Field of Science

Perry vs. Willingham

Governor Rick Perry (R-TX) is feeling the heat over the 2004 execution of Cameron Willingham. Basically, evidence had amounted in due time before the execution that Willingham was innocent, and yet Perry refused granting a 30-day deferment of the execution. Now criticism is amounting, I am guessing based on the New Yorker article from earlier this year detailing the circumstances of the case, and Perry's response is to cement his opinion that Willingham was a beast, obviously because he cares more about his future career than he does about the truth.
Last week Mr. Perry defended his decision and struck back at his critics. “Willingham was a monster,” he said. “Here’s a guy who murdered his three children, who tried to beat his wife into an abortion so he wouldn’t have those kids. Person after person has stood up and testified to the facts in this case.”
Fuck you, Perry.

Evolution highlights VI

PZ Myers is reporting from the Darwin/Chicago 2009 conference (schedule) organized by Jerry Coyne. Talks by Richard Lewontin on bad metaphors in evolution, and by Ron Numbers on the history of creationism.

Tomorrow Douglas Futuyma, Jerry Coyne, and Daniel Dennett, among others.

On his blog, Coyne has a post about the refutation of the worst paper of the year in PNAS: Caterpillars evolved from onychophorans by hybridogenesis. Complete dismissal of that zany paper.

Update: There's now even more good summaries from Darwin/Chicago 2009 by PZ:

Marc Hauser— where do morals come from? NOT religion
Douglas Futuyma—Evolutionary Ecology and the Question of Constraints
Peter & Rosemary Grant—Natural Selection, Speciation, and Darwin's Finches
Douglas Schemske—Ecological Factors in the Origin of Species
Paul Sereno— Dinosaurs: Phylogenetic reconstruction from Darwin to the present
Frederick Cohan—the Origins of Ecological Diversity in Prokaryotes
Jerry Coyne—Speciation: Problems and Prospects
Eric Lander—Genomics and Darwin in the 21st Century
Philip Ward—What do phylogenies tell us about evolution?

Like diarrhea from a babycalf.

Coyotes kill human hiker

A young woman was killed by two coyotes.
A young Canadian folk singer who had just set off on a solo tour to boost a promising musical career died Wednesday after being mauled by two coyotes in what is believed to be one of the country's first fatal attacks by the animals.
I am surprised. I live in Suthern California, and there are coyotes all around. A family of six lives close to where I work, in a suburban neighborhood. I see one on my way to work once in a while. They're cute. It does not for a second raise any alarms in me, despite stories of cats and small dogs being taken by them.

And then the authorities go out and shoot an innocent coyote, I am sad to say.
Officials shot a coyote late Tuesday, but Robichaud doubted that it was one of the two involved in the attack.
Let's just hope no influenza is named the coyote flu, prompting Canadians to kill all their coyotes, Egyptian style.

Woman can run but not walk (Dystonia)

This is some weird shit. This young woman recently got a rare neurological disorder, dystonia, which prevents here from speaking properly and walking without severe spasms. However, she can run normally, and talk meanwhile. She can also walk backwards normally. Still, horrible disorder.

Sadly, this case is being linked with the flu shot that she received ten days earlier. A spurious correlation is the only connection between the two, and yet it is enough for the media to scare people away from vaccines.

Important update:
News about the women now being mostly fine on Pharyngula.

Food for thought: give up meat to save the planet

Climate chief Lord Stern: give up meat to save the planet
“Meat is a wasteful use of water and creates a lot of greenhouse gases. It puts enormous pressure on the world’s resources. A vegetarian diet is better.”
I could live with that, but it's the tragedy of the commons. I like meat a lot, and I'll only do it if everyone gives it up, too. Otherwise I lose out for no good reason. But do raise the price of meats, and inform the public how they can change their diet without foregoing protein and how to make delicious vegetarian food. Anyhow, pork is a vegetable, right?

Padian pounds Darwin myths

Kevin Padian, Paleontologist at UC Berkeley and President of the NCSE, has written Ten Myths About Charles Darwin, in which he debunks common misunderstandings about the man.

I'll highlight two of them here. The first was a surprise to me: Darwin did not think of populations, a crucial entity in population genetics. Except, as Padian explains, he did talk about "groups of individuals in the same species", which I think sounds pretty god-damned close.
5. Population thinking

It is often maintained that Darwin was the first biologist to think in modern populational terms (e.g., Mayr 1982). There is no evidence for this view. For Darwin, natural selection operated on individuals. He did not recognize population structure within species as we do today. For one reason, he didn't recognize species as real. He made no distinction among species, races, varieties, and subspecies. More than any other biologist of his generation, he thought of them as stages along a continuum of evolutionary diversification and separation of lineages. The word “population” does not appear in On the Origin of Species, even though Malthus's Essay on Population was a principal stimulus to his idea of natural selection. The closest Darwin comes is in his discussions in Origin, The Descent of Man, and elsewhere that suggest how groups of individuals in the same species could diversify structurally and ecologically under different selective pressures in different geographical regions. Remember too that mathematical modeling, the basis of modern populational thinking, was not one of his strengths. He did not have a developed sense of the quantitative flow of inherited traits within and among populations—this was developed only in the early decades of the 20th century, and then by mathematicians (Fisher 1958, Provine 1971).
Secondly, the myth that Darwin thought evolutionary change must always happen in tiny, incremental steps. Gradualism meant something else to Darwin than it does to most people today. Personally I am not sure how large steps he considered plausible. Read this and let's hear what you think.
7. Gradual change is slow and steady

When in Chile during the voyage of the Beagle, Darwin experienced a huge earthquake that leveled Concepción and injured and killed many people. On the ship the next day he looked down the coast and saw that the cliffs had been raised several meters, and that this was simply the latest instance of such cataclysms. He referred to the event in his diary as a “gradual change.” It seems strange to our ears to think of the effects of earthquakes as “gradual,” but the etymology of the word comes from the Latin gradus, meaning “step.” In Darwin's day, “gradual” often meant steplike (the Oxford English Dictionary uses the example from Addison and Steele's Spectator of rows in an auditorium). Consider the discrete markings on a graduated cylinder, and that students all graduate on the same day, as opposed to all through the year. Yes, the gradual steps were small. But it is unlikely that Darwin would have endorsed the classic gradualism of the Modern Synthesis to the exclusion of punctuated equilibria (Eldredge and Gould 1972). On the other hand, he was opposed to any kind of large, sudden change, which is why he rejected Huxley's entreaty that he abjure the doctrine that “natura non facit saltum” (nature makes no leap).
Again, again, again, we celebrate Darwin's 200th birthday and The Origin's 150 anniversary this year. Next year is bound to be mundane.

Jesse Jackson votes against Obama?

Update: How did Jesse Jackson really vote? According to the government itself, Jackson voted Aye. I guess I'll have to run with that. Apologies for the mistake. The last paragraph, then, doesn't seem so terribly relevant now. But I'll let it stand as a general comment on political life. Can anyone think of any cases where it applies?

Jesse Jackson Jr. (D-IL) voted against Obama's hate crime bill, H.R. 1913: Local Law Enforcement Hate Crimes Prevention Act of 2009.

It's a shame how religious affiliation (he's a baptist) will cloud your political vision. Or, it's a disgrace when civil rights activists falls short of their calling because a selective reading of the Bible renders them homophobic.

Homeopathy explained

Dr. Charlene Werner explains physics and homeopathy. She is one of the funniest quacks I have seen in a long time. Watch and squirm.

Here's a summary of what she said:

"Einstein: All the mass in the Universe can fit into the size of a bowling ball, so in fact there is next to no mass in the universe, so E=mc2 becomes E=c2, which is why the vision system is so important, because we have lots of photoreceptors.

"String theory: Other particles are little strings, so we have both eyes and ears, so we have E=mc2, but mass is crossed out almost, and string/vibration. But that still doesn't tell us the whole picture, because what is a cell, right? A cell has cell wall, cytoplasm, etc., but is that mass? Not very much, really, right? So what is it? Tiny pieces of energy: electrons, protons, neutrons. So the whole body has a 'infantesimal' amount of mass, so what is the remainder? Energy. So we are energy. Something about conservation of energy, and guess what the definition of disease is: it's not mass, but the transformation of our energy state into something different. That's what the definition of disease is. So we should be able to transform our energy into a previous better state. We can use light, we can use sound, we can use homeopathy.

"Homeopathy: There is little mass, lots of energy, so that means everything has a vibration to it. If my neighbor's dog poops in my yard, literally, and I take a bomb and throws it at my neighbor, it destroys something, it changes its energetic state. Homeopathy can store energy and match it with your disease change in energy state and restore the energy state, and that's how homeopathy works.

"All of us vibrate, either with a plant, a mineral, or an animal. Something about curing a squeaky knee, and that is so miraculous and exciting, giggle giggle."

★ ★ ★

This is some weird shit, man! I really wonder where she gets it from. How anyone can make up such pure nonsense is completely beyond me. Can this not be classified as insanity? Please?

Via Pharyngula.

The quackery of chiropractic

Chiropractic, the "art" of treating a sleuth of medical conditions by manhandling the spine, is up there with homeopathy and reflexology. Except, to my surprise, it isn't innocuous at all. An article in the Skeptics Magazine details the dangers of this true branch of medicinal quackery: Fatal Adjustments: How Chiropractic Kills.
WHEN KRISTI BEDENBAUGH WANTED RELIEF FROM A BAD SINUS HEADACHE, the 24 year-old former beauty queen and medical office administrator made the mistake of consulting a chiropractor. An autopsy performed on Kristi revealed that the manipulation of her neck had split the inner walls of both vertebral arteries, resulting in a fatal stroke.
The chiropractor’s violent twisting of her neck caused the torn arterial walls to balloon and block the blood supply to the posterior portion of her brain. Studies confirmed that the blood clots formed on the two days she received her neck adjustments.
Kristi died in1993. Four years later, South Carolina’s State Board of Chiropractic Examiners fined the chiropractor $1000 and sentenced him to 12 hours of continuing medical education in the area of neurological disorders and emergency response.
This was news to me, but the fact that there is no science to support the practice wasn't. Chiropractic is bogus:
The public is led to believe that physicians disparage chiropractors out of some sort of professional jealousy. Yet there is only one reason that physicians judge chiropractors so harshly. Medicine is scientifically based, whereas chiropractic is not supported by a single legitimate scientific study.
The human urge to make an easy dollar is great, I suppose. Most of us have a deep aversion to cheating others out of their money, but I imagine that some finds it somewhat easier to get over the shame of scamming thy neighbor if they can make the patients believe they are being helped.

Which they aren't.

Einstein on evil?

In this little video Albert Einstein refutes the argument from evil against God's existence by saying that, like cold and darkness do not exist except as the absence of heat and light, so does evil not exist except in the absence of good. Evil is what happens when man does not have God's love present in his heart.

What a load of utter bullshit!

Of course a God who created everything is equally responsible for good and evil. Evil is not the absence of good. That would be neutrality. Evil deeds are done, and isn't automatically what's there when no good is done.

Albert, methinks you were a bit daft at times.

Update 10/21: Please see James' comment below on the question of the origin of this quote.

Update 11/2: While the quote attributed to Einstein is apparently a hoax (see comments), the argument falls all on its own, and... I still think Einstein was daft at times.

Update February 1st, 2010:
This comment below has now earned tsharp811 the inaugural "Best Apologetic of the month" January 2010. Congratz!

Nothing makes sense...

Nothing is biology makes sense except in the light of evolution.
Theodosius Dobzhansky.

Nothing in evolution makes sense except in the light of genetics.
William Rice.

Nothing in genetics makes sense except in the light of epistasis and pleiotropy.
Bjørn Østman.

More statements of this nature could be added under Dobzhansky's and next to Rice's, and similarly more under Rice's. It would be a whole tree of nothing makes sense's. Please feel free to contribute your own.

This was prompted by two articles on epistasis and pleiotropy in Nature Education. Excellent reads:

Epistasis: Gene Interaction and Phenotype Effects by Ilona Miko in Nature Education 1(1).

Pleiotropy: One Gene Can Affect Multiple Traits by Ingrid Lobo in Nature Education 1(1).

Arrived in Hungary


I arrived at a colleagues house in Budapest to spend the night. Tomorrow I will check out Budapest and then go to the conference venue at Balatonfüred.

The driver of shuttle from the airport drove like a madman, with Rick Astley's Never Gonna Give You Up, Vaya Con Dios, and Hungarian pop best classified Eurovision Song Contest material on the radio. *Shudder*

I arrived in Budapest airport after a pleasant flight with Malev just minutes before the Hungarian football team was going to make their entrance for their return from Copenhagen, where they beat Denmark. I made my exit before they arrived.

I met my mother between flights in Paris, and we had lunch close to Saint-Michel metro station.

Horrible, horrible flight from Salt Lake City to Paris. Fat guy next to me sleeping the whole way, and I got no sleep. Back to now, I am jet-lagged and tired, but unable to sleep at midnight local time.

Conference in Hungary

Tomorrow I am leaving for a conference in Hungary:

COST-ESF Conference

I will be giving a short talk on my new paper (of which you can find a preprint here) - a very short talk. 15 minutes only, and it looks like that includes time for questions.

The conference is mainly on questions regarding the transition from organic chemistry to biochemistry, i.e. the origin of life. This is of course highly interesting, even though chemistry isn't exactly my cup of tea. The organizers have stipulated that
New ideas and results discussed at this meeting should not be cited in publications without the explicit and prior permission of their author.
That will make blogging about it rather difficult, as I have to ask every presenter if doing so is okay with them. We'll see.

Particularly interesting speakers include Stuart Kauffman (Origins of Order + NK), Peter Schuster (quasispecies), John Odling-Smee (niche construction), and Eörs Szathmary (The Major Transitions in Evolution with John Maynard Smith).

The uncanny valley

On this blog, fisheye perspective, I've just read about the uncanny valley for the first time. If you don't know what that is, go over there and check it out: Monkeys exhibit the uncanny valley effect.

Otherwise, just watch Emily here for the state of the art in animation. Do you agree they have crossed the uncanny valley?

Genomic obesity

ResearchBlogging.orgYou don't usually think of plants as being fat, but they do really have an issue - at least on the genomic scale. Their genomes can be huge.

They expand their genome size with the help of transposable elements - sequences of DNA that copy and insert themselves somewhere else in the genome.

Maize, for example, doubled its size in only three million years. That makes it the Oprah Winfrey of plants genomes.

But, luckily, there is a way for the plants to lose the extra pounds (i.e. megabases). They remove the extra DNA through recombination.

For three different species of cotton from the genus Gossypium (G. herbaceum, G. raimondii, and G. exiguum) and the sister group of the genus as an outgroup (Gossypioides kirkii), they used genomic shotgun sequences to estimate numbers of accumulation and deletion of a retrotransposon, Gorge3.
Surprisingly, Gorge3 copy numbers were more abundant in, pre-Gossypium than at any other time point, for all taxa. Copy number estimates from this oldest time point in G. kirkii (3,001 ± 2,445) and the D-genome [G. raimondii] (4,731 ± 2,725) were not significantly different from one another, but many retained ancient copies of Gorge3 were identified in the A-genome [G. herbaceum] (22,272 ± 6,331) and twice as many ancient copies were recovered from the K-genome [G. exiguum] (43,037 ± 9,063).
A nitpick: I'm not sure what they mean. The second comma in the first sentence seems misplaced to me. Removing the comma (comma), it says that the outgroup, G. kirkii, has more Gorge3 copies than the three species, and yet the numbers in this paragraph tell a different story (I think, but I could be wrong). I wonder if text is missing before that comma? Generally it is not a carefully written paper. They write "posses" (and don't mean the sheriff's search party), and the paper is written in passive voice, which is generally discouraged (but often done). Just saying.

Using a simple growth model the authors were able to infer the changes in the rate of gain and loss for all four species. The results are that two species have lost a considerable amount of Gorge3, while two other have be gaining.

Fig. 3. Phylogenetic relationships and estimated rates of Gorge3 gain and loss among diploid members of Gossypium. Branch lengths are to scale. Numbers above the branches represent the estimate of the exponential rate of change in Gorge3 DNA with confidence intervals in brackets. Taxa are shown at tips with entire genome size as well as the amount (in Mb) of extant DNA from Gorge3 elements. (Click for larger image.)

Even among closely related species there is ample variation in genome sizes. Why do some genomes have a ‘‘one-way ticket to genomic obesity,’’ while others couldn't gain weight if they tried (sort of like Michael Phelps and other people with tapeworms)?

It is not known why genome expansion is differently tolerated in different lineages. One could imagine that some external, environmental factor is responsible; the three Gossypium species evolved on different continents. There can be benefits to adding extra DNA to the genomes, since this gives material that evolution can work with, but at the same time it is energetically costly to make all that extra DNA every time a cell is duplicated.

Something in one environment could favor large genome sizes (perhaps this could be investigated by comparing with different species in the same environment?) while there not being the same selection pressure in another. Or, the environment affects the fitness of the transposons differently (say, when it's really hot Gorge3 is more successful at jumping around). Or, Gorge3 is really different in the four different species, and that explains their different rates of proliferation.

Hawkins JS, Proulx SR, Rapp RA, & Wendel JF (2009). Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants. Proceedings of the National Academy of Sciences of the United States of America PMID: 19815511

Observations from the zoo

During a family trip to Los Angeles Zoo I made a couple of observations that made the trip for me. My kids are becoming more autonomous, not requiring constant attention anymore, so I can do other things than just following them around.

Meerkats keep a lookout even though it clearly offers no survival benefit when there are no predators. This behavior is an instinct, not learned, and therefore difficult to get rid of. Assuming this instinct is currently neutral with respect to fitness, it might take a long while for it to disappear. But that might be beneficial in the long run, because the environment might change and their vigilance again become adaptive.

Giraffes are smaller when they are young (surprise!), so it seems unlikely that leaves on high branches that adults could barely reach would result in the selection pressure that eventually led to their long necks (and legs - that the legs are long too is a much overlooked fact, I think). Rather, sexual selection looks like a much better explanation. Males fight not just using their necks, but they also kick each other.

This is some serious, serious headbutting. Imagine if they evolved sharper horns.

Chimpanzees within a group are violent at dinner time, but disputes over the right to mate is settled in a much more peaceful fashion. A male and a very beautiful female were grooming and hugging each other (people watching going "hnnn, so sweet"), then the male stood up and did a brief dance (people watching going "oh wow, look!"), and then she put up her ass they had sex (people watching going "oh, erhm"). Then the much older male came over and interrupted them with his presence. He did the same dance, and the female got scared and ran away. The younger male pretended nothing had happened. Then the old one left, and the female returned. They repeated all of this a couple of times, with a lot of grooming in between. But why? If the old male had any power, why did he allow them to be close at all? If the other male was higher in the hierarchy, why did he not defend the female from him? At one point the old male attempted to mate with the female, but she moved a little bit, and that was enough to discourage him. Again the other male did nothing. I know from other primates that hierarchies are often very tight with everyone aware of their place in it. But here it seems like the hierarchy is in dispute, and yet it doesn't lead to fighting between the males.
Apparently, male chimpanzees prefer older females.
"Chimpanzee males may not find the wrinkled skin, ragged ears, irregular bald patches, and elongated nipples of their aged females as alluring as human men find the full lips and smooth complexions of young women, but they are clearly not reacting negatively to such cues," the researchers concluded.

Guns don't kill people?

You wake up in the middle of the night and hear someone in the hallway. You are certain it's a robbery. What do you do?

1. Take the loaded gun from the drawer and shoot the first chance you get?
2. Leave the loaded gun in the drawer and pick up a candlestick?

Option number one:
Brunelle said 62-year-old John Tabutt told investigators he thought he heard an intruder, got his gun and fired at a figure in the hallway. It was his live-in girlfriend, 62-year-old Nancy Dinsmore, who family members say he was going to marry Saturday during a small ceremony. Tabutt said he thought she was next to him in bed the whole time.
(Miami Herald)

Option number two: You approach slowly and is just about to whack the intruder over the head when she turns around goes "What are you doing with that candlestick, dear?" You go back to bed and get married the next day.

Guns don't kill people, but they do make it a hell of a lot easier for people to kill people.

Death penalty for Iranian protesters

Okay, alright, death penalty to demonstrators who have been in contact with the opposition. I mean, at least that a clear signal. If you talk to people who are against us politically, then we'll kill you.
The sentences were said to be for involvement in the countrywide protests that followed Mahmoud Ahmadinejad's re-election as president in polls many Iranians said were rigged. The authorities have rejected the charges and portrayed the protests as a foreign-backed bid to undermine the Islamic republic.
Just fuck that ridiculous theocracy.

Lectures on applied evolution

UC Riverside has a series of lectures on the application of evolutionary theory this fall. All talks are given by faculty members of the department of biology:

The Battle Within: Our Evolutionary Struggle with Cancer
Leonard Nunney, Department of Biology
Thursday, October 15, 2009

Born to Run: Evolution of Hyperactivity in Mice
Theodore Garland, Department of Biology
Thursday, October 29, 2009

The Silent Majority: How Symbiotic Bacteria Evolve to Help and Hurt
Joel Sachs, Department of Biology
Thursday, November 12, 2009

Because evolution mostly takes place over long periods of time, evolutionary theory does not have a huge range of applied uses. But there are some, with cancer and drug-resistance being the most famous (first and last lectures). I actually don't know how the second lecture on hyperactivity in mice is applied evolutionary thinking...

Despite being really close by, I have never been to UC Riverside. Perhaps I will make it to one of these lectures. Anyone else?

Evolution highlights V

When Being a Cuckold Makes Evolutionary Sense
In one species if fish, the females lay more eggs in nests where several males contribute sperm. This makes cuckold males more fit.

Chinese fossil find gives clue to ear's evolution
123 million year old mammalian fossil shows how the bones of inner ear evolved by separating from the jaw bone.

Do birth control pills alter mate selection?
Being on the pill changes which kind of man women find attractive. One expert said "Just because you like someone with a square jaw in the middle of your cycle probably doesn't affect who you end up with." I find that an extremely ignorant statement. Of course who you find attractive matters for who you end up with. There are apparently 100 million women on the pill world wide, and even a short monthly change in preference will have a significant effect in such a large population.

How Did Evolution Begin?
A new numerical model of "prelife" - a chemical system that can lead to information and diversity, and that is capable of selection and mutation, but does not yet have the ability to self-replicate.

Researchers discover a new antibacterial lead
Novel chemical compound targets the cell wall during bacterial development.

Top universities for natural science

The Times Higher Education ranks the 10 best universities in the world for the natural sciences like this for 2009:

That's three countries: UK, US, and Japan. Or, England (3) , US east coast (3), US west cost (3), and Japan (2).

Did I ever mention here that I'm expecting to graduate at the end of spring 2010, and that I am looking for a post doc. position starting then?

This is not a "thought crimes" bill

The American Family Association is against the H.R. 1913: Local Law Enforcement Hate Crimes Prevention Act of 2009.

Under the title Tell Congress to vote “No!” on “thought crimes” bill they write that
Politically incorrect thoughts about homosexual behavior will result in enhanced criminal sanctions under this law.

Everywhere hate crimes laws have gone into effect, they have been quickly used to intimidate, silence and punish people of faith who express deeply held religious objections to the normalization of homosexuality. [Selective deemphasis added.]
Come now! First it is 'thoughts' and then it is 'express.' A very unclever attempt at cleverly manipulating the reader into thinking this bill is going to punish people for their thoughts.

No bill is going to criminalize anyone for their thoughts, and that should be obvious to anyone. Apart from anything else, it would be completely impossible to enforce.
In fact, such laws actively discriminate against heterosexual Christians who are victims of crime, since they will get less legal protection than homosexual victims.

And since "sexual orientation" is nowhere defined in the legislation, this law will give pedophiles, voyeurs, and exhibitionists special protections, which is why the bill has correctly been called "The Pedophile Protection Act."
"Correctly"? The law should protect those who need it, and no one that I have heard of are going after heterosexual Christians because they are heterosexual Christians*. Pedophiles, who have been convicted for their crime, should be given protection against vigilantism. I personally think pedophiles who abuse children sexually should be locked away forever, but whatever the law says on the matter should not leave room for them being unprotected against hate-crimes. That sort of behavior leads to anarchy. Man.

But, what does the bill actually say? Here's a summary:
Section 6 -
Amends the federal criminal code to prohibit willfully causing bodily injury to any person through the use of fire, a firearm, a dangerous weapon, or an explosive or incendiary device because of the actual or perceived race, color, religion, national origin, gender, sexual orientation, gender identity, or disability of any person.
Nothing there about heterosexual Christians sitting at home thinking - or expressing - bigoted thoughts of any kind. In fact, it is explicitly stated that they can do so even in public (or, at least according to this bill they cannot be prohibited from doing so):
Section 8 -
Declares that nothing in this Act shall be construed to prohibit the exercise of constitutionally-protected free speech.
This bill is about violent hate-crimes. Construing it to be about thoughts is disingenuous.

* Notice that in section 6 it says "because of the actual or perceived race, color, religion, national origin, gender, sexual orientation, gender identity, or disability of any person." Heterosexual Christians are equally protected under this bill. What to conclude from the AFA's dislike of this bill? It reeks of indignation that the law will not allow them to follow the word of the Bible and bomb abortion clinics and so forth.

Bill Donohue attacks sinister anti-Christian movie (that he didn't watch)

Bill Donohue of the Catholic League did not see a movie, The Invention of Lying, and didn't like it one bit. Specifically, he doesn't like that the bigotry is subtle. He prefers his bigotry straight up, just as he is used to, I suppose.
Jeff Field, policy analyst and editor of the Catholic League’s monthly journal, Catalyst, provided Bill Donohue with a review of “The Invention of Lying”; Field saw the movie today in New York City. Here are Donohue’s thoughts on it:

[As I said, he didn't personally see it.]

The trailer to the movie gave no indication of its atheistic-themed plot, but there was enough of a buzz about the agenda of screenwriter Ricky Gervais that we decided to check it out. We’re glad we did. “The Invention of Lying” is not the kind of in-your-face assault that Hollywood often serves up, but therein lies its perniciousness: because this anti-religion—make that anti-Christian—film is laced with some romance and humor, the message it sends is all the more sinister.

[But when you lace child abuse with promises of paradise the perniciousness is forgiven? Or when the Pope condemns the use of condoms with the result that thousands die of AIDS the sinisterness at least isn't laced with romance or humor? So that's okay? Lacing the message with superstition is so much better?]

The movie centers on a world where no one lies. But that changes when the lead character’s mother is dying and the dutiful son finds utility in spinning a tale about a place that resembles heaven, thus saving her from being consigned to an “Eternity of Nothingness.” He subsequently floats the idea that there is a God-like “Man in the Sky,” a belief accepted by most, though some cynics wonder why AIDS exists (it’s never diabetes that Hollywood flags). In mockery, the lead character later shows up looking like a fat Jesus, and an image of him appears on a stained-glass window holding the Two Tablets (of Moses), posing as if on the Cross. In the end, he and his girl are the only two people who haven’t drunk all the moonshine about “The Man in the Sky.”

[Diabetes... Okay, so Hollywood uses AIDS (which, again, the Vatican helps spreading by discouraging the use of condoms), and it's worth mentioning that they don't use diabetes, because... what? But indeed, assuming your benevolent creator, why does diabetes exist? Or AIDS?

Otherwise, it sounds like a not so subtle message.]

We at the Catholic League prefer our bigotry straight-up. We don’t like bigotry-lite, which this is not. But we also don’t like it slipped into our drink. It is not for nothing that the Office for Film & Broadcasting of the bishops’ conference slammed the movie as “morally offensive.” But we are pleased to note that the atheists still use our religion as the model, and still portray God as male. There is hope for them yet.

[I wonder how this movie is morally offensive. The bishops should of course be outraged by the blasphemy. The anti-Christian message should offend them, or Catholicism wouldn't have made it this far, I bet. But morally?

Still portray God as male. I recall a Danish movie from decades ago where Jesus came back as this woman who traveled through toilets. Somehow a non-toilet traveling man works better, I am sure. And as for hope, and apart from the sarcasm, Donohue of course means hope for him and his his religion.]
Has anyone seen The Invention of Lying? It sounds boring, I must admit, but might be worthwile to watch just for the bigotry.

Homophobianizing football

A French football team consisting of Muslims, Créteil Bébel, is refusing to play another team with some homosexual players on it, The Paris Foot Gay team.
Zahir Belgarbi, identified as a spokesman for Creteil Bebel, told France-Info radio he apologized if "anyone felt upset or hurt."
Right. If you are sorry that you upset someone, then you either regret that you did what you did, and won't do it again, or you regret that idiotic rules are forced upon you. Neither of these are true in this case; the Muslims players will of course refuse next time as well, and they do not think that Islam is idiotic.

But I suppose Mr. Belgarbi could just be sorry that the people his team upset are hurt, because he is sorry that those people don't agree with him.

Scientia Pro Publica 13 is live

Scientia Pro Publica 13: Nobel Prize Edition is up at Living the Scientific Life.

One post on Science of Board Games contains Python code for the famous Monty Hall problem:
To demonstrate how I use rejection sampling, we can use it to confirm the Monty Hall riddle. Basically, you are a contestant on a game show, and are asked to pick on of three doors, behind one of which is a new car that you win if you pick it. After picking a door, the host then reveals one of the other doors without a car in it, and offers to let you switch your choice. So, should you switch? The answer is always yes, though I won't go into details: suffice it to say that it's a non-intuitive probability calculation. If you switch, you have a 2/3 chance of winning the car, and if you stay the course, you have a 1/3 chance of winning.
I wrote code for it, too, once, and if you're interested I suggest you try to modify it so that the host opens a door at random, and then see if switching still gives probability 2/3.

Nagging conundrums

Celebrating the 150th issue of the British Psychological Society's Research Digest, the editor invited twenty-something of the world's leading psychologists to answer the what nagging thing they still don't understand about themselves. Many of them are quite good reads, and one of them, Alison Gopnik, wrote that she does not understand why she would love her children so intensely when they are young, but look forward to see them go when they become adults. I personally don't think that's such a big mystery, but it reminded me of the one nagging thing I still don't understand about myself (yes, there's really only one thing left by now).

Why do I expect that I will be different from everyone else?

When people get older they tend to become more conservative, more scared of strangers, and less interested in learning new things. Set in their ways, people often say. Nobody picks up the banjo when they're forty (not literally), and no one learns a new language when they reach sixty. Why not? Because when you get old you get less flexible and less able to learn new things. Less interested in life? But why? No one can tell me. It's one of those things that are so ingrained in our life experiences that we never question it. I look forward to either disprove that those symptoms must not come with old age, or learn why it is that we end up like that. I fully intend to learn to play banjo when I turn forty, and plan to learn a new completely new language when I am sixty (e.g. Arabic or Mandarin). I don't understand why I shouldn't be able to.

Cheese banks (really!)

I love cheese. To eat it. In Italy they put cheese in the bank. They really roll the cheeses into a vault, where they age for a year or two.
Row upon row of 85-pound wheels of straw-colored Parmesan cheese, stacked some 33 feet high at a secure warehouse, age for as many as two years under the care of bank employees trained in the centuries-old art of Parmesan making.
So how much can that be worth?
Typically, a Parmesan maker who produces 7,000 wheels a year might put up 2,000 as collateral for a loan. According to Morini's calculations, each wheel is worth as much as 300 euros ($425), valuing the cheese collateral at 600,000 euros. The bank would then issue a loan of 60 percent to 70 percent of the value, so around 420,000 euros.
I wonder if they have similar arrangements elsewhere... Sheep banks in Australia? Pilsner banks in Czech Republic? Opium banks in Afghanistan? Vanilla banks in Madagascar?

Ardipithecus ramidus in the news

The new 4.4 million year old fossil of the newly found hominid, Ardipithecus ramidus gets it's fair share of attention in Science with 11 article in one issue. Science has made all the articles free, here's your chance to print out great readings for the whole weekend.

Carl Zimmer at The Loom
Great review, as always.

Matthew Cobb at Why Evolution is True
Spells out the fact that we don't know whether Ardi is a human ancestor or not (though she definitely isn't an ancestor of both chimp and humans).

PZ Myers at Pharyngula
As usual, cranky about the science reporting.

Someone at
Lots of links to press coverage.

Mailund on the Internet
Even more links to blogs on Ardi.

Not quite evolution or just plain crazy

Here are a few posts that didn't make it into the Carnival of Evolution 16 (which requires that they really be about evolution, and that they aren't batshit crazy).

How to Become a Highly Effective Problem Solver
And the answer is: Ethos, Pathos and Logos. (Not really evolution.)

Top 100 Science Professor Blogs
A list of 100 blogs run by science professors. 19 in biology, though not all are really by professors. (Not really evolution.)

To eat or not to eat…meat. Do animals know that we eat them?
The author of this post not only believes in reincarnation, but that animals choose which organisms to be born as. They know their lives are going to be short and nasty, but they don't mind that, because the consider it an honor to help humans in this way. The author knows these facts having communicated with the animals. Seriously! (BS crazy.)

Carnival of Evolution 16 - the [find modest synonym for outstanding] edition

I am pleased beyond measure to welcome you to this 16th edition of the traveling Carnival of Evolution. Very pleased! Pleased beyond... measure.

So welcome. We all love statistics like [find appropriate idiom], so let's start with some of that.

This edition of the carnival consists of 36 posts (far too few) about evolution on ≈26 blogs (far too few), with a total of 50,228 words, for an average of 1,395.2 words per post. Standard deviation is 1,307.6. Count of words for each post is listed in brackets after each title, where I also note if the post is about a peer-reviewed paper (PR). Shortest post is 314 words, while the longest is 5,584 (counting Carl Zimmer's post and NYT article as one). Both praiseworthy achievements.

In a pitiful attempt at bringing some order to chaos, the posts have been forced into categories that many of them are quite uncomfortable with. I suspect I shall concomitantly receive much hate-mail, and will of course bend over backwards to please everyone by making any changes strongly suggested. I am serious.

To see the previous editions, please visit Carnival of Evolution, the blog, where you can also find the form to submit to next month's edition.

One of the posts this time is about a fine paper about experimental evolution, which I was intending to blog about myself. However, since it is also my desire to eventually publish papers in scientific journals myself, I never got further than writing this footy list of explanations of evolutionary terms particularly important for that paper. I'll link right here to the first who can guess which paper/post I'm talking about.

Organism: A uni- or multi-cellular automaton with the ability to reproduce.
Fitness: A measure of the organism's ability to reproduce.
Genotype: The genetic make-up of the organism; the particular DNA.
Mutation: Any change in the organism's genotype (recombination, insertions, deletions, SNPs, inversions, duplications, translocations, etc.).
Beneficial mutation: Having an advantageous effect on fitness.
Deleterious mutation: Having a detrimental effect on fitness.
Neutral mutation: Effectively no change in fitness.
Population: A competing group of organisms.
Trait: A characteristic of an organism encoded by part of the genotype.
Selection: The increase of genotypes or traits in a population due to their fitness advantage.
Drift: A random fluctuation of genotypes or traits in a population.
Fixation: The event of a mutation becoming universal or very common within a population.
Substitution: A mutation that has gone to fixation.
Adaptation: The process by which the population increases its fit to the environment.

Lastly, before we begin, I must surprise everyone by revealing that this year Charles Darwin would have turned 200, and The Origin was first published 150 years ago. Both of which makes this carnival very special. Next year is going to be a real bummer.

Human Evolution

AK's Rambling Thoughts
Diagonal Postures & The Descent from Human to Ape (3,213, PR)
Guest blogger and author of The Upright Ape: A New Origin of the Species (2007) goes into details with a paper that argues that humans did not evolve from a knuckle walking ancestor.

A Primate of Modern Aspect
What microcephalics can tell us about human evolution (1,004, PR)
This post, to my surprise, is not about hobbits, but about the fact that humans with smaller brains than some chimpanzees can still do things chimpanzees can't (use tools and make fire, and restrict themselves to one lover).

Evolving Thoughts
Rudiments and vestiges (983, PR)
Does phylogenetic analysis support the claim that the human appendix has a function, or is it rather evidence that humans are primates?

Mailund on the Internet
Doubts about complex speciation between humans and chimpanzees (932, PR)
A paper argues that hybridization between humans and chimpanzees is not necessary to explain the lower divergence between their X chromosomes, compared to that between humans and gorillas.

Greg Laden's Blog
Is the latest claim regarding "chimp-human" inbreeding a bunch of hooey? (469, PR)
Another take on the paper about complex speciation between humans and chimpanzees.


A DC Birding Blog
A Man-eating Bird? (390, PR)
Did Haast's Eagle eat humans? At least it could have.
Figure: Comparison of the huge claws of H. moorei with those of its close relative the Hieraaetus morphnoides, the “little” eagle. The massive claws of H. moorei could pierce and crush bone up to 6 mm thick under 50 mm of skin and flesh.

Fresno, Evolving
A punk-size T-rex and an Eagle that ate children?! (1,752, PR)
Evolutionary pressures can cause body size to become smaller as well as larger. Not all Tyrannosaurs were huge (though nine-footers would still be scary), and Haast's Eagle wasn't as puny as the extant ones.

Natural Selection

Fence lizards versus fire ants: Evolutionary fail? (559, PR)
Lizards fail to adapt to venomous ants after seventy years. Perhaps a case of too little variation present for natural selection to act on?

Ionian Enchantment
Chameleons DO change their color to blend in with their environment (658, PR)
Does color change in chameleons serve only as social signaling, or also as camouflage? Which function was first selected for?

Mauka to Makai
Sperm Wars (552, PR)
Ironically, the selection pressure for females to get their eggs fertilized has resulted in the female reproductive tract making it difficult for sperm to get through.

Why do atheists have fewer kids? (604)
Do the religious have more children than atheists because of honest signaling?

Adaptive depression? (736)
Two scientists argue that depression is an adaptation for thinking harder about our problems. Perhaps this is an example of applying positive selection where it doesn't belong?

Mailund on the Internet
A Method for the Simultaneous Estimation of Selection Intensities in Overlapping Genes (868)
A new method to estimate selection finds no evidence of positive selection in two influenza A genes, contrary to what is inferred in elsewhere.

AK's Rambling Thoughts
Homeotic Mutationism (5,584, PR)
Mutations in homeotic genes (e.g. Hox genes) can cause large developmental changes. Here we learn about the definition, causes, and possible consequences of homeotic mutations, with a nod to the otherwise universally predominantly dismissed “hopeful monsters.”

The Primate Diaries
Laboratory Evidence for the Breakdown of the Selfish Gene (1,674)
In The Selfish Gene (1976) Richard Dawkins championed selection on individuals, and group selection hasn't been regarded with much sympathy since. This is slowly changing, as experiments show that selection can work on groups.

Deep Thoughts and Silliness
Kin are a Group (1,480)
A reply to the post at The Primate Diaries: Selfish gene theory need not be expanded, because it already encompasses group selection via kin selection.

[Note: Both bloggers have promised me to continue the debate about group selection, and I will be adding links here when they get around to it.]

Molecular Evolution

The Chromosome Chronicles
Sexual Reproduction for Same Sex Couples? (1,170)
Pluripotent stem-cells can be made into either male or female gametes (sperm or egg), so it might be possible to have children who are genetically descended from two males or two females. I can't wait for the conservative Christians to go bonkers over this one. Note: Two females can only have female offspring. Wrap your head around the consequences of that.

The Atavism
Where did you get that preposterous hypothesis (1,774, PR)
A paper in PNAS suggests that metamorphosing organisms are hybrids between two distinct lineages (e.g. butterflies descend from a mating between a flying insect and an onychophran). The hypothesis is crazy, so why did it get published in a prestigious journal, PNAS? Get the answer here.

The Loom
The Continuing Adventures of the Blind Locksmith: You Can’t Get There From Here (165+846, PR)
Epistasis makes evolution irreversible. Make sure you click through to the NYT article.

Greg Laden's Blog
Evolutionary enamel loss linked to molecular decay of enamel-specific gene (437, PR)
Mammals evolved from an ancestor with enamel (hardest substance in the vertebrate body) covering its teeth. Genetic analyzes verify that enamelless and toothless mammals still have the gene to make enamel, but that mutations have made it a pseudogene.

Adaptive Complexity
Physical Chemistry Makes Us Different (1,722)
Key to understanding evolution is understanding genetic variation. How does genotypic variation generate phenotypic variation? Can biochemistry and genetics solve this problem?

Ionian Enchantment
Silver fox domestication (844, PR)
In the famous experiment on domestication of Silver Foxes the animals were selected for tameness, but also evolved other developmental traits that we know from dogs: shorter snouts, droopy ears, white patches of hair, &c. The hypothesis is that pleiotropy links these traits, so that tameness and the physical traits go together. But were the foxes really only selected for tameness?

Mousy blondes: Ready for evolution textbooks? (810, PR)
A skeptical angle on a paper that got a lot of press coverage. “This research would fail as a textbook example right now, fine work though it is.”

The Tree of Life
The Tree of Life: Why endosymbionts rule ... (314, PR)
A GC-rich bacterial symbiont with an alternative genetic code.

Lab Rat
Living without a cell wall... (723, PR)
How is living and replicating without a cell wall possible, and what does it have to do with the origin of life?


Sympathy for Creationists (5,364)
Can we find some sympathy for creationists through understanding their beliefs?

Birds & Science
Feather mites and God? (1,042, PR)
Roger's paper is picked up by creationists who conclude that feather mites knowing which bird feather will fall off next is proof of God.

Weird Things
Harder, better, faster, stronger? (384, PR)
Humans are still evolving and this is presented as evidence against creationism. If humanity would be the pinnacle of creation, then why are we still evolving?

The Tree of Life
Dembski still trying to play scientist (1,044)
Dembski published a paper in a peer-reviewed journal. It has been mauled and masticated, just like we like it.


Skeptic Wonder
The Myth of Evolutionary Ascent (4,531)
If you still think that evolution has a goal, then this is the post for you.

Cubik's Rube
So You Think You Are a Darwinian? (2,501)
“Also, nature has given some creatures gills, also by Darwinian processes. Doesn’t mean humans have a moral imperative to breathe underwater.” Precious!

Evolving Thoughts
Dreams of memes and replicator machines (1,409)
Should we replace the notion of replicators by reproducers?

Skeptic Wonder
The Tree concept is quite alive and well, thank you (551)
Revisit the “Darwin was wrong” mess of the New Scientist for another argument that the tree of life is still a good description.

Beetles In The Bush
A Silver Anniversary (1,453, PR)
Beetle taxonomy. 25 years ago a new species of beetle was discovered in Missouri.


Adaptive Complexity
The Indiana Jones Method Of Science (990)
A favorable review of Sean B. Carroll's newest book, Remarkable Creatures: Epic Adventures in the Search for the Origin of Species.

NSCE reviews (696)
The NCSE reviews evolution books, and a review of the review of Donald Prothero's Evolution: What the Fossils Say and Why it Matters gets axed.

☆ ☆ ☆

We have reached my only friend, the end. I hope you have enjoyed reading this 16th edition of Carnival of Evolution as much as I have writing it. Hopefully it has inspired you to learn more, and perhaps even to contribute to next month's edition, which will be hosted at Adaptive Complexity. So long.