Putting together a curriculum in evolutionary medicine

At a life science institution where most research is related to human health, my adviser's lab is one of the few exception. We do evolution (mostly), so it would be great to teach a course on evolutionary theory. At our weekly lab meeting, I suggested that he put together a course on evolutionary medicine. What's that, then?

Chris, here are some resources:

The great evolution website at Berkeley has an easy-to-read section on why evolution is relevant that includes a few pages about medicine.

Five Reasons Why Evolution Is Important, by Steven Newton, NCSE.

1. H1N1 & Emerging Diseases
2. HIV
3. Vaccines
4. Antibiotic Resistance
5. Drug Development

Making evolutionary biology a basic science for medicine, Randolph M. Nesse et al., PNAS 2010 107:1800-1807.

Evolution: medicine’s most basic science, R.M. Nesse, The Lancet, Volume 372, Pages S21 - S27, 1 December 2008.

Oh, and references therein...

I won The Tangled Bank!

I was just on a webminar with Carl Zimmer and Chris Mooney, talking about their new books. Carl went first, and at the end of his presentation there was a drawing for a copy of his book, The Tangled Bank, and he chose 18, and that was me, and now I'm so excited, and they will send me the book, and I will read it, and, and, and (gasping for air)...

It's hard to get anyone else here at work to see just how exciting this all is, but surely you and I can share the excitement, right?

I wasn't really able to listen to much of what Mooney said after the excitement!!!

Happy anniversary, E. coli experiment

One of the most important evolutionary experiments in the laboratory, Rich Lenski's long term evolution experiment with E. coli began 22 years ago today:

More than 20 years ago, Rich Lenski, then at University of California, Irvine, started a simple experiment. On a Wednesday morning, the 24 February 1988, he started the parallel evolution of 12 populations of Escherichia coli, all clonally derived from a single bacterium and competing for limited sugar in Erlenmeyer flasks. Each day, roughly half a billion new copies of the E. coli genome are made in each flask as the bacteria multiply, along with about a million mistakes, meaning that in the span of a few days, virtually all conceivable mutations in the bacteria’s five million base pair genome will have been attempted. Most of these mutations make no difference or are deleterious, but a few make the bacteria grow a little bit faster — providing up to a 10% growth advantage over their predecessors. The fastest ones are extremely rare and the population must ‘wait’ a couple of days for them to show up.

Every night, the bacteria run out of the sugar glucose and go dormant. The following day around noon, a researcher plunges a pipette in and sucks up 1% of the culture to inoculate a fresh flask. Those faster at gobbling up glucose will send more of their descendants to the following day’s pipette and, after a few weeks, descendants of the fastest one will be the only ones transferred as the mutation ‘sweeps’ to fixation.

The text is taken from a review in Nature, Evolution: Revenge of the hopeful monster, about how natural and lab experiments are changing how we think about the mutations that create the phenotypic variation that enables organisms to evolve. In Fisher's model (see yellow spheres →) a single mutation of large effect is bound to either "move" the organism in the wrong direction, away from the fitness optimum (center of spheres), or it will mostly overshoot the optimum, landing the organism on the other side, and the mutation will still be detrimental. on this basis, Fisher argued that adaptation only takes place by many small mutations. However, this assumes two things which both are unrealistic: 1) That there is only one fitness optimum. And there aren't. A model of a realistic fitness landscape would have many peaks and valleys (we call such landscapes 'rugged'), which immediately makes Fisher's model nonsensical. A large mutation may indeed take the organism further away from one optimum, but that might land the organism near another peak in the fitness landscape, and thus be beneficial anyway. 2) Adaptation occurs when the organisms are not sitting right on top of a local fitness peak, and this situation can occur when the fitness landscape changes, because the "real" environment changes. For example, in Lenski's experiment the bacteria were removed from the natural environment, and that changed the fitness landscape accordingly. If a fitness peak disappears, then the organisms may not find themselves near another peak, as Fisher's model assumes, but may be really far away. (Note that adaptation is a process that occurs for one or more traits that are no longer optimal after an environmental change, while most other traits are fine.)

Tedious footnote:

That we learn new things from experiments about how evolution proceeds should be a cause for celebration, so it is with irritation that I came across this blog-post on the same article by a fellow of the Discovery Institute, Cornelius Hunter. After reading the discussion on his blog, I realize that Hunter is equating evolutionary theory with "Darwin's theory", which means that when something turns out not to be quite right with "Darwin's theory" (as is the case of gradualism, or small effect mutations, vs. mutations of large effect), then he thinks it's a problem for current evolutionary theory, to the extent that it is then falsified.

When some people have made up their mind that there is a world-wide conspiracy going on among evolutionary biologists to keep the truth from the public, and when their belief in this is motivated by their desire to prove evolution wrong because of their religious faith, then at some point all discussion becomes futile. But, one point in still arguing with them, is that hopefully the younger generations will come away with a more rational view of evolution and science.

Presidential failure

Dangnabbit, Obama wouldn't presidentially proclaim February 12 as Darwin Day. What a surprise bummer.

Thank you for signing our Darwin Day Petition. Unfortunately, we were unsuccessful in obtaining a presidential proclamation this year, but we plan to keep growing our movement in hopes of a proclamation next year.

Darwin Day is administered by the American Humanist Association (AHA). The mission of the AHA is to be a clear, democratic voice for Humanism in the United States; to increase public awareness and acceptance of humanism; to establish, protect and promote the position of humanists in our society; and to develop and advance humanist thought and action. In short, we strive to bring about a progressive society where being "good without God" is an accepted way to live life. Become a member!

It really ought to be up there on Obama's list of priorities along with health care, the economy, and ending American hegemony (and maybe it is, but this one is just a much tougher nut to crack). Maybe next year...

Gays in the military?

The always odious AFA has a poll on whether homosexuals should be allowed to serve in the US military. So far the results look like this:

President Obama and liberal members of Congress now strongly urge repealing current law for a new “LGBT Law,” allowing for open and practicing homosexuals, bisexuals and transgenders to serve in the military.

Should open homosexuals, bisexuals and transgenders be allowed to serve in the U.S. Military?
Yes 344
No 5,335

Cast your Vote in the Online Poll

We are not surprised.

I suggest you go cast your vote, too.

We have a nominee for best apologetic

Exciting! The awards live. We have the first nominee for Best apologetic of the month (click for January) of February, 2010: Juan Carlos Bordes for the comment

Do you think Jesus would be happy by reading your blog?

Only ten days left to say something stupid in the name of Jesus, so get your comment in. Pick any post about evolution or atheism, tell evolution-lovers to eat dirt because Jesus rode a triceratops, or whatever, and you can be nominated too.

Fun!

Elton John: Jesus super-intelligent homosexual

Here's are the words in the interview that are making headlines today:

His take on Christianity.
"I think Jesus was a compassionate, super-intelligent gay man who understood human problems. On the cross, he forgave the people who crucified him. Jesus wanted us to be loving and forgiving. I don't know what makes people so cruel. Try being a gay woman in the Middle East -- you're as good as dead."

Come one, he had twelve guys in dresses following him around 24/7. Totally.

Bill Donohue, president of the Catholic League (job description: take yourself very, very seriously) takes offense to calling Jesus super-intelligent! For real.

Jesus was certainly compassionate, but to say He was “super-intelligent” is to compare the Son of God to a successful game-show contestant. More seriously, to call Jesus a homosexual is to label Him a sexual deviant. But what else would we expect from a man who previously said, “From my point of view, I would ban religion completely.”

Okay, so the gay comment is worse, but that was of course expected. As for Jesus being a sexual deviant, I wonder what Donohue thinks normative sexual behavior is. Celibacy?

We’re not sure what’s worse—John’s ignorance or intolerance. In any event, if we thought we could persuade him to issue an apology, we would try. But given his recidivism, we won’t even bother to ask. One thing is clear: someone needs to straighten John out.

Translation: "Ignoring our own intolerance of sexual diversity, we'd really like to get more attention (please?), for example by calling for an apology (God needs our help) from the most brazenly gay man in the world, who by the way ought to join one of those groups who heal homosexuals though prayer."

Christopher Maloney is a quack

Category: Skepticism

Maloney is a naturopath in the state of Maine, where quacks like him get to call themselves "doctors". These so-called "doctors" get to make recommendations like this, in which he disparages standard flu vaccines and suggests these useless prescriptions:

Parents waiting for vaccinations can provide their children with black elderberry, which blocks the H1N1 virus. A single garlic capsule daily cuts in half the incidence and the severity of a flu episode for children.

There's another way you can tell he's a quack. When a student, Michael Hawkins, dared to criticize him, pointing out that "Naturopathic medicine is pure bull" and stating that naturopaths are underqualified and do not deserve the title of "doctor," Maloney took action to silence him. After all, we can't have people questioning quacks — that just makes them look even more ridiculous, which could lead to a loss of business.

So Maloney complained to Wordpress, where Hawkins blog was located, and got them to shut it down. This does not speak well of craven Wordpress; if you're using Wordpress hosting, you might want to reconsider it and move elsewhere. You know, to someplace that respects reality.

Now not only is Maloney a quack, but he's a stupid quack. Shutting down blogs that criticize him? That never, ever works. In fact, it tends to backfire rather severely — because now a much bigger blog is going to spread the word that Christopher Maloney is a quack. I'm also going to ask all of you out there who reads this to echo the message: Christopher Maloney is a quack. Won't that be fun? Poke the net, and the net pushes back.

Share the message. Let the whole world know that Christopher Maloney is a cowardly quack.

He's also tasteless. This is possibly the ugliest youtube video ever.

Posted by PZ Myers at 9:14 PM • 41 Comments • 0 TrackBacks

Scientia Pro Publica 21

Grrlscientist herself is hosting the all round science blog carnival this time: Scientia Pro Publica 21: Darwin's 201st Birthday Edition.

Here's an excerpt from a post by Bob O'Hara about how wrong anti-evolutionists can get the theory wrong, even if they aren't all-out creationists:

We can see their confusion even where they are trying to agree with evolutionary biologists: they are even ignorant of what fitness means. This is how they define it:

we’ll follow the current consensus according to which an individual’s relative fitness co-varies with the probability that it will contribute its phenotypic traits to its offspring.

This is not just wrong. To see why, imagine an individual that passes on its phenotype to every one of its offspring. According to Fodor & Piattelli-Palmarini, it has maximal fitness: transmission is 100%. But imagine that the trait is for only having two offspring. Compare that to an individual who half the time passes on the trait of having 10 offspring, and the rest of the time the offspring are sterile. Fodor & Piattelli-Palmarini may think that these individuals are less fit, but if these are the only two phenotypes in the population, the “fitter” phenotype will be lost. For the rest of us fitness is defined in relation to the population (and the environment!), not transmission within a family.

... co-varies with the probability that it will contribute its phenotypic traits to its offspring... Hilarious!

Comment moderation

Has anyone else been getting comments like this one?

Cool article as for me. I'd like to read something more concerning that theme. The only thing it would also be great to see on this blog is some photos of any gizmos.
David Stepman
Cell phone jammer

The cell phone jammer is a link to a store that sells something. I bet the post Evidence says no life on Mars could really use pictures of gizmos, yeah.

This is why I now moderate comments on posts that are more than 7 days old.

Facebook battle over evolution

Today's Darwin's birthday. Here's his present.



On Facebook I have joined the group We can find 1,000,000 people who DO believe in Evolution before June (go here to join it).

It was created as a reaction to the creationist group we can find 1,000,000 people who don't believe in Evolution befor June.

[sic]

So how's that going for them?

Well, the pro-evolution group now has a little over a quarter of a million members. The number of members by date looks like this:



Since the goal is to get a million by June, I here add that datum, and as we can see, the increase in members per day would have to fall considerably to fail reaching that goal.



I didn't take the data for the creationist group, but for the past couple of weeks the evolutionists have had approximately 4.5 times as many members as the creationists, and if we assume that that ratio holds all the way to June 1st, then the creationists won't make it.


Here I have taken the member count from the evolutionist group and added (June 1st; 4,500,000).

This little analysis assumes that the member increase per day in both groups won't change, which is arguably a bad assumption. Growth curves like these are usually exponential, and the blue one above might be that, even though if we take out the first and last data points, then the curve looks pretty linear. Either way, it looks plausible that the evolutionists will reach a million by June, and probably much earlier (my money is on March 10th), while the creationists aren't going to make one million by June 1st. Depending on the slope of the exponential they just might, but I wouldn't hold my breath if I were them.

New photos of WTC on 911

Newly released aerial photos of the World Trade Center coming down on September 11th, 2001.

That day really changed the world - for the worse.






...

Ancient brains revealed by microRNA?

Detlev Arendt's lab at EMBL looks at the evolution of the central nervous system in Bilateria. A brand new letter in Nature, Ancient animal microRNAs and the evolution of tissue identity, explores the link between the birth of ancient microRNAs and body plan evolution.

In the press release (read it on ScienceDaily), as is not uncommon, the conclusion of the work is taken just a little bit further than what the study warrants, I think:

Animals from different branches of the evolutionary tree -- different lineages -- possess specific microRNAs that evolved only in their lineage. But they also have microRNAs in common: ones which they inherited from their last common ancestor, and which have been conserved throughout animal evolution.

(...)

The scientists reasoned that if an ancient microRNA is found in a specific part of the brain in one species and in a very similar location in another species, then this brain part probably already existed in the last common ancestor of those species. Thus, they were able to glean a glimpse of the past, an idea of some of the traits of the last common ancestor of worms and humans.

MicroRNA are short RNA nucleotide sequences regulating gene expression mainly by supressing it. So they say that because one specific microRNA is found working in a specific part of the worm's brain, and this same microRNA also works in the same part of the human brain, then the common ancestor also had this same brain part. Saying that this microRNA has been conserved since the last common ancestor - something that the conclusion hinges on - is a bit of a mouthful. It could be true, but it is an assumption that could be contested.

From their abstract in Nature:

We reason that any specific localization shared between protostomes and deuterostomes (the two major superphyla of bilaterian animals) should probably reflect an ancient specificity of that microRNA in their last common ancestor.

This last common ancestor lived sometime during the Cambrian (say 555 million years ago), and we are supposed to infer that a 22 long microRNA could not have changed its role on regulating genes expressed in the brain?

Somehow I am not convinced that it would be impossible, or even unlikely, that microRNA and other regulatory factors change affinity frequently enough to render such inference dubious. In the paper they say this.

At the present state of analysis, we can only speculate about the tissue-specific ancient roles of these microRNAs, by extrapolating from observations in other animal models. [Emphasis added.]

And that's a fine thing to say. But going from this to "Last Ancestor Humans Shared With Worms Had Sophisticated Brain, microRNAs Show" is a little over the top.


a–d, Apical view of 48 h.p.f. Platynereis with expression in dorso-medial brain (green, acTub; red, microRNAs). e, Apical view of 72 h.p.f. Platynereis brain section showing colocalization of microRNA (red) with serotonin (cyan) (blue, DAPI, green, acTub). f, g, Apical views of 5 d.p.f. Platynereis brain. h, 3D reconstruction of 5 d.p.f. apical brain with superficial expression at the base of antennae.

Reference
Christodoulou F, Raible F, Tomer R, Simakov O, Trachana K, Klaus S, Snyman H, Hannon GJ, Bork P, & Arendt D (2010). Ancient animal microRNAs and the evolution of tissue identity. Nature PMID: 20118916

Yes, we can be homophobes

Obama's new military: Gays showering with straights

It's been a while since I've heard something really juicy from the always odious AFA. Of course, they are fundamentalist Christians, so they think sex between two men is the most repugnant thing they like to think about every night after they save their prayers. Making it their business what other people do in private is a religious right. (AFA website.)

So of course they are going to freak when Obama tells them to take shower with gays.

Gays showering with straights? Absolutely.

If President Obama, congressional Democrats, and homosexual activists get their wish, your son or daughter may be forced to share military showers and barracks with active and open homosexuals who may very well view them with sexual interest.

Talk about creating a hostile work environment for people who practice normative sexuality!

As former General Colin Powell observed in 1993 (before bowing to pressures of political correctness), "...it would be prejudicial to good order and discipline to try to integrate gays and lesbians in the current military structure."

Gotta love pretty much every word of it.

What exactly do they think is going to take place in the showers? Erections? Soap just lying on the floor for months and months?

Military morale will break down because now the straight men (somehow I have trouble seeing this being a problem in the women's showers, but what I don't know but wish I did) will be harassed by the gay military activists? So the gays will view the straights with sexual interest, and so... what? Orgies? Rape?

I get the point that the homophobes for Christ (say that they) fear that allowing homosexuals in the military (as though they weren't there already) would

undermine recruiting and retention, impact leadership at all levels, have adverse effects on the willingness of parents who lend their sons and daughter to military service, and eventually break the All-Volunteer Force.

So much for patriotism, eh? Do you imagine enforcing a no-sex policy in the showers? And impact leadership? Why? Because of sexual harassment? I think they imagine the effect of the first gay general. "Camouflage is out, men. Rainbows are in.

"Overturning the ban will likely preclude advancement and promotions for officers and chaplains who do not publicly affirm homosexual behavior, essentially ending their military careers.

I'm not sure what "affirm" means in this context, but surely you can be promoted whether or not you publicly state that you support gays in the military, or homosexuality in general. If, on the other hand, affirm here means that they cannot live with working side by side with homosexuals, then they are, in my mind, unfit for leadership. I mean for officers. Chaplains? No, it seems like a prerequisite to be a homophobe, so perhaps that does present a genuine problem. My solution would be to get rid of army chaplains, but that's another story.

If we do not insist that the ban on homosexual military service be retained, our military will no longer be the place America's families want to send their best and brightest young men and women.

Oh, is that where they are going now?



Full disclosure: I have not been in the military. I am not homosexual. I am not a homophobe. I am not religious. I am not a democrat. I am not a republican. I am not even American. Nobody cares what I think.

---

Update Feb 10th:
The AFA also wants the government to force homosexuals to get psychotherapy.

Evolution highlights XIV

Bunch of interesting new papers on evolution came out recently. Here are links to ScienceDaily, which is really the best resource on the web for easy reads on all things science.

Moral intuition does not come from religion, if we are to believe Marc Hauser, again.
Morality Research Sheds Light on the Origins of Religion

As if it wasn't hard enough to come to grips with birds evolving from dinosaurs, now it is being suggested that birds preceded the dinosaurs, and that velociraptor really was more of a big bird on steroids.
Bird-from-Dinosaur Theory of Evolution Challenged: Was It the Other Way Around?

Two distantly related butterflies (genus Heliconius) with similar wing patterns have had their genomes sequenced, and it turns out that similar genes (homologs) are responsible.
How the Butterflies Got Their Spots

This sentence is a clever reduction of both methods and results of something about the evolution of mitochondria. This sentence explains how fascinating and important this research is.
Did Bacteria Develop Into More Complex Cells Much Earlier in Evolution Than Thought?

From the abstract:

How did the process of protein import in mitochondria—which facilitated the evolution of this organelle, and thus, eukaryotic cell evolution—arise? Was the process driven by the ancestral host cell or by the prokaryotic endosymbiont, or by both?

Framed

Last year I sat in on a course where a student presented the well-known idea of framing. How you present two alternatives influences the choice of those that make it. For example,

A take-away restaurant near my house offers customers free home delivery or a ten per cent discount if you pick up. It sounds much better than saying you get no discount for picking up and suffer a ten per cent fee for delivery – this is the power of ‘framing’.

(Via BPS Reseach Digest.)

The student presented the following intriguing example: Two pipe-loving novices discusses smoking and praying at the same time. One asks their priest/pastor/father if it is okay to light up his pipe while he is praying, which is given the answer that that is certainly not okay. The other novice ask the p/p/f it it would be okay if he starts reciting a prayer while he is smoking his pipe, and to this inquiry the answer is that that is of course quite acceptable.

Then the student explained that the priest/pastor/father gives two different answers because the question is framed differently. Framing makes all the difference in the world.

However, I object (and did in class, but this student never really got it): those are two different situations - the difference is not in how the questions are asked, because those two situations are not the same at all. In the first, the novice would be concentrating on the prayer, but then distracting himself with something un-devine, thereby ruining the prayer. The second is presenting a situation where he interrupts smoking his pipe and starts concentrating on the prayer instead. Clearly not identical situations. Would you mind if your lover turned on some music while you were making out? Would you mind if your lover started kissing you while she was turning on the music? Very different answer, but not because of framing, but because those are different situations.

So the irony is that the pipe-prayer example is framed as an example of framing, when it is really not. If the student in question had afterwards revealed that this was the intent all along, then I would have been delighted.

Incidentally, in the first example of the discount at the take-away restaurant something similar is at play. Yes, if the patron is given no other information about prices, then this framing would make a difference. But, if the patron knew what the going rate of that kind of take-out was, then the 10% discount vs. 11.11% increase would be real.

I love Immanuel

Here's a line I overheard in a philosophy class yesterday:

"I'm starting to see the value of Kant."

RMAOTLF! About time, I'd say.

Deepak Chopra warming up to debate Shermer

Deepak Chopra is proud of being the King of woo woo.

It used to annoy me to be called the king of woo woo. For those who aren't familiar with the term, "woo woo" is a derogatory reference to almost any form of unconventional thinking, aimed by professional skeptics who are self-appointed vigilantes dedicated to the suppression of curiosity.

Any form of thinking must be dealt with with skepticism, at first. It's just that Chopra's thinking, when skeptically evaluated, doesn't hold up to reality. It goes against all the evidence.

It's such a tired old argument that people who are skeptic are against curiosity. On the contrary, scientists are the really curious ones. But they also come equipped with the filter that makes them able to evaluate the ideas generated by our curiosity: skepticism.

I get labeled much worse things as regularly as clockwork whenever I disagree with big fry like Richard Dawkins or smaller fry like Michael Shermer, the Scientific American columnist and editor of Skeptic magazine. The latest barrage of name-calling occurred after the two of us had a spirited exchange on Larry King Live last week. . Maybe you saw it. I was the one rolling my eyes as Shermer spoke. Sorry about that, a spontaneous reflex of the involuntary nervous system.

I'm going to a debate with Chopra vs. Shermer next month. Will look for rolling eyes.

Afterwards, however, I had an unpredictable reaction. I realized that I would much rather expound woo woo than the kind of bad science Shermer stands behind. He has made skepticism his personal brand, more or less, sitting by the side of the road to denigrate "those people who believe in spirituality, ghosts, and so on," as he says on a YouTube video. No matter that this broad brush would tar not just the Pope, Mahatma Gandhi, St. Teresa of Avila, Buddha, and countless scientists who happen to recognize a reality that transcends space and time. All are deemed irrational by the skeptical crowd. You would think that skeptics as a class have made significant contributions to science or the quality of life in their own right. Uh oh. No, they haven't. Their principal job is to reinforce the great ideas of yesterday while suppressing the great ideas of tomorrow.

Oh come on, Deepak. It is through skepticism that scientists increase our knowledge about the world. And let me fix that sentence for you: "happen to recognize believe in a reality that transcends space and time"

Chopra wants Shermer to debate these questions:
• Is there evidence for creativity and intelligence in the cosmos? [Yes, on Earth. Other than that, no evidence yet.]
• What is consciousness? [It's the information the brain has in excess of its modules.]
• Do we have a core identity beyond our biology, mind, and ego? [No.]
• Is there life after death? Does this identity outlive the molecules through which it expresses itself? [Yes, my life after your death. And no, consciousness and mind are tied to matter, so when the matter that supported them disappear, so does the mind.]

I've baited this post with a few barbs to see if Shermer can be goaded into an actual public debate. I have avoided his and his followers' underhanded methods, whereby an opponent is attacked ad hominem as an idiot, moron, and other choice epithets that in his world are the mainstays of rational argument. And the point of such a debate? To further public knowledge about the actual frontiers of science, which has always depended on wonder, awe, imagination, and speculation.

And skepticism. Without skepticism there is no shield against the woo woo. I can't wait to hear what the 'actual frontiers of science' are, as Chopra sees them. More evidence for life after death, is my bet.

Oh wait, there is a new P.S.:

P. S. In light of a few of the comments I would like to clarify something. I hold great value and trust in the scientific method when practiced honestly. Also, I have nothing against healthy skepticism which retains an open mind to future possibilities in science. What I am really addressing here is the brand of professional skepticism that Shermer stands for that borders on cynicism and which leads to a rigid attachment to materialist science. It is the cynicism and prejudice that refuses to explore the new frontiers of neuroscience, genomics, epigenetics, information theory and the understanding of consciousness that I am speaking to. [Emphasis added.]

I'm baffled. Those fields of science... skeptics refuse to explore them? Scientists, skeptics, and Shermer as well, happen to be very interested in those frontiers. I don't get it. Please explain how Chopra can claim those as i) dismissed by skeptics, and ii) beyond materialism.

Dinosaur in colors

If you haven't already seen this feathered dinosaur in colors, do take a good look:



Stunning, innit?

Carl Zimmer writes about it in The New York Times.

The researchers removed 29 chips, each the size of a poppy seed, from across the dinosaur’s body. Mr. Vinther put the chips under a microscope and discovered melanosomes.

(...)

Dr. Shawkey can accurately predict the color of feathers from melanosomes alone. The scientists used the same method to decipher Anchiornis’s color pattern.Anchiornis had a crown of reddish feathers surrounding dark gray ones, and its face was mottled with reddish and black spots. Its body was dark gray, but its limb feathers were white with black tips.

Turkeys voting for Christmas

Fascinating article about why voters vote against their own interests:

Gore: "Under the governor's plan, if you kept the same fee for service that you have now under Medicare, your premiums would go up by between 18% and 47%, and that is the study of the Congressional plan that he's modelled his proposal on by the Medicare actuaries."

Bush: "Look, this is a man who has great numbers. He talks about numbers.

"I'm beginning to think not only did he invent the internet, but he invented the calculator. It's fuzzy math. It's trying to scare people in the voting booth."

Mr Gore was talking sense and Mr Bush nonsense - but Mr Bush won the debate. With statistics, the voters just hear a patronising policy wonk, and switch off.

In other words, half of voting America vote they way they do because they are stupid. Very, deeply, and profoundly stupid. In twenty, fifty, or ninety years historians will look back at this period shaking their heads, grappling with the inanity. Hard to believe people really were that dumb.

Faroe Islands out of Denmark now

Important update Feb 6th: I am very well aware that several of the comments in this video are factually wrong. As I have explained in the comments below, it is also unimportant in regards to the reason I abhor the killing of dolphins, which is due exclusively to the amount of physical and emotional pain I believe they suffer. In addition, I do not hate the Faeroese, only their practice of killing Pilot Whales (which is a species of dolphin). Same goes for any other people who kill any other living creature that I believe feel a comparable amount of physical and emotional pain.

I am from Denmark, but I am NOT from the Faroe Islands. And quite frankly, with all the places in the world where people crave independence from the nation they belong to, I say, again, that we let the Faroe Islands go. Cancel their membership of Denmark.



Bastards.

Petition the Pope to pay for his own travels + Feb 12th Darwin Day

Two petitions worthy of my signature, and perhaps of yours:


We the undersigned petition the Prime Minister to ask the Catholic Church to pay for the proposed visit of the Pope to the UK and relieve the taxpayer of the estimated £20 million cost. We accept the right of the Pope to visit his followers in Britain, but public money would be better spent on hard-pressed schools, hospitals and social services which are facing cuts. [Sign.]



Now, Therefore, I, Barack Obama, President of the United States of America, by virtue of the authority vested in me by the Constitution and laws of the United States, do hereby proclaim February 12, 2010, as Darwin Day. I call on all Americans to recognize the importance of Charles Darwin and his theory of evolution by natural selection, to endeavor to preserve scientific discovery and human curiosity as bedrocks of American society, and to commemorate this day with appropriate events and activities. [Sign.]

As always, PZ Myers is first with thing sort of thing (Pope + Darwin).

Carnival of Evolution #20 - blog phylogenetics

In Carnival of Evolution #20, which is just out this morning, Psi Wavefunction has taken the URLs of the submitted posts and analyzed them as if they were proteins.

Psi then constructed cladograms, and find that blog-posts that we know come from the same blog actually form clades. Except one clade, which is paraphyletic (see the red branches on this figure →). Apparently I have a paraphyletic blog, which completely blows my mind. So Darwin's Bulldog must have branched off from one of my posts, even though it has existed for longer than my blog. Hmmm....

On top of that, the submitted posts this month - all about evolution - are both abundant and exceptionally good, and that's despite the fact that we're are now in the year 2010. The official Not Darwin Year. Evolution for the win!

Next edition, CoE #21, will be on Mauka to Makai. Submit your posts already using this form.

Curious Scientia Pro Publica #20

Scientia Pro Publica #20 is up on Kind Of Curious. This time it includes a post by Nature Blog's Henry Gee about the recently discovered oldest tetrapod footprints.

What does it all mean?

It means that the neatly gift-wrapped correlation between stratigraphy and phylogeny, in which elpistostegids represent a transitional form in the swift evolution of tetrapods in the mid-Frasnian, is a cruel illusion. If – as the Polish footprints show – tetrapods already existed in the Eifelian, then an enormous evolutionary void has opened beneath our feet.

And a challenge:

Note: the first person to find any part of this post quote-mined in support of creationism will receive the highly prestigious and coveted Order of the Unicycling Girrafe.

Not sure what a girrafe is, though. Exciting!

Best apologetic of the month Jan/2010

With fanfare, it is my pleasure to bestow the inaugural "Best apologetic of the month" for January 2010 to Taylor Sharp, 21, from Orange County. He posted this comment here on Pleiotropy:

Proving Evil exists doesnt mean anything. Yes God created Evil but without it human life could not exist.

Good cannot exist without Evil, aka you cant know one thing without knowing its opposite and thats why human life could not exist without Evil. God created Evil knowing that it is the only possible way human life could exist.

So in the end - Evil is in itself Good, because without it we could not exist in this world at all.

Seeing as probably nobody will believe or understand that u can email me if u want and i'd be happy to explain further. tsharp811@yahoo.com

Congratulations to Taylor!

The competition was steep, at least if comments found anywhere on the web are eligible (and I say they are). Still, Taylor's is by far the best comment I've seen arguing for the existence of God by apologizing for his inadequacies.

Do you believe in evolution?

There is a happy little Facebook competition going on between evolutionists and creationists. First the creationists created we can find 1,000,000 people who don't believe in Evolution befor June, which today has an impressive 25,696 fans. Spelling errors and all.

From that evolved the We can find 1,000,000 people who DO believe in Evolution before June, which now sports 111,880 fans.

Why don't you join your group of choice?

Liberia on drugs and human flesh

Monrovia, Liberia. Man. It's so fucked up you won't believe it. Deep, deep, crazy bad all over. You gotta, gotta! see this video - the Vice Guide to Liberia - if you EVER watch any on the web at all, you must see this video of an American team intervieweing ex-warlords in Liberia. Murder, rape, drugs, shit, piss, malaria, more drugs, and cannibalism. And that's with the UN there.

Just everything about it is so depraved and horrible that I didn't know it was even possible. One ex-warlord, General Butt-Naked, converted to Christianity and was acquitted of his war crimes. (And they say religion poisons everything.) He moniker came from the fact that he and his men fought naked. They were also cannibals. Butt Naked is now an evangelist. And I believe he is sincere.

In less than a year from now the UN will leave Liberia, and war will break out again. Coming soon to the news station of your choice...