism, but I've just seen that he is almost even greater when he's totally serious:

(Yes, I am aware it's a cover.)


A: "5."
Q: "What is the number of lines without the word "fuck" (or derivatives) in Tim Minchin's Pope Song?"

P.S. I don't mean to imply that Tim is not serious when he's funny. On the contrary.

P.P.S. If you haven't, listen to White Wine In The Sun - one of my favorites.

Welcome to the Anthropocene

The Anthropocene has begun:
Among scientists, there is now serious talk that the Holocene has ended and a new era has begun, called the Anthropocene, a term first used in 2000 by Paul Crutzen, who shared a Nobel Prize for his work on the chemical mechanisms that affect the ozone layer.


Those of us alive today may well be able to say we were present when the Anthropocene epoch was formally adopted. But we will not be able to say we were present at the start of the Anthropocene. There is a strong case that the Anthropocene begins with the Industrial Revolution, around 1800, when we began to exert our most profound impact on the world, especially by altering the carbon content of the atmosphere.
In that regard, I submit these figures that I use in talks on my research on nitrate reductase in bacteria:

Clearly the rise begins at around year 1800. Here is atmospheric concentration (left axis) and radiative forcing (right axis) of methane, which is a potent green house gas, about a third as bad as carbon dioxide. Nitrous oxide, which is in part produced by bacteria in agricultural soils, is even less potent, at about a tenth the radiative forcing of carbon dioxide. But the point is that all three gases closely mirror the human population growth.

From IPCC 2007 Synthesis Report (the x-axis is identical to the human growth curve, starting at 1000 and ending at 2000.)

WTF in the blogosphere*

Satoshi Kanazawa arguing that the US militia should have access to nuclear warheads, or is he playing devil's advocate? Dangerous game either way.

"Santorum is a sexual neologism for a "frothy mixture of lube and fecal matter that is sometimes the byproduct of anal sex," and was proposed by American humorist and sex-advice columnist Dan Savage in 2003 to "memorialize" then-Republican U.S. Senator Rick Santorum from Pennsylvania due to the controversy over his statements on homosexuality.[1] Savage asked his readers to submit new definitions for the term.[1] The word became a successful Google bomb when Savage created a website for it, which unseated the Senator's official website as the top search result for his surname on the Google web search engine.[2][3]On February 21, 2011, Stephen Colbert proposed that the definition be changed." Click here to spread Santorum.

* And other related spheres.

Dawkins and Moran on neutral evolution (and me)

It's not every day that Richard Dawkins comes to your defense.

But he just came to mine. Larry Moran is a biochemist at the University of Toronto, and he runs a great blog writing a fair bit about evolution. He is on the side of Gould and Lewontin in the neutralist/selectionist debate in evolution. In the comments to a post from this morning, Dawkins, Darwin, Drift, and Neutral Theory, I asked for examples of traits that are known to have evolved via drift, rather than natural selection. Not that there aren't any traits that are thought not to be adaptive, but to make the point that we know that they are neutral just as much or little as we know others are adaptive, and that many traits must be adaptive, and that I think Moran is overemphasizing the importance of drift in evolution. Here's Moran's response:
It's shocking to me that you would have to ask such a question in 2011. As a graduate student interested in evolution you should be very familiar with the common examples and the debate.

Lewontin likes rhinoceros, I like tongue rolling. Some people can roll their tongues and some can't? Is this an adaptive trait?

I admit that these particular examples aren't going to change the course of evolution but it's all that's required to establish the real possibility that alleles with visible phenotypes can be neutral.

Once we've agreed on that point we can discuss whether the evolution of blood types in different human populations is due to selection or drift. (The answer is drift.)

Your other examples are more complicated but many of them arise from a combination of all the important mechanisms of evolution, not just natural selection.

I anticipate that you are going to fall back on the old canard that none of these traits have been proven beyond all reasonable doubt to be the result of random genetic drift acting on nearly neutral alleles, therefore it's permissible to say they all must be adaptations. If you don't see the flaw in that logic then there's no point in continuing.
I honestly didn't appreciate that much if at all, and neither did Richard Dawkins:
"Shocking"? Isn't that rather a patronising and arrogant response to Mr Østman?

Lewontin's guess that the difference between two-horned and one-horned rhinoceroses is non-adaptive is just that: a pure guess. Here is what Lewontin wrote:

"For example, the Indian rhinoceros has one horn and the African rhinoceros has two. Horns are an adaptation for protection against predators, but it is not true that one horn is specifically adaptive under Indian conditions as opposed to two horns on the African plains." (cited, together with my reply, in The Extended Phenotype, the chapter called 'Constraints on Perfection':

Actually, it seems unlikely that horns are an adaptation against predators. Lewontin is being too adaptationist here. Horns are more likely an adaptation against other rhinos, both as weapons and as displays. In which case it could very well be the case that one horn is best for Indian rhinos and two horns best for African rhinos (because a rhino has to match whatever is the norm for its competitors in its own region).

Never mind Lewontin's ignorance about the biology of rhinoceroses. The point is that Moran has no more right to assume, with Lewontin, that the number of rhinoceros horns is neutral than anybody else has the right to assume that they are under selection. Even if I could not invoke sexual selection (which makes it positively likely that Lewontin is wrong) Moran would have no right to assume that this is a good example of a neutral trait, still less would he have the right to patronise Bjørn Østman in that way.

Tongue-rolling is a polymorphism (I can 't do it, you very possibly can) which makes it more complicated. In this case we are not seeking an adaptive advantage in tongue-rolling per se. We are seeking some kind of balance between the two sides of the polymorphism. I don't know enough about it (nor does Moran) but I would keep an open mind, and the first place I would look would be for some kind of balancing selection (or perhaps heterozygous advantage) with tongue-rolling as a pleiotropic byproduct. Once again, the last thing I would do is simply assume in my ignorance (and Moran's ignorance) that selection is not involved.

Richard Dawkins
It's Dr. now, btw.

Do go read the full exchange.

Cruelty towards animals all around

I posted this video of some humans having fun poking a half deep-fried and half alive fish on Facebook the other day:

Here's one that isn't better (though I am not saying that it makes no difference whether one is having fun with cruelty, or not):

To erase any doubts, I am am by no means at all saying that things are better in Denmark; the way pigs, for example, are treated there is often downright despicable.

There was a big case some years ago in Denmark about transportation of live pigs. Here's a similar one somewhere else in Europe:

So, it seems to me animals are treated with unnecessary cruelty no matter where we look. I am no vegetarian, and I don't think that there is anything wrong with killing animals for consumption. However, I would like to insist that they are treated well on their own terms while alive, and that they are killed without excessive or unnecessary suffering (though I personally think that some moments of suffering in death at the end of an otherwise enjoyable life is acceptable).

Eat less meat. Choose the more expensive meat of animals that have been treated well. Don't eat halal. Don't mistreat animals - especially not for the fun of it.

Mankind has not stopped evolving

Watch this.

Last sentence: "Chances are decades from now, we'll look pretty much the same."

"Decades from now"?!?! Are you absolutely kidding me? What a ridiculous thing to even consider. Decades from now nearly all species will look pretty much the same as they do now. When humans evolved big brains, did it happen in "decades"? That's like saying there is no galaxy evolution (= development), because decades from now all galaxies will look just the same as they do now.

It is true that some selection pressures have been removed, such as selection against bad eyesight, diabetes, low sperm count, and many other diseases. There is probably also not selection for being more intelligent - people of low IQ (for one measure) do not appear to have any less children than those of high IQ (is it in fact the other way around?). But this is now. Selection pressures are dictated by the environment, and we can only say anything about what selection will do as long as we know what the environment will be like. And does anyone really think nothing will happen in the future to our environment? No global climate change will affect us? No loss of species diversity, habitat loss, continental drift, changes in the Gulf Current, nearby gamma-ray bursts, meteors, supervolcanos, or other things that we don't know of?

The statement that there is no selection pressure anymore is also wrong. There is lots of purifying selection, meaning selection that makes sure that humans do not change. This selection pressure is in fact exactly why we do not evolve - for example selection against having larger brains, since babies with larger heads tend to die in child birth (if it were not for c-sections, my oldest son would likely not have been born, his mother dying with him). But note that this need only be true for some aspects of human morphology - while one trait is under purifying selection, another may be under positive selection, forcing a change in the long term.

Additionally, evolution does not equal natural selection. Random chance can change populations, too. Genetic drift is weak when the effective population is large, which is arguably is with humans right now, but that may quickly change when famine or disease or other catastrophic events suddenly kill off everyone in the northern hemisphere, for example. And then in one fell swoop the human population will have changed, and we call that evolution too.

One aspect of human morphology that interests me are feet. I don't think we are presently under selection for having five distinct toes. My guess is that a human born with just two toes would be totally fine. I know people with some toes fused, and it makes no difference in the lives. They can walk like the best of them, and since we wear shoes, no potential mate will react negatively to gross toes (okay, I'm putting things a little on edge here). Toe morphology drifts, and once humans lose the ability to make shoes, we may have changed significantly since we first started wearing them.

No, mankind has not stopped evolving. At all. Some selection pressures have changed, but they may change again when the environment changes. Evolution takes time, not "decades".

Also, Michio Kaku is a string theorist. Here's one for you: String theory is not a field of physics, but of mathematics. Please stop saying what the real world is like based on string theory, at least until you can actually verify your hypotheses experimentally.

Victory in the whaling wars?

Japan has suspended their whaling for research™ for fear of the safety of the crew members. They haven't announced that they won't start again, but it's still a victory in my mind for a couple of reasons:
  • Some whales will live to see another day.
  • Killing in the name of science is a lie, and doesn't exactly give science a better reputation.
  • The Nisshin Maru whaling ship gave in to the harassment of the conservationists.
Sea Shepherd Conservation Society ships have been chasing the whaling fleet for weeks in the icy seas, trying to block Japan's annual whale hunt, planned for up to 945 whales.
The latter point proves that aggressive actions by conservationists actually works. Three cheers!

Again, this may not be a permanent halt, but I still regard is a step in the right direction. The fact that eating whales is tradition in Japan matters none.
The country kills hundreds of whales every year in a hunt which appalls conservationists but which is also deeply embedded in traditional Japanese culture.
[Source.] Slavery. Beheadings. Torture. Discrimination. Bullfights. All sorts of things were practiced for hundreds of years, condoned by governments and leaders, and yet no longer considered morally defensible. It's got to fucking stop.

Citron pudding for Darwin's birthday

It was Charles Darwin's birthday yesterday, and at MSU we of course had a big party to celebrate the day. Unfortunately, two days ago I had two wisdom teeth removed, and I was in a lot of pain yesterday, despite a decent acetaminophen/codeine cocktail, so I couldn't go. Besides, I'm also on penicillin, and not being able to drink alcohol at a party is like partying without alcohol to me.

But, Rob Pennock did introduce me to the idea of looking up Emma Darwin's recipes at The Complete Works of Charles Darwin Online. So yesterday I made the Citron Pudding:

I didn't have cream, so I used yoghurt. And cane sugar instead of sifted sugar. I used both lemon juice and lemon skin. Here's how it turned out:

I baked it at 375 Fahrenheit for about 20 minutes, and the result was superb. Thank you Emma, and congratz to Charles.

Loss of anus?

ResearchBlogging.orgIt's nice when we are somewhat certain that evolutionary trees are accurate, so it is unsettling when researchers suggest that they aren't. This time it's Acoels, which were are thought to be older than both Protostomes (mouth develops before the anus) and Deuterostomes (anus first). But now a team of evolutionary biologists is suggesting that Acoles belong within the group of Deuterostomes. This even though Acoles don't have a separate mouth and anus at all, but an opening that serves both functions.
Zoologists have generally placed acoels on the earliest branch of the bilaterians — before the split between protostomes and deuterostomes — because the worms lack so many key features such as a separate mouth and anus, a central nervous system and organs to filter waste.
(From Nature News).

Click for larger version.

After analysing sequences from nuclear DNA, the group made a separate evolutionary tree based on genes in mitochondria. They also studied microRNAs, which regulate gene expression but do not code for proteins. According to co-author Kevin Peterson, a palaeontologist at Dartmouth College in Hanover, New Hampshire, microRNAs are particularly useful for studying deep evolutionary relationships. The team found that acoels have a type of microRNA known to be specific to deuterostomes, suggesting that they are related. [Emphasis added.]
Really? This microRNA evidence weighs more than the fact that Acoels have no anus, etc.? The researchers did not only use microRNA:
Here we assemble three independent data sets—mitochondrial genes, a phylogenomic data set of 38,330 amino-acid positions and new microRNA (miRNA) complements—and show that the position of Acoelomorpha is strongly affected by a long-branch attraction (LBA) artefact. When we minimize LBA we find consistent support for a position of both acoelomorphs and Xenoturbella within the deuterostomes.
Okay, but since I don't give much credence to microRNA compared to presence/absence of separate mouth/anus and central nervous system, what would happen to the inference if the microRNA data were taken out?

Unlike some other researchers who like very much that we have a living form ancestral to all bilaterians (organisms with bilateral symmetry), my problem here is that we are asked to believe that an ancestor of Acoels had separate mouth and anus, etc., but then lost those later on. The hell?! One biology lab manual I used once had the text "the critical invention of the anus", and I think this is apt. What happens to a lineage that makes it lose it's anus, and instead start barfing out excrements?

Very strange.

Philippe, H., Brinkmann, H., Copley, R., Moroz, L., Nakano, H., Poustka, A., Wallberg, A., Peterson, K., & Telford, M. (2011). Acoelomorph flatworms are deuterostomes related to Xenoturbella Nature, 470 (7333), 255-258 DOI: 10.1038/nature09676

Regicide in evolutionary psychology

I missed a blog post by Satoshi Kanazawa about a month ago: Why Are Stepparents More Likely to Kill Their Children? In it, Kanazawa describes research carried out by a Swedish team that sounds pretty damning for what is one of the "foundational empirical findings" in evolutionary psychology, namely the so-called “Cinderella Effect”. The effect is that children are more likely to be killed by stepparents than biological parents, and the explanation that evolutionary psychologists have given is that this is because "stepchildren do not carry any of the genes of the stepparents, so there is absolutely no evolutionary reason for stepparents to love, care for and invest in their stepchildren."

Science like that makes me vomit. Figuratively.


First interjection: How can anyone with any knowledge of biology even write something like this?
Stepchildren do not carry any of the genes of the stepparents, so there is absolutely no evolutionary reason for stepparents to love, care for and invest in their stepchildren.
Wrong. On the semantic level: Stepparents share ALL genes with the stepchildren. All humans have all the same genes*. A gene can be approximately thought of as a sequence of DNA that codes for a particular protein. Many genes then come in different versions in the human population - they are called alleles. One famous example is the gene coding for Hemoglobin for which there are two versions, one of which makes sickle-celled Hemoglobin. This may seem like a minor mistake, and I am sure that Kanazawa knows the difference.

But then, what sense does it really make to say that "stepchildren do not carry any of the genes of the stepparents"? Suppose we here substitute "allele" for "gene", is it then true? No, it is not at all. It's not just Kanazawa, of course. It is very common to hear people saying "each parent shares 50% of their genes with each child." But it's bogus, because we are all related, and there are many genes for which two random people will have the same allele. I am not saying that therefore parents aren't more like their children genetically than any random person - parents and children look alike for genetic reasons, of course. But it remains that the statement as given is factually false. Let me just remind you that when people speak of the genetic relatedness of humans and chimpanzees, then we are all of a sudden 98% (or whatever) identical. Taken together, these statements of course make no sense. Apples and oranges.

Second interjection: It does emphatically not follow that there is no reason to love, care for, or invest in children that one is not the parent of. Not even in evolutionary terms. Humans cooperate, and in evolutionary terms it potentially benefits a parent to care for stepchildren in many ways. How about protecting each other? Stepchildren caring for children, for example. I know the story of male lions taking over a pride and killing the cubs that aren't theirs, so that the females come into estrus quicker, and in the light of this, the hypothesis that parents are more likely to kill their stepchildren than their own children does make sense. But always watch out for "making sense". My high school physics teacher liked to tell how "common sense" had been put into an urn and shelved away so that it may not delude the scientist.

Third interjection: The Swedish team examined data that suggest that stepparents are from the beginning more likely to be violent, and Kanazawa readily admits that this could explain the "Cinderella effect". Single mothers perhaps aren't the kind of women in the highest demand, and neither are violent males, so it seems like a good hypothesis that stepfathers are more likely to be violent than the average male. And this is the problem: If one evolutionary psychology hypothesis - trusted and expounded for many years - cannot explain the data, then it is dead easy to come up with another that can. And that's the danger of how evolutionary psychologists practice science. It's not that studying human behavior is not good science (it is). It's not that the link between genetics and behavior is bogus (it isn't). It's the readiness to attribute an evolutionary explanation to psychological data that is problematic. Not because such explanations can't be true (and in some cases they likely are), but because of the ease and certainty with which "common sense" is applied. This sordid affair is a perfect case in point.
The only major weakness of Temrin et al.’s study, which the authors themselves openly acknowledge, is their extremely small sample, taken from one small nation. There just aren’t many homicides in Sweden, child homicides or otherwise. So their findings must be replicated, with larger samples and in other societies. But, at the very least, their paper has begun to throw one of the foundational principles of evolutionary psychology into possible doubt. In my experience, this is the first and (so far) the only study ever to do so. If their findings are replicated, and if their explanation for the greater risk of homicide faced by stepchildren is true, then Hans Temrin and his colleagues have secured their places in the Evolutionary Psychology Hall of Fame for their act of successful academic regicide.
Kanazawa writes this apparently without any kind of reflection, which I think is appalling.

* There may be super rare cases where a whole gene is deleted or added in offspring.

Update 2/6/2011:

Jerry Coyne writes about human-chimp genetic similarity in Why Evolution is True. His estimate is that at least 80 percent of genes differ in at least one codon coding for amino acids:

Culturomics does not exist'Culturomics' does not exist. As far as I'm concerned, if it isn't on Wikipedia, it doesn't exist. However, it is listed on Wikipedia's Word of the year for 2010 under the designation 'Least likely to succeed'. As an amusing side note, it also says this: Most Unnecessary: refudiate (Blend of refute and repudiate used by Sarah Palin on Twitter. The laughs.

Quantitative Analysis of Culture Using Millions of Digitized Books was published online december 16th 2010, and in print January 14th, 2011. Unfortunately, 'culturomics' does not appear in the title. Big mistake. Twice in the abstract, 17 times in the paper (including 'culturomic' and, but not in the title. Tsk.

Using the Books Ngram Viewer is indeed addictive. Comparing 'Bjørn', 'Bjorn' and 'pleiotropy' I get this:

Clearly there is a correlation between 'Bjorn' and 'pleiotropy', as there should be. That this trend takes off in 1940 is of course curious (should be 2008), but I'll take what I can get (that only (4% of all) books are parsed is another important detail, I guess). And I'm just not going to comment on the fact that people can't spell 'Bjørn'.

The really interesting thing in the article is this figure:

Even before the origin of the Modern Synthesis of evolutionary biology in the 1930's, interest in evolution waned, and neither 'the cell' nor 'bacteria' was enough to revive interest. Then came along 'DNA', and 'evolution' picked up again, and has been increasing ever since. And so it is. Our understanding of evolution is contingent upon what studying DNA has taught us. It has revolutionized biology, and now pervades evolutionary biology. Without DNA, I would be without a job. Or this job, at least.

Michel, J., Shen, Y., Aiden, A., Veres, A., Gray, M., , ., Pickett, J., Hoiberg, D., Clancy, D., Norvig, P., Orwant, J., Pinker, S., Nowak, M., & Aiden, E. (2010). Quantitative Analysis of Culture Using Millions of Digitized Books Science, 331 (6014), 176-182 DOI: 10.1126/science.1199644