2009 Atheist Convention

The Atheist Alliance International 2009 Conference is a couple of days away, and, for me, only a couple of miles away. Lots of great interesting speakers will be there, but, alas, I cannot go. Why? Because it's too freaking expensive! $279 for an all weekend pass. I'm not just upset that I cannot go because I am too poor (though I am very upset about being poor), but also that they insist it must cost this much. Give me a break! If I were to lash out, I'd say that the result of that will be that only retirees with nothing left to offer but their money will be going, while all the young people with ideas and a future to put them to use are going to be left out. But I won't lash out. Just advertise the event:

October 2-4, Los Angeles.

Speakers:
And many more.

From Tierra to... Spore?!

From an NYT article on artificial life:
Later artificial life researchers created programs to take advantage of the growing power of computers to model evolution in simple, abstract universes. Tierra, in particular, first developed by the ecologist Thomas Ray in the early 1990s, drew a great deal of attention. The program, which ran on more than 100 workstations, demonstrated the mutation of digital forms and elementary aspects of evolution. More recently, Spore, from Will Wright, popularized many of the aspects of artificial life in a game that is now widely available on desktop computers, videogame consoles and even iPhones.
Tierra and its successors are computer programs in which digital organisms really do evolve. Spore, on the other hand, is nothing like it. Rather, it's a lot like creationism.

Save the environment through eating

Christie Lynn, at Observations of a Nerd, has an excellent post about Lionfish, which are wrecking havoc on Caribbean coral reefs. The great news is that YOU can do something:
This lionfish invasion is an ecological distaster. We need a plan of action to manage this invasive species, a plan which will stop the spread of these quick-breeding sea-vermin and help protect the native populations from the advancing threat.

We need to eat them.
That's right. All you need to do is request them at restaurants and your local supermarket, and you can help save the environment. And they taste great, too.

If you want to do more, the Monterey Bay Aquarium has suggestions and guidelines about how to be a conscientious fish consumer.

For example, if you live on the US west coast, here are the fish to void:



Fish to avoid on the US west coast.

If you live somewhere else, choose a different Seafood Watch Pocket Guide.

It's a homo's devil machine!



Think . . .

Carnival of Evolution Trailer

Carnival of Evolution is only three days away, and it's going to be HUGE. I know none of you can wait, and that you all have a hard time going about your daily lives with so much great evolution stuff just around the corner, so here's a trailer with some highlights from the 16th edition of Carnival of Evolution:
Chimps are very promiscuous, humans somewhat less so, while gorillas would argue that the selfish gene theory also needs expanding. Do the animals know that we have evolved a light coloured fur coat in a relatively short geological period of time? A small brain can result from pleiotropy, the phenomenon of a single gene having multiple and seemingly unconnected phenotypic mice. Dembski grades his students on how well they troll, and was wrong about the utility of the surprising connection between mite behavior and God existence. Chimps and humans continued to interbreed long after they split in evolutionary time, so humans therefore did not evolve from a knuckle walking ancestor.
Carnival of Evolution 16 - coming to a blog near you on October 1st ! ! !

Session chairs listen up!

If there is even the slightest risk that you are ever going to chair a session at a conference, please (please!) do read these Ten Simple Rules for Chairing a Scientific Session (click for thorough explanations):

Rule 1: Don't Let Things Overrun
Rule 2: Let Your Speakers Know the Rules
Rule 3: Be Prepared to Give a Short Introduction
Rule 4: Write Down the Actual Start Times of the Speakers
Rule 5: Do Have a Watch
Rule 6: Communicate How Much Time is Left to the Speaker
Rule 7: Don't Be Afraid to Move on Without Questions
Rule 8: Get to the Venue Early and Be Audiovisually Aware
Rule 9: Prepare Some Questions in Advance
Rule 10: Keep Control of the Question and Answer Sessions

If only because there is a non-zero chance that I will be in the audience, and I HATE when the schedule isn't kept (because I am just waiting to go to lunch or hit the bar).

NCSE reviews

On NCSE's website there are three new reviews of three books on evolution and creationism:

  • Kenneth Miller's Only a Theory, reviewed by Andrea Bottaro,
  • Jerry Coyne's Why Evolution is True, reviewed by Donald Prothero, and
  • Donald Prothero's Evolution: What the Fossils Say and Why it Matters, reviewed by Peter Dodson.
I have only read the Prothero's book, and, like Dodson, I love it. Also like Dodson, I have my complaints, but they aren't the same as his. Dodson ends his review thus.
I do have a complaint, however. The book preaches to the converted. Its polemical tone can become wearying and may produce the unintended effect of nudging undecided readers in the wrong direction. Poorly disguising his contempt, Prothero's rhetoric is sometimes over the top, as when he refers to "hard working, dedicated, self-sacrificing biologists who spend years enduring harsh conditions in the field" in contrast to "creationists who sit in their comfortable homes and write drivel" (p 113). Please! The facts of paleontology stand on their own. They do not need to be undermined by rhetorical shenanigans.
Dodson seems to favor writing that strokes the creationists and/or the fence-sitters by the hair. I agree that Prothero's rhetoric is at times over the top, but the whole situation, the level of discourse between scientists and creationists, is already over the top. I personally find it relieving to hear Prothero vent his frustration, but I guess that's because I share it. I am part of the choir, I suppose you could say. However, I don't think there's much chance that Prothero's polemic tone is going to nudge anyone in the wrong direction (i.e. towards creationism), because the book - being detailed and technical and spanning almost 400 pages - is highly unlikely to be read by anyone who isn't extremely interested in (and on the side of) science in the first place. [Update: Turns out I am wrong about that - see Don's comment below.]

Also, the statement that Prothero's style of writing "may produce the unintended effect of nudging undecided readers in the wrong direction" really is pure guesswork. People may have anecdotal evidence that this is so (or not so), but as far as I know there aren't any studies that have examined this at all. (If someone can point me to such work, I'll be thankful and apologetic.)

Besides, if "[t]he facts of paleontology stand on their own," then what do we need the NCSE for?

My complaint with Prothero's book is his accommodationism. Of course, since the NCSE has chosen to bet that accommodating those who believe that the science that contradicts a literal reading of the Bible can be unified with being a Christian (or the same for other creationisms of other religions) is the best way of promoting the teaching of evolution in schools, they are not likely to publish reviews disagreeing with that position. Jerry Coyne would not likely be reviewing Prothero's or Miller's book on NCSE's website, for example.

I have previously tried to formulate my views on this matter. And a question for the Christians who believes in God and evolution at the same time: How is it that you choose what to take literally, and what to read as allegory? If you make up your own mind about it, then how do you know that you (or your clergyman) didn't make a mistake? If you discard some verses, then how do you know where to stop? I have asked a lot of people this, and no one has given an answer better than "it's obvious" or "from the context." Well, if it's obvious, then why is there so much disagreement between the denominations?

The answer is, evidently, that while there are some good teachings in the Bible (love your neighbor, the golden rule, etc.), in no way do these point to the existence of God, nor are they unique to the Bible. Which in turn means one can live a perfectly "Christian" life with Christian values without needing to ever the read bible, nor having to believe in any deity.

Related posts about the NCSE:
Why teach Intelligent Design?
10 minutes on Intelligent Design

Evolution highlights IV

Flatfish support Darwin's evolutionary theory, research claims
An examination of fossil flatfish revealed that the eyes moved gradually to the same side of the skull.

First Evolutionary Branching For Bilateral Animals Found
First evolutionary divergence within bilaterians.

Getting a leg up on whale and dolphin evolution
Phylogenetic analysis suggests that cetacean ancestors transitioned to water before becoming carnivorous but that the meat-eating diet developed while these ancestors could still walk on land.

Did comet crashes help spark Earth life?
Researchers fire bullets into metal containers with a liquid core to show that the rise in temperature in comets crashing on Earth would not destroy the amino acids inside the comets.

Mass extinction event spared Europe — mostly
When a meteor hit the Yucatan peninsula 65 million years ago, the effects were global, but not equally so. Europe was apparently less affected, and species diversity grew faster there in the years that followed. But, as we all know, the non-avian dinosaurs didn't make it anyway:
It wasn't enough to save the dinosaurs, though. The findings suggest there was no global inferno, but instead a blanket of debris that cast a dim pall over the planet.

Unable to access sunlight, plants that were critical sources of food quickly died. Even areas like western Europe, where the effects were less severe, the famine lasted long enough to wipe the big animals out.

The edge of atheism

If you're serious about learning about transitional fossils, then Daniel Prothero's, Evolution: What the Fossils Say and Why It Matters (2007), is the book to read. After reading it, the creationist claim made on a daily basis that there are no transitional fossils becomes utterly laughable. I highly recommend it.

In the last chapter on creationism, Prothero directs the reader to this page written by a geologist and former creationist, Glenn Morton. Morton stopped being a creationist when the young-earth creationists rejected his presentations of the geological data that points unequivocally to the Earth being much older than 10,000 years. I applaud his adherence to the data.

And yet, what happened in the end? Did he become an atheist? No. He read an accommodationist book, and that saved him from the curse of atheism:
And being through with creationism, I very nearly became through with Christianity. I was on the very verge of becoming an atheist. During that time, I re-read a book I had reviewed prior to its publication. It was Alan Hayward's Creation/Evolution. Even though I had reviewed it 1984 prior to its publication in 1985, I hadn't been ready for the views he expressed. He presented a wonderful Days of Proclamation view which pulled me back from the edge of atheism. Although I believe Alan applied it to the earth in an unworkable fashion, his view had the power to unite the data with the Scripture, if it was applied differently. That is what I have done with my views. Without that I would now be an atheist. There is much in Alan's book I agree with and much I disagree with but his book was very important in keeping me in the faith. While his book may not have changed the debate totally yet, it did change my life. [Emphasis added.]
Hilarious. Sad.

Kurzweil is off his rocker

"Within 25 years we will be able to do an Olympic sprint for 15 minutes without taking a breath, or go scuba-diving for four hours without oxygen."
These are the words of Ray Kurzweil, whom the Telegraph calls a scientist. I wouldn't go that far.

Here's another pearl:
"Nanotechnology will extend our mental capacities to such an extent we will be able to write books within minutes.
Look, I also believe that nanotechnology will result in many interesting and beneficial additions to our lives (if society doesn't crash sooner), but these things are a tad foolish. Okay, so if he turns out to be right in 25 years, then I'll have to say that I wasn't the big visionary. The unfairness is that he just has to see one of his far-fetched predictions come true, and he will be named a living oracle (presuming he is still alive at 86, of course, but then I know that Kurzeil is 100% certain of that).

Either way, his singularity is humbug. PZ Myers has a great critique of it from February: Singularity silly singularity. Read it!

To shoot or not to shoot

In the US, we are expecting H1N1 (“Swine Flu") vaccines to be available this fall. In the Skeptic magazine Harriet Hall, MD, exposes a bunch of fradulent claims about the effects of such a vaccine. Read Swine Flu Vaccine Fearmongering.

The vaccine will be offered to
  • Pregnant women
  • Household contacts and caregivers for children younger than 6 months of age
  • Healthcare and emergency medical services personnel
  • All people from 6 months through 24 years of age
  • Persons aged 25 through 64 years who have health conditions associated with higher risk of medical complications from influenza.
One claim I find particularly interesting is the one that doing something contrary to nature is bad.
Claim: [Joseph] Mercola says “Injecting organisms into your body to provoke immunity is contrary to nature.”

Fact: Nature kills people. Doing something contrary to nature is what medicine is all about. It’s a good thing.
Generally, whether our actions are contrary to nature or not is insufficient argument to determine whether we should carry them out or not. Death from disease is natural, yet we try to prevent it. The use of DDT in agriculture is unnatural, and we try to prevent it (c.f. Stockholm Convention).

The article ends with a really funny one:
[One] person pointed out that shots hurt and that alone should tell you something. “Yet you are willing to trust these people with your lives to make a vaccine that the Creator never intended the human body should need, and let them inject it into your body? You people are scary or insane!”
Shots hurt, and that should tell me... what? Love hurts. Diarrhea hurts. Physical therapy hurts. As for the “Creator" who created Loa loa, I really don't see how anything he supposedly did* could have any bearing on what we should do.


Loa loa in a human eyeball.

* As the most casual readers of this blog will know, I don't believe in any form of a creator (and yet I hate his actions intensely).

Evolution highlights III

Big dicks preferred
Get this: the researchers cut the genitalia of the mosquitofish males and found that among males of large body-size, females preferred gonopodia that weren't cut as short as others. For males of small body-size, no correlation was found. [1]

Why do females have horns?
Talking about ungulates (e.g. cattle, goats, deer, antelope - just to mention a few that actually have horns, as opposed to pigs and horses). Results: in large species, the horns are for defense against predators, and for the small species that have horns, they have them for intrasexual competition over territory or mates. [2]

Evolutionary biologist receives MacArthur 'genius' award
Beth Shapiro, 33, evolutionary biologist at Pennsylvania State University (lab page). She works on ancient DNA, and already has six publications in Science! For example, Flight of the Dodo (2002) - one page.

References:
1. Females prefer to associate with males with longer intromittent organs in mosquitofish
Andrew T. Kahn, Brian Mautz and Michael D. Jennions
Biology Letters published online before print September 15, 2009.
(intromittent = penetrating)

2. Evolution of weaponry in female bovids
Theodore Stankowich and Tim Caro
Proc. R. Soc. B published online before print September 16, 2009

Zoological nomenclature

When I first started learning Japanese, I was confused why rats and mice are referred to by the same name, nesumi. It is possible to qualify which one is meant, but this is generally not done. On the other hand, there are two species of ducks that go by completely different names, kamo (the mallard), and ahiru (domestic duck), but there is no common name for ducks.

At least, that is as far as I understand the meaning of the words, and I could be wrong. Nevetheless, it got me thinking.


Ahiru.


Kamo.

I was thinking that rats and mice are clearly different enough that they need to have different names, and that kamo and ahiru, while different species, clearly are both ducks (in fact, most domestic ducks are bred from mallards) . But... if we go to Wikipedia and check, then the result is that rats and mice are very closely related (same family, but different genera)

[When I was working in New York I often went to Peebler Point in Central Park. One year a lone domestic duck was trying to hang out with a group of mallards, but that didn't go so well. It was clearly the odd one out, being much larger and white, and the mallards were not very welcoming, though also not directly chasing the outsider away.]

Then I was asked why alligators and crocodiles have different names. (I should note that I am not a zoologist, so all information I have to share is amenable to correction.) My first thought was that they are not just different species, but probably different families of crocodilians, and I further had the hunch that most common names of animal groups in English describe families. But it turns out that there is a lot of variation. Incidentally, alligators belong to one genus, while all crocodiles is a family. The list below includes some of the most common names of animal groups that I could think of, and as can be seen, the names cover genera through superorders. While surprised at this range, I wasn't exactly expecting that the old names for the animals wold confirm to taxonomic nomenclature. This inconsistency probably has to do with
  • the closeness and utility of the animals to humans,
  • where we draw the lines between taxonomic clades, which partly has something to do with morphology and species diversity, and
  • (least interesting) my particular choice of what I consider "common animal groups."
Does it really matter how we group the animals semantically? No, I suppose it doesn't, even though it would be terribly nice if we could stop using paraphyletic terms, such as "monkey" (see below). And speaking of monkeys, I would also really appreciate if Zoo visitors would stop referring to apes and lemurs as monkeys. Not that there is anything wrong with being a monkey, 'cause there's not, but they just aren't monkeys, is all.

Unless noted otherwise, the groups are Monophyletic, meaning that all the species in the group share a common ancestor that they do not share with species that does not go by the listed name (e.g. all ants species are members of the family Formicidae, and all member of the Formicidae are ants).

Pig - Genus (Sus)
Mouse - Genus (Mus)
Rat - Genus (Rattus)
Alligator - Genus (Alligator)
Crocodile - Family (Crocodylidae)
Horse - Family (Equidae)
Dog - Family (Canidae)
Cat - Family (Felidae)
Duck- Family (Anatidae1)
Eagle - Family (Accipitridae)
Bear - Family (Ursidae)
Ant - Family (Formicidae)
Ape - Superfamily (Hominoidea)
Bee - Superfamily (Apoidea)
Monkey2 - Superfamily (Cercopithecoidea)
Shrimp - Infraorder (Caridea)
Dinosaur - Suborder (Dinosauria)
Snake - Suborder (Serpentes)
Parrot - Order (Psittaciformes)
Bat - Order (Chiroptera)
Fly - Order (Diptera)
Whale3 - Order (Cetacea)
Shark - Superorder (Selachimorpha)

1 Anatidae is paraphyletic (i.e. not monophyletic) and includes swans and geese.
2 "Monkey" covers both old world (superfamily Cercopithecoidea) and new world (pavorder Platyrrhini) monkeys, and is a paraphyletic group.
3 Includes dolphins and porpoises.

Bonus fact: Here's a mallard without webbed feet. It hates water. I can imagine why.

The Quaternary now includes the Gelasian

They changed the beginning of the Quaternary! And here I thought the eras, periods, and epochs were written in stone.
In June 2009, the Executive Committee of the International Union of Geological Sciences (IUGS) formally ratified a proposal by the International Commission on Stratigraphy to lower the base of the Quaternary System/Period to the Global Stratotype Section and Point (GSSP) of the Gelasian Stage/Age at Monte San Nicola, Sicily, Italy. The Gelasian until then had been the uppermost stage of the Pliocene Series/Epoch. The base of the Gelasian corresponds to Marine Isotope Stage 103, and has an astronomically tuned age of 2.58 Ma.
← The quaternary period formerly started at 1.8 million years ago, but it has now been extended to include the Gelasian stage going back to 2.58 mya.


The vote was not unanimous; a significant (by the 5% level) of the 18 members of the International Commission on Stratigraphy (ICS) did not concur.

The results of the voting were overwhelmingly in favour of the SQS recommendations. In the final ballot, 89% of the ICS voting membership supported the Quaternary case. In May 2009, the ICS forwarded the results to the IUGS Executive Committee, and on 29 June 2009 that body formally ratified the SQS proposal. This brings closure to a debate that has run for more than six decades and, from a Quaternary perspective at least, the outcome is entirely satisfactory. In addition, with the imposition of the 10-year moratorium, this matter cannot be revisited until 2019 at the earliest.
The begging question is, of course, does it matter? Will this change anything we know? I'm fairly certain it won't, but that it's all just about agreeing on what to call what - even though this of course has to reflect what we know.

Reference:
Formal ratification of the Quaternary System/Period and the Pleistocene Series/Epoch with a base at 2.58 Ma
Philip L. Gibbard, Martin J. Head, Michael J. C. Walker, the Subcommission on Quaternary Stratigraph
Journal of Quaternary Science (2009)

Will the religious out-breed the atheists?

Tom Rees has an interesting post about the effect of religiosity on fertility, Why do atheists have fewer children? Here's my comment to his post:
And modern people have retained a capacity for atheism, which suggests some competing reproductive benefit.
I would be very skeptical of the idea that a 'capacity for atheism' must have a reproductive benefit. You basically saying that just because there are atheists around, this capacity must be selected for. That does not need to be so. Besides, if the numbers are really true, and assuming religious belief is heritable, then it is hard to argue that a capacity for atheism increases fitness.

However, I would also doubt that religiosity is heritable enough that it can overcome 'cultural evolution,' meaning that even though religious people have more children, atheism might still grow when the children are influenced by factors that cause them to lose their faith (education, in the broadest sense).
That post let me to another on the same subject, The Reproductive Advantages of Religiosity, where I posted this comment:
For religiosity to be adaptive, it is not enough to show that religious people have more children. Rates at which people change their religiosity must be incorporated. Do you have these data?

For example, assuming that all children born of religious parents become religious themselves, it is very hard to explain that there are any atheists around at all.
But from an evolutionary as well as philosophic perspective, it may seem rather odd to try to defeat nature with naturalistic arguments."
Why? Nature can inform us, but that does not mean we should bow to it. This is the same thing with many other aspects of human life. It is "natural" to get diseases and die before the age of thirty, and yet we fight it.

Lastly, I gather that when you say that there is no consensus on the meaning of the biological terms you mention (adaptation, etc.) that you mean among social scientists like yourself? Evolutionary biologists have strict definitions of the terms, of course.
Basically, I think people are over-eager and extrapolate wildly from the data they have, which is not enough to draw the conclusions that they would like to make. Crucially, religiosity is a meme, not a gene. How many children you have might be influenced by how often you go to church/mosque/temple/shrine, but as any Christian missionary knows very well, conversion* happens on a daily basis, and so the heritability of religiosity is not perfect (H2<1).

* Both ways, of course. And I suspect that in the developed world the trend is away from religiosity - in the US there is reason to conclude that atheism is "on the rise."

Evolution highlights II

The Greatest Dying - A fate worse than global warming.
Jerry Coyne and Hopi Hoekstra explain in The New Republic how the current mass extinction is a far worse threat than global warming to human and other life on earth. (2007)

'Evolutionary forecasting' for drug resistance
Biochemists at Rice University are trying to predict how pathogens will acquire drug resistance by performing evolutionary experiments on them. (Today)

Animals Cool Down at Six Flags
"Odin, a white Bengal tiger, swims with his eyes wide open as he dives under water for a piece of meat at Odin's Temple of the Tiger exhibit at Six Flags Discovery Kingdom, Vallejo, California, on July 23, 2009. In the wild, all of the big cat species will will dive under water to get its prey or just cool off."

A message from Mr. West

Kanye West likes Beyonce's website better. Gotta try it.

Carnival of Evolution teaser

October 1st important events in history:

1050 years ago, Edgar the Peaceable becomes king of all England (959).
820 years ago, Gerard de Ridefort, grandmaster of the Knights Templar since 1184, is killed in the Siege of Acre (1189).
180 years ago, South African College is founded in Cape Town, South Africa (1829).
140 years ago, Austria issues the world's first postcards (1869).
70 years ago, after a one-month Siege of Warsaw, hostile forces entered the city (1939).
60 years ago, the People's Republic of China is declared by Mao Zedong (1949).
40 years ago, the Concorde supersonic transport plane breaks the sound barrier for the first time (1969).
30 years ago, the United States returns sovereignty of the Panama canal to Panama (1979).
20 years ago, Denmark establishes the World's first legal modern same-sex civil union called "registered partnership" (1989).
0 years ago, Carnival of Evolution, the 16th edition, will air on Pleiotropy (2009).

Paper finally submitted to PLoS

I finally submitted my manuscript to PLoS Computational Biology. Woot! Can't quite believe the rigidity of the submission process, though. Lots of HTML editing of figure captions in order for the paper to be posted online. The layout rules for the manuscript are also burdensome, and, including a submission to the e-Print archive, it has taken most of today to get it all done. I'll be pretty upset if the editors decide not to send it out for review after all that trouble.

The paper, Impact of Epistasis on Evolutionary Adaptation, will be viewable at the arXiv shortly, I trust...


Update 9/20-09:
It's now available on at the arXiv.

Obama calls Kanye West 'Jackass'

Listen to it right here. Then take the poll below and vote 'Way to go!'
The audio was recorded just before Obama went on camera to do an interview with CNBC. Before the interview began, Obama -- referring to Kanye's antics on stage -- said "I thought that was really inappropriate," then adding, "He's a jackass."
Obama on Kanye...
Way to go! 93%
Inappropriate 7%
Total Votes: 456,550

P.S. I just killed a fly in mid-flight. It was bugging the hell out of me.

The rare footed snake from China

A snake with a rare atavism was discovered (and clubbed to death) in a Chinese bedroom. It had a single foot.



As freaky as this is, an atavism - the occurrence of an ancestral trait otherwise lost in the extant species - is good evidence for evolution. Given the right mutation(s), an organism may develop a trait as it was in all the ancestors of the species. There are many examples of this, such as humans with tails.



So what caused this? Contrary to what the snake expert on the site said, an autopsy won't reveal the cause. For that the snake's genome has to be sequenced. Was it a mutation in the germ-line (either egg or sperm), or a somatic mutation during early development? The fact that the snake only had one leg suggest that it would be somatic, or it would most likely have had two. (My youngest son has two different eye-colors, and no doubt that is caused by a somatic mutation.) What kind of mutation (single nucleotide, or a larger scale event)? And note, that if it is a somatic mutation, offspring of this individual would not have had legs. Shame that. I'm sure lots of people would fancy havinga rare legged snake, for a pet or for dinner.


Update 9/16/09:
Other good hypotheses have surfaced. Ironically, PZ Myers is guessing that pleiotropy is to blame (the irony being that I should have thought of that), by way of some gene(s) that control limb development also have other functions, and that constraint then prevented the gene(s) from being destroyed. Instead it could be silenced specifically for limb development, and it is this repressor that PZ guesses has been suppressed during early development by an environmental factor, leading to activation of the genes that make the limb. Another hypothesis is that the whole thing is a photoshop hoax, and yet another that it is the leg of the snake's last meal protruding through the skin. I highly doubt this last idea, seeing that the limb and digits are very well defined, which seems unlikely if the skin belongs to the snake.

Reform the grant application process

The way research grants are evaluated and awarded makes bureaucrats out of scientist.

That's the bottom line as presented in a perspective article in PLoS Biology.
Real Lives and White Lies in the Funding of Scientific Research:
The granting system turns young scientists into bureaucrats and then betrays them

Here's the cause of the problem (wrong selection pressure):
The peculiar demands of our granting system have favoured an upper class of skilled scientists who know how to raise money for a big group [3]. They have mastered a glass bead game that rewards not only quality and honesty, but also salesmanship and networking. A large group is the secret because applications are currently judged in a way that makes it almost immaterial how many of that group fail, so long as two or three do well. Data from these successful underlings can be cleverly packaged to produce a flow of papers—essential to generate an overlapping portfolio of grants to avoid gaps in funding.
And here's the consequence (better grant-writers, less innovative research):
Thus, large groups can appear effective even when they are neither efficient nor innovative. Also, large groups breed a surplus of PhD students and postdocs that flood the market; many boost the careers of their supervisors while their own plans to continue in research are doomed from the outset. The system also helps larger groups outcompete smaller groups, like those headed by younger scientists such as K. It is no wonder that the average age of grant recipients continues to rise [4]. Even worse, sustained success is most likely when risky and original topics are avoided and projects tailored to fit prevailing fashions—a fact that sticks a knife into the back of true research [5]. As Sydney Brenner has said, “Innovation comes only from an assault on the unknown” [6].
And, finally, the solution:
Drastic simplification of this grant-writing process would help scientists return to the business of doing science. Grant applications should be much shorter, and if so, scientists would spend less time writing them and less time reviewing other applications.

(...)

The solution is to allow, say, only three to five of the best papers of the group from over the previous five years to be offered for assessment (as Howard Hughes Medical Institute already do in the US). The evaluation of these papers should be corrected for the size of the group, i.e., productivity would be rated per person, not per group. If these reforms were enacted, the pressure to rush out many papers would be replaced by pressure to complete projects that report stories of value and present them well.
Asses grant applications on previous work, rather than future work. Previous work documents that the P.I. can get research done, and what the quality of that research is. This would also, crucially, free up time for researchers to do research, rather than writing grant applications.

Seems like a no-brainer to me.

Wilson + Watson

E. O. Wilson and James Watson met at Harvard last week to discuss enemies in science. They once were, but now appreciate that fact.

Memorable quote:
Watson believes that scientists ought to push themselves to be stars, making at least one great achievement, going for the gold.

"Why should scientists be stars?" Krulwich prods.

Watson answers without missing a beat. "It's better to be bright than dim."
Ha! Not bad for the old guy (which in no way means I concur with any of his views about intelligence...).

Mr. Pink on solving complex problems

Totally share-worthy talk at TED: Dan Pink on the surprising science of motivation.

Bottom line: Rewards don't work for problems where thinking out of the box is part of the solution. Science knows it, but apparently business managers don't. Doing it for money does not get the job done faster, except for very straight-forward tasks.

Mr. Pink is basically saying that when complex tasks needs to be solved, don't set monetary incentives. Sounds very much like grad-school to me.

Evolution highlights

Here's a few recommendations for short reads about evolution:

Study examines the evolutionary fate of 'useless' traits, about relaxed selection, costly traits, and loss of function.

Scientists Use MicroRNAs To Track Evolutionary History For First Time, about how microRNA can improve our knowledge of phylogenetic relationships.

Ancient Fossils Shed New Light on Evolution of Humans, about how 1.8 million year old fossils from Georgia might change our understanding of the evolution of Homo erectus (i.e. not Homo sapiens).

Evolutionary constraints permeate large metabolic networks, about an approach showing that metabolic pathways are highly constrained. (This article is written by Andreas Wagner, who does great science, but is not my favorite science-writer.)

Ebert on creationists

I await 'Creation' not with anticipation, for as Roger Ebert predicts, those who admire Darwin are likely to be disappointed. Read Ebert's non-review.

Ebert muses over what caused Darwin to delay publication of The Origin, mentioning the possible theological implications of his theory. Then he says,
Did it occur to Darwin or his wife that nothing in his ideas precluded the existence of God? Today, no major religion finds conflict between God and the theory of evolution. The majority of Christians can live with both ideas; religious opposition to Darwin is limited primarily to a fundamentalist minority of American Christians.
Beg your pardon?

Oh sure, nothing about evolution precludes the existence of God, unless one has specific ideas about what 'God' means. And I think we can all agree to be fairly certain that to Charles and Emma it meant Yahweh - the one who created the heavens and humans in their present form, etc. etc. The creation myth that goes with that interpretation of the Bible is too in direct conflict with evolutionary biology. It does not preclude the existence of some god, but it does preclude that God did the things that Emma and (earlier) Darwin most likely attributed to God.

No major religion finds conflict between evolution and God?! Ebert, do you spend all your time inside a theological seminary? Because that's the only place where Christians are 100% comfortable with evolution, and those Christian professors of theology are really atheists. (If you don't believe me go to a talk about 'Ground of Being' and other such stuff, or read Tillich.)

Baptists, Evangelicals, Mormons, and Pentecostals are definitely not very comfortable with evolution, and many lutherans are likely to profess some sort of ID preference (whether they know of the discotute or not). At least, none of these denominations are deists, and evolution, astronomy, geophysics, nuclear physics, and geology together pretty much thwart anything but strict deism. If it wasn't for cognitive dissonance the heads of most of 'the majority of Christians' would be seen exploding on a daily basis.

Perhaps we can designate those American Christians who oppose evolution as 'fundamentalists', but then we would have to include more than what can be called a minority. Or vice versa.

Also, have Ebert heard what followers of that other major religion of the world, Islam, think about evolution? Muslims are hardcore creationists, and the vast majority are totally unable to "live with both ideas."

But, while I think Ebert is wholly uninformed on this matter, he ends with a good point:
Meanwhile, have you wondered why, if the Mayans were able to pinpoint the end of time in 2012, they were unable to see that their own civilization would collapse in the ninth century?
Indeed.

Math-challenged reverend hijacks plane with cans of hommus

Josmar Flores tried to hijack a plane in Mexico yesterday.
“He is a reverend,” Garcia Luna said. “He said it was a divine revelation that drove him to this action.”
What a lunatic! Praise the Lord that this is the only case ever where divine revelation has driven anyone to commit dangerous acts like this one.
The hijacker was wearing jeans and a white shirt when he was paraded in front of reporters after his arrest and appeared to be smiling and chewing gum. He took action because yesterday’s date, Sept. 9, 2009, represented an upside-down 666.
I guess that's why nothing like this happened on June 6th, 2006, because that's 999 upside-down, and that doesn't mean anything.

The story gets better:
Flores is a born-again Christian who had been on the verge of suicide. He spent time in jail in Santa Cruz, Bolivia, for armed robbery, Garcia Luna said.

Flores threatened the crew from Aeromexico flight 576 with a fake bomb made from a red light affixed to three cans of hummus about an hour after takeoff from Cancun, Garcia Luna said. The pilot told the authorities and later acted as interlocutor between Flores and officials once the plane landed in Mexico City at about 1:40 p.m. local time.
Three cans of hommus. As the saying goes, you can't make this stuff up. Soon they'll ban food on planes altogether.

The bat-eating tits

Others have already blogged it, so I'm writing this just to make absolutely sure that no one misses the bat-eating tits (with footage). They almost make my heart swell with pride.

Erasmus Darwin for some credit

A correspondence in the newest edition of Nature, quote in full:
Nature 461, 167 (10 September 2009) | doi:10.1038/461167b; Published online 9 September 2009

Evolution pioneers: celebrating Lamarck at 200, Darwin 215

William E. Friedman1
1. Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
Email: ned@colorado.edu


Sir

I take issue with the contention that Erasmus Darwin, the grandfather of Charles, tackled evolution only in poetic terms, as implied by Dan Graur and colleagues in their insightful Book Review ('In retrospect: Lamarck's treatise at 200' Nature 460, 688–689; 2009).

Erasmus Darwin's most important contributions to evolutionary thought will be found in the very unpoetic prose of the first volume of his major medical and zoological treatise, Zoonomia, published in 1794.

Here, notably in Section 39, are discussions of deep time and the descent of all life from a single ancestor, bauplan homology among vertebrates, the analogy of artificial selection as a means of understanding descent with modification, and a brief but clear enunciation of the process of sexual selection.

One need only to look at the backlash against Erasmus Darwin's evolutionary ideas, in the savage political cartoons of James Gillray in 1798 and of others, to understand that — years before Lamarck made his contributions to evolutionary thought — Erasmus Darwin was triggering strong reactions for promoting a transformist view of biodiversity.

This year is justly celebrating the history-altering contributions of Charles Darwin. But it is equally important to take stock of the critical intellectual steps before 1859 that made scientific and social acceptance of evolution possible.

Besides Erasmus Darwin and Jean Baptiste Lamarck, a host of other influential evolutionists, including Etienne Geoffroy Saint-Hilaire, Robert Chambers, Baden Powell, Herbert Spencer and Alfred Russel Wallace, deserve to be recognized (as well as read) for having laid a path to a modern view of descent with modification.
(Emphasis added.)

This is most fascinating information. I had no idea that Erasmus Darwin had written about so many of the concepts that Charles are famous for. I just checked out Zoonomia on Amazon. It can be downloaded to the Kindle for free (as can many other books). However, next best to that, my library has a free electronic version that I have just accessed online. Yeah!

On the second page of that is a humorous erratum:


ERRATA.
THE reader will pleafe to excufe en error of the corrector of the prefs - the paging from 154 - 171 is omitted, although the fubftance and fubject of the work is correctly continued - and he will pleafe to alter one figure with his pen that follows 235, by making it 236, &c. to page 250.

The Bookbinder will pleafe to obferve, that there is no fignature M, and that the book is perfect wanting it.
I have noticed before that old s's looks like f's, but in this case there are also properly looking s's, such as in 'prefs.'

Also, you gotta love the request for the reader to add page-numbers by pen. I seriously think I'll do the same with my first book.

Does that last sentence mean that, apart from the missing signature M, the book is perfect?

"Pundit" will become a derogatory term

FOX News is notorious, I know, for its "fair and balanced" approach to keeping viewers entertained. I don't watch news on TV at all, though, but get all updates from the web. Still, I don't particularly frequent FOXNews.com either. However, on Google news one item caught my eye: Why the Obama Administration Will Implode In Weeks, by Kevin McCullough, a pundit who "was the first pundit to predict Obama's presidency (back in December 2006)." That would be except for my friend, Ed, who predicted in way back in 2004 when Obama was elected senator of Illinois. Ed is not a pundit, but still. Anyone else who can make that claim?

Of course, now that he's pals with Nostradamus, his duty as a political pundit is to share his prediction for Obama's precidency. As he says "it behooves me to tell you the course I believe the next few weeks will take."

And as the title says, the Obama administration is going to implode with the the next six to eight weeks (published September 1st). Why? He lists the reasons:
  1. Health Care's Long and Painful Death
  2. Cap-and-Trade Will Be the Largest Tax Increase in American History
  3. Unemployment Will Remain
  4. Obama's Integrity Has Been Tarnished in August
  5. A $3 Trillion Dollar Budget
  6. A Coming Middle Class Tax Hike
Problems, indeed, should any of it become reality. But, "implode?" What does that even mean? That all confidence in this administration will have evaporated in five to seven weeks from now? That Obama will be on his knees begging McCain and Palin to take over the White house?

I, on the other hand, hereby make the prediction that the word "pundit" is going to become a derogatory term within the next, say, 4 to 5 months. I could be wrong, and pundits everywhere could become the heros they deserve to be for the expert advice they give on their radio shows syndicated on 197 stations across the country and in fair and balanced columns on FOX News.
But I'm not holding my breath, and I'd advise you against it as well.

Soliciting posts for Carnival of Evolution

Next month, on the first of October, I will be hosting Carnival of Evolution here on Pleiotropy, and I predict a number of great posts about evolution will be submitted. However, I don't expect especially many to be submitted, and I would like to change that.

You are hereby strongly recommended sending at least one, but preferably two, posts that you have written on any subject that relates to the study of evolutionary biology. Posts about evolution might include
  • reports on peer reviewed papers,
  • experiences teaching evolution,
  • debunking of creationism,
  • evolution related op-eds,
  • book reviews,
and anything else that you can think of that deals with evolution in any way.

The previous 15 carnivals averaged 13 and a third posts per carnival per edition, with a standard deviation of 4.8, with a range from 5 to 24. It's time to top that. There is more evolution going on in the blogosphere, and we need to hear about it on CoE.

If I don't see my inbox filling up with submissions really soon, I will probably solicit posts directly from people who I know blog about evolution.

Submit your evolution posts at Blog Carnival or email me directly at bjorn@bjornostman.com.

Babu's back belching bible and biology

Sorry to say, but Babu Ranganathan (B.A. in Bible and Biology from Bob Jones) is at it again, spewing forth utter nonsense about molecular biology, evolution, and abiogenesis. In a short article, DNA by chance impossible, he puts forward some conjectures that he has dealt with many times before.

I had at first written a snarky rebuttal, but deleted it because I couldn't figure out what the hell the point would be. Babu has written this very thing so many times, and he is both not too well educated about biology, and married to a Christian creationist ideology that he must make the facts fit. Just go read the darned thing, and then ask yourself how it is that he knows that DNA could never have originated by chance alone. What does it mean, in Babu's interpretation, that something came about by 'chance'? Then ask yourself if that is what serious scientists actually posit about the origin of DNA.

He does end the article by a statement that I have not seen the likes of before:
Both sides of the evolution/intelligent design controversy should have the opportunity to present their scientific arguments to students. No one is being forced to believe in God, so there is no real violation of separation of church and state.
No one is being forced to believe in God... so we can say anything we want to anyone anywhere? Tell elementary school students that evolution is wrong and creationism is right, and that if they don't believe that, they will end up in Hell. As long as you don't force them to believe it, this is not separation of church and state? Then what does this word 'force' really mean? That you enter their brains and force the neurons to fire in a manner that makes the brain believe in creationism?

What the hell is the point of these inane articles? Is this really what he does for a living? How does that work?

Innocent man executed

Liveblogging a reading* of a New Yorker article about a man who was exceuted in Texas for the murders of his own children, Trial by Fire. Was he innocent?

(* For the record, I've liveblogged reading an article once before, and I take full responsibility for inventing the procedure.)

Willingham's house burned one morning in 1991 or 1992, and the firemen found him outside, while his three toddlers had died from smoke inhalation. Two fire investigators examined the house after the fire was put out, and found evidence that the fire had been started by a human dousing the children's room with a flammable liquid. Other evidence also pointed to arson, and Willingham was the only suspect. He was convicted and sentence to death. He never admitted of any wrongdoing.

Interesting fact which I have often wondered about: Why is it more expensive to execute someone than to keep them in prison for the rest of their life? Sounds like it shouldn't be true.
because of the expense of litigation and the appeals process, it costs, on average, $2.3 million to execute a prisoner in Texas—about three times the cost of incarcerating someone for forty years.
Willingham couldn't afford a lawyer, so he had one assigned. I often wonder if those lawyers that are assigned are the bottom-of-the-class kind of lawyers, of what the deal are with those.

Part of the evidence against Willingham was that a fellow inmate said that Willingham told him that he took “some kind of lighter fluid, squirting [it] around the walls and the floor, and set a fire.”

Willingham was offered a deal to serve a life sentence rather than getting the death penalty if he would plead guilty. He declined the offer.

Here's an odd fact:
Willingham’s refusal to accept the deal confirmed the view of the prosecution, and even that of his defense lawyers, that he was an unrepentant killer.
Then, either way the prosecutor and the defense lawyers would conclude that he was a killer. I'm not saying Willingham was innocent, but this is like throwing a woman into the river and saying she' a witch if she floats. Apparently no one could understand why he would not plead guilty, but I think I can. Perhaps he'd rather die than serving a life sentence and admitting something he did not do. And, if he did do it, perhaps he didn't really want to live any longer.

The trial took only two days.

Years later a woman, Gilbert, corresponds with and visits Willingham in jail. She becomes interested in the case and reads the trial records. She finds that several witnesses were inconsistent. For example,
An even starker shift occurred with Father Monaghan’s testimony. In his first statement, he had depicted Willingham as a devastated father who had to be repeatedly restrained from risking his life. Yet, as investigators were preparing to arrest Willingham, he concluded that Willingham had been too emotional (“He seemed to have the type of distress that a woman who had given birth would have upon seeing her children die”); and he expressed a “gut feeling” that Willingham had “something to do with the setting of the fire.”

Dozens of studies have shown that witnesses’ memories of events often change when they are supplied with new contextual information. Itiel Dror, a cognitive psychologist who has done extensive research on eyewitness and expert testimony in criminal investigations, told me, “The mind is not a passive machine. Once you believe in something—once you expect something—it changes the way you perceive information and the way your memory recalls it.”
Interesting facts, those.

So this woman, Gilbert, talks to a lot of people who knew Willingham, and some of them weren't so sure that he was guilty. Some said they "could not imagine him killing his children." At this point I feel like saying, though, that I regard this kind of statement as not meaning anything much, really. I don't think it plausible that of all the guilty criminals it isn't possible to find someone they knew who would say such a thing. Most of the time people who commit crimes are probably behaving themselves very well, not showing signs of sociopathy or any such thing.
When Stacy [Willingham's wife and mother of the three children] was on the stand, Jackson [the prosecutor] grilled her about the “significance” of Willingham’s “very large tattoo of a skull, encircled by some kind of a serpent.”
“It’s just a tattoo,” Stacy responded.
“He just likes skulls and snakes. Is that what you’re saying?”
“No. He just had—he got a tattoo on him.”
The prosecution cited such evidence in asserting that Willingham fit the profile of a sociopath
Think about that before you get your first tattoo. And don't listen to heavy metal:
At one point, Jackson showed Gregory Exhibit No. 60—a photograph of an Iron Maiden poster that had hung in Willingham’s house—and asked the psychologist to interpret it. “This one is a picture of a skull, with a fist being punched through the skull,” Gregory said; the image displayed “violence” and “death.”
Gilbert finds that more evidence is bogus, particularly the testimony by the fellow inmate, who looks like he lied about that whole confession-in-prison thing.

Another wow-fact:
During America’s Colonial period, dozens of crimes were punishable by death, including horse thievery, blasphemy, “man-stealing,” and highway robbery.
Even blasphemy? One more of those:
In 1868, John Stuart Mill made one of the most eloquent defenses of capital punishment, arguing that executing a murderer did not display a wanton disregard for life but, rather, proof of its value. “We show, on the contrary, most emphatically our regard for it by the adoption of a rule that he who violates that right in another forfeits it for himself,” he said. For Mill, there was one counterargument that carried weight—“that if by an error of justice an innocent person is put to death, the mistake can never be corrected.”
But it happens:
In 1993, Ruben Cantu was executed in Texas for fatally shooting a man during a robbery. Years later, a second victim, who survived the shooting, told the Houston Chronicle that he had been pressured by police to identify Cantu as the gunman, even though he believed Cantu to be innocent. Sam Millsap, the district attorney in the case, who had once supported capital punishment (“I’m no wild-eyed, pointy-headed liberal”), said that he was disturbed by the thought that he had made a mistake.
Liberals are pointy-headed? What does that mean? But true, I have read elsewhere that one of the traits of conservatives is that they don't have a huge problem with some innocent people suffering when it's for the sake of the whole community; they can live fine with social injustice. Liberals not so much. Me, not a chance. Scalia just denies that it has ever happened:
Supreme Court Justice Antonin Scalia, in 2006, voted with a majority to uphold the death penalty in a Kansas case. In his opinion, Scalia declared that, in the modern judicial system, there has not been “a single case—not one—in which it is clear that a person was executed for a crime he did not commit. If such an event had occurred in recent years, we would not have to hunt for it; the innocent’s name would be shouted from the rooftops.”

• • • • • • •

But, ladies and gentlemen, the really phenomenal part of this story in the New Yorker comes in the end (it's an article of over 16 thousand words).

It turns out that the evidence that the fire was lit by a human was all bogus. Bogus science. The two investigators didn't really know what they were talking about, and they made the usual assumptions about what causes certain tell-tale signs, and they turned out to be wrong. The science didn't hold up, and when a third expert, Hurst, examined the evidence only weeks before Willingham was to be executed, he found that all the signs of arson really pointed to “flashover”—the point at which radiant heat causes a fire in a room to become a room on fire.

But Hurst was too late.
The warden told Willingham that it was time. Willingham, refusing to assist the process, lay down; he was carried into a chamber eight feet wide and ten feet long. The walls were painted green, and in the center of the room, where an electric chair used to be, was a sheeted gurney. Several guards strapped Willingham down with leather belts, snapping buckles across his arms and legs and chest. A medical team then inserted intravenous tubes into his arms. Each official had a separate role in the process, so that no one person felt responsible for taking a life.
(Emphasis added.)
After his death, his parents were allowed to touch his face for the first time in more than a decade. Later, at Willingham’s request, they cremated his body and secretly spread some of his ashes over his children’s graves. He had told his parents, “Please don’t ever stop fighting to vindicate me.”
Remember Scalia's claim?
There is a chance, however, that Texas could become the first state to acknowledge officially that, since the advent of the modern judicial system, it had carried out the “execution of a legally and factually innocent person.”
Suck on that, Scalia!

Abolish the death penalty now!

Recommended reading: Conservapedia

The exchange of letters between Rich Lenski (of the famous E. coli experiments) and Andy Schlafly (founder of Conservapedia) came up in a lab meeting today.

I just read the whole thing again, and highly recommend this thoroughly enjoyable read for those who didn't see it back in June, 2008: Conservapedia:Lenski dialog.

Also check out the Conservapedia Commandments:

4. When referencing dates based on the approximate birth of Jesus, give appropriate credit for the basis of the date (B.C. or A.D.). "BCE" and "CE" are unacceptable substitutes because they deny the historical basis. See CE.

Carnival of Evolution #15

Carnival of Evolution 15 just went up at Southern Fried Science, from where I'll highlight this post by Satya where she asks this question:
The Rexes and Spots of the world have been man’s best friend for 15,000 years. But when and where did humans begin domesticating these furry companions?
I'd like to argue, though, that perhaps it wasn't really humans that domesticated dogs, but rather the other way around. Seriously.

Anyhow, the paper that the post is about is from Carlos Bustamante's lab and their collaborators, and they call into question the hypothesis of an East Asian origin for dog domestication, which could mean that when humans trotted out of Africa, they did it with dogs at their sides. One could then wonder whether it was the dogs who followed the humans, or the other way around...

Looking forward to Dawkins' newest book

The prose of Richard Dawkins is getting stronger. He newest book, The Greatest Show On Earth, will be a really reasonable read if it's as good as this appetizer from last week:
Evolution is a fact. Beyond reasonable doubt, beyond serious doubt, beyond sane, informed, intelligent doubt, beyond doubt evolution is a fact. The evidence for evolution is at least as strong as the evidence for the Holocaust, even allowing for eye witnesses to the Holocaust. It is the plain truth that we are cousins of chimpanzees, somewhat more distant cousins of monkeys, more distant cousins still of aardvarks and manatees, yet more distant cousins of bananas and turnips . . . continue the list as long as desired. That didn’t have to be true. It is not self-evidently, tautologically, obviously true, and there was a time when most people, even educated people, thought it wasn’t. It didn’t have to be true, but it is. We know this because a rising flood of evidence supports it. Evolution is a fact, and [my] book will demonstrate it. No reputable scientist disputes it, and no unbiased reader will close the book doubting it.
I hasten to say that while I agree with Dawkins that the theory of evolution is such a well tested model of what happens to living things on Earth, I'll say that doubt is to be cherished. It is with doubt in hand that any theory is understood, always being questioned at every turn along the way. As a researcher, there is no reasonable doubt left that evolution has, is, and will continue to occur, but both the fine and the coarse details are still diligently worked on, and doubt is a prerequisite of skepticism, and skepticism is the sine qua non of any scientist.