Pleiotropy is 100 years old

This year, the term pleiotropy was defined 100 years ago, and Frank Stearns, graduate student at the University of Maryland biology graduate program has written a perspective in Genetics, which I highly recommend.

Looking around umd.edu, I found that Stearn's research topic is "mutations in adaptive landscapes", which explains his interest in pleiotropy. I have the same interest for the same reason (see preprints here and here).

ABSTRACT

Pleiotropy is defined as the phenomenon in which a single locus affects two or more distinct phenotypic traits. The term was formally introduced into the literature by the German geneticist Ludwig Plate in 1910, 100 years ago. Pleiotropy has had an important influence on the fields of physiological and medical genetics as well as on evolutionary biology. Different approaches to the study of pleiotropy have led to incongruence in the way that it is perceived and discussed among researchers in these fields. Furthermore, our understanding of the term has changed quite a bit since 1910, particularly in light of modern molecular data. This review traces the history of the term "pleiotropy" and reevaluates its current place in the field of genetics.

Apparently this Ludwig Plate was a nazi and a misogynist. Sighs. Onward, upward.

Pleiotropy can be caused by one gene making two or more different proteins (alternative splicing) which then affect different traits, or by a single protein affecting multiple traits. The former used to be termed "genuine" pleiotropy, and the latter "spurious" pleiotropy. I'm not so hot on these terms, since the connotation is that there is something less real about pleiotropy caused by a single protein. But no one uses these terms anymore, so never mind. Incidentally, I previously worked with Drosophila gene expression data, and there it was evident that mRNA (which is what gets translated into protein) was found in multiple tissues (we called them domains, but think of them as traits, e.g. 'hind gut', 'glial cells', 'rectum', etc.). Studies mostly confirm that pleiotropy is largely owing to one protein's involvement in several traits, so it doesn't seem so spurious.

Stearns argues that alternative reading frames (where the DNA strand is read at different starting positions, yielding different proteins), which is common in bacteria, is an instance of pleiotropy, since there is information shared between the two 'genes'. I totally concur, since for me the issue is whether a mutation can affect more than one trait, and in this instance it certainly can, given that the different proteins affect different traits.

Current research questions about pleiotropy

One avenue of research on pleiotropy is how extensive it is. Recent research has shot down the assumption of universal pleiotropy made by the founders of the Modern Synthesis (Fisher, Wright, Mayr), which states that all genes has the potential to affect all traits. However, we now know something about the distribution of number of traits affected, i.e., the level of pleiotropy. For example, Wang, Liao, and Zhang (2010) found that in yeast, nematode and mouse, the number of traits that a gene affects ranges between 0 and about 150, with averages of up 5-8 traits for nematode and mouse.



Staerns quotes earlier studies that found the level of pleiotropy to be 4-5 (in yeast, Droshoplia and nematode), 6-7 for eight vertebrate species, and 7.8 for mouse in a study of skeletal genetics.

Since this is counting traits per gene, you may be excused for asking what a trait is (and what a gene is, but that's not my purview). For one thing, the nomenclature is a little confusing. What is meant by trait here, is what is formally known as a character, which is a property of the phenotype. Trait can sometimes mean the value of the character, such as character=hair, trait=brown, but I like to refer to that as the trait value (and I'm not alone). Phenotype can also mean two things, namely the whole physical/biological manifestation of an organism, and that's what I meant here, but it can also refer to a trait, like when they say that knocking out a particular gene causes a particular phenotype. This may all not be very enlightening if we're interested in what a trait is; the pornographic definition seems to be what people apply: "I'll recognize it when I see it". And one may wonder how many traits a species has. The caption to the figure above from Wang et al. reads

Frequency distributions of degree of gene pleiotropy in (A) yeast morphological, (B) yeast environmental, (C) yeast physiological, (D) nematode, and (E) mouse pleiotropy data. Mean and median degrees of pleiotropy and their SDs are indicated. The numbers in parentheses are the mean and median degrees of pleiotropy divided by the total number of traits. After the removal of genes that do not affect any trait and traits that are not affected by any gene, the total numbers of genes and traits in these datasets are (A) 2,449 genes and 253 traits, (B) 774 genes and 22 traits, (C) 1,256 genes and 120 traits, (D) 661 genes and 44 traits, and (E) 4,915 genes and 308 traits.

"Traits that are not affected by any gene..." Strange. Describing the methods they say

Using the yeast morphological pleiotropy data, we calculated the number (n) of traits that are significantly affected by each gene. We then measured a gene’s total phenotypic effect on these n traits, using either the Euclidian distance (TE) or the Manhattan distance (TM).

I'm not sure, but it doesn't seem that even if they looked at all 6,000 yeast genes that they then necessarily identified all traits. Their number of 253 morphological traits... is that enough to completely characterize Baker's yeast? And are 308 really enough to characterize a mouse? How many traits to humans have?

Okay, I'm done. Go.

References:
Stearns, F. (2010). One Hundred Years of Pleiotropy: A Retrospective Genetics, 186 (3), 767-773 DOI: 10.1534/genetics.110.122549
Wang, Z., Liao, B., & Zhang, J. (2010). From the Cover: Genomic patterns of pleiotropy and the evolution of complexity Proceedings of the National Academy of Sciences, 107 (42), 18034-18039 DOI: 10.1073/pnas.1004666107

Historian predicts demise of evolutionary theory

His name is Enézio Eugênio de Almeida Filho, and he is a post-Darwinist. He predicts that evolutionary theory will soon meet its demise, following a grand scale of people recognizing that the evidence does not support it.

Science gave me this conviction. I learned at university, when a scientific theory is not supported by evidence, it must be revised or dropped. I'm post-Darwinian anticipating imminent and impending rupture paradigm in evolutionary biology. Time to say goodbye to Darwin.

This is a Google translation of his Blogger profile - he's Brazilian, and only blogs in Portuguese.

His background is in history of science. He has a PhD in it from 2009, and no apparent background in science at all. The obvious question is "what the hell does he know?" I don't mean to say that he could not know a substantial amount about evolutionary theory, and has a good overview of the evidence. But I doubt it both for the reason that he has no formal education in the natural sciences (doing research about Darwin is not that), which does not really leave one a lot of time to concentrate on the science, and also for the reason that I do know a lot about evolutionary theory through my education and work, and I understand the theory and know the evidence for it (scoop: it's pretty solid).

So, how long are we to wait for this imminent demise? He predicted this formally in 2006: 3. ALMEIDA FILHO, E. E. . An imminent paradigm shift in evolutionary biology?. 2006. (Presentation / Conference or Colloquium). [Via his CV.]

Still waiting...

He just launched a new website, DarwinLeaks. Again, all in Portuguese, which is a hassle. The translation reveals a post asking Why correspondence between Darwin and Mivart has not yet been published online? As far as I can gather, certain letters between Darwin and George Jackson Mivart - who criticized Darwin on scientific grounds (though arguably with a religious motivation) - has not yet been made available to the public. My guess is that de Almeida Filho is very upset about this, as it hinders progress in his own research. But form there to claim that revealing these documents would spell the end of evolutionary theory as we know it... Unconvincing.

Supply and demand doesn't work for universities?

Seems to me Madhusudan is onto something here:

Let me get this straight: we have MORE students enrolling in college, competing to get into overfull classes taught by FEWER faculty every year, and TOO MANY PhDs who would love to have those faculty jobs that are clearly needed to teach all the new students! Does that sound about right? How does this make any kind of economic sense even with a supply-and-demand analysis? Seems to me that the demand is there, as is the supply, yet they aren't exactly meeting up! WTF is that about?!

I can't explain why capitalism is not working in this case. But then, my PhD isn't in economics...

No Santa, no Jesus

Don't dare to miss Ricky Gervais' reasons for being an atheist. I seriously wonder if this stuff is funny for believers, too.

But anyway, there I was happily drawing my hero when my big brother Bob asked, “Why do you believe in God?” Just a simple question. But my mum panicked. “Bob” she said in a tone that I knew meant, “Shut up.” Why was that a bad thing to ask? If there was a God and my faith was strong it didn’t matter what people said.

Oh … hang on. There is no God. He knows it, and she knows it deep down. It was as simple as that. I started thinking about it and asking more questions, and within an hour, I was an atheist.

Wow. No God. If mum had lied to me about God, had she also lied to me about Santa? Yes, of course, but who cares? The gifts kept coming.

As for myself, I've always been an atheist. Even when I chose to be baptized at age ten. But as for Santa, I had a very specific reason never to believe him. In Copenhagen, chimneys are simply too narrow that anyone could get through them. I swear that was the reason.

Why don’t I believe in God? No, no no, why do YOU believe in God? Surely the burden of proof is on the believer. You started all this. If I came up to you and said, “Why don’t you believe I can fly?” You’d say, “Why would I?” I’d reply, “Because it’s a matter of faith”. If I then said, “Prove I can’t fly. Prove I can’t fly see, see, you can’t prove it can you?” You’d probably either walk away, call security or throw me out of the window and shout, ‘’F—ing fly then you lunatic.”

Not possible to absorb alcohol through feet (of course)

Being from Denmark myself, this Danish study caught my eye. It examines what is apparently an urban legend (they call it urban myth, though) in Denmark, namely that one can get drunk by submersing one's feet in alcohol.

I have never heard of this ridiculously credulous idea, but I am not surprised that some idiots were stupid enough to believe it. But wasting vodka in that way...? But then, it's been over a decade since I moved from Denmark.

The researchers tested the hypothesis in a study aptly named the Peace On Earth study, for Percutaneous Ethanol Absorption Could Evoke Ongoing Nationwide Euphoria And Random Tender Hugs. Bravo!

However, they used three bottles of vodka per person, to which I cannot say any bravos. More like, stupid gits!

At this pint it really doesn't seem to matter much what the results were, both because people with half a brain could foresee the outcome, and also because we already know a really good way of getting alcohol into the blood (two*, actually).

And yet, here are the results:

Plasma ethanol concentrations were below the detection limit of 2.2 mmol/L (10 mg/100 mL) throughout the experiment. No significant changes were observed in the intoxication related symptoms, although self confidence and urge to speak increased slightly at the start of the study, probably due to the setup.

The method section is well worth a gander.

Methods
The Peace on Earth study was open labelled and self experimental, with no control group. It evaluated the effect of submerging feet in 2100 mL of vodka (three bottles’ worth) on the concentration of plasma ethanol. Secondary end points were intoxication related symptoms.

Three healthy adults (all authors, CSH, LHF, and PLK) agreed to participate. None had any chronic skin or liver disease or was dependent on alcohol or psychoactive drugs. None was members of local Alcoholics Anonymous communities or had been implicated in serious incidents or socially embarrassing events related to alcohol during the week before the experiment.

Yep, those three participants are the authors of the study. And there's the real clue for us all. There's no reason we cannot combine fun times in the office with research. I've always known this, and yet I've never really been able to get anyone else here in the puritan states to agree to have beer in the office (I have, however, brought beer in a mug to lab meetings, which I highly recommend).

* The other one is the swedish method of inserting a cotton ball dipped in vodka into one's rectum. That REALLY works, and three bottles of vodka is enough for several high schools to go around.

Reference:
Hansen, C., Faerch, L., & Kristensen, P. (2010). Testing the validity of the Danish urban myth that alcohol can be absorbed through feet: open labelled self experimental study BMJ, 341 (dec14 2) DOI: 10.1136/bmj.c6812

Replies to arsenic criticism

An article in The Washington Post describes how Felisa Wolfe-Simon and the team behind the work on arsenic-loving bacteria pushed by NASA are planning to respond to criticism. And indeed, how they have responded as of yesterday. On Felisa's website you can find the FAQ, which I repost here slightly(!) paraphrased:

Some people have questioned whether the DNA was sufficiently cleaned by your technique using gel electrophoresis, to separate it from other molecules. Do you feel this is a valid concern?

(Shorter) Answer: No.

Others have argued that arsenate-linked DNA should have quickly fallen apart when exposed to water. Could you address this?

(Shorter) Answer: No experiments have previously been done relevant to our study.

Is it possible that salts in your growth media could have provided enough trace phosphorus to sustain the bacteria?

(shorter) Answer: We think not.

Is there anything else you’d like for the public to understand about your research, or about the scientific process?

(Hmm, I wonder who asked this question. It's not really one of those very critical questions that this whole debacle included.)

(Shorter) Answer: We love science, and we love you.

I'm not saying that is what the team intended to say in reply to that lat question, but that's the feeling I got from it. Overall, good answers, because they are standing their ground. That means that vindication will be sweet, or that the fall is going to hurt even more. Fun in the blogosphere either which way it goes. And science progresses, but that was never in doubt.

The Washington Post article also includes this bit of cluelessness:

He said that when people launch online attacks on the work done by him and biochemist Felisa Wolfe-Simon, he doesn't really know who is behind them. "I don't want to get involved in what can end up in a Jerry Springer situation, with people throwing chairs," he said.

Oremland is pretty senior, i.e., trained before the advent of the internet. So no wonder. However, practices change, and we must, too. I was trained to write job applications on paper and send it by mail, but (next to) no one does that anymore either. Deal. Also, yes, we do know who is behind much of the serious criticism. Rosie Redfield. George Cody. Steven Benner, surely. The internet is great for looking people up.

But either way they will respond, so all is well on that front.

Yet not only was Oremland on the panel Thursday because of the blogging, but the research team also put out a series of answers to questions frequently asked about their work, and promised to respond by next month to more than 20 letters and e-mails sent to the the magazine Science questioning their work. The team announced as well that it would make samples of the microbes available to other scientists for their research.

Earth, we've got a problem

According to Darryl Cunningham we've got a major problem:



Of course, this isn't merely according to Darryl Cunningham, but rather according to nearly all the scientists who work on this particular problem.

Go see of yourself what it is.

When you get back, we can discuss why it is that people who deny this problem for the reasons given by Darryl, are motivated to do so. I mean, it's not all deniers who are oil-billionaries...

Inside North Korea - true to his behest

Man, I cry for the North Korean people. I look forward to the death of Kim Jong-il, and to the events that will follow (hoping they're not going to be devastating).

Here's a courageously recorded documentary from North Korea by VBS.TV. You should see this fascinating documentary, true to my behest.


(Clip takes you to SnagFilms for the whole video.)

It is chilling to imagine the lives of the people that Shane meets on his secret mission to film inside North Korea. Watching the people in this land of the people, all the time I'm thinking that these aren't even real people, but facades that cover up indoctrinated souls yearning to be free. I imagine a nagging suspicion that they have that the outside world is not that evil, that their lack of food is not necessary (why are the foreigners so well fed?), that laws agains humor are not in their own best interest, etc. etc.

Frozen Evolution book review

Dan Graur reviews Frozen Evolution: Or, That's not the Way It Is, Mr. Darwin: A Farewell to Selfish Gene by Jaroslav Flegr in The Quarterly Review of Biology.

And thank Dan for that, because I know what an awful book that is. As Dan says

I regard this book review as a public service. Life is much too short to waste it on bad books. So, do not even touch this sloppily written, unprofessionally translated, inadequately conceived, improperly edited, dubiously syntaxed, and horribly pompous and tedious stream‐of‐consciousness monologue masquerading as a scholarly work.

I few years back I saw a message somewhere on the web that Flegr was looking for people to review his book, which is in part about epistasis (a topic of my research), so I asked him, and he subsequently sent me a copy. However, I was never able to get through it (apologies), because the writing is indeed sloppy, and the core idea as I perceived it - that because epistasis makes a mutation have different effects on different genetic backgrounds, a mutation can't lead to workable changes in the genome in sexual species, since recombination makes the genetic background in the offspring different from that of both parents - is patently crackpotty. Better things to do, kind of thing.

I have one final piece of advice for those masochists who will imprudently decide against my very strong admonitions to read this book. Have a fun experience by using a “crackpot‐index measure” (see e.g., F. J. Gruenberger. 1964. Science 145:1413–1415) to compare Frozen Evolution against a checklist of the most significant attributes of scientists and quacks. I am looking forward to finding out whether your conclusions will be similar to mine, which I shall keep to myself for the present time.

Mistreating animals for pleasure

For the record, you and I can't be friends if you crush animals for pleasure. It's Julia Galef on Rationally Speaking discussing what the difference is between taking pleasure in acts of violence against animals, and taking pleasure in eating animals that have suffered at the hands of humans with the intent of slaughtering them.

The closest thing that I can find to a morally relevant distinction between industrial farming, dogfighting, and crush videos is this: While it’s true that all three acts cause animal suffering in order to give people pleasure, the nature of that tradeoff differs. The consumers of crush videos and dogfighting are taking pleasure in the suffering itself, whereas the consumers of industrially-farmed meat are taking pleasure in the meat that was produced by the suffering. From a purely harm-based perspective, the moral calculus is the same: the animal suffers so that you can experience pleasure. But the degree of directness of that tradeoff makes a difference in how we perceive your character. Someone whose motive is “I enjoy seeing another creature suffer” seems more evil than someone whose motive is “I want a tasty meal,” even if both people cause the same amount of suffering.

I think Julia's right that the difference to many people will be that the animal suffering of pigs, cows, chicken, etc., is a by-product, and not the main point. But I also think that difference a distraction.

Personally, I'd really very much like if we all ate less meat, and paid more for that meat, with the result that no animals were treated cruelly.

So, we can continue to be friends even if you eat meat of animals who suffered for that, but if you in any way promote suffering of animals because you or someone else take pleasure in that suffering, then you can fuck the right off.

Alligator electrocution

It's really rare that I squirm so much that I have to stop watching something. Here's an alligator attacking an electric eel, and that took me two attempts to finish.



Via Denim and Tweed.

Christopher Maloney doesn't want to be called a quack

I get mail
Category: Kooks
Posted on: December 7, 2010 4:52 PM, by PZ Myers

Some people just don't get it. Christopher Maloney wants to silence a message he doesn't like on the internet by serving a cease & desist order.



The last time I mentioned Maloney was eight months ago, and even then it was to point and laugh at his page throwing crazy paranoid accusations at me. So now, after eight months of neglect, he has decided to stir the pot and remind everyone that Christopher Maloney is a quack and that he keeps on quacking? That makes no sense.

So, once again, the web will start echoing the Christopher Maloney is a quack message.

It must be handy for a quack to marry a lawyer, but I don't think she's giving him good advice in this case. You might as well serve a writ on the tides to stop flowing as ask the internet to erase a piece of its data—your best bet is to allow it to take its course and hope that the wavelet that disturbs you gets lost in the incessant volume.

I'm just quoting, again.

Israel behind Egyptian shark attacks?

This is too funny to be believed, and yet it is not The Onion.

Egyptian Official: Israel Could Be Behind Deadly Shark Attack

An Egyptian official believes that Israel's intelligence agency might be behind the fatal shark attack of a German tourist in Sinai over the weekend, the Jerusalem Post reports.

"What is being said about the Mossad throwing the deadly shark (in the sea) to hit tourism in Egypt is not out of the question, but it needs time to confirm," South Sinai Gov. Muhammad Abdel Fadil Shousha told egynews.net.

Right. Mossad caught a shark, pumped it full of adrenaline, made it smell a pair of swimming pants, and then let it loose near the Egyptian resort. Clever!

Israel is also - somehow - behind festering stupidity among Egyptian officials.

Prothero reviews Conway Morris

Daniel Prothero, author of one of the best yet most neglected book about evolution for the general public, Evolution: What the Fossils Say and Why It Matters, reviews Simon Conway Morris' book, Life’s Solution: Inevitable Humans in a Lonely Universe.

The thesis of the book is both that humans are an inevitable outcome of evolution, and that life is unlikely to exist anywhere else in the universe.

Prothero discovers why.

This change in tone makes one wonder about the underlying motivation of the author. He’s an optimist about the possibility that humans are the inevitable by-product of evolution, but a pessimist that any other planet has humanoids — how can someone take those two mutually contradictory positions? The mystery is answered in the last chapter, when the author reveals that the whole motivation for his position is religious. Early in the book he trashes and dispenses with the fundamentalist Creationists, but by the end his arguments appear equally slanted and biased. His final chapter bashes agnostic materialists like Gould and Dawkins and veers abruptly off into his own philosophical beliefs, musing about why he finds materialism and agnosticism inadequate to provide “meaning” to life.

As Prothero laments, Morris seems to be aiming for the Templeton Price...

I have written about Prothero since I first started blogging. Search for all posts about him here.

Carnival of Evolution #30 has set sail

The thirtieth edition is hosted by Bob O'Hara on This Scientific Life. Enjoy! And spread the word.

Here's my favorite post this time: Mapping fitness: landscapes, topographic maps, and Seattle by Steve Matheson at Panda's Thumb. Particularly because of the discussion, where Joe Felsenstein himself enters the discussion in the comments, as does Arlin Stoltzfus, and the whole thing is quite a good read.

Ark Park or the P'Ark?

Feast your eyes on this beauty!


Arc Encounter

They are actually going to build the arc. Right next to the Creation Museum in Kentucky, of course.

An office mate of mine wants it to be called the Ark Park. I think The P'Ark is much better. What do you think?

Now point and laugh, and wait for the flood. Except, if they build it, and I hope they won't, they might likely attract lots of people to the P'Ark, and make a ton of money and misinform a bunch of people. Shame.

Also, as PZ points out, I am very upset that they will employ hundreds of people to build it, while for "the real" arc, only eight people were involved. If NOah had divine help, why can't Ken Ham?

Can science tell us right from wrong?

That is the question* posed at this ASU Origins debate that I found my way to via Rationally Speaking I was referred to this debate in which one Patricia Smith Churchland asks which higher mammal babies died unpleasant deaths at high rates in the time before humans started to destroy everything (some paraphrasing), rhetorically. Suggesting that this was not the case. Hmm, I think, what an odd statement, because I imagine that even when humans weren't destroying gorilla habitat, lots of other dangers lurked everywhere and the young ones paid the price.



But then I think I better look her up before I dismiss her remark as a silly ignorant one, because just maybe she has reasons to believe that higher mammals didn't lose their young children much before humans made them. And then I have another experience that I have had several times before, because I see that she is a philosopher, and I immediately realize that what she says is based on no evidence whatsoever. She's doing research in "the interface between neuroscience and philosophy." In other words, no expertise in the field of mammalian suffering™.

However, I find her comment on Hume's is-ought fallacy later (at 8:49 in part 2) very, very true, that all right, no deduction is possible, but other kinds of inferences - the ones we use on a daily basis most of the time.

*And my answer is that all by itself, science cannot tell us right from wrong, but that is not the relevant question. The right question is whether it can inform us on questions of right and wrong, and that it so very clearly can. We don't like poverty (well, some rich people do like that others are poor, but you know what I mean), and science can inform us how to alleviate it, so there.

A challenge from Hitchens

Hitchens debated Blair, and then he wrote about it in the Washington Post:

As for religious charity and good works, this is not even a bad argument. Examined for a moment, it doesn't amount to an argument at all. Suppose you observe me debating with an opponent who catches me out in a logical fallacy or an apology for crimes against humanity, or both. Nothing daunted, I have my riposte all prepared. On the way to the symposium or panel, I announce as if proudly laying down my four aces, I handed a fifty dollar bill to a homeless person. Why, I even specified that ten per cent of my donation would be set aside to build a school where the man, and his children, could be taught my own beliefs as if they were true. Now try to tell me that my logic was unsound, or my ethical claims contradicted! When faith reduces you to this level of "debate" you should feel a distinct blush of shame.

Herewith given up as a challenge to anyone who would find themselves around these parts.

On stochasticity

Some days I think stochasticity is an important phenomenon in evolution, and some days I don't.

The peacock's tail is not only a product of sexual selection

Oh.. dear, I'm becoming one of those annoying obsessed types - with the peacock tail. For the I don't know what time, someone is stating as fact that the peacock's tail evolved via sexual selection. Here's one Denis Dutton on TED:

The peacocks magnificent tail is the most famous example of this [sexual selection]. It did not evolve for natural survival. In fact, it goes against natural survival. No, the peacock's tail results from the mating choices made by peahens.

I've said it somewhere before, but I'll just go on and say it as many times as the editor* of this blog allows me: THE PEACOCK'S TAIL SCARES AWAY PREDATORS! (I'm told all-caps gets the message across).



Now, I admit immediately that this is not a well tested hypothesis. Here are the two pieces of evidence that I have: I have myself seen a peacock raise its tail** in San Diego Zoo when it was approached by... children. They were going too close, and as a result it raised its tail feathers (yeah, I know, correlation/causation - maybe the peacock was horny at the sight of humans its own size).

Another is a story I've heard about a peacock in a garden and two golden retrievers. The first time the dogs saw the bird, they ran barking towards it, and in response (or, again, just maybe because it was at that very moment getting all horny thinking about a certain peahen it had met earlier that morning) it raised its feathers. And the dogs cowered and retreated, and never bothered the bird again.

In addition, I have also once heard that eyes generally confuse animals, which might be why there are "eyes" on the feathers. And of course, if you can fool the predator into thinking you're the bigger one, they may just forget about the peacock meal.

The story for how the tails would increase the likelihood that a predator catches the peacock usually describes a peacock on the run, with the tail feather in the "neutral" position, and the predator grabbing on to the long feathers. But that of course only works if the peacock retreats in the first place.

Now for some testing. Next time you see a peacock somewhere (zoos, public gardens - there are many in California, but I haven't seen any here in Michigan - or did I see one in Detroit Zoo?), try to ask a child to approach it too closely and see what happens. If you're against involving children in research (why would that be?), get down on all fours yourself. Tell me what happens.

And here we damn well go:



And here is a great dramatization of a peacock scaring off a pesky dog.



And here's one interacting with humans.



Lastly, I do not at all contest that sexual selection is also involved. It is unlikely the the peacocks fan their tails at peahens in order to scare them away.



Dutton's talk, by the way, is about a Darwinian theory of beauty. Watch it here, if you must.


* Fortunately, that's also me.
** Okay, so it's also called a "train", and those feathers are not on the tail at all, but "highly elongated upper tail coverts." [Source.]

Blair/Hitchens on the goodness of religion

To my elation, the much anticipated debate between Tonay blair and Christopher Hitchens is up on YouTube. To see it, and to skip the first 19 minutes of introduction by someone I don't know, go here (h/t to Physicalist). See the YT channel for all eight 15 minute segments, but note it is likely to be taken down at some point...

The motion that Hithcns and Blair were to discuss was this. "Be it resolved that religion is a force for good in the world."

Hitchens recently debated William Dembski, and in comparison, this was a far better debate. Blair is actually a worthy opponent to Hitchens, whereas Demsbki is just feckless, really.

Admittedly, Dembski had a much, much harder question to deal with than Blair: "Does a Good God Exist?" This question opens up, and the debate did get deep into, all the good reasons why the very idea of a god is so ridiculous, which is much harder to defend than the question of whether religion is a force for good in the world.

Do go watch - it is a delight to see them both.

A few points I felt like jotting down:

Hitchens mentions the famous quote by Steven Weinberg: "With or without religion, good people can behave well and bad people can do evil; but for good people to do evil—that takes religion."

I'm now reading Malcolm Gladwell's The tipping Point, in which he makes the point that otherwise well-behaved people can do bad things in the proper context. I agree with this, and would then rather say "for good people to do evil—that takes context (and often that can be religion)." But it can often be that the good people experience distress and fear without religion, and that can lead to evil, too.

But that's about as far as I would disagree with Hitchens today (okay, I also disagree about the invasion (Blair and Hitchens both say "liberation") of Iraq).

Blair, though, brings up the same point quite a few (i.e., many) times, namely that, yes, religion causes many bad things, but many people also do good things exactly because of their religion. Much charity is done by the religious, and, Blair contends, this work is inspired by the faith of the religious. Whatever that exactly means, we can then either surmise that without faith they wouldn't do that, or that they would. If they would, then faith is of no relevance. If they would not, then the question becomes if the good things thus impelled by faith outweighs all the bad ones (which both Blair and Hitchens agree are plentiful). That is an empirical question.

On top of that, if the truth is that people who do charity based on faith would cease to do it if they lost their faith, then that's actually a pretty dismal inference. How uncharming that would be, don't you think?

Blair doesn't seem altogether certain what the answer is, because he manages to both say "fact is that's what motivated them," and that while they might do it anyway, their faith is an impulse to do charitable work. The latter sentiment would seem to give faith a minor role. Does he resolve the ambiguity by saying that "love of fellow human beings [are] bound up with their faith"? I'm not entirely sure what he means, and I'm not sure Blair himself is completely resolved on the issue.

Near the beginning Blair also speaks well of humility, and not so well of "swagger". But, I implore you all, do tell me what it is that is so great about humility. True, people who are not humble can be arrogant. Maybe the idea is that the starving poor would rather not receive sacks of flour with statements like "are the rich countries great or what?" on them? But seriously, are we really sure that humility is such a big issue (it does get mentioned by pretty much all religious people who i have seen debate)? I agree that arrogance is many times a bother, and humility is less confrontational, but it does not, as far as I can see, have much do with the motion of the debate, nor about the truth of the claims of the religious.

Another one from Blair: "Get rid of religion, and you still won't get rid of fanaticism." And that would be true, at least in the century of Stalin and Mao. However, maybe we would get rid of most most most of it? Seem likely to me. Also, turn the statement around: Get rid of fanaticism, and you still won't get rid of religion." That's also true, but you'd get rid of the a lot of it, and I think that speaks volumes. There is no need to debate the extremes; I would like to hear Blair admit that while not all religion is bad, weighing the good vs. the bad does clearly suggest that getting rid of religion would do the whole world a lot more good than bad.

As for the motion, before the debate the vote in the audience was 21% in favor, 56% 57% against, 21% undecided. I don't know what it was afterwards.

---

Update 11/28: The post-debate vote was 32% in favor, and 68% against. Both increased about 10%. I agree with Larry Moran that this makes it a tie.

New Trends in Arabic Anti-semitism?

Can anyone confirm or deny the accuracy of this translation?



If true, this is just fantastically disgusting.

Comments on Pleiotropy

A few posts from the past are still generating comments now and then:

Warning: don't go to La Sierra University.

Islamic crud stones innocent girl in Somalia.

¡Buenos dias, Catalonia!

I'm both sad and unsurprised that it's these posts that generate heat, rather than those on evolution and other science.

Professional writing for academic cheaters

Fuck!

Things will never be the same again, for me. If we are what we write, then forever there is no knowing who we are. Am I even who I claim to be, and are these words written by me at all, or by someone with no name who charges for helping the misplaced incompetents?

The request came in by e-mail around 2 in the afternoon. It was from a previous customer, and she had urgent business. I quote her message here verbatim (if I had to put up with it, so should you): "You did me business ethics propsal for me I need propsal got approved pls can you will write me paper?"

I've gotten pretty good at interpreting this kind of correspondence. The client had attached a document from her professor with details about the paper. She needed the first section in a week. Seventy-five pages.

I told her no problem.

It truly was no problem. In the past year, I've written roughly 5,000 pages of scholarly literature, most on very tight deadlines. But you won't find my name on a single paper.

Do read this essay. The details and anecdotes should shock you. If for no other reason than marveling at the incapability of American students (how difficult can it be to use a spell-checker? Answer: nigh impossible).

But if this person cashes in on the apparently rampant cheating in American academics, I find it less apparent to decide where the blame for this disastrous state of affairs lie. As he says:

I work hard for a living. I'm nice to people. But I understand that in simple terms, I'm the bad guy. I see where I'm vulnerable to ethical scrutiny.

But pointing the finger at me is too easy. Why does my business thrive? Why do so many students prefer to cheat rather than do their own work?

Rather than blaming anyone, I personally prefer to think ahead to when I will (hypothetically) be reading papers written by students myself. It really should not be much of a trouble to test whether the student is at all capable of writing, for instance by having them do it once while in class.

Given the nature of the essay, it of course becomes imperative to question its veracity in the first place. If the author can make up stories about any subject, and write them well, then why not his own story? Could this simply be some aspiring writer's term project? Or, how about a meme-based virus? Educational malware? Can we trust that his business is as booming as he contends, and that he writes papers on ethics for the ethically challenged on a regular basis?

Yet, contemplating human nature and the current (permanent?) state of financial affairs, I don't doubt that there is at least a market for this kind of cheating. Given the suspicion, I wonder if other businesses won't now crop up to root out these dens of academic deceit. Like removing access to guns from people who are naturally homicidal, so I find it does make sense to eliminate the access to professional sources of cheating.



I wonder what he charges for blog posts...

Do atheists not have any songs?

Well, here's one on the topic.



But I object. There are many songs that do not have any affiliation with anything religious, but they are perhaps better designated agnostic songs? Then, there are also many songs written by atheists, but that doesn't make them especially atheist songs, I suppose. As when a religious person writes a song nothing to do with religion (does that happen?). But then, songs about non-belief? How about John Lennon?

---

Update 11/10: Via the comments, more atheist songs:

Ignoring you

This blog post is for all those things going on in the blogosphere and affiliated^* that I am ignoring. There is lots of crazy stuff out there that are both inane and annoying that they are best ignored out of existence. Things not like that are those inane and amusing, like Babu Ranganathan, or those stupid and evil, like the Koch^† brothers, or the dogmatic and oblivious, like those who think no evidence ever has anything to say about gods. This post is not about them, but about those things that I will not mention:

...

...

...

These people are both stupid and annoying, and they don't need to be taken seriously anymore, and they are also not funny, but just tedious and puerile. I suppose if you sent me a personal email, I could tell you who we are ignoring. But be forewarned that you will probably regret it.

^*Online newspapers and journals, for the most part (for as long as they exist).

^†Pronounced 'coke', don't you know?

Belated review of Why Evolution Is True

I have just finished reading Jerry Coyne's latest book, Why Evolution Is True. Jerry is one of the world's most famous living evolutionary biologists, and an expert on speciation. This book collects a fair amount of evidence for the fact of evolution (i.e., that evolution has occurred), and spares us from most of the intricacies of the theory of evolution (i.e., the details of how it proceeds). It's an easy piece to read, and lays out very convincing evidence for those who are amenable to such (as he recounts towards the end, not all people are). In a little over 200 pages he describes evidence from paleontology, embryology, and biogeography, and evidence for natural selection, sexual selection, speciation, and human evolution. If you haven't decided what to believe in terms of evolution, this book is for you.

Coyne is, famously, an advocate of the primacy of natural selection in evolution, in addition to being of the observation "that the biological species concept is the way to go, that allopatric speciation is the dominant mode of formation of new species, and that the Modern Synthesis of the 1930s and '40s is an adequate framework for evolutionary theory". [Source of quote, but do read Speciation by Coyne and Orr*, if you must see for yourself.] I largely agree on the point of natural selection, that it is the only driver of adaptation (I am not a big believer in neutral theory having much to say about adaptation). However, in this book aimed at an audience outside of academia (as opposed to Speciation), I am not so happy with some of chapter 5 - The Engine of Evolution. That "engine" is natural selection, and on several occasions he attributes selection with the power to build complex biological systems. "Has there really been enough time for natural selection to create both complex adaptations as well as the diversity of livings forms?", he asks on page 140, and goes on to explain that there has. If he had said "evolution" instead of natural selection, then I would have been all for it, but it is as if Coyne assumes that there is no problem generating all the needed genetic variation for selection to act on, and that is not true. That must also be explained, and he skirts the issue entirely. Natural selection has the power to promote or suppress novel genetic changes in a population. However, within a population, natural selection only diminishes the amount of genetic variation, by selection of (for?) genotypes and phenotypes that produces more offspring, because of some adaptation produced in the first place by mutations (I count any genetic change as a 'mutation'). In this sense natural selection is only half the story, and by my reckoning the most trivial and therefore least interesting part of the story of how to build complexity. Adaptations are not "built by selection" (page 137), but by mutations and selection together. One or two mutations here, then selection for those, then a couple more mutations, and more selection, more mutations, and finally selection can ensure that a new trait goes to fixation (everyone in the population shares the new trait).

A second point of dissatisfaction is that Coyne has elected not to talk about the great abundance of molecular evidence for evolution. [This is not true. See important update below.] The book has next to nothing in molecular evolution.
He could, for example, well have included a discussion of the story of the fusing of two chimpanzee chromosomes to create human chromosome 2 (humans is the only ape with 23 pairs of chromosomes, the other all have 24). [Incidentally, that Wikipedia page contains a clueless comment stating that this fusion cannot be used as evidence for evolution. Contrary to what it says, it indeed can, because when it was found that humans have one chromosome less than the other apes, that presented a bit of a problem for the idea of common descent, but it was eventually resolved when it was discovered that human chromosome 2 contains all the genes of the two chimp chromosomes in addition to telomeres in the middle of the chromosome!] If he didn't like that story, there are a plethora of other ones to choose from. And he knows this, which is why I wonder why he didn't.

Apart from these two points, I was happy to read the many stories of amazing evidence for evolution. However, only once must I admit that he caught me quite off guard, and this point made the whole book a valuable read for me all by itself. This was his assessment of the genetic difference between humans and chimpanzees (page 210). The seminal paper by Wilson and king (1975) quantified that this difference in protein coding sequence DNA is about 1%. He uses the more accurate value of 1.5% to show that humans and chimp are actually not very similar genetically after all:

A 1.5 percent difference in protein coding sequence mean that when we line up the same protein (say, hemoglobin) of humans and chimps, on average we'll see a difference at just one out of every hundred amino acids. [Because about three quarters of substitutions change the amino acid, while the rest - the synonymous substitutions - do not.] But proteins are typically composed of several hundred amino acids. So a 1.5 percent difference in a protein three hundred amino acids long translates into about four differences in the total protein sequence. [Given that 74.3% of all nucleotide substitutions are synonymous, I think that number should be 0.743*0.015*300=3.34, though.] That oft quoted 1.5 percent difference between ourselves and chimps, then, is really larger than it looks: a lot more than 1.5 percent of our proteins will differ by at least one amino acid from the sequence in chimps. And since proteins are essential for building and maintaining our bodies, a single difference can have substantial effects.

Point taken. Even though not all amino acid changes make much difference for the function of the protein - the functional sites of proteins are often a small fraction of its entire length, and the rest of the amino acids are somewhat less constrained (but rarely totally so) - so that the number of proteins with a changed function will be smaller by some number, it had previously not dawned upon me that the King and Wilson estimate made humans and chimp that different. The argument being a quantitative estimate, I still don't really know how different the actual proteins of humans and chimp are†, but I am nevertheless now more open to the possibility that the obvious morphological differences between us that I observe when I go to the zoo have something to do with differences in the proteins, and not only in how the genes that produce the proteins are regulated. In fact, one of my earliest insights when I just entered biology in 2003 (I studied physics first) was that gene expression was of such importance that all developmental, morphological, and physiological differences could be explained by changes in the part of the genome that regulates expression of genes (e.g., same protein for making hair, but turned on less in humans, and same proteins for making the skeleton, but in different patterns). While I knew that there are differences in some proteins between the two of us, my point was that changes in gene expression was potentially waaay more powerful to make actual changes in evolution. Now I'm not so sure. I do recall, however, a great picture of Coyne and Greg Wray shaking hands after having debated the relative importance of exon vs. cis-regulatory changes (i.e., changes in protein coding sequence vs. changes in gene regulatory sequences), and reading somewhere an estimate that two thirds of evolution is regulatory, and one third exonic (but don't quote me on that).


Greg Wray and Jerry Coyne leaves their scientific differences aside for just long enough for someone to take a picture of them striking these adorable poses.

In summary, even though I have presented two points which upset me, I highly recommend this book. It's boring to talk much about the points we agree on, which in this case is the rest of the book. If you read only one book on science this year, let this be the one™.

* Incidentally, when he came to visit MSU last week, I spoke with H. Allen Orr about their fondness of the Biological Species Concept. My view is that species is a real(ly useful) concept, but that several definitions are all sufficient criteria for determining whether a population is a separate species or not. Orr of course agreed that the BSC doesn't always apply (say, to asexual species like bacteria), but that for sexual species it is more than just one way of looking at it. In the talk he gave he presented evidence for post-zygotic reproductive isolation in Drosophila which is thought to have led to a speciation event, thus supporting the notion that speciation is caused by reproductive isolation, rather than being a side-effect.

† In the paragraph after that one, Coyne writes that it is now known that about 80% of the genes shared differ by at least one amino acid. However, how big the effects of those difference are is harder to get at.

---

Important update 11/8:
Coyne has pointed out in an email that he did write about pesudogenes, for an example of evidence from molecular evolution. Pseudogenes are defunct genes. Our understanding is that they used to have a function like other genes, but now are no longer expressed. Loss of expression can happen when mutations cause changes in gene regulation, or when mutations create stop-codons in the protein coding sequence. The model/theory we have of evolution and molecular biology predicts that genomes should be more or less full of pseudogenes.

And the evolutionary prediction that we'll find pseudogenes has been fulfilled - amply. Virtually every species harbors dead genes, many of them still active in its relatives. This implies that those genes were also active in a common ancestor, and were killed off in some descendants but not in others, Out of about thirty thousand genes, for example, we humans carry more than two thousand pseudogenes. Our genome - and that of other species - are truly well populated graveyards of dead genes.

(Page 67.) Coyne then goes on to discuss some human pseudogenes: GLO (used to make vitamin C) and olfactory receptor genes (some of our ancestors had a much better sense of smell than we do).

Yet more on whether adequate evidence for God could exist

I swear I was gonna leave this subject alone, but a new post by Greta Christina has just said something on the topic of what evidence is needed to persuade atheists of the existence of God that I so disagree with:

Even if a 900-foot Jesus appeared in the sky tomorrow, healing amputees and unambiguously stating his message in all languages and whatnot, a religion would have to explain why God was making all this happen now...and not at any other time in human history.

Notice she says "religion would have to explain". No. The deity that appeared could do that. Suppose the reason for doing godly stuff now, and not in the last 200 or 2000 years, or ever before, was not shared with any humans, then how is any religion supposed to hypothesize about it? Suppose the deity just was busy with other things, or was observing us as an experiment, or was not able to do so (a deity need not be omnipotent). If all current religions are wrong, because the deity had not shared anything with us, then that does not preclude evidence from being adequate.

If I one day let everyone know (in their heads, in their language, at the same time) that I am that deity, and then went on to tell everyone that I could do anything I wanted (let animals talk, create a new planet, sink Australia, make Australia reappear in the Atlantic, let your dead loved ones come back to life, make anything appear that you ask again and again, make you larger than the Earth, make everyone observe and agree that you were made larger than the Earth, suspend the most trusted laws of physics (2nd law of thermodynamics, for starters), and repeat all of the above on command, etc. etc.), and then continued to tell you that, look, I don't care about you, I just happen to have the powers of Q and more, and I did in fact create the whole solar system and life on Earth (and on Europa - go have a look see), but in fact not the entire universe, then just because no "religion" has hypothesized all of these events before it does not follow that I should not be called a god.

Sure, again, it depends on the definition of 'god', but I honestly think we've got it covered by now.

But then, I can just see PZ standing there looking at all that evidence, and say "mighty fine powers, but you're not God, because I you don't look anything like Jesus."

Seriously.

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Update 11/8: For some odd reason I cannot comprehend, PZ feels he is all alone on this issue, and is happy (I infer, with all the uncertainties that incurs) to link to two bloggers who agree with him, even though (imo) both posts are senseless supercilious screeds.

Carnival of Evolution logo competition

← Carnival of Evolution has a splendid logo, don't you think? We don't need a new one. However, I'd like to get another one for a specific purpose.

When people have their posts included in a CoE edition, wouldn't it be nice if they could put a little image on the post to identify it as a CoE-post? I think so. Like a stamp of approval, similar to the image that posts on Research Blogging has (see example here).

However, I have zero skills in that direction, so I'd like to ask someone else to make one.

Logo Competition:

What: Make a 70x85 pixel logo that CoE contributors can put on their CoE posts.

Why: So that we may make more people aware of the carnival, and promote both reading and writing about evolution.

How: I don't know how, but once you have figured that out, send it to me at bjorn@bjornostman.com.

When: No hard deadline, but I won't start choose among any submissions before the next edition of CoE is out (which will be on December 1st).

What's in in for me? The creator of the new CoE button will of course be featured both here and on the CoE site, but beyond that I'm afraid CoE has no funds for a monetary prize.

The button should be recognizable and distinct, so that people will quickly learn that it refers to Carnival of Evolution. I could suggest that it used the same colors as the CoE logo, for example, but that's not a strict requirement.

If you have any other questions, please do not hesitate to contact me.

The carnival carnival

New editions of various science blog carnivals have been posted recently:

Scientia Pro Publica is now at edition #44. It runs weekly now, so should reach #52 by the end of the year. Posts on all things science.


Carnival of the Blue about all things oceany. Click through to the 42nd edition.



The MolBio Carnival is for lovers of molecular and cellular biology. It's a new carnival and is just up to its fourth edition.


Carnival of Evolution of course runs every month, and is up to edition #29.



Carnival of the Vanities is the original blog carnival, and is still going strong. At least if by that you mean just pasting all submissions from Blog Carnival uncritically. I have one in there in the god only knows which edition that is.


Another great carnival, Carnival of the Godless, now seems to be defunct. Shame.

Namesake missionaries

I am very dismayed that namesakes of mine are Christian missionaries. They have a blog that keep popping up in my reader, so I read what they say once in a while. Here's what they say today:

This of course reminds us of a different harvest; the harvest of souls! Those who have yet to hear the good news of Christ’s death on the cross!

Yeah! Good news, Christ died. Painfully. For you (no reason to feel guilty). It's such great news (though somewhat old news, by now). And these people who have never even heard that they are living in sin, we go tell them so that they may feel bad, but then tell them about Jesus dying for those sins, so you can believe in him. And if you don't, you can go to hell.

Please, don't give me that sophisticated theology, 'cause that's not how you harvest souls, is it? In fact, as he tells in Don't Sleep, There Are Snakes Daniel Everett, who was a missionary to the Pirahã, was told by a senior missionary that "sometimes you've got to get them lost before they can be found." If they aren't broken, there's nothing to fix. So break them, and then fix them.

Everett ended up living with the Pirahan for many years, and eventually he became an atheist. Hardy people, the Pirahã are.

Lance and Laura Ostman continues.

Sonà, one of the church leaders, stopped by the house for a visit recently. During the course of conversation he named off six villages that are ASKING for someone to come teach them! One of these villages had missionaries living there in the early 80’s but their leaders forced them out. Now that they are gone, the younger generation wants to hear the teaching.

He said, “We need prayer for more laborers. It’s just like what Christ said that the harvest is great but the laborers are few.”

This is an exciting problem to have. Please pray with us for more Higaunon believers to go out with the message that they have been privileged to now have in their own language.

Right. "We need more people to help with the harvest, so come and teach us how your magical god can be persuaded to send more hands. Do we really really need to hear about sins, too? Oh, okay, but then we don't go to this hell-place, right? As long as we what...? Well, okay, as long as Jesus sends people to help with the harvest, I suppose that's a fair trade-off. Also, really looking forward to those 69 virgins waiting for me in the sky... Relax, I'm kidding!!!!!"

29th Carnival of Evolution kicks off

The 29th edition of Carnival of Evolution is now ready at Byte Size Biology. It's a great game of evolution this time.

Kick-off is a post about how penguins got their coats:

According to an international team of researchers, a close examination of feathers from a recently unearthed giant penguin fossil revealed that it was clad in reddish-brown and grey, instead of the familiar black-and-white colors worn by its modern relatives. Additionally, the researchers found differences in feather structure between ancient and extant penguins; differences that may offer clues for how modern penguin feathers evolved.

At Punctuated Equilibrium.

Next month our host is This Scientific Life, and you can submit one (good) or two (better) posts about evolution here. Go on, don't be shy now.

Six digit cat

Today a very affectionate cat walked up to my son and me as we were walking back from basketball practice. He wanted a lot of attention, and I noticed he had very peculiar front paws.



He really wanted some company, so my son and I obliged.




As I took a closer look, I realized he had six claws on each front paw. Looked like double thumbs. Nice!



I ran inside and got my camera, and tried to take some pictures for documentation, but they weren't good enough to show the six digits. I then held up his paws pretty firmly. He was good enough not to put his claws in my flesh, even though he clearly didn't much care to be constrained like that. I think he understood that this was a very important scientific investigation. No anthropomorphism here, I swear.


Click images to enlarge in order to see both claws on the thumb.



So why does he have six digits? Well, it could be a developmental "defect", even though I hesitate to even call it a defect - he was clearly doing very well, and my fitness assay was inconclusive (I didn't see any offspring). In that case, his kittens wouldn't have six. More interesting, if was a genetic "defect", then it could be heritable. Wouldn't that be cool? With some human artificial selection, the trait might even become established (i.e., appear in non-vanishing numbers, without going to fixation, i.e., the whole population sharing the trait). I hope he already had offspring, because he looked neutered, the poor thing. If true, that would be a real waste.