Second day at Cold Spring Harbor

Friday at the symposium had many great talks, For example, Hopi Hoekstra from Harvard told us about the experiments with wild mice that have recently expanded their range to include white sand beaches, favoring mice with a lighter fur color. The mice living in habitats with brown soil have brown fur, and are predated by birds of prey, so the question was if coat color actually matters for camouflage. To test this she and her colleagues painted clay figures of mice white and brown and put them out on the beach ("to the field, where few molecular biologists have gone before"). More molested brown clay mice confirmed that there is indeed strong selection for a lighter fur coat on the beach. Mutations in three genes are observed to have an effect on coat color:
Mc1r: single amino acid change reduces receptor signaling
Agouti: no amino acid changes, but increases mRNA expression
Corin: increase in expression
They investigated the effects in the mice of the order of these mutations, and found epistatic interactions; the order in which the mutations occur matters.

Whenever the mutation in Corin happens last, each mutation has a significant effect on color, but if Corin is first (or second, then that mutation does not result in a significant change in color:

In other words, Corin and Agouti (or Mc1r) interacts to produce a higher effect on color (and thus fitness) than each one has on its own. Epistasis.

However, then Hopi made a strange assumption. She then assumed that each mutation must have an effect on fitness, and that in the order of mutations, Corin must necessarily come last. I still haven't caught at the meeting, but when I do I'm going to ask why she makes this assumption. Since the effect of Corin alone is effectively neutral, there is nothing wrong with it coming first in the ancestral line that includes all three mutations.

---

Update 5/31: At the picnic I spoke to Hopi about the matter (btw, she's of Dutch ancestry, so her name is unpronounceable to Americans, but instead goes by Hoe-sktra, as in "that ho(e) is extra good"), and she told me that she agrees that the mutations could indeed come with Corin first (or second), but that the emphasis is not on the order of mutations, but on the order of selection pressures. Additionally, the story is more complicated than what she could present in 20 minutes (that undoubtedly goes for all 75 (or so) talks). There are subpopulations with only two of the three mutations. Which ones were they? Sorry, I don't recall. There were five different populations. Check out her publications.

First day a Cold Spring Harbor

My first real day at the 74th Cold Spring Harbor Symposium on Quantitative Biology, Evolution: The Molecular Landscape was a huge disappointment. My flight was supposed to arrive at La Guardia at 6:35pm, but it didn't get in until an hour after that. My luggage, however, was not on the flight, and not on the following flight from the same airline also coming from Dallas. It was on the third flight from the Dallas, and this delay resulted in me arriving at the meeting after 10pm, as Marc Hauser was just finishing his talk. I had missed E. O. Wilson's talk on the evolution of sociality in ants, and that really pisses me off.

Today has been very exciting, even though I have had some reservations about the talks. Usually I like shorter than one hour talks, but the length here is limited to 20 minutes, and speakers are really rushing through things. Given that, I had a really hard time following the morning lectures, which were on the interesting but (for me) difficult subject of RNA and proteins, with a lot of focus on elements of abiogenesis (origin of life). For example, Gerald Joyce talked about his recently published work on self-replicating and evolving RNA. I read the paper, which was very technical, and so I was looking forward to the talk to get a better understanding of the experiment. Not much luck with that, and on top of that I didn't get to ask him about, what I think is, his very strange definition of life. He argues that his replicating RNA has many of the traits of life, but not two that makes it non-life. The list is

1. Replication (yes)
   
2. Heritability (yes)
   
3. Mutation through recombination (yes)
   
4. Selection (yes)
   
5. Evolution of pre-existing function (yes)
   
6. Replication contingent on other functions (yes)
   
7. Capability for invention of novel function (no)
   
8. Open-ended evolution (no)
   

Why these points are good determinants of whether something is life is beyond me. I think life is not required to be able to evolve. We see that all life (that we see) evolves, but that doesn't make it a requirement, I should think. Or I am missing what his point with this was (that might be the case), and I will try to catch him tomorrow and ask him. I am giving a poster and I expect him to stand in line for it like everybody else.

However, the poster session was amazing. Michael Behe is here, and on his poster he argued from experiments with bacteria that, contrary to the observation that organisms increase in complexity (defined as number of promoters and genes), evolutionary theory predicts that it should decrease, because by far the most beneficial mutations result in loss of promoters and/or genes. I wholeheartedly disagree, because gene duplication, by his definition, increases complexity without having any effect on fitness (mostly). He countered that the rate of duplication is too low (1e-8 - 1e-9), but I don't see why that should be too low - it has to be compared to the rate of beneficial mutations, which is also very low (and perhaps comparable to that of gene duplications).

Another good poster was by Paul Bingham, Stony Brook, who argued that there is a causal correlation between human brain size and village size, as he put it. And the link... is throwing. Have you ever seen a chimp throw? It doesn't even throw like a girl. It simply isn't built for it. But humans are, and the advantages are clear: aggressive scavenging and low cost to ostracize. There is evidence of correlation from 1.8 million year old artifacts, but I was not alone about wishing for a testable hypothesis and some quantitative data.

Susan Lindquist from Cambridge, MA gave a an excellent talk in the evening on the influence of protein folding on evolutionary change. Chaperones (e.g. Hsp90) can facilities the evolution of new traits by three mechanisms, one of is by buffering the effect of small mutations, allowing the storage of cryptic genetic variation that is released by stress.

Check back tomorrow for words about Hopi Hoekstra (molecular phenotypic optima), Nick Barton (sex and recombination), Daniel Dennett (cultural evolution of words), and Matt Ridley also on some cultural evolution thing. And, the posters look even better again tomorrow. There's a great looking one on peaks in artificial fitness landscapes.

Here's a list of abstracts.

Self-help book for the ultimate man

Aha! So this is what is constantly bugging me. Finally, here's a book describing what I need to become a real man.

In a time when everyone is looking for a bailout, headlines highlight John Edwards' affair, and books detail A-Rod's steroid use, what has happened to men of honor and integrity? Once upon a time, a real man fought for his country, treated women with respect, and was a hero to his children.

Dare I say that one of them recently became president?

The Ultimate Man's Survival Guide explains how to fight off alligators, identify poisonous spiders, mix a perfect martini, and more. From tying a tourniquet to tying a bowtie—Miniter teaches men the skills, attitudes, and philosophies they need to be the Ultimate Man.

It should come as no surprise that I got this ad in an email from a conservative group - the ideals of a real man fighting off alligators and tying a bowtie fit right in with that, while I myself have other ideals. Not that I disagree that those are nice things to be able to do (especially mixing the perfect Martini), but I fear that the philosophies that this ultimate man must adhere to are of the conservative kind.

I wonder how learning from a book how to be the ultimate man squares with being the ultimate man. Seems kind of sissy ass liberal to me.

Encourage the use of condoms

Sex is repugnant. Animalistic. Unhygienic. Wrong. Can be tolerated between husband and wife only, exposing only a minimum of bare skin, under cover, lights off. And only as a means of procreation. No oral, no anal, no hand, no boobs. Keep pleasurability to a minimum.

Thus, no need for condoms. Condoms are contrary to the proper use of genitalia. Condoms encourage sex for other purposes than impregnation. Using a condom results in five million lost souls instead of just 4,999,999.

Is Condom Distribution Smart Health Policy?

Go vote, so that our views may dominate the interwebs.

Answers in Genesis goes to a Darwin exhibition

The irony is raining men. Someone with Answers in Genesis (Ken Ham, Kentucky creation museum) went to a Darwin exhibition in London, and predictably found it to be a clever form of mind-control.

In fact, before Darwin came along, people were breeding different sorts of dogs, cats, pigeons, and so on. Even in the Darwin exhibit, it is stated that “he [Darwin] was aware that people often bred animals with desirable traits and that over time such breeding exaggerated small differences. . . . Dogs were dogs but a tiny lap dog and a large lean greyhound look nothing alike.” I just wonder how many visitors noticed this gross inconsistency.

There is no inconsistency. The small differences that are exaggerated accumulate to create very large differences, as in the dog example, and this is precisely what many creationist will say they do not believe. They can accept microevolution, but not macroevolution. As for the case of dogs, which everyone unanimously continue to call one species no matter how great the differences, I beg to differ. Why continue to call them one species? There are so many breeds that differ enormously, and in some cases so much that for example two birds differing that much are routinely named different species. Would we continue to do so with dogs if we only knew of chihuahuas and great danes? Surely not. And who knows, perhaps there really is a reproductive barrier between those two breeds, designating them different species by the most pervasive definition (the Biological Species Concept). Not that I adhere strongly to that definition. I regard it as a proxy that can be used successfully in some situations, but far from all (asexual organisms is an obvious area where it clearly doesn't work).

The writer then lists the ways in which the Darwin exhibition performs mind-control:

1) Setting up straw-men arguments that totally misrepresent what Bible-believing Christians accept.

2) Showing how wrong Christians are for believing the things they supposedly believe (which they don’t believe in the first place!).

3) Convincing visitors that Darwinian evolution is true, and that one is a fool to believe otherwise (and certainly foolish to believe the Bible).

Actually, this kind of mind control is already being used constantly on America’s children through the public education system, the secular media, and science museums (even in many Christian schools and colleges, sadly).

This is the stuff of crazies. The alleged straw-man is that Christians believe in an unchanging world, but that that is clearly not the case, because just look at Genesis: the entrance of sin, the event of Noah’s Flood, and its account of the Tower of Babel. So there, things change, Christians all know it, and the Darwin exhibition thus attempts to control minds. Trying to convince visitors of the fact of evolution is the business of such a museum. Explain the science, show the evidence. By this standard any education can be labeled mind-control. And the point is that if ample evidence leads to evolution being true, then it is foolish to believe otherwise.

I wonder how this person sees AiG's Creation Museum in Kentucty. Totally free of straw-men? Are they not trying to convince visitors that evolution is a lie, and it is foolish to believe in it? Reality is that both scientists and creationists attempt to educate children, but that the scientists are the only ones with actual evidence to support their beliefs. You may consider this my attempt at mind-controlling readers of this blog, if you like.

On a related note, a long lost 400,000 year old axe has just been recovered at a museum, after having been lost for 150 years. The axe's old age shatters Ussher's calculation that the Earth is 6,000 years old. I realize that AiG won't accept this age, thereby denying the science not only of biology, but also of physics.

Bad, bad Tripp

From the cover of People magazine:

Gov. Sarah Palin's daughter talks about her life with baby Tripp. "If girls realized the consequences of sex, nobody would be having sex," says Bristol. "Trust me. Nobody"

Wow! I hope Tripp never finds a copy of that magazine when she gets older. What a bummer. That really sounds like an awful experience you're having with your baby, Bristol. I know babies are a lot of work, but surely your smiling face holding that baby is not a complete mock-up, or? Having babies, even at your very, very young age, must have at least some of the blessings that I myself have felt, even though I had children at a wee bit older age than you did.

However, I think that I will not trust you anyway, Bristol. Lust is a very strong force, and despite your insight into motherhood, I feel fairly certain that early motherhood horror stories are not enough to keep folks your age from giving in to their desires. Rather, complete sex education is required so that unwanted pregnancies can be avoided, and free access to condoms. Preferably those with strawberry taste.

Creationist erudition 101

Ouch, my God, that burns! Of all the attempts to attack evolution and defend creationism, this article on rightsidenews.com is one of the most pitiful I have ever read. It's a collection of misunderstandings, logical errors, semantic mistakes all rolled into one, and then coated with an air of erudition (which to creationists largely means quoting someone with a Ph.D. in whatever). Nothing is said that hasn't been said a hundred times over in letters to the editors of American local newspapers across the nation. This article is such a piece of junk that I just can't get over it. Hopefully blogging about it will be the cure of that plague.

But first, who are these people?

The subjects and thrust were selected and developed by Greene Hollowell, the research and composition by Evan Moore.

I googled their names, but all it got was this article. Hollowell supplied the Christian bias and selected which misconceptions to reiterate, and Moore did the hard work of copying and pasting from conservapedia or some such conservative Christian source of Truth.

Damning Christian bias:

In light of today's growing focus on science, it is essential to address the issue [of the conflicting views of evolution and creationism]. Through this treatise, we hope to show that God is the true creator of all life on earth and that evolution is a biased and illogical explanation for the creation and sustaining of life. [Setting yourself up for failure.]

Misrepresenting scientists:

What Scientists Say...

Evolution is derived from Naturalism, which assumes that things made themselves. [Wrong.] Naturalism suggests God had no part in the creation of life and assumes He has not attempted to share with humanity any information about the past.[1] At its core, evolution is the belief that "nothing" became "something." [Is not!] Non-living matter developed into living matter. It assumes that "single-celled organisms gave rise to many-celled organisms." It goes on to propose that "invertebrates gave rise to vertebrates, ape-like creatures gave rise to man, non-intelligent and amoral matter gave rise to intelligence and morality, and man's yearnings gave rise to religions."[2] Evolution is one of the major cornerstones of modern biological theory, taught in most school around the world. In Refuting Evolution, Jonathan Sarfati states, "The whole secular education system in America (and most other countries around the world) is underpinned by evolution."[3] Many scientists believe in evolution because it is the most practical alternative to believing in Creation [that's mostly not the reason - it is the only model supported by evidence], which they consider too incredible.[4] [Here I agree.] Most scientists will also admit evolution is not a proven fact, yet they treat it as fact and teach it as fact. [It is not proven with mathematical rigor (because that is never possible in science), but is so well supported by evidence that the occurrence of evolution is considered a scientific fact. Careful of the semantics!] Ironically, evolution is just as faith-based as Christianity. [Many people will confuse the blind faith in scripture of religions with the "faith" that seeing the same event a thousand times will make it likely that it will occur again. It is called induction, and contrary to religious faith, it actually works.]

Getting some core concepts wrong:

It is important to understand several key principles [Then try a little harder next time.]:

First, "the scientific method is limited to the study of processes as they occur at present." [Nonsense!] Science cannot speculate about past occurrences. [Sure it can. And does. As do everyone else all the time. In courts of law, and returning from the movies: "The house is a total mess, the kids are not in their beds, and the babysitter is nowhere to be seen. I must conclude that she took the money and ran without doing her job."] It can only deal with "how," "what," and "where" questions. "When" and "why" are out of bounds.[5] ["Judging from the body temperature and the fact that his broken wristwatch shows 4:03 AM, I estimate that he has been dead for about 3 hours."] Therefore, it is impossible to apply the scientific method to a concept like the Creation because it occurred so long ago. [No, historical sciences are very solidly based in evidence.]

Second, the word "science" means "knowledge." Since evolution is rooted in science - or so scientists say - it would seem essential to "know" with all certainty that evolution is true. [You are just making up stuff, now. Since we know that nothing about nature can be known with absolute certainty, the goal of knowing this about evolution (or any other scientific theory) is futile. No one in science would accept such a statement.] But no one has actually seen evolution occur. [I have. Many other scientists have.] There is no actual "knowledge" of evolution. [...!] In The Modern Creation Trilogy, Morris and Morris write, "The changes we do see in living species are either "horizontal" changes, at the same level of organized complexity [or] "downward" changes (e.g., mutations and extinctions)."[6] [And Henry Morris is just the person to ask about these things?] There is no scientific evidence for evolution. [There is plenty.] Believing in evolution requires faith.[7] [No, just induction.] Ultimately, neither creation nor evolution can be proved or disproved through evidence. ["Rabbit fossils in the Cambrian" would disprove a large part of evolutionary theory. Go look or shut up!] Both concepts occurred in the past, which the realm of science cannot touch. But creationism can be deemed the more logical faith. [With your interpretation of logic I trust you can deem anything you like.]

Third, one must understand evolution is not a fact. There is a strong difference between the terms "hypothesis," "theory," "law," and "fact." A hypothesis is "a statement that can be tested scientifically by some kind of experiment that could refute it if it is wrong."[8] A theory is a hypothesis that has been tested many times but hasn't been refuted yet. And a law of science is "a theory that has been tested, with positive results, so often and in so many different ways that it is almost certainly a confirmed fact of science."[9] However, many scientists are careful to confess that even a law could eventually be refuted. It is impossible to officially deem a law as absolute fact. Evolution should be called a theory rather than a law or fact of science. [This is one of the most tired semantic fallacies around. The relationship between hypothesis law, etc. is just not as described here. Evolution has occurred, that is the fact. The knowledge we have about how it occurs, and what did occur, is the theory. Within the theory various laws describe, for example, how evolution occurs (e.g. Dollo's law), and hypotheses are continually generated by scientists to be tested in order to increase our knowledge. That really isn't so hard to grasp, though I realize it is much easier to deliberately misconstrue.]

Fossil record inadequacies:

One of the strongest [unsubstantiated] arguments against evolution is lack of evidence in the fossil record. Many evolutionists claim the fossil records prove evolution, but they do not [sic! There is only one fossil record.]. If evolution was the true process of creation and all living things developed [no, evolved] from something else over time, there should be fossils that indicate their transitions. [And many have been found (Tiktaalik is a favorite of mine.)] There should be fossils that depict creatures with "incipient eyes, [half-way wings, half-scales turning into feathers, and partially-evolved forelimbs]."[10] [You say there should be, but evolutionary theory does not predict your ridiculous half-eyes.] Morris and Morris make a valid [no, uninformed] point: "It seems very strange that the fossilization process selected only those individuals for preservation that already had completed particular stages of evolutionary progress, and yet preserved these in great abundance and variety."[11] Billions of fossils have been preserved around the world, but none depicting transitional forms have been found. [I don't know about billions, but either way, many transitional fossils have been found. You can keep saying it all you want, but doing so will not constitute evidence. Read Prothero's Evolution: What the Fossils Say and Why It Matters for a long list of transitional fossils.]

Funny conclusion:

While this discourse has only taken a cursory look at the information and research surrounding the debate between creationism and evolution, it has hopefully shed a little light on some modern misconceptions about evolution and its place in the world as "scientific fact." [Blinding light.] Ultimately, Darwinian Evolution is merely a theory, and, although it seems rooted in science, it is actually rooted in faith. [In science, "theory" is the highest attainable attribute.]

It is crucial for Christians to understand the Creation and to accept it as truth, because the Creation story is the keystone of Christianity. If one does not believe in the Genesis account, why should they believe anything else the Bible says? [Indeed!] The Creation is the foundation of the Bible, and it is imperative to the Christian's walk with God that they believe in His role as the Creator. [Vaya con Dios, then, ignoranimuses.]

Biblical destruction

An email from Human Events - Headquarters of the Conservative Underground (*chuckle*) - expresses outrage over the destruction of Bibles in Afghanistan:

A Pentagon spokesman under the Obama Administration has just acknowledged seizing and burning the privately owned Bibles of American soldiers serving in Afghanistan. The Bibles had been printed in the local Pashto and Dari languages, and sent by private donors last year to American Christian soldiers and chaplains, for distribution to American troops on overseas military bases during optionally-attended Christian worship services. Had the Bibles not been recently seized and destroyed, they could have legally been given as gifts during off-duty time to Afghani citizens who welcome our troops in their homes, as an expression of American gratitude for Afghani hospitality, promoting the democratic ideals of freedom of religion and freedom of the press.

It is against regulations for troops to proselytize. Imagine what image it creates if soldiers go around distributing Bibles (conveniently translated into local languages). And I must admit I have a hard time seeing troops and locals fraternizing, Bibles being passed out, and the Muslim hosts being ever so grateful. Rather, it would create resentment and be seen as another act in a fourth crusade.

The homeschooling trap

Only conservative Christians can publish an article in which this opening paragraph is actually meant as an endorsement:

One flustered parent who was disillusioned with public school systems and what she believed to be lack of personal attention and creeping propaganda has chosen an alternative, where she may opt out of lessons on evolution, sex education and teaching that goes against her Christian beliefs – and her tax dollars pay for it all.

But then, the WorldNetDaily is a bastion of inanity. Notice that when conservatives agree with some use of taxes, they will say "her tax dollars pay for it all," but when they condemn it (as is most often the case - in fact this is a first that I see in print such a an endorsement of spending), they will say "my tax dollars pay for it all."

Opting out of any lessons is opting out of education. Most likely Susan Lockhart has trouble with letting her children learn about evolution.

"We had reached a point where the indoctrination in the schools was just untenable," said Susan Lockhart, a homeschooling mother. "I was going down there and complaining on a nearly daily basis about things. It got to the point where I had to do something. I had to get them out of there."

I wonder what things she felt she had to complain about all the time. They don't teach evolution every day of school. What else is did she find so disagreeable? The article does not say.

When the subject of evolution was addressed in Kristin Lockhart's marine science course, she was given an assignment to create a marine life that would evolve and adapt to its environment over time.

"I spoke to the teacher and told her we don't believe in evolution. We believe in creation," Lockhart explained. "I told her my daughter was going to do this assignment in terms of creationism, which she did. The teacher had no problem with it, and she got an 'A.'"

They've got to be kidding! That's an awesome assignment. I wonder how any teachers expect school children to do what professional researchers have a hard time doing. If she could really shown marine organisms adapting, she could publish in Nature overnight. But, appallingly, it is possible to reject the assignment and make another based of ideology rather then evidence.

"My kids don't have to put up with bullying. They don't have to put up with indoctrination. They don't have to have sex education. We're allowed to pray all we want at home," she said. "It's really a lifesaver for Christian parents."

Bullying is bad, but if you avoid it by staying home then the children are missing out on what I consider to be very important social lessons with other kids. I seriously have doubts that children who don't go to school with other kids are as capable socially as the rest of them, and that would be a real handicap. As for indoctrination, that's apparently also dependent on your point of view. I don't actually know what kind of it Susan Lockhart is referring to, but in my book indoctrinate means to instruct in a doctrine, principle, ideology, etc., esp. to imbue with a specific partisan or biased belief or point of view (my book is a dictionary). Christianity is of course a doctrine, and barring your children from arguments against it is indoctrination. Why, why, why would any parents prevent their children from getting sex education? Studies have shown that the better educated children are about sex, the better they know how to prevent unwanted pregnancies and sexually transmitted diseases. Besides, learning about something does not necessarily mean that you condone it. I have learned about ideas and theories that I dislike and that have been proven wrong (Maoism, Intelligent Design), but learning about them is still a good thing. It's like refusing to learn about the Holocaust. It was a bad thing, and exactly because of that it is so important that we all learn about it.

Lastly, I would very much like to see some statistics comparing the education of homeschooled vs. properly schooled children in the US. I predict that homeschoolers will choose science in college less often, will do worse in science, and those that do well in science start doubting their homeschooled ways. I predict that homeschoolers stay closer to home when they grow up, are more unhappy in their relationships, and have lower incomes. I predict that homeschoolers are more likely to accept the religious beliefs of their parents (which is not an endorsement, though I suspect that this is the main reason why some prefer to homeschool their kids), and I predict that homeschoolers are more ignorant as well as less tolerant of different cultures and ways of living.

Please, please do not homeschool your children. Give them the best chances in life by sending them to a real school. If the schools in your city are all bad, move or pay for a private school. When they get home, tell them that YOU don't believe in evolution, but let them make up their own minds. Anything else is indoctrination.

Darwinius has landed

I give in to the pressure:



Details all around: National Geographic, Pharyngula, Ed Yong, Laelaps, Carl Zimmer, and, of course, the actual paper in PLoS ONE.

Placebo works

Placebo is funny! Harriet Hall, MD, in the newest edition of eSkeptic, explain that placebo treatments actually work, and suggest a few way in which they do. For example:

• Placebo surgery works better than placebo injections
  
• Placebo injections work better than placebo pills
  
• Sham acupuncture treatment works better than a placebo pill
  
• Capsules work better than tablets
  
• Big pills work better than small
  
• The more doses a day, the better
  
• The more expensive, the better
  
• The color of the pill makes a difference
  
• Telling the patient, “This will relieve your pain” works better than saying “This might help.”
  

The main hypotheses about how placebo works are expectancy, motivation, conditioning, and endogenous opiates. These sound like good things, and in fact they are used in conventional medicine all the time.

We can’t isolate placebo effect from conventional medicine — it gets us thinking the wrong way. As the neurologist Robert Burton says, “Even given our advanced state of medical knowledge, much of routine medical care — from treating backaches to the common cold — relies primarily upon reassurance and hope, not disease- specific treatments … we need to reconsider how to facilitate the placebo effect with minimal risk and cost, and without deception.”

Humans work in mysterious ways. One of the most important lessons of science, in mind mind, is that we are not in control of ourselves by far - lots and lots of things go on in our minds that "we" are not in control of, or even aware of. We are masters at deluding ourselves, and placebo treatments is a testament to that.

Jared Diamond sued by tribesmen

Jared Diamond is being sued for $10 million (email me for a free pdf). He wrote an article for The New Yorker last year, telling a story of revenge warfare in Papua New Guinea. The two tribesmen who waged war on each other, Wemp and Mandingo, have joined forces with each other and none other than Stephen Jay Gould's widow, Rhonda Roland Shearer, to sue Diamond and Advance Publications Inc. over alleged errors concerning the events that Diamond reported on.

Diamond explains that he interviewed Wemp in 2006 and took detailed notes on which the article is based. Part of the story is that Diamond was reporting not as a scientist, but as a journalist, and that for those two spheres very different rules apply. In science one would report in a neutral fashion, not naming names. But in journalism including names is the default practice, in part so that people can check what is written.

This lawsuit should be thrown out immediately, in my opinion. Wemp et al. charge that some of the events reported on are erroneous, such that the war started when a pig destroyed a garden and lasted three years. Instead they say that the cause was a gambling dispute and lasted only a few months. So... demand $10 million in damages? Kick me if that makes any sense! But still, Diamond contends this is all irrelevant, because he took careful notes during the interview with Wemp. So Wemp exaggerated, gloated, and lied, and Diamond got some facts wrong. What of it?

Imagine the negative consequences if Wemp, Mandingo, and Shearer wins the suit. Every time an interview is made, the journalist has to fear that he is being lied to, and that the interviewee will later demand retributions for defamation. If the article is factually wrong, it should be retracted (in fact that did happen to the free online version), but anything more than that makes little sense to me. And consider the consequences of filling the pockets of the likes of Wemp who kill people in tribal wars:

Whether or not Diamond got the facts of Wemp’s case right, it is true that the tribes of PNG do practice revenge warfare, says [anthropologist Pauline] Wiessner, who has studied war in PNG’s Enga Province, just north of the region where Wemp and Mandingo live. In Enga, more than 300 tribal wars have taken the lives of nearly 4000 people since 1991. That’s one reason Wiessner, who is active in local efforts to bring peace to PNG clans, is worried about the outcome of the case if it results in a large monetary award: She fears that the money could eventually go to buy weapons that would make the wars even more deadly. “When these wars first started, they were fought with bows and arrows, but now they have M-16s,” she says.

Hard evidence for allopatric speciation

A question was posed to me, and I have been thinking about it on and off for a couple of days. Peter and Rosemary Grant has been studying Darwin's Finches (Geospiza) for decades, and at the talk they gave at Caltech last Thursday, he presented this map.



It details how the finches originally arrived at San Cristóbal from the mainland, and then radiated from there to Española, Santa Maria, Santa Cruz, and back to San Cristóbal, during which time they had speciated, resulting in two different species on San Cristóbal. The inference from the observations of living birds is that the finches speciated allopatrically. That is to say, that the genetic differences resulting from mutations took place in two different populations of finches, between which there was no gene flow (i.e. no mating between the two populations). This is the mode of speciation that is most easy to comprehend: two pupolations of the same species are reproductively isolated from each other by some physical barrier (such as a large body of water between San Cristóbal and Española), and as mutation and natural selection (or genetic drift) cause the two populations to diverge from each other, they eventually become different species.


Different species of Darwin's Finches have different beaks adapted to different types of foods.

My question to Peter Grant was what hard evidence there is that the mode of speciation was allopatric, and if sympatric speciation could be ruled out. Peter's reply was to ask me what I thought would constitute "hard evidence", and that is a good question indeed.

Sympatric speciation is a mode of speciation where there is no cessation of gene flow between any individuals - everyone continues to be able to mate with everyone else (of the opposite sex). Recent work on computer simulations have shown that this mode of speciation is possible with one or more of limited dispersal, assortative mating, and competition for resources. Since Darwin's Finches have specialized feeding on different foods, by changing the depth of their beak to match the seeds etc., it is at least possible to imagine that sympatric speciation occurred. Can that be ruled out given the evidence available? Is there any hard evidence for allopatric speciation in this case, or is that a conclusion arrived at because it is so much easier to understand allopatric speciation?

With that I am left pondering what evidence would satisfy me that this is a case of allopatric speciation.

My answer so far is to say that if among remnants of dead birds on San Cristóbal from the time that they are thought to have speciated, only finches morphologically similar to the birds that lived there at that time are found, but the remnants of birds on Española show signs that they changed there, then I would say that's pretty solid evidence of allopatric speciation. On the other hand, if it is found that among remnants of the first population if birds on San Cristóbal there is a continuous change in morphology, then I would consider that as evidence for sympatric speciation.

My question to you, dear reader, is whether you can think of anything else that would provide evidence either way?

Scientia Pro Publica #4

Scientia Pro Publica - the best science blog carnival around - has a new edition at The Primate Diaries.

Venemous Komodo dragons

I wonder why Kurt Schwenk, evolutionary biologist, thinks the evidence that Komodo dragons are venomous is not convincing. Bryan Fry dissected jaw tissue from a terminally ill lizard, and found venomlike proteins that keep blood from clotting and others that lowers blood pressure. This seems like fairly indicative evidence to me, but Schwenk calls it “meaningless, irrelevant, incorrect or falsely misleading.” Strong words indeed.

Even if the lizards have venomlike proteins in their mouths, Dr. Schwenk argues, they may be using them for a different function.

Sure, but the simplest hypothesis seems to be that they are used for attack.

Dr. Schwenk also doubts that venom is necessary to explain the effect of a Komodo dragon bite. “I guarantee that if you had a 10-foot lizard jump out of the bushes and rip your guts out, you’d be somewhat still and quiet for a bit,” he said, “at least until you keeled over from shock and blood loss owing to the fact that your intestines were spread out on the ground in front of you.”

Look, the effect of the proteins found in a gland in the mouth of the Komodo dragon are known to have the effect that its bite has on its prey. That's not conclusive evidence - finding those proteins in prey would help - but I am curious why Schwenk is so dismissive.

A personal case of swine flu

Last week, after my wife and two kids had just returned from a vacation in Japan, we all got sick with influenza-like symptoms. We went to the hospital, and there they downplayed the risk that this had anything to do with swine flu. Yet, they tested our oldest son and my wife, who had the most severe symptoms, and the results showed that my son was positive for Influenza A, while my wife was not. A second test confirmed that my wife did not have Influenza A. The test for Swine Flu takes ten days, and we expect to hear from them this coming week. In the meantime we have all had fever etc., but are now symptom-free and feel well.

At the hospital we were given prescriptions for TamiFlu, and instructions to stay home for a while. Now, what I am wondering is why more care wasn't given, considering the scare swine flu is causing, and the potential pandemic that it might cause? First, we were given the option to have a test done. They didn't advise it, but just agreed to do it when we asked for it. Second, we had to get the prescriptions filled at a local pharmacy ourselves. This is a far cry from the precautions of, say, the authorities of Hong Kong, which quarantined a whole hotel for a week. I believe that was over the top, but somewhere between that and sending people off to the pharmacist on their own feels like a better approach to me.

No one has offered us any explanation for how one of my sons could have Influenza A, while the rest of us apparently did not. My wife was the first to show any symptoms, with my oldest son following shortly after. Then myself and then my youngest son, who luckily had the fewest symptoms. So, how could the virus strains be different? If he really had Influenza A, how come the rest of us didn't catch it? How could we get two different viruses, and not all contaminate each other?

I fear that no one will ever be able to tell us.

Inward Catholic outrage

Catholics have been flamed a lot over their dogmatic attitudes towards freedom of speech, abortion, and especially their reaction towards people who disagree with them. At University of Notre Dame a rather miniscule group of Catholics protested today against Obama speaking at commencement, and/or against him receiving an honorary degree from there. All because he supports women's right to choose to have an abortion, which the Catholic church continue to be against. More than 100 people gathered in protest. So? Notre Dame is a Catholic university, and with nearly 13,000 students and faculty, one might expect a wee bigger group of protesters if the general attitude weren't favorable of letting Obama speak and receive the honorary degree. So probably it is.

But mostly I wanted to share the good feeling of a Catholic who is justly ashamed of her church:

genia on May 16, 2009 10:28 PM

All this protest and judgement...condeming...this is against everything I was taught as a Catholic.
As a Catholic I wonder why my religious leaders chose to embarrass us. I wonder why they chose to make fools out of my faith...I wonder why they chose to take a stand against the President of the United States...my president?
But mostly I wonder where these Catholic leaders were when Bush decided to attack an innocent country, starting an unprovoked war.... bombing sleeping cities...killing thousands of woman, children..men...and our military....where were the bishops and archbishops then? Are these victims not God's children?
Shame on the Catholic church...shame for spectacle they are making of my religion... shame on them.

Where were these Catholic leaders indeed?! Thanks genia, for sharing your outrage.

Retrospection

Retrospection is a very powerful way of looking at things.

Ruse and Grants

*LIVEBLOGGING from the Darwin Symposium at Caltech*

It's seven-thirty and I'm at the Beckman Auditorium at Caltech. In a minute or so Michael Ruse will be speaking about Darwin's famous book. "The Origin at 150: Is It Past Its Sell-by Date?" I predict he's going to say that while evolutionary theory has evolved (pun planned for months) since then, The Origin still has a lot of useful stuff to tell us. And I predict that when he finally says that, I will go "pfft!"

---

8:34. They changed the schedule. Peter and Rosemary Grant were on first. Here's my questions to them (for after Ruse's talk):
Allopatric speciation is easier to picture, and to infer, but I wonder about the hard evidence that Geospiza speciated allopatrically. Can we rule out sympatric speciation in this case? In times of stress it may be advantageous to specialize on a subset of resources, and one population may split into two specializing on different resources.

[The Grants' lecture ("Darwin's Finches") was great, but my battery was running low, so I decided just to sit and listen instead of typing.]

Michael Ruse is on. So far about how rich Darwin's family was. Darwin was not a rebel. He speaks of Darwin in present tense, which is confusing to me. "He's a great revolutionary, but not a rebel." Ruse quickly goes over the history of the voyage in six sentences. Then he's back.

---

8:49. Ruse remarks that there is absolutely no doubt whatsoever that Wallace and Darwin came up with their ideas of natural selection independently of each other. I beg to differ. There is at least doubt, as I have written about before.

---

9:16. In 165 lectures at South Kensington, Huxley gave natural selection ten minutes only. He just wasn't interested.

So far it's been a historical perspective of Darwin and his contemporaries. For instance, Ruse makes the point that while The Origin was published in 1859, we have to compare Darwin's thinking on the matter of evolution to his contemporaries of the 1830's. But then after 1859 evolution was widely accepted, except in the American south (laughs).

---

9:20. Pffft! "Thank God! No part of Darwin's theory is still standing. And thank God! All of Darwin's theory still stands.

Ruse's lecture was entertaining. It's always good to hear about the details of the lives of great scientists.

I'll have to send my question to the Grants by email, because we left before the question session, at about 10pm.

Irrelevant and ignored

The AFA is advertising their own failure.

On April 15, concerned and caring individuals held TEA Parties in over 2,000 cities. Hundreds of thousands of Americans participated in the TEA Parties. Despite those numbers, the liberal media practically ignored the event. When asked if he knew about the TEA Parties, President Obama said he was unaware of them.

Are all the media liberal to the AFA? Bill O'Reilly? Rush Limbaugh? Perhaps an acknowledgment that only crazy fundies support them would make the AFA come to their senses.

The email also informs us that the next TEA party is scheduled for the 4th of July. That should prove effective! I mean, because people aren't doing anything else that particular day...

74th Symposium at CSHL

In a couple of weeks I will be attending the 74th Symposium at Cold Spring Harbor Laboratory: EVOLUTION: THE MOLECULAR LANDSCAPE, and I just can't wait. The list of abstracts is here, and includes such luminaries (and others) as

Behe, M.: "Four decades of experimental adaptive evolution of microorganisms—A review"
Carroll, S.: "Endless flies most beautiful—Cis-regulatory sequences and the evolution of animal form"
Charlesworth, B.: "Genetic recombination and molecular evolution"
Davidson, E.H.: "Evolution of the animal body plan by cis-regulatory alteration of gene network architecture"
Dennett, D.C.: "The cultural evolution of words and other thinking tools"
Hauser, M.: "The origins of a generative brain and the possibility of impossible cultures"
Hoekstra, H.E.: "White mice on white sand—The molecule steps to a phenotypic optimum"
Joyce, G.: "Evolution in an RNA world"
Koonin, E.V.: "Search for a tree of life in the midst of the phylogenetic forest"
Lenski, R.E.: "The dynamics of phenotypic and genomic evolution during a long-term experiment with E. coli"
Levine, M.: "Transcriptional precision in the Drosophila embryo"
Miller, K.R.: "Deconstructing design—A strategy for defending science"
Pääbo, S.: "A Neandertal perspective on human origins"
Pinker, S.: "The cognitive niche"
Scott, E.C.: "The evolution of intelligent design"
Szostak, J.W.: "The origin of cellular life and the emergence of Darwinian evolution"
Wilson, E.O.: "The molecular landscape—A journey along the highway of evolution"

Crash this poll

A Dutch political party wants creationism taught in schools. Arie Slob (gotta doubly love that name), leader of the orthodox ChristenUnie party, says

'It is as if there are no other ideas and theories,' Slob was quoted as saying. 'There are more thoughts about the beginning of this earth than the one printed in the text books.'

There's more than one myth, but only one scientific theory that holds water. That's why evolution is taught, and not creationism.

Then there's a poll to crash:

What is the best explanation for how we got here?
Evolution 65.7%
God created the world in six days 17.1%
God created the world but it took longer 7.0%
Intelligent design 5.9%
Don't know 4.2%

Total votes: 286

Not much to crash, I know, since "evolution" is well in the lead. But with the hordes of Pleiotropy readers, we could surely get that number up to a full 68% !!!

Evolver Zone

Evolver Zone is a newly launched site with various evolution resources aimed at students, teachers, and researchers. For example, it has a very nice list of journals related to evolution, and you can buy this t-shirt with the only figure Darwin drew in The Origin.

Blame the demons

A man at the pharmacist was on his cell phone:

"I have been having trouble staying on a straight path, blamelessly.... Yeah.... Can the church help me?.... Yeah... Yeah.... I keep going to all the wrong places, and I can't help myself.... Yeah.... I have been to many different churches, but no one has been able to help me.... Yeah.... Yeah.... Yeah.... It is the demons inside of me that's taking over, and I was wondering if you could help me get rid if them?.... So you have classes starting tomorrow?.... Yeah."

What I wouldn't give to hear the other end of the line. My suspicion is that whoever he was talking to - I presume a clergyman - was thinking the same as I (why not?), that no demons have possessed him, and as soon as he accepts that the human nature is frail he will be able to take responsibility for himself and stop blaming imaginary beings. I don't know what the wrong places he is going to are, but he may have a real problem (gambling? drugs? prostitutes? atheist meetings?), and if that's the case he ought to get some real help. A quick search finds many people who can help with addictions for gambling, drugs, and prostitution.

Keep it fucking real!

The American Family Association emailed me again today to tell me what a bottom-slapping bad boy Pepsico is (remember to look for their products: Pepsi soft drinks, Frito-Lay chips and snacks, Quaker Oats, Tropicana, and Gatorade). What have they done now? How have they upset the chaste and righteous this time?

Pepsico is a sponsor of the 2009 New York City Gay Pride Parade. On AFA's site you can watch a new amusing video-clip of participants in a parade having the time of their lives, it seems. They warn you that

The video below shows what type of activity occurs at this parade. WARNING: The content is offensive content, including one very strong profanity (at the end).

Ooh, I was expecting something really nasty - I've been to Bar'Do, and I know they can make you spin on your behind with delight over the obscenities. But, sigh, the last line was just a simple "keep it fucking real!" That's it. That's all it takes for the AFA to swoon, I suppose.

Losing our freedom to discriminate

To no one's surprise, there is an awful lot of resentment against the bill introduced in Maine to end discrimination against same-sex marriage. For example, a bishop calls gay marriage dangerous, Pat Robertson (televangelist) claims it leads to bestiality and pedophilia, and at Pro-Polygamy.com (eh?) they say the bill in fact discriminates against polygamists (I can just imagine two straight couples deciding to get married all to each other).

In today's Kennebec Journal, there is a (largely insignificant, I know) letter by one Angela Fletcher, Same-sex marriage like Darwin's evolution theory, which is so arrestingly inane that I feel i must display it here in its entirety, with my comments in red:

Even if the governor signs the bill to make same-sex marriages legal in Maine, I will no more let my children or my future grandchildren [why stop there?] believe [are people told what to believe?] that it is OK for same-sex couples to marry, than I did before it becomes a law. This idea of marriage is no more acceptable to me than Darwin's Theory of Evolution. [And you have just labeled yourself as a conservative Christian bigot.]

It is my right to teach my family my religious beliefs without being discriminated against. [Is anyone saying anything else? Or is it the homeschooled peasant's way of interpreting this bill?] That is exactly what would be happening in the public schools -- No thank you. [Your personal beliefs are not discriminated against with this bill - it is you who think that your beliefs entitle you to discriminate against others.]

The demoralization of our great country can be blamed on the fact that our forefathers separated religion from state. [What demoralization? Some people are demoralized by the sexual acts that they get off on picturing others having in private, and others are demoralized by the discrimination against people who want the same rights as you (e.g. health care and inheritance rights).]

It seems to me that those of us of religious descent [no one is of 'religious descent' - being religious is a choice, or?] are losing more and more of our religious freedoms. [Which? Those freedoms to discriminate against others?] Little by little, from state to state, our country's morals are deteriorating. [Or, again, improviong, depending on your level of bigotry.] Why is murder still wrong? [Because it doesn't happen between consenting adults?] Oops, I forgot it's legal in some states, but that's a whole different ballgame. [Hear hear! Too many states still have the death-penalty, and those will have to change. Otherwise, I have no idea what you are referring to.]

Ode

Tomorrow I will see my children for the first time in six weeks. If you're a parent and haven't tried being away from them for that long, my recommendation is never to try it. Not that all parents hate it as much as I do, I know, but given that I feel like someone has cut off my left arm, I just can't tell anyone that it's all the good things one can imagine six weeks alone to be.

My kids are a lot of trouble. Two boys ages five and two, and they are every bit as active and exhausting as it sounds. But they are also my reason to live. Since they were born other important things in life went from top priorities to I hope to get those done when I retire. Or when my kids retire. Not that I plan to retire, but they might. I do go to work, but otherwise spend all my free time together with them. So six weeks suddenly alone is something to adjust to.

For me, one of the worst things things about being away from them is talking to them on the phone. Another bad thing is not talking to them on the phone. On more than one occasion they have been too busy playing or doing something else, and have only reluctantly agreed to talk. And I realize that they are fine without me. And that hurts. It's good for me because it's good for them that they can easily do without me, but it's bad for me for me. I want them to need me, but they don't need me, they need someone. In theory, it would be beneficial for me to have someone else spend all their time and energy on them, and spend my own time pursuing other goals. But then why is it that I feel this way? Are these emotions adaptive, or do they make no sense at all? Am I an example of an organism locked in an indefinite loop of love, neurons firing at will without sense? Admittedly I don't have access to the inner feelings of other fathers, but the ones I overhear here and there from time to time talking to their buddies about their offspring don't strike me as all that emotionally invested. Enough to be great fathers, but not this festering fondness.

In less than twelve hours my boys are back, and my daily life makes another revolution. Coming home to an empty apartment will be substituted with jumping, tickling, sword fighting, drawing, screaming, eating, bathing, laughing. Sleeping in my arms. I recommend.

Why are all the songs about love for a woman, and none of them about the love for children? Lennon is the only writer that comes to mind:

Third ever Scientia Pro Publica

Scientia Pro Publica is the blog carnival that replaces The Tangled Bank (which inexplicably has gone the way of baiji). It's is now up, and has tons of sciency posts: Scientia Pro Publica 3: the Swine 'flu Edition.

Umpteenth Carnival of the Godless

Don't overlook the Carnival of the Godless on Relatively Science. I recommend this post on The Evolving Mind: The Spirit World's Interest in Sex, which concludes like so.

Relationships are important, so don’t deceive others. Perhaps the sexual relationship is the most important to any animal. And thus the focus on sex and offspring in the Bible and other so-called sacred texts. And who better to monitor the sexual lives of people than an all-knowing, all-might, invisible alpha?

Go read it all.

Or you can just enjoy Tim Minchin here:

Darwin symposium at Caltech

For those of you in SoCal here's a tip on how to spend Thursday May 14th: At the Beckman auditorium at Caltech, because that's the time and place of

THE SCIENCE OF EVOLUTION/THE EVOLUTION OF SCIENCE
A symposium on the occasion of:
The 200th anniversary of Darwin’s birth
The 150th anniversary of The Origin of Species
The 20th anniversary of the Beckman Institute at Caltech

It's free for all, and speakers include among others:

Eric Davidson: "Some New Ways of Thinking About, and Working on, Evolution of the Body Plan"
John Grotzinger: "Geologic and Environmental Context of the Early Cambrian Radiation of Animals"
Christoph Adami: "The Free-for-All" Effect: A Mechanism for a Drastically Varying Rate of Evolution"
Frances Arnold: "On Beyond Nature: Protein Evolution in the Laboratory"
Michael Ruse: "The Origin at 150: Is it past its Sell-by date?"
Peter and Rosemary Grant: "Darwin's Finches"

Full program is here.

LOLcat is a Christian

Edward Current's cat is a Christian. Of course.

Hobbits perhaps not cretins

Vacation, jet lag, and deadlines all conspire to drag me away from blogging. But no more. Vacation is over, jet lag almost gone, and deadlines have been crossed. No matter.

So, remember John McWhorter's untestable hypothesis that the hobbits (H. floresiensis) were responsible for simplifying a group of Indonesian languages?

For those of us who have doubts that the hobbits were not just... well, retarded humans, new evidence leads anthropologist Dean Falk of Florida State University in Tallahassee to surmise that they perhaps were endowed with vamped up brains:

An analysis of the inner surface of an 18,000-year–old skull assigned to Homo floresiensis, a species also known as hobbits, indicates that this tiny individual possessed a brain blessed with souped-up intellectual capacities needed for activities such as making stone tools

From ScienceNews:

Falk compared a cast of the cranium’s inner surface, or endocast, obtained from the partial hobbit skeleton LB1 to endocasts from both modern humans and from other fossil skulls in the human evolutionary family, called hominids for short. These casts bring into relief impressions made by various anatomical landmarks on the brain’s surface.

“LB1 reveals that significant cortical reorganization was sustained in ape-sized brains of at least one hominid species,” Falk said.

One legitimate concern is that the hobbits were otherwise normal humans who suffered from cretinism: the condition of severely stunted physical and mental growth due to untreated congenital deficiency of thyroid hormones (hypothyroidism) or from prolonged nutritional deficiency of iodine.

So how can we know when all we have is fossils? Pleiotropy! The genetic mechanism - not the blog.

Why pleiotropy? Because

Low levels of thyroid production cause an array of skeletal abnormalities in cretinism, as well as dwarfism.

CT scans of LB1 show no signs of dental, skull or limb conditions associated with cretinism, [William] Jungers [of Stony Brook Health Sciences Center in New York] said. People with cretinism generally have much larger brains than that of LB1, he added.

I must admit that I am emotionally invested in the hypothesis that the hobbits weren't mere humans. Just imagine how cool it would be to meet and communicate, even, with another species. Talk about what that would do to our own image of ourselves as the pinnacle of evolution.