McWhorter + Behe on Bloggingheads.tv

Oh ....! John McWhorter really made a fool of himself talking to Michael Behe. He think Behe nailed it in Darwin's Black Box, and has a big problem with random mutations being responsible for skunks and okapis, etc. I recommend either sticking to linguistics or taking a few courses on evolution.

No wonder he asked the video to be taken down. No such luck, though: On Uncommon Descent, of course. They are loving it.

Swedish newspaper sued

The Swedish newspaper that published an article by a freelance journalist claiming that Israeli troops harvested organs from Palestinians, is being sued. See previous post about the freedom of the press.

Behind the suit is an Israeli lawyer from New York:

Attorney Guy Ophir filed a $7.5 million libel suit in New York on Tuesday against Aftonbladet, the Swedish tabloid that published the report Aug. 17. Ophir said the article's allegations were anti-Semitic and amounted to a "racist blood libel" against Jews.

The article as well as Aftonbladet's journalistic methods have been heavily criticized in Sweden, but the right to publish the article has been unanimously defended.

"Aftonbladet was within its rights to publish the article, and neither the Chancellor of Justice, nor the Israeli government, nor the Swedish ambassador has the right to interfere with that decision," wrote the editor-in-chief of [Expressen's, Aftonbladet's major tabloid rival] culture section, Björn Wiman.

Project Steve is going well

If you've never heard about Project Steve, then amuse yourself by catching up.

The NCSE launched Project Steve to mock the Dissent From Darwinism and related projects to amass signatures of scientists who are "skeptical about evolution."

Over 1,100 scientists named Steve has signed the document.

Among the 1101 current signatories to Project Steve are 100% of eligible Nobel laureates (Steven Weinberg and Steven Chu), 100% of eligible members of President Obama's Cabinet (Steven Chu, the Secretary of Energy), at least ten members of the National Academy of Sciences, the authors of widely used textbooks such as Molecular Biology of the Gene, Psychology: An Evolutionary Approach, and Introduction to Organic Geochemistry, and the authors of popular science books such as A Brief History of Time, Why We Age, and Darwin's Ghost. When last surveyed in February 2006, 54% of the signatories work in the biological sciences proper; 61% work in related fields in the life sciences.

I just might change my name to Steffen so I can sign it too.

Adaptive depression?

Sorry to be so blunt, but here's what I consider to be one of those crazy evolutionary stories of this and that human trait being adaptive: Depression.

Being depressed somehow increases your fitness (your long-term rate of reproduction)?

In an article in Scientific American, Depression's Evolutionary Roots, it is argued that depression is adaptive because it makes us think harder. Think about that for a moment.

Depression seems to pose an evolutionary paradox. Research in the US and other countries estimates that between 30 to 50 percent of people have met current psychiatric diagnostic criteria for major depressive disorder sometime in their lives. But the brain plays crucial roles in promoting survival and reproduction, so the pressures of evolution should have left our brains resistant to such high rates of malfunction.

Perhaps I think the current psychiatric criteria for major depressive disorders are rather liberal, but that's a different story. I'll accept that many people experience being really, really sad at some point in their lives.

Here's the link between depression and thinking:

One reason to suspect that depression is an adaptation, not a malfunction, comes from research into a molecule in the brain known as the 5HT1A receptor. The 5HT1A receptor binds to serotonin, another brain molecule that is highly implicated in depression and is the target of most current antidepressant medications. Rodents lacking this receptor show fewer depressive symptoms in response to stress, which suggests that it is somehow involved in promoting depression. When scientists have compared the composition of the functional part rat 5HT1A receptor to that of humans, it is 99 percent similar, which suggests that it is so important that natural selection has preserved it. The ability to “turn on” depression would seem to be important, then, not an accident.

(...)

Studies of depression in rats show that the 5HT1A receptor is involved in supplying neurons with the fuel they need to fire, as well as preventing them from breaking down. These important processes allow depressive rumination to continue uninterrupted with minimal neuronal damage, which may explain why the 5HT1A receptor is so evolutionarily important.

Okay, so 5HT1A promotes depression by binding to serotonin, but it also helps fueling neurons so we can think well. They therefore argue that depression is good for you, because you think better when you are depressed.

How fast can you say cum hoc ergo propter hoc?


By xkcd.

Of course, correlation alone is not enough to imply causation, and the authors do attempt to suggest a mechanism that would make sense of depression causing better thinking:

Many other symptoms of depression make sense in light of the idea that analysis must be uninterrupted. The desire for social isolation, for instance, helps the depressed person avoid situations that would require thinking about other things. Similarly, the inability to derive pleasure from sex or other activities prevents the depressed person from engaging in activities that could distract him or her from the problem. Even the loss of appetite often seen in depression could be viewed as promoting analysis because chewing and other oral activity interferes with the brain’s ability to process information.

Except that the two very things that usually make traits adaptive are precisely what are offered as damaging to thinking: sex and food. We are meant to believe that thinking about one's problems is so much more important than having sex and eating that having a depression is adaptive. That is one hell of a big mouthful that requires a few exclamation points.

Laboratory experiments indicate that depressed people are better at solving social dilemmas by better analysis of the costs and benefits of the different options that they might take.

In the meantime the rest of us will be over here having dinner and sex.

Here's how it's gonna go down: The brain is developmentally complex, with multiple proteins required to build each component, and proteins involved in building multiple components. Epistasis and pleiotropy, respectively, if you think of proteins as genes. The brain is not optimally designed, but has evolved using available proteins for new functions. It has had to make do with what was already present, at least in many cases, and that has resulted in some constraints that we now have to deal with. Such as being good at thinking analytically unfortunately comes at the cost of higher risk of being depressed, for example.

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Related post: Head injury as a cause of ADHD.

Scientia Pro Publica 10 is finally up

Scientia Pro Publica is up on Grrlscientist's blog, Living the Scientific Life.

One of the posts is about a paper that has been blogged about extensively, namely
Kivell, T., & Schmitt, D.
Independent evolution of knuckle-walking in African apes shows that humans did not evolve from a knuckle-walking ancestor
PNAS August 25, 2009, vol. 106 no. 34 14241-14246

Here's a bunch that I trust will satisfy your urge for commentaries on that paper:

• Laelaps (~700 words)
• Afarensis (~500 words)
• Lawn Chair Anthropology (~500 words)
• AK's Rambling Thoughts (~3,500 words)
• A Primate of Modern Aspect (~1,200 words)

Enjoy the anthropocentric knuckle-gazing!

Darwin was wrong about the human appendix being vestigial

"Ever since Darwin"™ [1] it has been thought that the human vermiform appendix doesn't serve a function any more, but that the function was lost, and the remnant lingers on - something that is easily explained by evolution, but not so easily explained by creationism.

Then a research team from Duke University came along and changed all that.

First they demonstrated that the appendix does have a function [2]:

the human appendix is well suited as a “safe house” for commensal bacteria, providing support for bacterial growth and potentially facilitating re-inoculation of the colon in the event that the contents of the intestinal tract are purged following exposure to a pathogen.

Proposed function of appendix as providing support for growth of bacteria essential to the function of the intestine.

Then they show [3] that

Although the appendix has apparently been lost by numerous species, it has also been maintained for more than 80 million years in at least one clade, supporting the idea that the structure has a vital biological function.

Part of the phylogenetic tree showing that the appendix most likely evolved more than once (red, appendix present; gray, appendix absent). Note that this part of the tree doesn't show that the monotremes (platypus, echidna) and some marsupials also have something that looks like an appendix.

Both of these papers separately point to evidence that the human vermiform appendix is not a useless structure. The interpretation is not in question - no biologist do (should) not have any problem understanding the implication of this, namely that the status of the appendix has changed to one of use, but that while Darwin was wrong about this particular point, this conclusion in no way takes anything away from evolutionary theory as a whole. Creationists are guaranteed to jump out and imply that this means there is a problem with evolution, but it cannot be said with enough emphasis that it in no way means that. Again, evolution can explain such organs of no use, but creationism can't. That one structure is no longer considered neutral with respect to fitness does not mean that such neutral organs don't exist. Examples:

• leg bones in whales
• eyes of blind cavefish
• pelvis remnants in snakes
• the human tailbone
• human goose bumps
• human muscles to move the ears (I'm very skilled at this myself)

There are many more. Some of these may one day, like the human appendix, be demonstrated to have a function (i.e. increase fitness), but it is highly doubtful (it is unthinkable) that the status will change for all of them.

A question of semantics

What do we call such organs/structures/behaviors that no longer serve any function? If we distinguish between those that used to have one function but now has another (penguin wings, for example) and those that used to have a function, but now doesn't at all (see list above), then I personally find it most useful to call only the latter vestigial. However, some people use the term in both cases (Jerry Coyne is said to do so in Why Evolution Is True, for example), but I find it more informative to call the former structure exapted, preadapted, or co-opted (I use co-opted, because the first to are usually used a nouns, exaptation and preadaptation - and that reminds me that Todd Oakley still owes me to explain what the difference between these three are).

So, I'll say that the human appendix is not a vestigial organ.

A question of politics

All of the above is really fairly straightforward (but exciting) science discourse. However, our own PZ Myers has reacted rather strongly in a post, Darwin and the vermiform appendix.

Before I go on, let me make a few things clear before anyone says otherwise: PZ is a great blogger, when blogging about science as well as about creationism and all things related to either one. I happen to be fairly aligned with him in terms of politics as well as on religion (we are both atheists), and I agree with him on most issues that he brings up on his blog. Notably, I side with him on the question of "Crackergate," "Expelled from Expelled," and share his disdain for the faitheists, just to name a few.

The post from today about the human appendix paper is the first example where I strongly disagree with PZ. He doesn't so much talk about the scientific paper itself, but instead about an article in ScienceDaily, Evolution Of The Human Appendix: A Biological 'Remnant' No More, in which we are introduced to the evolutionary significance of the study:

Now, some of those same researchers are back, reporting on the first-ever study of the appendix through the ages. Writing in the Journal of Evolutionary Biology, Duke scientists and collaborators from the University of Arizona and Arizona State University conclude that Charles Darwin was wrong: The appendix is a whole lot more than an evolutionary remnant. Not only does it appear in nature much more frequently than previously acknowledged, but it has been around much longer than anyone had suspected.

"Maybe it's time to correct the textbooks," says William Parker, Ph.D., assistant professor of surgical sciences at Duke and the senior author of the study. "Many biology texts today still refer to the appendix as a 'vestigial organ.'"

[Emphases added.]

Parker then said

Darwin simply didn't have access to the information we have. If Darwin had been aware of the species that have an appendix attached to a large cecum, and if he had known about the widespread nature of the appendix, he probably would not have thought of the appendix as a vestige of evolution.

He also was not aware that appendicitis, or inflammation of the appendix, is not due to a faulty appendix, but rather due to cultural changes associated with industrialized society and improved sanitation. Those changes left our immune systems with too little work and too much time their hands – a recipe for trouble.

That notion wasn't proposed until the early 1900's, and we didn't really have a good understanding of that principle until the mid 1980's. Even more importantly, Darwin had no way of knowing that the function of the appendix could be rendered obsolete by cultural changes that included widespread use of sewer systems and clean drinking water.

Here is, then, the relevant passage from Darwin [1]:

Not only is [the vermiform appendage of the caecum] useless, but it is sometimes the cause of death

[Emphasis added.]

He doesn't use the term vestigial, but instead is very careful (I gather) to say that it no longer has any use (in fact, it isn't even just neutral, per Darwin's observation, but detrimental).

Here are a few quotes from PZ's post about the ScienceDaily article, and my answers to each of them:

It's rather unseemly to collect a lot of data that Darwin did not have, run it through PAUP 4.0 on a fast computer, map the data onto a molecular consensus phylogeny, and cackle gleefully over discovering something Darwin did not know. Really, it doesn't make you a better scientist than Darwin.

"Cackle gleefully" ? Who, Parker? "Make you a better scientist" ? Where does this come from? Parker isn't implying any such thing.

To make it even worse, people who do this can't even make the corpse-fight a fair fight — they have to stuff the pathetic dead body with straw. In this case, they're padding Darwin's investment in the appendix a fair amount. They cite one work by Darwin, The Descent of Man, which mentions this issue. He wrote one whole paragraph on the topic, and here it is, in its entirety;

Go to PZ's post to see the quote, which includes the sentence I quote from Darwin above, where he labels the appendix as 'useless.' People criticize the work of dead scientists on scientific grounds as a matter of routine. There is absolutely nothing wrong with it. Indeed, this is the way things must be, in order for science to progress. PZ would agree, I know, and I am puzzled why he would scold Parker in this manner.

Note why Darwin classed this appendage as vestigial: because it is greatly reduced compared to the homologous organs in non-human relatives, and because it currently exhibits a great range of variation, which is apparently non-functional. These are criteria which the paper in question does not refute at all. Darwin does say that the appendix is "useless", and the paper will show some evidence that that is wrong. It's also irrelevant.

The reason why it is irrelevant is that the presence of some function is not part of the definition of a vestigial or rudimentary organ

It is not relevant that the appendix is useless? The hell?! PZ harps about the semantics - vestigial vs. useless - but then ignores the meaning behind Parkers's words. Parker clearly means 'useless' when he says 'vestige'. Of that there can be no doubt. How can it be irrelevant whether the appendix has a use, when that is what both papers are all about? (It can't, and it isn't.)

If a portion of the gut, a digestive organ, is diminished in size such that it no longer contributes to the primary function of the organ, but does retain a secondary function, such as assisting in immunity, or as the authors of the recent paper will argue, in acting as a reservoir of bacteria for recolonizing the gut, then it is still a vestigial organ. It has lost much of its ancestral function.

PZ is using one definition of the word, and not the other (see semantics above).

I mentioned that I'd point out errors in Darwin's understanding. They're there, but note that seeing them now 150 years after he wrote his big book does not make me smarter than Darwin, nor does it invalidate the overall picture of his theory.

And Parker neither said nor implied anything to that effect. In fact, he goes to great length to emphasize that "Darwin simply didn't have access to the information we have," and "If Darwin had been aware of the species that have an appendix attached to a large cecum, and if he had known about the widespread nature of the appendix, he probably would not have thought of the appendix as a vestige of evolution." That, and the rest of the Parker's words above from the ScienceDaily article.

Most of my complaints here are with the abysmal presentation of the ideas in it by the popular press, aided and abetted by the scientists themselves. Just keep in mind that whenever these press releases that declare "Darwin was wrong" appear, it's usually an example of grandstanding and the regrettable tendency of competitive scientists to think the way to impress people with the importance of their work is to get into a penis-measuring contest with poor dead Chuck.

I was very careful to put "Darwin was wrong" in the title of this post. This is the "abysmal presentation" that PZ is referring to. PZ co-authored a letter to the New Scientist, when they printed those exact words in big letters on the cover of the January 2009 issue. (That cover story was about the uprooting the tree of life, and how parts of it isn't at all like a tree, but a network. I agree it was foolish to choose that headline for the cover, but, luckily, as things have turned out, it didn't really have much of an effect as far as I have seen.) I also think it is impressive when scientists can finally prove Darwin wrong on something. If no one else have been able to do it for almost 150 years, then let us indeed celebrate it with much fanfare whenever someone can. Darwin would have been proud.

I think PZ has got the heebie-jeebies. He is at the forefront of defending evolution against creationist imbeciles, so it is understandable that he dislikes it when scientists gives them ammo for their cannons (note to self: find a better idiom). However, when communicating science, we should not be hesitant to say things the way they are, and in this case "Darwin was wrong: The appendix is a whole lot more than an evolutionary remnant." Trying to boost your scientific work in the popular media by such statements is fair game. It's very hard to get people interested, and I personally applaud Parker for the way he did it, and for standing up for "poor dead Chuck" at the same time. Yeah!

Lastly, let me briefly say how disagreeable I find the discourse in the comments to many of PZ's posts, this one in particular. People call each other names for voicing opinions not shared by the majority of the commenters. Accusing them of trolling is standard practice, akin to shouting 'witch' back in the middle ages, and one is a 'fucktard' when they don't like you. But worse than that, ScienceBlogs is a place for science bloggers, and the number one trait of a good scientist is skepticism. Pharyngulites as a group don't have too much of it; commenting how much they are in agreement with PZ on whatever he writes about, spiced with sublime derogatory terms, seems to be a hobby of hundreds of regular visitors. A few quotes from comments to the post in question:

"some idjits think that makes the whole work of the innovator wrong."
"As Prof. Myers points out, Darwin was wrong about a lot of things. So what?"
"Picking a fight with Darwin over it is just stupid."
"So, basically, they didn't understand what Darwin meant by "vestigial" because they didn't do all their homework."

It's not all bad, though. Here's one dissenting voice: "If we are to refer to all homologous structures with different functions as vestigial, it seems to have become a useless term."

Exactly my point.

References:

[1] Darwin, C. 1871. The Descent of Man and Selection in Relation to Sex.

[2] Randal Bollinger, R., Barbas, A., Bush, E., Lin, S., & Parker, W. (2007). Biofilms in the large bowel suggest an apparent function of the human vermiform appendix Journal of Theoretical Biology, 249 (4), 826-831 DOI: 10.1016/j.jtbi.2007.08.032

[3] Smith HF, Fisher RE, Everett ML, Thomas AD, Randal Bollinger R, & Parker W (2009). Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. Journal of evolutionary biology PMID:19678866

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Update 11/2:
Bill Parker sent me an email in reply, and I have elected to make it a separate post: More on the appendix.

Israeli official lectures Swedish government on the meaning of a free press

The irony kills me.

Israeli Foreign Minister Avigdor Lieberman doesn't seem to understand what it means to have a free press. Just like the days when the Danish Prime Minister was asked to censor Jyllands-Posten for publishing the drawings on Muhammad, now, despite Lieberman's request, Sweden's Foreign Ministry is refusing to condemn an article (CNN, BBC, Politiken) published in a Swedish newspaper, Aftonbladet, in which Israeli troops are accused of harvesting organs from dead Palestinians (original article in Swedish).

"It's a shame that after the Swedish ambassador to Israel did the right thing and condemned the report, clarifying that this newspaper does not represent Sweden in any way or form, the Swedish Foreign Ministry chose to dismiss her statement instead of supporting it," Lieberman said.

"The meaning of freedom of press is the freedom to publish the truth, not the freedom to lie and slander. A country which really wants to defend democratic values must strongly condemn false reports that reek of anti-Semitism like the one published this week by the Aftonbladet newspaper."

The free press in Scandinavia is really free. Without fear of government intervention of any kind, they really can write whatever they want. Private parties can sue them for libel, but the government is never involved. I find it ironic that Lieberman here thinks he is in any position to tell the Swedes what it means to have a free press. As for his insinuation that the article is not the truth, it is baffling that he suggests that the Swedish government should believe his word on the matter, without any prior assessment of the facts.

The free-lance author of the op-ed article (need i say 'of course') received threats on his life:

"I have an e-mail here ... saying, 'The Nazis should die and you will be next. We will meet you outside, you will be the next news very soon. Meet you outside,' " Bostrom said.

Just to be fair and balanced I am now looking for death threats made by Danish and Swedish citizens against other nationals writing articles criticizing anything Danish or Swedish, or drawing indecent cartoons of Jesus or our royalty (actually, Danish people take pride in doing just that themselves - see below).

Here's a Turkish drawing from 2005 of then Danish prime minister Fogh Rasmussen in bed with Kurdish leader Abdullah Öcalan. Fogh Rasmussen said his honor had been challenged, and then ordered a nuclear attack on Ankara.

Oh wait. Strike that. It says he just shook his head a bit and laughed about it.


Jesus!


Queen Margrethe (center, smoking, as usual).


Danish roligan stops evolution? Looks like Fogh Rasmussen third from the left. That's probably not a coincidence.

Still looking...

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Update 8/28: A lawsuit has been filed against Aftonbladet.

Hindus go fanatical over paintings

Here's a story reminiscent of the ruckus caused by (the reaction to the) Danish cartoons of Muhammad back in 2005.

(Some) Hindus are crazy like the rest of them. An Indian artist depicted Ganesh, god of intellect and wisdom (among other things), performing a Maori dance, walking naked carrying a garden rake, and in the pose of Auguste Rodin’s The Thinker. As a result he was received threats on his life and on his fingers.

The artist added that the threats began when Sanatan Sanstha, a hard-line group which presents Hinduism as a form of science, told Hindus to call him and “express their anguish” at the images.

As a form a science. Right. If you're that far out it's no wonder a depiction of your beloved god will make you threaten someone on their life. (No, I am not saying I would ever threaten anyone because they dissed Issac or Charles.)

One, the extremist organisation Hindu Janagruti Samiti (HJS), called for demonstrations at the exhibition venue.

“We intend to have peaceful protests, but we are not responsible for any law and order problem if it arises,” said Jayesg Thali, an HJS convener.

Oh, and we were so worried, but this of course makes it completely safe! No instigation of religious mobs with hurt feelings going nuts can be imagined now.

Affirmative action in science in Japan

Hokkaido University in Japan have an advertisement in Nature (July 9th, 2009) where they invite Ph.D.s to apply for faculty positions. They will hire 25 professors (assistant/associate) and lecturers over the next five years for science, technology, and agriculture positions. "Applications are open only for female researchers." (original emphasis)

Ultimately, who are hired in faculty positions should only be based on merit. The best candidates should be hired, giving no consideration to gender, species, race, height, religion, food preference, martial status, sexual preference, vertigo, et cetera, et cetera, given that none of these would interfere with job function. It therefore seems unfair that Hokkaido University will earmark positions for females, when there might be better qualified males who would have liked to apply.

However, society (Japan in particular) is already heavily biased in terms on merits. Women do not have the same opportunities as men for at least two different reasons.

1. Role models. It will become much more likely that other women will find becoming a professor a reachable goal once they see others achieving it. We may not think that this should be the case - after all the whole point is that gender doesn't matter, but that only qualifications do - but the fact is that it does. Who we identify with is demonstratively influenced by the characteristics that we share.

2. Remedying Discrimination. Women has a tough time being hired as professors in Japan, probably for several reasons. I recall reading that a female applicant was turned down because a male applicant "needed the job to provide for his family, while the female applicant had her husband to do that." (Paraphrasing from memory.) Additionally, the reason that there are fewer female professors do of course have something to do with there being fewer qualified female candidates, but that is most likely because fewer women see that path as one that is viable for them, in part because there is a bias in what students are encouraged to pursue in the educational system (boys do math, girls do language, or some such stereotype). Discrimination continues to exist in the favor of males for hiring professors, and to remedy that, tipping the scale in favor of women will arguably have a positive effect.

For more information on the positions at HU go to F3 project: fortississimo affirmative action in Hokkaido University. (It's only in Japanese, so it appears application is also open only for Japanese speakers?)

P.S. A couple of places here I have made some assertions that I believe to be true. I have read, for example, that who we identify with influences our career choice, and that we identify with those who are similar to. Forgive me for not listing references, but I trust the enthusiastic reader will have no problems locating sources that argue this and other points.

Libya honors convicted terrorist

Abdel Basset Ali al-Megrahi, the only person convicted in the 1988 Lockerbie jet bombing, has been released from prison in Scotland because he is expected to die soon from prostate cancer. You can think what you want about that (and I think it's crazy), but the thing I really want to object to is the reception he got when he returned to Libya (see picture).

Ignoring American demands that Mr. Megrahi not be celebrated as a hero returning to his homeland, hundreds of young Libyans were bused to the military airport in Tripoli to welcome him home, cheering and waving Libyan and Scottish flags as he sped off in a convoy of white vehicles.

Pissed me off, it did.

Evolving robots

Very interesting experiment is blogged on 80beats of the Discover Magazine, To Win the Evolutionary Race, Robots Learn to Deceive. Brains of real robots were subjected to evolution, and the result was that they learned how to horde the most food for themselves, doing what they could not to attract other robots to the food, so they could have more for themselves.

Effect of prayer on rainfall in Georgia

May I recommend the feature article of this week's eSkeptic, A Governor’s Prayer for Rain?

On Tuesday, November 13, 2007, Sonny Perdue, the Governor of Georgia, led a group of approximately 250 persons, including many state officials, in a prayer for rain on the steps of the state capitol in Atlanta.1 Georgia had been suffering an extreme drought, and the level of Lake Lanier, an important water reservoir near Atlanta, had been decreasing dramatically over several months. Governor Perdue believed that a divine intervention was necessary and so he boldly asked God to bring rain.

It rained. The author, Gary J. Whittenberger, compares the amount of rain before and after the prayer with rainfall in the previous ten years to show that it wasn't an unusual increase in rainfall, especially considering that the prayer was done during a time of drought. As Allan Donald comments, regression to the mean explains the increase in rain all by itself.

Interestingly, several readers belittle the article, saying that it is ridiculous to even discuss the idea of praying for rain, that if people want to believe in the power of prayer, then you should just let them (note this is the Skeptic Magazine!), and that it’s silly and counterproductive to spend time "on an analysis that the author knew ahead of time couldn’t prove anything." The last remark I find quite true. There is no way that even a torrent of water the minute the prayer was over could convince me that the prayer was resposible, as long as there are other and better hypotheses. However, apparently, for the citizens of Georgia, less would suffice.

Many Georgians considered Perdue a hero and thought that his prayer had influenced God to increase rainfall to the drought stricken vicinity of Atlanta.

And therefore I think this article is not such a bad idea after all. Let the Georgians read it, and perhaps some of them will realize that the increase in rainfall coinciding with the prayer does not need to be an act of God.

Evolution blurbs

Great article in the NY Times by Nicholas Wade on why humans have become (mostly) hairless: Why Humans and Their Fur Parted Ways. He quickly mentions the aquatic ape theory, but (rightly) leaves it at that. While some people are very much into the theory, certain isotopes would have been present in bones if humans had gone through an aquatic stage are absent (I can't find a reference for this at the moment, so instead take a look at other objections on Wikipedia). The hypothesis discussed is that loss of hair was adaptive because of fleas, which were highly beneficial to get rid of.

David Sloan Wilson discusses the evolution of war with John Horgan, Evolution and War: Basic and Advanced. Wilson said Horgan flunked Evolution 101, and Horgan then called Wilson arrogant. Wilson then takes a deep breath.

Gary Ruvkun: “My rule of thumb is to ignore the evolutionary biologists — they’re constantly telling you what you can’t think.” Again Nicholas Wade in the NY Times, Tests Begin on Drugs That May Slow Aging.

Cladistics does not resolve hobbit controversy

Homo floresiensis (nicknamed "the hobbit") is the name given to a hominin species whose remains were discovered in 2004 on the island of Flores, Indonesia. But do the bones represent a new species at all, or were they, mundanely, anatomically modern humans with some pathological disorder that caused them to have smaller brains (~400 cc) and be shorter (106 cm) than humans (~1130 cc and 147 cm, average for women and Indonesian women, respectively)?

I have previously made clear where I stand in that debate, and for what reasons, but at the same time I do have some reservations with a paper in the Journal of Human Evolution that applies cladistic analysis (also known as phylogenetics) to determine where in hominin evolution H. floresiensis fits in.

The authors, Argue et al., examined multiple morphological features of bones of H. floresiensis, H. ergaster, H. erectus, H. habilis, H. rudolfensis, A. africanus, A. afarensis, H. rhodesiensis, H. georgicus, and H. sapiens in order to compare them and construct cladograms (evolutionary or phylogenetic trees showing ancestral relationships). Because some scientists suggest that the smaller brain case could have been caused by microencephaly, they excluded cranial capacity from the comparisons.

The result is that two trees are the most parsimonious, meaning that they are the shortest of all the trees they examined. In other words, under the assumption that the fewer morphological changes between the species is the better model for the evolutionary relationship, these two trees are the most likely of all.


The two most parsimonious cladograms, with H. floresiensis branching off just after and just before H. habilis, respectively. Dmanisi is also known as Homo georgicus.

So the conclusion the authors make seems fair enough: H. floresiensis branched off either just after or just before H. habilis.

Skipping over the problems I have with the assumption of parsimony, does anyone else notice something really fishy so far?

The fishy part is that in order to construct cladograms like the ones above, the authors assumed that H. floresiensis and H. sapiens are different species. Once that is done, no other conclusion can be reached. It is perhaps interesting by itself to see what the evolutionary relationship is between them, assuming that they have one, but it can't address the question of whether they are different species or not. However, Argue et al. state clearly in their introduction that this is their goal:

Alternative interpretations include the possibility that the Liang Bua fossils represent a new hominin species, H. floresiensis (...), and that the holotype specimen, LB1, was a modern human, possibly afflicted with a pathological condition (...). These conflicting hypotheses are based on comparative analyses of the morphology of the bones with both archaic and modern Homo, typically using statistical methods to compare the Liang Bua bones with those of other hominins.
      The morphological and morphometric analyses have contributed much to the debate about H. floresiensis, but have not conclusively resolved the controversy about the position of the species in human evolution. We, therefore, use a different tool, cladistic analysis, which has not yet been applied to resolving this problem.

Again, I do not see how using cladistic analysis can be used to resolve this question of whether H. floresiensis was a human with a pathological condition or a separate species. In fact, the same issue exists between H. georgicus (Dmanisi) and H. erectus. H. georgicus is now thought to represent an early stage before H. erectus, rather than being a separate species. Yet, here they are assumed to be different species.

From their conclusion:

Based on rigorous cladistic analyses, we propose that H. floresiensis evolved in the Late Pliocene or Early Pleistocene. The first of our two equally parsimonious trees suggests that H. floresiensis branched after H. rudolfensis (represented by KNM-ER 1470) but prior to the divergence of H. habilis (represented by KNM-ER 1813 and OH 24). Alternatively, our results are equally supportive of H. floresiensis branching after the emergence of H. habilis.

Agreed. I too believe H. floresiensis to be a new species, and given that, I can accept the cladistic analysis (again, ignoring my issues with parsimony in cladistics).

Our results sustain H. floresiensis as a new species (Brown et al., 2004; Morwood et al., 2005) and favor the hypothesis that H. floresiensis descended from an early species of Homo (Falk et al., 2005; Argue et al., 2006; Larson et al., 2007; Tocheri et al., 2007).

In their earlier paper (Argue et al., 2006) the morphological data were used to support this conclusion, but, again, the results in the present paper does not "sustain H. floresiensis as a new species (...) and favor the hypothesis that H. floresiensis descended from an early species of Homo," when it is assumed that they are separate species.

Reference:
Argue D, Morwood M, Sutikna T, Jatmiko, & Saptomo W (2009). Homo floresiensis: A cladistic analysis. Journal of human evolution PMID:19628252

Apologize to Alan Turing

Campaign to win official apology for Alan Turing.

Alan Turing was the greatest computer scientist ever born in Britain. He laid the foundations of computing, helped break the Nazi Enigma code and told us how to tell whether a machine could think.

He was also gay. He was prosecuted for being gay, chemically castrated as a 'cure', and took his own life, aged 41.

The British Government should apologize to Alan Turing for his treatment and recognize that his work created much of the world we live in and saved us from Nazi Germany. And an apology would recognize the tragic consequences of prejudice that ended this man's life and career.

Via Pharyngula.

Bottle feeding simulates child loss

There is much reason to be critical of the field of evolutionary psychology, not because it isn't obvious at some level that the human mind is an evolved organ, but rather because much of the research comes down to evolutionary just-so explanations of otherwise interesting studies of human psychology. When, on the other hand, this process is reversed, it does have scientific merit. The right way to do it is to start hypothesizing based on our evolutionary history, and then set forth to do experiments that may reject or validate these hypotheses.

An example of that is a study of the effects of bottle feeding. Based on what we know of our evolutionary history, the only reason that a new mother would prematurely cease breastfeeding her infant would be in the case of the infant's death. Bottle feeding had not yet been invented. Consequently, a team of scientists at the Department of Psychology, State University of New York in Albany surmised that bottle feeding mimics this loss, and that mothers who breastfeed would be more likely than average to experience postpartum depression.

The researchers found this hypothesis to hold true in a study of 50 new mothers:

We recently completed a study of over 50 mothers recruited through local pediatric offices at 4–6 weeks postpartum [25]. Consistent with previous reports, we found that those who bottle fed their babies scored significantly higher on the Edinburgh Postnatal Depression Scale than those engaged in breastfeeding. The increased risk of depression among mothers who relied on bottle feeding held true even after we controlled for such things as age, education, income, and the mother’s relationship with her current partner.

The authors don't label their study as evolutionary psychology, but as evolutionary medicine, and I commend the emergence of this new discipline. What can it bring to the table, then? The authors conclude that

Bottle feeding practices and hospital procedures that simulate child loss may increase the risk of postpartum depression and fall within a growing number of medical issues that could benefit from an evolutionary perspective.

[The paper is published in a journal owned by Elsevier, and is not free. If you want a copy of the PDF, let me know and I will send you one.]

Reference:
Gallup Jr., G., Nathan Pipitone, R., Carrone, K., & Leadholm, K. (2009). Bottle feeding simulates child loss: Postpartum depression and evolutionary medicine Medical Hypotheses DOI: 10.1016/j.mehy.2009.07.016

Drink FIJI Water and support military dictatorship

How do we decide who we trust? When someone writes an article telling a mean story about someone else, how are we to know if this is the truth?

FIJI Water is doing very well, in part by promoting itself as Carbon negative, by boasting of various good deeds (e.g. permanently protecting a UNESCO World Heritage site and its rain forest from logging), and by being consumed by many famous people, such as Obama, Paris Hilton, and Mary J. Blige. At the same time the water really comes from Fiji, which is ruled by a military junta, and where many people ironically don't have access to clean water.

If you drink bottled water, you've probably drunk Fiji. Or wanted to. Even though it's shipped from the opposite end of the globe, even though it retails for nearly three times as much as your basic supermarket water, Fiji is now America's leading imported water, beating out Evian. It has spent millions pushing not only the seemingly life-changing properties of the product itself, but also the company's green cred and its charity work. Put all that together in an iconic bottle emblazoned with a cheerful hibiscus, and everybody, from the Obamas to Paris and Nicole to Diddy and Kimora, is seen sipping Fiji.

All this is from an article, Fiji Water: Spin the Bottle, by Anna Lenzer, who went to Fiji to see the bottling plant by herself.

Nowhere in Fiji Water's glossy marketing materials will you find reference to the typhoid outbreaks that plague Fijians because of the island's faulty water supplies; the corporate entities that Fiji Water has—despite the owners' talk of financial transparency—set up in tax havens like the Cayman Islands and Luxembourg; or the fact that its signature bottle is made from Chinese plastic in a diesel-fueled plant and hauled thousands of miles to its ecoconscious consumers. And, of course, you won't find mention of the military junta for which Fiji Water is a major source of global recognition and legitimacy. (Gilmour [the company's founder] has described the square bottles as "little ambassadors" for the poverty-stricken nation.)

It's not that I have seen Lynda Resnick (current owner of FIJI Water) excoriate Anna Lenzer's claims, but I'll be damned if FIJI Water is willing to admit that they are true. Assuming that someone financially involved in FIJI Water will eventually answer (and by 'answer' I mean 'deny') part of her criticisms, my question is how it is that we'll believe one or the other.

I don't drink FIJI Water, though I'm sure it's tasty. Since recently I don't drink any bottled water, actually, but that's a different story (though not entirely). But if I was a long-time consumer of FIJI Water, I can see that the emotional investment that I had made would make me more likely to dismiss claim's such as Lenzer's, until I saw solid proof. (By 'emotional investment' I mean the fact that while drinking it regularly, I would expect that doing so wouldn't cause all sorts of calamities in another country, for example, and if I then had to admit to myself that I had been wrong all that time, then I would be emotionally upset - we don't like when that happens.) On the other hand, now that I don't drink it, I don't really have anything at stake, and I don't have to face the fact that I am part of the problem (that FIJI Water causes disease, climate change and other human and environmental tragedy).

But if reading just one article that highlights good reasons why we shouldn't be drinking it isn't enough to rationally make up our minds on the subject, then what exactly is enough? Two considerations, I would say:

1. Consider that history shows that those who stand to make or lose a lot of money are usually the ones who are fine with screwing over other people. This is to be contrasted with what history tells us about investigative reporters' practice of making up complete falsehoods just to get a great story printed.

2. Independent evidence. Anna Lenzer isn't the first to write about FIJI Water's involvement with a military dictatorship and problematic environmental practices. See Message in a Bottle, What it takes to bring you Fiji water, and Fiji government yields to bottled water company pressure. We must of course be careful that we aren't reading more than one article from the same source, but apart from that, it would seem clear and hard to denounce that there is something fishy about the water from Fiji.

Incidentally, I went to Ontario Mills Mall this sunday, and almost every vendor the food court were aggressively pushing FIJI Water - at $2.99 per pint. I asked around and was told that the decision to do so comes from the Manager of HMS Host, whom I now intend to write a letter of complaint to.

---

Important update 8/17:
FIJI Water already had published a reply to Lenzer's article, and Lenzer has a reply to that on the same page. Bottom line is that while FIJI Water does do some charity work in the local Fiji communities, this does not excuse doing business with a dictatorship.

Bob Dylan mistaken for a hobo

Make sure you read how Bob Dylan was taken for a homeless guy, and had to show ID before the police believed who he was.

Attitudes towards homosexuals can change

ResearchBlogging.org is a great site for the latest research in the natural sciences. Here bloggers apply to register, and then when they blog about peer-reviewed academic research on their own blogs, they import and get a link with a blurb on the site.

The most active of them all, The British Psychological Society's Research Digest Blog has a new post that I find most fascinating: Intervention helps reduce homophobia.

It's about how a group of people imagining how it would be to live in a society where sex is not permitted, and how that affects the participants attitudes towards people who are homosexual. It turns out that

"[people who was in this experiment] were more able to take the perspective of homosexuals, than were the control participants [who attended a lecture on homophobia] , and this in turn was associated with more empathy towards people who are homosexual, a greater tendency to think of homosexuals and heterosexuals as all belonging to the same category (being human) and ultimately to more positive attitudes towards people who are homosexual."

On how to affect the anti-science nation

Unscientific America by Chris Mooney and Sheryl Kirshenbaum has been a hot topic in this realm of the blogosphere, but I haven't commented on it yet (since I have not and will not read it), leaving that to PZ and Coyne, whom I largely agree with on the issue (of whether to be a faitheist or a confrontationalist on the subject of compatibility between religion and science).

In an op-ed article today in the LA Times, Must science declare a holy war on religion?, they ask who is going to read Richard Dawkin's new book The Greatest Show on Earth (to be released this September) in which he makes the case for evolution. Their answer:

Surely not those who need it most: America's anti-evolutionists. These religious adherents often view science itself as an assault on their faith and doggedly refuse to accept evolution because they fear it so utterly denies God that it will lead them, and their children, straight into a world of moral depravity and meaninglessness. An in-your-face atheist touting evolution, like Dawkins, is probably the last messenger they'll heed.

But but but. While I would also guess that those who are firmly set in their religious beliefs and tenaciously anti-science aren't going to touch the book, those aren't the only audience that would benefit from reading it (in the eyes of pro-science folks). The people I hope will read it - as I know some have read The God Delusion - are younger people (teenagers, people in their twenties) who are perhaps fence-sitters, or even already totally pro-science, and these people will talk about it. Most won't know much about evolution at first, but with a book like this they will understand evolution better, be better able to have a conversation on the subject, and will talk about it with their friends, some of whom might be children of those very religious parents who would never read it. Perhaps they will start question the creation myth they hear in church, and stop accepting it on faith, as a result of reading a conflicting account.

The point is that these things take time. We won't persuade everyone in one fell swoop that evolution is true, but the more books out there, and articles on the internet, and public debates, and TV-shows, the higher the chance that the next generations will grow up being a little more skeptical than their parents, feeling some discomfort in having to read the Bible literally, and becoming more and more pro-science as a result.

Mooney and Kirshenbaum then invoke Darwin as an example of how they think the "New Atheists" should behave:

It turns out that late in life, when an atheist author asked permission to dedicate a book to Darwin, the great scientist wrote back his apologies and declined. For as Darwin put it, "Though I am a strong advocate for free thought on all subjects, yet it appears to me (whether rightly or wrongly) that direct arguments against Christianity & theism produce hardly any effect on the public; & freedom of thought is best promoted by the gradual illumination of men's minds, which follows from the advance of science."

Except that Darwin lived in a different time, where it might have been true that "direct arguments" had next to no effect (I am not sure of that either - just because Darwin said it doesn't make it so), but this is a different era, with mass communication and massive communication: while TV and radio aren't the media seething most with this controversy, the internet is constantly buzzing with it, and it is easy for anyone with internet access to find. Perhaps Darwin would have changed his statement had he known?