Genes, Phylogeny, and Orangutans

Jeffrey H. Schwartz is well known to talk.origins veterans because we discussed his book (Sudden Origins: Fossils, Genes, and the Emergence of Species) back in 1999. Schwartz tried to make the case for a "groundbreaking and radical new theory of evolution." This "theory" was based on the idea that new species spring into existence very quickly when a mutation in a homeobox (HOZ) gene arises in a population. It's a "theory" of saltation but it's based on such a flawed understanding of genetics that you really have to read to book to see just how bad it is. Sudden Origins is a leading candidate for the worst science book ever published.

In case you want to see a shorter version, the basic idea is explained in Schwartz (1999).

Over the years, Schwartz has published many other ideas that are controversial. Lately he has been pushing the concept that molecular phylogenies are unreliable. In part this is because he is opposed to gradual change as documented in the record of the genes. He thinks that real evolution takes place when alterations of regulatory genes result in major new phenotypes. Thus, the best way to discover the history of life is to examine anatomical homologies and differences.

But part of the problem lies in Jeffrey Schwartz's idiosyncratic understanding of genetics and molecular biology. When you put these together, this is what you get in Schwartz (2009).

This having been said, systematics and evolutionary biology need not remain estranged. Developmental biology increasingly makes clear that organismal change (and by extension, evolution), is not how it was imagined when the synthesis emerged (see reviews in Schwartz 1999, 2009b; Maresca and Schwartz 2006). Further, because of the interrelation between, e.g., the physical properties of cells, signaling pathways, epigenetic effects and development and consequently the origination of form, the false dichotomy of ‘‘molecules versus morphology’’ that resulted in the 1980s from the dethroning of morphology by the hegemony of molecular analyses is no longer tenable (Schwartz 2009a). Indeed, the undeniable hierarchical continuum from the molecular through the morphological, firmly centralizes morphology (as understood via development) in systematic endeavors (Schwartz 2009a).

Grahan and Schwartz (2009) have just published a paper in which they claim that orangutans are more closely related to humans that are chimpanzees. According to them, the molecular data is not reliable. They claim that detailed morphological comparisons show that orangutans are our closest ancestor.

John Hawks asks the question "Are orangutans our closest living relatives?" and he comes up with the best possible answer to scientists with a well-known history of promoting "unusual" positions on evolution.

It's a lesson that New Scientist should have learned. They devote several pages to the Grahan and Schwartz paper thereby giving it much more publicity than it deserves [Could the orang-utan be our closest relative?].¹ The article is written by Graham Lawton who you might remember from the "Tree of Life" episode [see: Explaining the New Scientist Cover]. The editors of New Scientist knew full well that their decision would be controversial so they took a proactive position by writing a short editorial [In praise of scientific heresy ].

If its claims are so outlandish, should the research even have been published? Some scientists would clearly have preferred it if the paper had never seen the light of day, and question the judgement of the journal.

That is territory we should tread with care. Ideas that mainstream opinion "knows" to be wrong occasionally turn out to be right. The insights of Galileo, Stan Prusiner - who discovered prions - and many others were once denounced as heresy. And even those that are wrong can be valuable.

Science proceeds by questioning its own assumptions and regarding every "fact" as provisional, so alternative hypotheses should be given an airing, if only to reaffirm the strength of the orthodoxy. Science that pulls up the drawbridge on new ideas risks becoming sterile. The journal recognised that and should be applauded for its decision to disseminate this challenging paper.

There's some truth here, but only some. You can't use Stanley Prusiner as an excuse to publish every crazy idea that comes along. Some ideas really are crazy—they are not revolutions in disguise. The plain fact is that Jeffrey H. Schwartz has already had his chance to make his case and he has not been successful. How many chances does he get before we draw the obvious conclusion?

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1. The article was two pages long and the editorial was much less than one page. This may not qualify as "several" pages by some definitions.

[Photo Credit: Daily Mail]

Grehan, J.R. and Schwartz, J.H. (2009) Evolution of the second orangutan: phylogeny and biogeography of hominid origins. Journal of Biogeography, published online June 22. 2009. [doi:10.1111/j.1365-2699.2009.02141.x]

Schwartz, J.H. (1999) Homeobox genes, fossils, and the origin of species. Anat Rec. 15:15-31. [PubMed]

Schwartz, J.H. (2009) Reflections on Systematics and Phylogenetic
Reconstruction. Acta Biotheor 57:295–305 [doi: 10.1007/s10441-009-9078-9]

What Can Scientists Do to Help Science Journalism?

 
This week's issue of Nature has a number of articles devoted to science journalism. Their publication coincides with the 6th World Conference of Science Journalists in London, UK.

One of the articles is an editorial, Cheerleader or watchdog?, about what scientists can do to help science journalism.

Scientists can do little to stem this bloodletting. But whatever they can do to engage with those caught up in it, and ensure that questioning and informed science journalism persists, will be worthwhile. If there is to be a transition to new — perhaps philanthropic — business models for in-depth reporting or new types of analytical media, science journalism will integrate into them all the better if scientists are taking an active interest in its health. And if the future of the media truly is a dire landscape of top-100 lists, shouting heads and minimal attention span, then such efforts might at least defer the grim end.

Even amid the turmoil, however, scientists can help ensure that reporting about science continues to be both informed and accurate.

I agree that scientists should work on trying to make science reporting more accurate. So far, we haven't been too successful.

But there's another important contribution we can make. We can help clean up our own act so that less bad science is published. This will not only make science better, it will have the spin-off effect of making life easier for science journalists. At the very least, we should make sure that press releases coming from our institutions are accurate. Every scientists should have to stand behind and endorse the press releases from their supporting institution. Let's take responsibility.

Also, wouldn't it be nice if most of the papers published in the scientific literature were careful to put their work in the proper perspective? Wouldn't it be nice if scientists themselves stopped exaggerating their contributions and stopped making outrageous claims? Science journalists have not done a good job of sifting the wheat from the chaff, in spite of what they think. They are far from blameless but scientists carry a bigger share of the blame for the sorry state of science literacy.

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Campus Excitement

 
There's usually something exciting happening on the University of Toronto campus during the summer.

It's a popular location for shooting movies and TV shows and you never know what you'll find on any given day. This is the scene that greeted me today when I emerged from the subway station. It took a few seconds to realize that I wasn't in the middle of a real emergency.

Last week the front campus was the scene of a bank truck robbery in Germany, just in front of a sidewalk café. I wish they'd left the outdoor tables and umbrellas and kept serving the wine and food.

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Monday's Molecule #127

 

Today's molecule stinks.¹ You have to identify it by giving me the common name and the IUPAC name.

There's only one Nobel Laureate whose name is linked to this molecule. The Laureate was responsible for determining its structure.

The first person to identify the molecule and the Nobel Laureate, wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Michael Clarkson of Waltham MA (USA), Òscar Reig of Barcelona, Maria Altshuler of the University of Toronto, Mike Fraser of the University of Toronto, Jaseon Oakley of the University of Toronto, Bill Chaney of the University of Nebraska and Ian Clarke of New England Biolabs Canada in Pickering ON, Canada.

Bill Chaney has donated his free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours.

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1. Opinions may vary.

Grandpa Burger

 
When I was (much) younger I used to order the Teen Burger when we went to the A&W. Even after I stopped being a teenager I still got the Teen Burger 'cause I wasn't really eligible for any of the others.

While we were living in Europe there were no A&W's in our part of the world so I didn't have a problem choosing what to order. By the time we returned to Canada, Jane had been born and I could order the Papa Burger without feeling guilty.¹

Here I am at the the A&W yesterday, trying out the Grandpa Burger. Technically, I won't be officially eligible for the Grandpa Burger until next January. Coincidentally, that's when my daughter Jane and her husband Michael will be able to buy the Mama and Papa Burgers.

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1. I sometimes cheated and ordered the teenburger anyway.

[Hat Tip: A&W Grandpa Burger commercial.]

Everything You Wanted to Know About Canada but Were Afraid to Ask

 
The Canadian system of government can be a little difficult to understand and recent political events in Canada don't make it any easier. Here's a brief and dumbed-down lesson on Canadian politics. It's intended mostly for Canadians but foreigners might also find it helpful.

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Thanks to Greg Laden most readers on his blog are now much more knowledgeable about Canada than most Canadians.

The Great, Profound, and Valuable Works of Evolutionary Psychology

A few weeks ago I was having an email discussion about evolutionary psychology with Gad Saad. Readers may recall an earlier posting about Gad's work on the correlation between the length of one's fingers and the kinds of things one likes to buy in a store [Psychology and Finger Length].

One of my criticisms of evolutionary psychology is that its proponents don't usually seem to have a good handle on modern evolutionary biology. Gad argues that, while this may be true for some evolutionary psychologists, it's not a widespread problem. He, for example, considers himself to be very knowledgeable about evolution. His undergraduate degree is in Mathematics and Computer Science. He then went on to obtain an MBA, an MS in Management, and finally a PhD in Marketing [Gad Saad].

He is currently an Associate Professor in the Marketing Department at Concordia University, Montreal, Canada. But over the years he has learned a great deal about evolution and in 2008 he was appointed to the "Concordia University Research Chair in Evolutionary Behavioral Sciences and Darwinian Consumption." Gad explained to me that this appointment was recommended by several experienced evolutionary biologists.

We weren't making much progress in our email discussions. It seemed that we had been reading different accounts of evolutionary theory because we couldn't agree on some basic concepts. Nevertheless, Gad advanced a number of vigorous defenses of evolutionary psychology including the following point that I reproduce from our email exchange with his permission. (Actually, he gave me permission to post his list of "great, profound, and valuable works" but not the actual paragraph where he made the claim. I posted the actual claim because it differs from what Gad said in the comment to my earlier posting.)

You are indeed correct that evolutionary psychology has at times succumbed to the allure of just-so storytelling. That said, it is unfair (and frankly dishonest of you) to place all evolutionary behavioral scientists under the negative umbrella that you repeatedly do. Evolutionary psychologists produce great, profound, and valuable works, and at times can produce weaker works with tenuous conclusions. This holds true of biochemists as well. Physicists disagree as to whether String Theory is valid or not. Should we equally view physicists as providers of shoddy and controversial work?

I was intrigued by the claim that evolutionary psychologists have produced "great, profound, and valuable works" and I asked for examples. He supplied them but around that time I got distracted by real life and didn't follow up on our email exchanges.

Now Gad has posted his list in the comments to yesterday's posting on Why Evolutionary Psychology Is False.

I think it deserves wider coverage so here, without comment, is Gad Saad's list of the great, profound, and valuable works of evolutionary psychology. This is the best of the best by one of the leading experts in the field. I think we can get a good sense of the overall quality of the discipline by examining the list.

1. Women alter their preferences for the facial features of men as a function of where they are in their menstrual cycles. When maximally fertile, they prefer men possessing markers of high testosterone.
2. Babies display an immediate instinctual preference for symmetric faces (at an age that precedes the capacity for socialization).
3. Children who suffer from congenital adrenal hyperplasia display a reversal in their toy preferences. Furthermore, using inter-species comparisons, vervet monkeys display the same sex-specific patterns of play/toy preferences as human infants. This suggests that contrary to the argument made by social constructivists, play has an evolved biological basis.
4. Individuals who score high on an empathy scale are more likely to succumb to the contagion effects of yawning. This is indicative that this particular contagion might be linked to mimicry and/or Theory of Mind.
5. How provocatively a woman dresses is highly correlated to her menstrual cycle (a form of sexual signaling found across countless Mammalian species).
6. Culinary traditions are adaptations to local niches. For example, the extent to which a culture utilizes meat versus vegetables, spices, or salt is a cultural adaptation (this is what behavioral ecologists study).
7. Maternal grandmothers and paternal grandfathers invest the most and the least respectively in their grandchildren. Whereas all four grandparents have a genetic relatedness coefficient of 0.25 with their grandchildren, they do not all carry the same level of "parental uncertainty." In the case of maternal grandmothers, there is no uncertainty whereas in the case of the paternal grandfather, there are two sources of uncertainty. This last fact drives the differential pattern of investment in the grandchildren.
8. Good male dancers are symmetric (paper published in Nature). One would expect that some behavioral traits might correlate with phenotypic quality as honest signals of an individual's desirability on the mating market.
9. Self-preference for perfumes is linked to one's immunogenetic profile (Major Histocompatibility Complex).
10. When a baby is born, most family members (especially those of the mother) are likely to state that the baby looks like the father. This phenomenon is found in countless cultures despite the fact that it is objectively impossible to make such a claim of resemblance. The reason for this universally found cultural tradition lies in the need to assuage the fears of paternity uncertainty.
11. Environmental stressors (e.g., father absence) and the onset of menarche (first menses) have been shown to be highly linked. In numerous species, the likelihood of a female becoming reproductively viable is affected by environmental contingencies.
12. Women are less receptive to mandatory hospital DNA paternity testing (for obvious reasons). In other words, their willingness to adopt a new product/service is fully driven by an evolutionary-based calculus.
13. Women can smell the most symmetric men. In other words, women have the capacity to identify men who possess the best phenotypic quality simply via their nose. This is what I have referred to as sensorial convergence.
14. Using fMRI, the exposure to ecologically-relevant stimuli (e.g., beautiful faces) yields distinct neural activation patterns in men and women.
15. In choosing a mate, humans tend to prefer the smell of others that are maximally dissimilar to them along the MHC. This ensures that offspring possess a greater "defensive coverage" in terms of their immunological system.

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Swine Flu Is Caused by French Fries

 
According the a report from Russia, the current swine flue pandemic is caused by genetically modified potatoes that are sold as French Fries in many Western industrialized nations [Russian Scientists Warn Of Genetically Modified Fast Food Link To Pandemic Flu].

Scientists from Russia’s Ministry of Health are warning in a secret report to Prime Minister Putin that they have discovered a ‘critical link’ between the H1N1 influenza (Swine Flu) virus and genetically modified amylopectin potatoes that are consumed in massive quantities nearly exclusively by Westerners and sold in fast food restaurants as French Fries.

According to these reports, the protease enzyme genetically modified in the potatoes being sold through Western fast food restaurants as French Fries to protect against Potato virus X causes an “explosive” replication of the H1N1 influenza virus by increasing the acidic conditions of the endosome and causing the hemagglutinin protein to rapidly fuse the viral envelope with the vacuole's membrane, then causing the M2 ion channel to allow protons to move through the viral envelope and acidify the core of the virus, which causes the core to dissemble and release the H1N1’s RNA and core proteins into the hosts cells.

Evidence confirming these dire findings by top Russian scientists is also supported by the World Health Organization who in their reporting on the current Influenza Pandemic, clearly shows that the H1N1 virus is nearly totally confined to those Western Nations allowing their citizens to consume these genetically modified potatoes, and which include: The United States with over 17,000 cases being reported with 45 deaths; Canada with 2,978 cases; the United Kingdom with 1,226 cases; and Australia with 1,823 cases.

This is very troubling. I'd like to be an accommodationist and pretend that the Russian kooks scientists are every bit as good as real scientists in other countries. On the other hand, my scientific instincts lead me to postulate that the claim is not very scientific and should be assigned to the urban legend category.

I'm in a quandary over whether I should believe this or not. We need the Russians as allies but we also need the French. Seems like one of them is going to be offended.

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The Glory for Christ Football League

 
Normally I don't like piling on and I don't like making fun of spelling errors (because I make so many myself). But here's a photograph from the New York Times that every blogger is reproducing and I just can't help myself.

The New York Times ran an article on football teams for home schooled children and this photo appears on their website under the caption ...

The Glory for Christ Football League in Georgia grew out of a desire to provide an option for young men who are home-schooled but cannot play in local football leagues.

It's pretty obvious that "acedemics" and "atheletics" are not the top priorities of these homeschoolers but who knew they were so far down the list?

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Why Evolutionary Psychology Is False

 
I haven't got time to review the recent publications on evolutionary psychology. The good news is that the popular press is finally waking up to the fact that the entire field is suspect. It sure took them long enough.

Read a summary on Why Evolution Is True: Genetic determinism? Not so fast.

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Lawrence Krauss on Science vs Religion

 
Lawrence Krauss was recently asked to participate in a debate about science and religion. Ken Miller and another Roman Catholic scientist were there. Miller argued the case for compatibility and Krauss defended the atheist position. Here's how Krauss describes some of the debate in an article entitled God and Science Don't Mix.

Faced with the remarkable success of science to explain the workings of the physical world, many, indeed probably most, scientists understandably react as Haldane did. Namely, they extrapolate the atheism of science to a more general atheism.

While such a leap may not be unimpeachable it is certainly rational, as Mr. McGinn pointed out at the World Science Festival. Though the scientific process may be compatible with the vague idea of some relaxed deity who merely established the universe and let it proceed from there, it is in fact rationally incompatible with the detailed tenets of most of the world's organized religions. As Sam Harris recently wrote in a letter responding to the Nature editorial that called him an "atheist absolutist," a "reconciliation between science and Christianity would mean squaring physics, chemistry, biology, and a basic understanding of probabilistic reasoning with a raft of patently ridiculous, Iron Age convictions."

When I confronted my two Catholic colleagues on the panel with the apparent miracle of the virgin birth and asked how they could reconcile this with basic biology, I was ultimately told that perhaps this biblical claim merely meant to emphasize what an important event the birth was. Neither came to the explicit defense of what is undeniably one of the central tenets of Catholic theology.

This is the problem. Whenever you encounter a religious person who claims that there's no conflict between their religious beliefs and science, you have every right to engage in a discussion about the specific beliefs that they hold.

Do they believe in miracles? In my experience, religious scientists tend to avoid answering such direct questions just like they avoid answering questions about the efficacy of prayer, the existence of a soul, and life after death. I wonder why they won't answer these questions?

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John Wilkins Is an Asportist

 
Some questions are really very simple in spite of the fact that people want to make them complicated. When I ask you, "Do you believe in God?" it really doesn't require a lot of thought for most people. True, there might be a few people who want more clarification about the meaning of God but those people are the exceptions. Usually you can get a response by asking, "Are you a theist?"

There are only two possible answers to the second question. If the answer is "yes" then you are a theist. If the answer is "no" then you are not a theist. Most of the world can be conveniently divided into two groups: theists and non-theists. The others, those who answer "I don't know," aren't worth the bother.

We have a word for those who are non-theists. They are called atheists by my definition of the word. I use the word "atheist" in the same sense as any other word that begins with "a" and means "not." As Antony Flew puts it, the word atheist has the same connotation as "amoral," "atypical," and "asymmetrical." It means that you are not a theist. I'm also an athoothfairyist and an asantaclausian.

John Wilkins disagrees. He thinks the word atheist should be reserved for the strong belief that gods do not exist. When used in that sense, he would argue that he is not a theist and he does not actively deny the existence of gods. He is an agnostic. John divides the world into two camps—those who have a position on the existence or non-existence of god and those who don't. The latter group is the agnostics and he is one.

That's fine by me as long as John makes his definitions clear and he doesn't try to impose his definition of atheist on the rest of us. It would be wrong of John to call me an atheist using his definition so he better be careful. He would have to include me among the agnostics if he is being consistent. He'd also have to include Richard Dawkins. As a matter of fact, John might find it difficult to find anyone who is a true atheist by his definition.

I will try and respect John's wishes and refer to him as an agnostic who doesn't believe in god but doesn't advocate the nonexistence of gods as a philosophical position. However, I don't think I can go along with him in all cases ...

So, to summarise, when an atheist says to me I am an atheist because I lack a view, I am minded to reply, “I am also an asportist” for failing to have a team in any sport that I support. It makes about as much sense.

I'm sorry, John. I'll respect your (strange) opinion and not call you an atheist, but you really are an asportist!

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Religion and the Templeton Foundation

 
From Jesus and Mo.

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Blogging about Scientific Meetings

 
The question is whether it is legitimate for bloggers to report on what goes on at scientific conferences and meetings. I've done it several times and I never thought there was a problem.

Well, apparently some people disagree. Read about it in the latest issue of Nature: Science journalism: Breaking the convention?.

Blogs and Twitter are opening up meetings to those not actually there. Does that mean too much access to science in the raw, asks Geoff Brumfiel.

Next month I'm going to a meeting on "The Tree of Life." I intend to let you all know what goes on at that meeting but it shouldn't be a problem since the participants know what I'm doing and I won't be the only blogger.

There was a time, forty years ago, when some scientific meetings were very closed affairs and scientists could talk openly and frankly about what they were doing without fearing that it would be widely disseminated to non-insiders. There are still a few meetings like that but the vast majority are not.

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Scientists Are no Different from Anyone Else

 
I admire Stephen Jay Gould for many reasons but his honesty ranks right up there near the top of the list.

Gould never pretended that individual scientists could be completely objective. He always said that they are no different than other people who have biases and prejudices. The special attributes of a scientist are that they recognize their biases and struggle to not let them influence their science.

He wrote a review of "Not in Our Genes: Biology, Idealogy and Human Nature" - a book by Richard Lewnotin, Steven Rose, and Leon J. Kamin, The review was later published in "An Urchin in the Storm."

In that review he acknowledged that he shared many of the opinions of the authors. He also wrote ...

... we scientists are no different from anyone else. We are passionate human beings, enmeshed in a web of personal and social circumstances. Our field does recognize canons of procedure designed to give nature the long shot of asserting herself in the face of such biases, but unless scientists understand their hopes and engage in vigorous self-scrutiny, they will not be able to sort out unacknowledged preference from nature's weak and imperfect message.

The problem in scientific discourse is not the background of the scientist but the strength and logic of the scientific arguments. It may be useful to see *why* certain scientists adopt certain positions at a particular point in time but that explains the history of an idea and not its correctness.

Leftist scientists are more likely to combat biological determinism just as rightests tend to favor this quintessential justification of the statu quo as intractable biology; the correlations are not accidental. But let us not be so disrespectful of thought that we dismiss the logic of arguments as nothing but an inevitable reflection of biases—a confusion of context of discovery whith context of justification.

Gould often laid his cards on the table when he confessed to his background. Whether it was baseball, a love of history, or a preference for New York, these were part of his personality and sometimes they crept into his science.

But honesty is not always the best policy. If you are honest enough to admit to prejudices and biases—even while you fight to suppress them—you aren't necessarily going to be admired. Especially if your opponents don't reveal their biases and pretend to be completely objective.

By drawing attention to the fact that scientists are no different than anyone else, Gould handed his enemies a weapon that could be used against him. How many of you have heard the charge that Gould is a Marxist, or (gasp!) a Liberal, and that's why he advocated Punctuated Equilibria? This is usually meant to discredit Gould because he revealed his background. Other scientists, who aren't so open, are given a free pass.

This is why you see a book about Gould and his politics but not a book about the politics of some of his opponents.

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