Wednesday, December 31, 2008

Religion may have evolved because of its ability to help people exercise self-control

 
Here's an example of evolutionary thinking by a psychologist at the University of Miami. Read the press release (below) and watch the video. It's only when you watch the video that you realize where Professor McCullough is coming from on this issue. He uses the word "evolution" to talk about cultural phenomena without necessarily including genetic changes. In other words, he is not talking about biological evolution.

This can be very confusing and I recommend that evolutionary psychologists change their practice. They should refer to "cultural evolution" and distinguish it from "biological evolution" whenever possible.
Religion may have evolved because of its ability to help people exercise self-control

A study by a University of Miami psychologist reveals that religion facilitates the exercise of self-control and attainment of long-term goals

CORAL GABLES, FL (December 30, 2008)—Self-control is critical for success in life, and a new study by University of Miami professor of Psychology Michael McCullough finds that religious people have more self-control than do their less religious counterparts. These findings imply that religious people may be better at pursuing and achieving long-term goals that are important to them and their religious groups. This, in turn, might help explain why religious people tend to have lower rates of substance abuse, better school achievement, less delinquency, better health behaviors, less depression, and longer lives.

In this research project, McCullough evaluated 8 decades worth of research on religion, which has been conducted in diverse samples of people from around the world. He found persuasive evidence from a variety of domains within the social sciences, including neuroscience, economics, psychology, and sociology, that religious beliefs and religious behaviors are capable of encouraging people to exercise self-control and to more effectively regulate their emotions and behaviors, so that they can pursue valued goals. The research paper, which summarizes the results of their review of the existing science, will be published in the January 2009 issue of Psychological Bulletin.

"The importance of self-control and self-regulation for understanding human behavior are well known to social scientists, but the possibility that the links of religiosity to self-control might explain the links of religiosity to health and behavior has not received much explicit attention," said McCullough. "We hope our paper will correct this oversight in the scientific literature." Among the most interesting conclusions that the research team drew were the following:
  • Religious rituals such as prayer and meditation affect the parts of the human brain that are most important for self-regulation and self-control;
  • When people view their goals as "sacred," they put more energy and effort into pursuing those goals, and therefore, are probably more effective at attaining them;
  • Religious lifestyles may contribute to self-control by providing people with clear standards for their behavior, by causing people to monitor their own behavior more closely, and by giving people the sense that God is watching their behavior;
  • The fact that religious people tend to be higher in self-control helps explain why religious people are less likely to misuse drugs and alcohol and experience problems with crime and delinquency.
McCullough's review of the research on religion and self-control contributes to a better understanding of "how the same social force that motivates acts of charity and generosity can also motivate people to strap bomb belts around their waists and then blow themselves up in crowded city buses," he explained. "By thinking of religion as a social force that provides people with resources for controlling their impulses (including the impulse for self-preservation, in some cases) in the service of higher goals, religion can motivate people to do just about anything."

Among the study's more practical implications is that religious people may have at their disposal a set of unique psychological resources for adhering to their New Year's Resolutions in the year to come.
I leave it up to you, dear readers, to decide whether non-religious people (atheists) tend to have higher rates of substance abuse, worse school achievement, more delinquency, worse health behaviors, more depression, and shorter lives. It would imply that countries like Sweden, where half the population is non-religious, are in much worse shape than America, where more than 80% is religious. It would imply that extremely religious countries like Saudi Arabia must be near-perfect societies full of very old people.

Incidentally, the idea of "self-control" is not well explained. If you behave in a certain way because you fear punishment from your god or your priests, then this isn't exactly what I think of when I use the term "self-control."




Tuesday, December 30, 2008

What Is the New Atheism?

Andrew Brown blogs at Helmintholog and also at AndrewBrown's Blog, part of the Guardian website. Andrew and I met in London a few years ago. We had an interesting discussion.

Yesterday Andrew posted a provocative article where he attempts to define the New Atheism [The New Atheism, a definition and a quiz]. He is not a fan, to put it mildly.

So, who does he rely on to construct a definition of the New Atheists?
The ideas I claim are distinctive of the new atheists have been collected from Richard Dawkins, Sam Harris, Christopher Hitchens, Jerry Coyne, the American physicist Robert L. Park, and a couple of blogging biologists, P Z Myers and Larry Moran. They have two things in common. They are none of them philosophers and, though most are scientists, none study psychology, history, the sociology of religion, or any other discipline which might cast light on the objects of their execration. All of them make claims about religion and about believers which go far beyond the mere disbelief in God which I take to be the distinguishing mark of an atheist.
That's very distinguished company. I'm flattered. I guess it means I'll have to take the quiz!

Quiz? Yes, that's right, Andrew proposes that we atheists 'fess up to six propositions that represent the New Atheist position, or at least the Andrew Brown version of New Atheism.
All of these propositions will be found in the authors I have cited as well as in the comments to religious articles here. I sometimes think that only the last two are unique to the new atheists: you can certainly find the others in earlier authors. But those are the six doctrines which I would reject when saying rude things about the new atheists.

What would be interesting in comments is if people would score themselves out of six. I expect that one of the most common forms of disagreement would be to claim that you are a three or a four, but none the less the believers are so repulsive and dangerous that the other two points just don't matter. That's how politics works, after all, and the new atheism is interesting as a political or social movement, not an intellectual one.
Challenge accepted.

Here are the six propositions and my position on each of them.
1. There is something called "Faith" which can be defined as unjustified belief held in the teeth of the evidence. Faith is primarily a matter of false propositional belief.

I agree.

2. The cure for faith is science: The existence of God is a scientific question: either he exists or he doesn't. "Science is the only way of knowing – everything else is just superstition" [Robert L. Park]

I agree, as long as we understand that science is a way of knowing that relies on evidence and rationality. The other, undefined, ways of "knowing" will reject either evidence or rationality.

The question before us is whether supernatural beings exist or not. I fail to see why a scientist isn't as competent to answer that question as those who study "psychology, history, the sociology of religion, or any other discipline which might cast light on the objects of their execration." The object of my attention (not execration) is supernatural beings. Why would a psychologist or a sociologist know more about their possible existence than I do?


3. Science is the opposite of religion, and will lead people into the clear sunlit uplands of reason. "The real war is between rationalism and superstition. Science is but one form of rationalism, while religion is the most common form of superstition" [Jerry Coyne] "I am not attacking any particular version of God or gods. I am attacking God, all gods, anything and everything supernatural, wherever and whenever they have been or will be invented." [Dawkins]

I agree, except for the minor quibble that science is not the opposite of religion. Religion is a set of beliefs based almost exclusively on the worship of supernatural beings. I think that religion is silly because these supernatural beings do not exist. Belief in such beings is not the opposite of the scientific way of knowing: it is outside of the scientific way of knowing. Such beliefs are based on some other, undefined, way of knowing that we may refer to as superstition for want of a better term.1 The battle is between rationalism and superstition.

4. In this great struggle, religion is doomed. Enlightened common sense is gradually triumphing and at the end of the process, humanity will assume a new and better character, free from the shackles of religion. Without faith, we would be better as well as wiser. Conflict is primarily a result of misunderstanding, of which Faith is the paradigm. (Looking for links, I just came across a lovely example of this in the endnotes to the Selfish Gene, where lawyers are dismissed as "solving man-made problems that should never have existed in the first place".)

I agree.

5. Religion exists. It is essentially something like American fundamentalist protestantism, or Islam. More moderate forms are false and treacherous: if anything even more dangerous, because they conceal the raging, homicidal lunacy that is religion's true nature. [Sam Harris]

I don't agree with all of this. While it's true that even moderate forms of religion are based on the irrational belief in non-existent beings, that only makes them false—not treacherous, and certainly not homicidal. Most modern religions are trying to promote good things that I support. The mistake theists make is in assuming that you have to believe in non-existent beings in order to be good.

6. Faith, as defined above, is the most dangerous and wicked force on earth today and the struggle against it and especially against Islam will define the future of humanity. [Everyone]

Nonsense. We will be better off when people abandon their belief in supernatural beings but that's a far cry from saying that such superstitious beliefs are the most dangerous and wicked force on Earth.2

I have never singled out Islam for special attention. As a matter of fact, I am very much opposed to characterizing the current struggles as a war between Islam and Christianity. I may not be an historian but I know enough history to understand that Islam has a solid track record of tolerance and understanding. Probably a better record than Christianity.
What's my score? I agree with the first four propositions and disagree with the last two. I guess that means I'm not a true New Atheist. I should have known that those other guys were too good for me.

Oops, PZ only gives himself 2 out of 6 [Oh, no! The New Atheists are getting attacked again!]. I guess I'm more of a New Atheist than he is. Go figure.


1. I anxiously await Andrew Brown's next essay when he defines the New Theism and reveals to us these other ways of thinking.

2. Earth, the planet, begins with an upper-case letter, just as the names of all the other planets do.

[Hat Tip: Richard Dawkins.net]

On Darwin and Atheism, by Richard Dawkins

 
Richard Dawkins posts a comment about an article written by Madeleine Bunting [Darwin shouldn't be hijacked by New Atheists - he is an ethical inspiration]. She repeats the rather boring complaint that the "New Atheists" are about to hijack the 2009 celebrations.

She says,
In particular, what would have baffled Darwin is his recruitment as standard bearer for atheism in the 21st century. Darwin kept his pronouncements on religion to a minimum, partly out of respect for his Christian wife. Despite continuing claims that he was an atheist, most scholars acknowledge that he never went further than agnosticism.
Richard Dawkins replied ...
It is true that Darwin declined to call himself an atheist. But his motive, clearly expressed to the atheist intellectual Edward Aveling (incidentally the common-law husband of Karl Marx's daughter) was that Darwin didn't want to upset people. Atheism, in Darwin's view, was all well and good for the intelligentsia, but ordinary people were not yet "ripe" for atheism. So he called himself an agnostic, largely for diplomatic reasons..

In any case, what Darwin chose to call himself, as a pillar of his local parish in the nineteenth century, is of less interest than the cogency of the arguments themselves. Before Darwin came along, it was pretty difficult to be an atheist, at least to be an atheist free of nagging doubts. Darwin triumphantly made it EASY to be an intellectually fulfilled and satisfied atheist. That doesn't mean that understanding Darwin drives you inevitably to atheism. But it certainly constitutes a giant step in that direction.
I stand with Dawkins1 except that I would include all of the modern scientific advances as additional facts that make it easy to be an atheist and difficult to believe in supernatural beings.

Science doesn't turn you into an atheist but it sure as heck poses a severe challenge to most established religions. That's why religions fear science.


1. On the issue of superstition vs. rationality, I'm in (almost) complete agreement with Richard Dawkins and I admire him greatly for writing The God Delusion. On the issue of evolutionary theory, I'm not in complete agreement.

An Adaptationist View of Stephen Jay Gould

 
In last week's issue of Nature, Steve Jones reviews Stephen Jay Gould: Reflections on His View of Life. Jones is part of the British school of Darwinism, along with Richard Dawkins, the late John Maynard Smith, and others.1 This group shares many perspectives on evolutionary theory including an emphasis on natural selection. They are also united in their dislike of, and misunderstanding of, Stephen Jay Gould.

The misunderstanding shows up in several places in the Jones review [A wonderful life by leaps and bounds].

Being part of the anti-Gould school means that Jones is obliged to trot out the famous quotation by Maynard Smith (it's part of their oath of allegiance).
Gould held fast to Darwin's maxim that "All observation must be for or against some view if it is to be of any service", and was among that band who felt that those not for him must be against him — which was not much help in keeping friends. The great biologist John Maynard Smith wrote that most evolutionists saw Gould as "a man whose ideas are so confused as to be hardly worth bothering with, but as one who should not be publicly criticized because at least he is on our side against the creationists".

Gould was hurt by that acidulous statement, which was without doubt unfair.
Of course it was unfair—so why repeat it? The statement says more about the British Darwinists than about Gould. The fact that they find Gould's ideas "confusing" isn't something to be proud of.

One of Gould's major contributions to evolutionary theory was punctuated equilbiria, with Niles Eldredge. The basic idea is that the fossil record shows millions of years of stasis (no change) and when change occurs it takes place relatively quickly during speciation by cladogenesis (splitting). After that, the two species (parent and daughter) continue to exist together in the same environment.

The morphological changes that occur when a new species is formed are not dramatic. They are similar to the differences between closely related modern species. In many cases it takes an expert to even recognize the new species in the fossil record.

Punctuated equilibrium is a theory of speciation and stasis. The changes during speciation may be due to natural selection or some form of random genetic drift. That's not what's important about punctuated equilbria—what's important is that change is coupled to speciation and nothing happens for most of the life of a species.

Here's what Steve Jones has to say about it.
Whatever the importance of sudden leaps in the fossil record, his notorious idea of punctuated equilibria, nicknamed 'punk eek' and referred to as 'evolution by jerks' by some of its critics — their own views characterized by Gould as "evolution by creeps" — gave the fossilized field of palaeontology a much-needed kick in the pants. Gould saw punk eek as a "coordinating centrepiece" that "congealed into a coherent critique" of evolutionary theory. Many biologists, by contrast, insist that what look like palaeontological leaps can be explained by simple Darwinism. To them, an instant in geology may represent almost an infinity in biology, leaving plenty of time for evolution by natural selection to do its normal job.
He just doesn't get it, does he? The speciation event takes place over a period of about one hundred thousand years as Gould and Eldredge explained. That's plenty of time for selection, or drift, or founder effect, or whatever. Punctuated equilibria is not a challenge to natural selection, it's a challenge to gradualism.

Furthermore, anyone who refers to punctuated equilibria as "sudden leaps" is revealing an understanding of the theory that's no better than that of the creationists. As is anyone who thinks that "Darwinism" explains speciation.
His other great passion, contingency — the notion that evolution goes on with sudden bangs rather than protracted whimpers — has also not held up particularly well. Wonderful Life, Gould's 1989 book on the Burgess Shale, suggests that the obscure fauna of the late pre-Cambrian represents a lost universe wiped out by some unknown disaster, but now we know that they have descendants among modern animals. Even so, scientific ideas often change, and that volume, like most of his others, remains a rattling good read. The fact that nature must build on what it has, and not on what it wants, is still at the centre of evolutionary thinking.
Talk about confused thinking! When did Gould ever say that contingency is "the notion that evolution goes on with sudden bangs"?

Gould and Lewontin made great play with the parallels between the Spandrel School and the many evolutionists who say that every character in every animal is there for an adaptive reason and if you look hard enough you'll find it.

There's some truth in their argument, but to accept it as the only truth is basically to give up and walk away, to stop being an ornithologist and turn into a bird-watcher. You become somebody who observes rather than analyzes. What they're saying to lots of biologists is, "Abandon hope, go home, and become a liberal-arts graduate!" I may be overcriticizing the Lewontin and Gould view; both of them like to poke people with their sharp pitchforks. The spandrels were a particularly successful poke. But what happened as a result of the famous spandrel paper? The answer is, not much.

Steve Jones in
The Third Culture
As for Wonderful Life, it is, indeed, a book about contingency—just like the movie from which it takes its title. One wonders whether Steve Jones has actually read the book, or seen the movie.

While it's true that some of the unusual Cambrian species that Gould once thought were separate phyla have now been lumped into modern phyla, it's also true that there are many that haven't. Gould's point is that some of those enigmatic Burgess Shale species have left no descendants and, if you could have observed them back then, you would not have been able to pick out the eventual winners and losers. In other words, if you re-wind and replay the tape of life it will come out differently.

Jones is not referring to these species however. He's talking about the "pre-Cambrian" fauna—presumably the Ediacara biota. It's not an important part of Gould's book. As far as I know the relationship between Ediacaran species and modern species is still very controversial. Perhaps Jones has studied this in more detail that I have.

One of the ideas to come out of punctuated equilibria is the idea of species sorting. This makes sense when you think about it. If most speciation occurs by cladogenesis and not by gradual transformation, then over time the number of species in a clade doubles every five to ten million years. Eventually there will be hundreds of similar species. The reason this doesn't happen is that species go extinct. They die.

If species within a clade are "born" and "die" then this looks an awful lot like evolution at a different scale than the birth and death of individuals within a population. The idea of species sorting, where the species in a clade are treated like the individuals within a population, is part of Gould's hierarchical theory of evolution. He claims that it is an extension of the Modern Synthesis.

Whether he's right or wrong doesn't matter. What matters is whether his critics have the intelligence to understand hierarchical theory in general, or species sorting in particular. I don't have much respect for evolutionists who refuse make a modest attempt to understand; it's not rocket science.

Here's what Steve Jones says.
Backwards ran his sentences, and some of his ideas were equally opaque. In support of punk eek, for example, he wrote that "species are individuals ... by all vernacular criteria", which is at best obscure, and at worst obscurantist.
No, Professor Jones, it is not obscure and it is not obscurantist. Gould explains it very well to those who can read his works with an open and intelligent mind. He's talking about species sorting and treating species as "individuals" that are selected within a clade.
As Reflections portrays, its hero showed an increasing regard for style over content, and was resistant to the notion that anyone should dare to edit his writings. The pinnacle — the very summit, crown and peak — of his great Olympus of orotundity was his last voluminous volume, The Structure of Evolutionary Theory, published in the year of his death. All the authors agree that this is not a book to be lightly tossed aside, but their motives for saying so vary. Its reviews are quoted with a certain relish: "an elephantine opus"; "pathological logorrhea"; "billowing clouds of verbal flatulence" — but Gould had no doubt of its value. In it he came out with the idea of life as a series of interlocking hierarchies and of a grand unification of its sciences into some post-Darwinian consilience, comprehensible only to the chosen.
The Structure of Evolutionary Theory is long and tedious but those who criticize its ideas are the ones who confuse style over content. I don't agree with many of Gould's ideas about species sorting and hierarchical theory and therefore I stand as the exception to Steve Jone's claim. It was comprehensible to this unchosen one so it must also be comprehensible to others who disagree with Gould. You just have to make the effort.

If you don't make the effort to understand Gould then you should refrain from criticizing him. It doesn't make you look good.


1. For examples of the Steve Jones perspective on evolution see Have Humans Stopped Evolving? and Steve Jones Says Human Evolution Is Over.

[Image Credit: The Cheltenham Ladies' College]

"Monkey Girl" and False Icons

 
Monkey Girl: Evolution, Education, Religion, and the Battle for America's Soul is a book about the Dover trial. It's written by Edward Humes, an ex-newspaper journalist turned author.

The cover of the book shows one of the common, but false, icons of human evolution. This series of skeletons depicts a steady upward march of human evolution from a chimpanzee to modern humans. The image is false in two ways: (1) humans did not evolve from something that looks like modern chimpanzees, and (2) the "progress" was not a linear transformation as depicted, instead, there where many side branches and lineages that went extinct.

This is the icon that Stephen Jay Gould attacked in Wonderful Life and elsewhere in his essays. Even the Intelligent Design Creationists recognize that this is a bad way to depict evolution. Casey Luskin writes in A Partisan Affair (Part 2): False Attacks Upon Discovery Institute in Edward Humes’ Pseudo-History of Kitzmiller, "Monkey Girl".
Any book with an icon of evolution on its cover — in this case, the fanciful diagram of ape-like skeletons transitioning into a human skeleton — is bound to be unfriendly towards intelligent design (ID).
For once I agree with Casey Luskin!!!! The diagram is a fanciful "icon" and the book is unfriendly towards creationists.

I realize that trade book authors don't get much say in cover design but that has to change. I urge all authors to insert a clause in their contracts that requires approval of the cover design and title. Let's try and prevent future embarrassments of this sort.


If Spiders Are Arthropods then Where Are the Segments?

 
Christopher Taylor of Catalogue of Organisms has the answer [Attercop].


[Image Credit: Commonwealth Scientific and Industrial Research Organisation (CSIRO)]

Trouble with Blogger

 
I'm pretty happy with Blogger, most of the time.1 However, every now and then the powers that be meddle with the code and screw up a feature that we've come to rely on. I don't understand why this happens—you'd think they would test all their changes before implementing them.

A few weeks ago Blogger decided to mess with the RSS feeds and other things. The changes had two obvious effects: I can no longer detect links to my blog via Technorati, and recent comments are stuck on old comments (June 20, 2007).

Blogger has a "Help Group" forum where you can post about problems with Blogger. There are hundreds of postings—most of them concern mistakes made by the users, many of whom don't read instructions very well. The thread concerning the RSS feed [Problem with the comments feed] was begun on December 19th, shortly after the problem first appeared. On December 21 the Blogger team indicated that they were aware of the problem.
Thanks for the heads up folks! We're looking into this right now and hope to have this sorted out shortly.

We'll make sure to update this thread when we have some news to pass along. Thanks for your patience,

Gatsby
The Blogger Team
As of today (Dec. 30) it still hasn't been fixed.

Why is it taking so long to fix a problem that they created in the first place?


1. After all, it's free. I shouldn't complain about such an excellent service at such a low price. (But I will anyway.)

Recreational Mathematics

 
Ms. Sandwalk has discovered a new game called Blokus. I recommend it highly.

She has a description of the game on her blog and an explanation of "polyominoes"—a term used in recreational mathematics. What she didn't put on her blog is her reaction on discovering that some people think that mathematics can be recreational!!

Incidentally, she hasn't yet won a game of Blokus. This makes up for all the times when she beats me at word games.



Saturday, December 27, 2008

Philosophers and the Existence of God

 
The existence of God is one of the exciting questions in philosophy. I firmly believe that all undergraduates should take a course in philosophy where they address issues like this and learn how to argue logically and rationally. Philosophy is the most important subject in university.

However, sometimes philosophers seem to get so badly off track that they fail to see the forest for the trees. The debate over the ontological argument for the existence of God falls into this category. I can't believe that modern philosophers would waste more than a microsecond on such a stupid argument.1.

Here's one version of the argument from Wikipedia.
  1. God is, by definition, a being greater than anything that can be imagined and is the cause of all things, but is not bound causally by anything (otherwise God would be ontologically dependent on something else which would in turn undermine "its" greatness).
  2. Existence both in reality and in imagination is greater than existence solely in one's imagination.
  3. Therefore, God must exist in reality: if God did not, God would not be a being greater than anything which can be imagined.
Alex Byrne wastes far more than a microsecond in the latest issue of Boston Review [God: Philosophers weigh in]. Check it out if you want to wade through some mind-numbing examples of tree-gazing. (There are other interesting bits in the article that might make it worth your while.)

Part way through that article, Byrne decides that philosophical arguments in general, and arguments for the existence of God in particular, are often not very significant. He says the following ...
A better complaint is that sound philosophical arguments with significant conclusions are as rare as atheists in foxholes: the track record of philosophical “proofs” is not exactly impressive, unlike the mathematical variety.
What the heck?

There have been millions of atheists in (metaphorical) foxholes throughout history. Does this mean there are millions of sound philosophical arguments with significant conclusions? Or does it mean that Alex Byrne is one of these people who think that atheists becomes believers whenever they're under stress, in spite of the fact that there are no sound arguments for the existence of God?

What a strange thing for a philosopher to say.


1. It's fun to debate the logic of the ontological argument and to try and construct proofs that it is false. That's not what I mean when I say that it's a stupid argument. What I mean is that it is stupid to actually think that such a clever twisting of words would actually cause someone to believe that a perfect supernatural exists.

[Hat Tip: RichardDawkins.net]

On the Origin of Eukaryotes

 
Theme

The Three Domain Hypothesis
If all you do is read the textbooks, you would think that the origin of eukaryotic cells has been discovered. Most textbooks describe the Three Domain Hypothesis as a done deal. Eukaryotes and archaebacteria share a more recent common ancestor than either group does with the remaining groups of bacteria. Thus, eukaryotes arose from archaebacteria.

The scientific literature does not reflect this confidence. In fact, there is general agreement that the classic Three Domain Hypothesis is no longer viable as a complete explanation for the origin of eukaryotic cells. The current consensus favors a more confused picture of early life with lots of gene swapping—the so-called web of life. It is not clear that eukaryotes as a group arose from any particular prokaryotic clade. It is likely that in addition to horizontal gene transfer, there were probably one or more fusion events where the cells from two separate lineages united to form a hybrid.1

This week's issue of the Proceedings of the National Acedemy of Sciences (USA) has a paper that addresses the problem, one more time. Cox et al. (2008) ask whether there is phylogenetic support for the Three Domain Hypothesis by analyzing 53 well conserved genes. The answer is no. But is there support for one of the alternatives, the Eocyte Hypothesis? The answer is, maybe.2

The commentary by John Archibald is worth reading. Here's an excerpt.
Evolving Views on the Tree of Life

Next to life itself, the origin of complex cells is one of the most fundamental, and intractable, problems in evolutionary biology. Progress in this area relies heavily on an understanding of the relationships between present-day organisms, yet despite tremendous advances over the last half-century scientists remain firmly divided on how to best classify cellular life. Many adhere to the textbook concept of 2 basic types of cells, prokaryotes and eukaryotes, as championed by Stanier and van Niel (7). Others posit that at its deepest level life is not a dichotomy but a trichotomy comprised of cells belonging to the domains Bacteria, Archaea, and Eukarya, each monophyletic and sufficiently distinct from one another to warrant equal status (5, 8). The conceptual and practical challenges associated with establishing a genealogy-based classification scheme for microbes have been fiercely debated for decades (see ref. 9 for recent review), and the literature is rich in philosophy and rhetoric.

The genomics revolution of the 1990s brought tremendous optimism to the field of microbial systematics: if enough genomes from diverse organisms could be sequenced and compared, definitive answers to questions about evolutionary relationships within and between eubacteria, archaebacteria, and eukaryotes would surely emerge. More specifically, it should be possible to discern how eukaryotes evolved from prokaryotes (if indeed that is what happened), and perhaps even who among modern-day prokaryotic lineages is our closest ancestor. Unfortunately, with the sequences of hundreds of eubacterial, archaebacterial, and eukaryotic genomes has come the realization that the number of universally distributed genes suitable for global phylogenetic analysis is frustratingly small (10). Lateral (or horizontal) gene transfer has shown itself to be a pervasive force in the evolution of both prokaryotic and eukaryotic genomes, and even if a “core” set of genes can be identified (and there is much debate on this issue), how confident are we that the phylogenetic signal in these genes reflects the vertical history of cells? How meaningful are sequence alignment-independent, gene content-based approaches to resolving the “tree of life” (11)? To what extent is a “net of life” a more accurate and useful metaphor for describing the full spectrum of life on Earth (10, 12–14)?
The bottom line is that the earliest stages of evolution are still very much open questions. It is wrong to assume that the Three Domain Hypothesis is correct and scientists, as well as textbooks writers, should stop making this assumption.


1. Most workers make the unstated assumption that eukaryotic cells are more recent than prokaryotic cells. The idea that archaebacteria could have arisen by a fusion of an early eukaryote with an early prokaryote is just as consistent with most of the data yet this possibility is almost never discussed.

2. Cox et al. use very "sophisticated" techniques for analyzing their sequence data. Much of the controversy in this field involves disputes over which computer programs give the most accurate results. What's really going on, in my opinion, is that the data isn't good enough to justify the kinds of manipulations that are being done. The trees give you a good approximation of the true phylogeny but subjecting the data to over-analysis isn't helpful.

Archibald, J.M. (2008) The eocyte hypothesis and the origin of eukaryotic cells. Proc. Natl. Acad. Sci. (USA) 105:20049-20050. [doi:10.1073/pnas.0811118106]

Cox, C.J., Foster, P.G., Hirt, R.P., Harris, S.R., and Embley, T.M. (2008) The archaebacterial origin of eukaryotes. Proc. Natl. Acad. Sci. (USA) 105:20356-20361. [doi:10.1073/pnas.0810647105].

My Christmas Jigsaw Puzzle

 
According to Wikipedia, the first commercial jigsaw puzzles were marketed in England by John Spilsbury in 1760.

I haven't been putting them together for nearly that long. Every Christmas we buy a jigsaw puzzle and try to assemble it before the end of the holidays. Ms. Sandwalk usually gives up after the first day.

Do you know what "tessellation" means?




Wednesday, December 24, 2008

Pop Evolutionary Psychology

 
David J. Buller is a Professor of Philosophy at Northern Illinois University (USA). He is an expert in his field, He is not a professional science journalist although he has written a book and many articles.

This is relevant because many science journalists have written favorable articles about popular evolutionary psychology. This is the field that promotes evolutionary explanations for many human behaviors. They are the classic examples of adaptationist just-so stories.

Buller has just published an article in Scientific American where he argues against these popular stories [Evolution of the Mind: 4 Fallacies of Psychology].

Here's part of what he says ...
Some evolutionary psychologists have made widely popularized claims about how the human mind evolved, but other scholars argue that the grand claims lack solid evidence

...

The most notable representatives of Pop EP are psychologists David M. Buss (a professor at the University of Texas at Austin and author of The Evolution of Desire and The Dangerous Passion) and Steven Pinker (a professor at Harvard University whose books include How the Mind Works and The Blank Slate). Their popular accounts are built on the pioneering theoretical work of what is sometimes referred to as the Santa Barbara school of evolutionary psychology, led by anthropologists Donald Symons and John Tooby and psychologist Leda Cosmides, all at the University of California, Santa Barbara.

According to Pop EP, “the human brain consists of a large collection of functionally specialized computational devices that evolved to solve the adaptive problems regularly encountered by our hunter-gatherer ancestors” (from the Web site of the Center for Evolutionary Psychology at U.C.S.B.). Just as evolution by natural and sexual selection has endowed all humans with morphological adaptations such as hearts and kidneys, Pop EP says, so it has endowed all humans with a set of psychological adaptations, or “mental organs.” These include psychological mechanisms, or “functionally specialized computational devices,” for language, face recognition, spatial perception, tool use, mate attraction and retention, parental care and a wide variety of social relations, among other things. Collectively, these psychological adaptations constitute a “universal human nature.” Individual and cultural differences are, by this account, the result of our common nature responding to variable local circumstances, much as a computer program’s outputs vary as a function of its inputs. The notable exceptions to this rule involve sex differences, which evolved because males and females sometimes faced distinct adaptive problems.

Moreover, because complex adaptation is a very slow process, human nature is designed for the hunter-gatherer lifestyle led by our ancestors in the Pleistocene (the period from 1.8 million to 10,000 years ago). As Cosmides and Tooby colorfully say, “our modern skulls house a Stone Age mind.” Pop EP proposes to discover our universal human nature by analyzing the adaptive problems our ancestors faced, hypothesizing the psychological mechanisms that evolved to solve them and then testing those hypotheses using standard-fare psychological evidence, such as paper-and-pencil questionnaires. Pop EP claims that a number of psychological adaptations have been discovered in this way, including evolved sex differences in mate preferences (males prefer nubility; females prefer nobility) and jealousy (men are more distressed by a mate’s sexual infidelity, women by emotional infidelity).

I believe that Pop EP is misguided. The ideas suffer not so much from one fundamental flaw as from many small mistakes. Nevertheless, recent critiques of evolutionary psychology point to some general problems of Pop EP.
There's nothing remarkable about this article. The majority of evolutionary biologists know full well that pop evolutionary psychology is a farce. For most biologists, it's an embarrassment.

The real puzzle is why most science journalists seem to be completely unaware of the controversy. They haven't been doing their job. Next time you see an article promoting the "latest discoveries" of pop evolutionary psychology look for the balance. Do you see the disclaimers questioning the relevance of the entire field? If those points aren't mentioned then you know that science journalists have not done their homework.


Top Ten Intelligent Design Creationist Stories

 
Denyse O'Leary is one of the best of an excellent group of science journalists.1 When she selects her top ten science stories of 2008 it's time to pay attention, especially since these are stories about Intelligent Design Creationism [The top ten Darwin and Design stories of the year.

Here's the list ...
The Altenberg 16
Atheists and Agnostics Defend ID
Expelled #1 Political Documentary of 2008
Louisiana Academic Freedom Act
Biologic Institute Releases Stylus: A System for Evolutionary Experimentation
A Molecular Clutch Discovered in the Flagella
Royal Society Expels Director of Education
Leading Biologists Marvel at the "Irreducible Complexity" of the Ribosome
Have Cosmologists Lost Their Brains?
Design-based Biomimetics Yields Tangible Results
What a sad list.


1. Not. I wonder what George Johnson thinks of science journalists like Denyse O'Leary?

The "Best" of Genetics Science Writing from New Scientist

 
The blogosphere is discussing the conflict between scientists and science journalists. The issue is not whether science journalists can write for the general public—I take that as a given—it's whether what they write is scientifically accurate. Do articles by science journalists fairly represent the state of science?

New Scientist has risen to the challenge by listing it's top ten article on genetics [Genetics: Top 10 articles from 2008.

Here's the list of titles. Judge for yourselves.
Me and my genome
DNA dating: Can genes help you pick a mate?
Genes make mice squeal during sex
Are political leanings in the genes?
Cloning 'resurrects' long-dead mice
Genetically modified humans: Here and more coming soon
MicroRNAs: The cell's little emperors
Solar-powered sea slug harnesses stolen plant genes
Cancer special: Living with the enemy
Goldmine bug DNA may be key to alien life



Monday, December 22, 2008

Webpages as Graphics for Sandwalk

 
Here's the Webpages as Graphics for this blog. I have no idea what this means.




Who the Heck Is George Johnson?

 
A few weeks ago I wrote about Epigenetics at SEED. The article in SEED was written by a scientist who wants to change evolutionary theory in order to accommodate epigenetics. I pointed out that this was a poorly written article. One of the worst problems was the definition of epigenetics, which was broad enough to include the kitchen sink.

Abbie Smith picked up on this on her blog ERV. She agreed that the SEED article was not helpful [ew... epigenetics in SEED...].

Along comes someone named George Johnson. He interprets Abbie's criticism of the science, and mine, as a rant against science journalism. Well, he's right, even though in this case it's science journalism being written by a scientist. Apparently science journalists (I assume George Johnson is one) are very sensitive about criticism from scientists. Apparently science journalists are very good at what they do ... how dare scientists criticize what they write about science!!!

Watch George Johnson make a fool of himself on this bloggingheads video with John Horgan. Johnson reads my name from the ERV posting but it seems he didn't bother to read my posting. If George Johnson has the courage to show up here I'll be happy to explain to him why this particular SEED article is bad. He's welcome to read all my other criticisms of science journalism and and attempt to defend the science journalists.

Pay close attention to Johnson's comments when he reads the passage from Abbie's blog. It's clear that he doesn't know what chromatin is and he doesn't know what epigenetics is. On the other hand, he is certain that Nicholas Wade, who writes about molecular biology, is a great science writer. How would George Johnson know this? Johnson may be able to tell whether Nicholas Wade is a good writer but he sure isn't in a position to judge whether he's a good science writer since the most important thing about science writing is accuracy and Johnson knows nothing about molecular biology.

This may be one of the biggest problems with science writers. They can't tell the difference between science and writing. And they don't like it when scientists point this out to them.






Friday, December 19, 2008

Name That Research Scientist

 
I'd love to know the name of this "research scientist" and the name of the pharmaceutical company he works for.

From DonaldM at Uncommon Desent:
Today, I had the privilege to have lunch with a research scientist who works in the area of bio-pharmaceuticals for a pharmaceutical company. He told me about their research with proteins and genes that enable them to develop products that alleviate or cure a wide range of diseases at the cellular level. Of great value to the research they do was the Human Genome Project because it made available the entire database to whoever needed it. That information enabled them to move several projects forward.

He knew from our conversation that I had been involved in the Intelligent Design/Evolution debate, so I asked him what role evolution played in all thier research. Now, this is a research facility that is carrying on a huge number of projects across a number of areas in cellular biology, bio-chemistry, hemotology, oncology and other related areas. He said that evolution plays no role whatsoever in their research and that evolutionary theory doesn’t make one whit of difference to the outcome of any of their research projects and never has. To clarify, I said, "so the heuristic value of evolutionary theory to your biological research is…." and he answered "Nil!".


Center for Inquiry World Congress 2009

 

The Center for Inquiry's 12th World Congress:
Science, Public Policy, and the Planetary Community
April 9-12, 2009
Bethesda, MD Hyatt Hotel (just outside of Washington, DC)


2009 marks the bicentennial of both Charles Darwin's and Abraham Lincoln's birth and the 150th anniversary of the publication of On the Origin of Species. There can be no more fitting opportunity to discuss and consider the appropriate relationship between science and public policy. Please join us as scientists and scholars from around the world analyze the role of science, explain how it works, explore its connection to public policy, and examine its significance for the global community.

Speakers
Norm Allen
Mona Abousenna
Tom Beauchamp
Roger Bonnet
David Contosta
Austin Dacey
Tarek Fatah
Barbara Forrest
Ren Fujun
Christopher Hitchens
Pervez Hoodbhoy
Leo Igwe
Philip Kitcher
Lawrence Krauss
Paul Kurtz
Ronald A. Lindsay
Elizabeth Loftus
John C. Mather
Joe Nickell
James Randi
Michael Ruse
Armadeo Sarma
Patricia Scott Schroeder
Drew Shindell
Eleanor Smeal
Eddie Tabash
Floris van der Berg
Toni Van Pelt
Ibn Warraq
Mourad Wahba
Richard Wiseman




Student Perceptions of "The Spandrels of San Marco"

 
Hopeful Monster asked his senior biology majors to read "The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme." [Student perceptions of San Marco].

I think he was disappointed.


How Women Got Their Menopause

The December 13 issue of New Scientist has an article about the evolution of menopause in humans [Are daughters-in-law to blame for the menopause? ]. The author is Alison Motluk, the Toronto corresponent for New Scientist.

She begins with ..
IT FLIES in the face of natural selection, yet in humans it seems fixed and universal: at around age 50, not far past the midpoint of life, normal healthy women lose their capacity to bear children. Following a decade of gentle winding down, the whole reproductive system screeches to a halt. It is as though, after a few years of wearing bifocals, all women suddenly went blind.

Menopause is a mystery. It leaves women with 20, 30, perhaps even 50 years of life - squandered time in evolutionary terms, because no further genes can be passed on. Yet the selection pressure for menopause must have been strong: there are no known pockets of women around the world who do not go through it. All the evidence suggests menopause has been around a long time, and that the age at which it hits has changed little. Increased longevity seems not to have budged our closing hours. Nor, apparently, has lifestyle; it hits hunter-gatherers at pretty much the same age as hip New Yorkers.
The search for an adaptive explanation for menopause has been going on for over fifty years.

The most common just-so story is called the "Grandmother Hypothesis." It imagines a time in the distant past when humans females were fertile until the day they died, which for 75% of women who survived childhood was before the age of 30 according to a recent study. A mutation arose in one individual and the effect was to induce menopause, or sterility, at about age 50. This new mutation proved to be so beneficial that it spread throughout the species. Today every woman undergoes the pain and frustration of menopause.

Why was it so beneficial? Because post-menopausal women whose partners were still alive could invest their time in looking after their grandchildren instead of having more children of their own.

To its credit, the New Scientist article reviews the latest work on the Grandmother Hypothesis and concludes, correctly, that the effect on ancient hunter-gather societies could not possibly have been significant enough to be adaptive.

The same reasoning applies to the "Mother Hypothesis," which claims that by going through menopause a mother will avoid the risks of future childbirths enabling her to concentrate on raising her existing children. Both of these hypotheses assume that "just saying no" was not a reasonable strategy in ancient societies and that's why menopause was necessary.

So what's the alternative if you are committed to an adaptive just-so story? You are going to be shocked ... menopause evolved to benefit daughters-in-law!!! (Our daughter-in-law will be so pleased.)

I'm not even going to dignify such a stupid idea by pointing out the obvious flaws.

In case you haven't clued in by now, the bottom line is that all these hypotheses are flawed from the get-go because they all make the unnecessary assumption that the pain and suffering of menopause are adaptive. What if they aren't? What if menopause is neutral with respect to evolution or even maladaptive? What's the point of making up irrational just-so stories when there's no evidence to suggest that menopause has any positive effect of fitness?


Get a Job

 
Assistant Professor, Tenure Stream
Dept. of Cell & Systems Biology
University of Toronto


The Department of Cell & Systems Biology at the University of Toronto invites applications for a tenure track faculty position to be appointed at the Assistant Professor level in the field of Systems Biology to begin July 1, 2009.

We particularly encourage applications from candidates who have demonstrated excellence in addressing fundamental questions in biology using high-throughput approaches or gene/protein network analyses with bioinformatic, genomic, proteomic, or imaging tools. Our vision is to advance systems biology-based research, with a specific interests in developing expertise in systems neurobiology, but we welcome applicants from all others areas of systems biology which complement existing strengths in the department (www.csb.utoronto.ca).

Candidates should have at least two years of research experience beyond their doctoral degree. In addition to pursuing a vigorous, internationally-recognized research program, the successful candidate will contribute to undergraduate and graduate teaching in the molecular life sciences. The successful candidate would also be expected to network with researchers university-wide to take advantage of the extensive resources in systems biology at the University of Toronto and its affiliated institutions. A generous start-up package will be provided. Salary will be commensurate with qualifications and experience.

We encourage qualified applicants to submit their applications online at: www.jobs.utoronto.ca/faculty.htm. Applicants should submit their curriculum vitae, copies of significant publications, and statements of research and teaching interests. Applicants should also arrange for three confidential letters of recommendation to be sent directly to: Professor Daphne Goring, Chair, Department of Cell & Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Ontario M5S 3G5, Canada; or by email to search@csb.utoronto.ca by January 31, 2009.

The University of Toronto offers the opportunity to teach, conduct research and live in one of the most diverse cities in the world, and is responsive to the needs of dual career couples. The University of Toronto is strongly committed to diversity within its community and especially welcomes applications from visible minority group members, women, Aboriginal persons, persons with disabilities, members of sexual minority groups, and others who may contribute to the further diversification of ideas.

All qualified candidates are encouraged to apply; however, Canadians and permanent residents will be given priority.



Poinsettias Are Poisonous

 
Friday's Urban Legend: False

From 6 Medical Myths Debunked For Christmas.
Dr. Vreeman and Dr. Carroll found that the largest study of poinsettia "toxicity" to date involved an analysis of 849,575 plant exposures reported to the American Association of Poison Control Centers. None of the 22,793 poinsettia cases revealed significant poisoning. No one died from poinsettia exposures or ingestions, and more than 96 percent did not even require treatment in a health care facility. Another study, looking at poinsettia ingestion by rats, could not find a toxic amount of poinsettia, even at doses which would be the human equivalent of consuming 500-600 poinsettia leaves or a pound and a half of the plant's sap. Dr. Vreeman cautions, though, that you should always call a poison control center if someone eats a plant not intended for consumption.



Suicides Increase Over the Holidays

 
Friday's Urban Legend: False

From 6 Medical Myths Debunked For Christmas.
The holidays can bring out the worst in people, and the stresses of family get-togethers, loneliness, and the cold, dark winter months are commonly thought to increase the number of suicides at Yule time. But studies conducted around the globe show that, while the holidays may be a difficult time for some, there is no scientific evidence to suggest a holiday peak in suicides, according to Dr. Vreeman and Dr. Carroll. Furthermore, suicides are actually more common during warm and sunny times of the year.



Sugar Makes Kids Hyperactive

 
Friday's Urban Legend: False

From 6 Medical Myths Debunked For Christmas.
This is without a doubt false, report Dr. Vreeman and Dr. Carroll, who are both pediatricians at Riley Hospital for Children. They write that "in at least 12 double-blinded, randomized, controlled trials, scientists have examined how children react to diets containing different levels of sugar. None of these studies, not even studies looking specifically at children with attention deficit-hyperactivity disorder, could detect any differences in behavior between the children who had sugar and those who did not." This includes sugar from candy, chocolate and natural sources. Even in studies of children who were considered "sensitive" to sugar, children did not behave differently after eating sugar-full or sugar-free diets.



Thursday, December 18, 2008

Let's Count the Ways a Creationist Can Go Wrong

 
The latest posting on Uncommon Descent tries to undermine the concept of a natural origin of life [Life From Chiral Crystals . . . Really?]. Maybe one of these days they'll actually put up some evidence to support Intelligent Design Creationism instead of always attacking science.1

Patrick is worried about the chirality problem, which can be pretty well explained by just applying a bit of common sense [Amino Acids and the Racemization "Problem"]. Unfortunately, it's not just the IDiots who are confused about the chirality problem. Many chemists and biologist also seem to have weird ideas about the requirement for 20 L-amino acids when life began.

Patrick quotes Timothy Standish who says,
Much as the Miller-Urey experiment demonstrated that it is possible to produce insignificant yields of a very few biologically important monomers in a laboratory device, Noorduin et al. demonstrated that chemists are capable of producing enantiomerically pure crystals under laboratory conditions. This laboratory technique fails to show a mechanism by which enatiomerically pure solutions of all 20 amino acids used in protein construction may have existed before the advent of life, not to mention the other chiral molecules found in living things. As a consequence, the chirality problem for chemical evolution remains unresolved by this technique.
How many things are wrong with this paragraph?


1. Not holding my breath.

Speciation in Monkeyflowers

 
Within a species there may be distinctive subspecies that have different allele frequencies. The differences are maintained because there is restricted gene (allele) flow between them. The two subspecies may look very different or they may be very similar in appearance.

Genetic exchange between the subspecies is often prevented because the subspecies are geographically separated. This is the first step on the path to allopatric speciation. But genetic exchange can also be restricted by other mechanisms, for example the timing of reproduction, that occurs even if the subspecies inhabit the same environment. This could lead to sympatric speciation.

In either case, the two subspecies will become distinct species—as defined by the biological species concept—when it becomes impossible to form hybrids due to genetic incompatibility. The study of actual speciation events is a hot topic in evolution these days. One of the goals is to identify the genes responsible for preventing the formation of fertile hybrids. The other goal is to identify the mechanism by which the alleles of these genes become fixed in the subspecies. Is it by natural selection or random genetic drift? (Shuker et al. 2005)

One of the best studied examples of speciation in action is due to the work of H.D. Bradshaw and Douglas Schemske at the University of Washington in Seattle, Washington (USA) (Schemske is now at Michigan State University). They studied two species of monkeyflowers that grow near streams and rivers in the mountains and valleys of western North America.

Mimulus lewisii (top) is found primarily at higher elevations (1600 m to 3000 m) while Mimulus cardinalis (right) grows at lower elevations (sea level to 2000 m). Their ranges overlap at moderate elevations in the mountains of California but hybrids are exceedingly rare.

The species differ in a number of characteristics including leaf shape and stem height but the most obvious differences are in the flowers. Mimulus lewsii has pink flowers that are quite open. They attract bumblebees and in the wild 100% of pollinations within this subspecies are by bees. Mimulus cardinalis has red flowers with a more narrow shape. These flowers attract hummingbirds who are responsible for 98% of pollination events in M. cardinalis.

When crossed in a greenhouse, the two species produce fertile hybrids so technically they are not really species but subspecies.

Ramsey et al. (2003) have studied the barriers to gene flow in the wild. Much of it is due to ecogeographic isolation, which is a fancy way of saying that the species don't often come in contact. They grow at different elevations and each species has become adapted to that elevation so that M. lewisii, for example, does not survive well at low elevations and M. cardinalis can't take the cold and the shorter growing season at high elevations.

The fact that the two species have different pollinators is a major factor in preventing gene flow between them. Hummingbirds hardly ever visit M. lewisii and in the overlapping zones there were very few recorded instances of bees visiting flowers from both species. Thus, the opportunities for cross-pollination were effectively zero. What this means is that, "even in sympatry these species are isolated to a large degree by pollinators" (Ramsey et al. 2003).

There are other factors contributing to genetic isolation. The hybrid plants are somewhat less fit and cross-pollination results in fewer seeds than pollination within a (sub)species. The sum of all these factors means that, in the wild, the total reproductive isolation between the two species is 0.9974 to 0.9998. In other words, they don't mix! (But recall that they can readily form fertile hybrids when crossed in the greenhouse.)

In this example, a major component of the restricted gene flow is due to physical separation of the species and that separation is the result of adaptation to different environments. In that sense, the path to speciation is driven, in part, by natural selection. The species are not genetically incompatible so we're not dealing with mutations that prevent hybridization as would be the case if they were true biological species.

Attention has focused on flower color and shape since that determines whether an individual is pollinated by bumblebees or hummingbirds. It's another step toward preventing gene flow between the species. Is it due primarily to selection or drift?

Schemske and Bradshaw (1999) identified a locus, called yellow upper (YUP), that plays a large role in determining flower color in the two species. The locus affects carotenoid distribution in the petals. In M. cardinalis carotenoids are found throughout the petals and the flowers are red. Bees are not attracted to red flowers. The YUP allele in M. lewisii results in less carotenoid and the flowers are pink. These flowers attract bees.

A subsequent study by Bradshaw and Schemske (2003) established that the YUP alleles are directly responsible for much of the pollinator discrimination observed in monkeyflowers. In the second study the authors created near-isogenic lines (NIL) that differed only at the YUP locus.

The normal M. lewisii flower is pink and the petals are in an open shape (a). The normal M. cardinalis flower is red and the shape of the flower is quite different (c). The dominant YUP allele from M. lewisii prevents carotenoid deposition and when it is bred into M. cardialis the flowers are pink (d). The recessive yup allele from M. cardinalis causes more carotenoid to be deposited making the flowers orange in an M. lewisii background (b).

The plants were tested in a natural environment where the ranges of the two species overlapped and both bees and humingbirds were common. Bees preferred the pink flowers whether they were in an M. lewisii background or an M. cardialis background. Conversely, hummingbirds preferred the orange and red flowers in both backgrounds. Thus, the two species have adapted to different pollinators and a large part of this adaptation is due to flower color.

Here's where it gets tricky. Is the switch from bee pollination to hummingbird pollination driven by natural selection? In other words, when the mutation causing red flowers first arose did it confer a fitness advantage on the individuals that came to be pollinated by hummingbirds?

Here's how Bradshaw and Schemske (2003) address this question,
As ‘mutations’ at the YUP locus decrease visitation by the current pollinator guild, and simultaneously increase visitation by a new pollinator guild, are there plausible ecological circumstances in which the mutant might be favoured by natural selection? The combined rate of bumblebee and hummingbird visitation to the yellow-orange-flowered ‘mutants’ of M. lewisii is just 26% of that to the wild-type pink flowers, and the combined rate for dark-pinkflowered ‘mutants’ of M. cardinalis is 95% of the wild type. This implies that a change in the relative abundance of bumblebees and hummingbirds, compared with the pollinator assemblage present during our field experiments, would be required for the mutant to be favoured by natural selection in the common ancestor of M. lewisii and M. cardinalis. The change in relative abundance of pollinators necessary to produce equal visitation to both flower colour phenotypes can be estimated from our data. A ninefold decrease in the relative abundance of bumblebees would produce equal combined visitation rates in the wild-type pink-flowered and ‘mutant’ yellow-orange-flowered M. lewisii NILs. At the equilibrium point, 99% of visitors to wild-type M. lewisii flowers would be bumblebees, whereas 87% of visitors to ‘mutants’ would be hummingbirds. In the M. cardinalis NILs, a twofold increase in the relative abundance of bumblebees would produce equal visitation rates to pink and red flowers. At the equilibrium point, hummingbirds would be virtually the only visitor to the wild-type red M. cardinalis flowers, and remain the major visitor (89% of visits) even to the dark-pink ‘mutants.’
In order for the red flower allele to be fixed by natural selection there would have to be a significant decline in the bee population at the time the mutation arose. Presumably, this decline would have only occurred in a small part of the range leading to a subpopulation with red flowers while the main, wild-type, population (pink flowers) continued to be visited by bees.

The authors don't mention the other possibility; namely, that the red flower allele (yup) spread in a subpopulation by random genetic drift. In this scenario, there is no selective advantage to individual plants if they are pollinated by humingbirds. Clearly the evolution of pollinator discrimination by flower color will lead to restricted gene flow between the two species but it is not clear whether this epiphenomenon is due to selection for hummingbird pollination or random genetic drift.


[Photo Credits: Mimulus lewisii or Purple monkey-flower (top) is from flickr. Mimulus cardinalis or Cardinal monkeyflower (second from top) is from the Arizona-Sonore Desert Museum.


Bradshaw, H.D. Jr. and Schemske, D.W. (1999) Allele substitution at a flower colour locus produces a pollinator shift in monkeyflowers. Nature 426:176-178. [doi:10.1038/nature02106] [PDF]

Ramsey, J., Bradshaw, H.D. Jr., Schemske, D.W. (2003) Components of Reproductive Isolation between the Monkeyflowers Mimulus lewisii and M. cardinali (Phrymaceae). Evolution 57:1520-1534. [PDF]

Schemske, D.W. and Bradshaw, H.D. Jr. (2003) Pollinator preference and the evolution of floral traits in monkeyflowers (Mimulus). Proc. Natl. Acad. Sci. (USA) 96:11910-11915. PDF]

Shuker, D.M., Underwood, K., King, T.M., and Butlin, R.K. (2005) Patterns of male sterility in a grasshopper hybrid zone imply accumulation of hybrid incompatibilities without selection. Proc. Biol. Sci. 272:2491-2497. [DOI: 10.1098/rspb.2005.3242]

Is Bill O’Reilly Really this Stupid?

 
Don't answer that. It's a rhetorical question.

Honestly, I just don't understand how someone who's a prominent television personality can be so totally ignorant of the very issue that he rants about. It's not rocket science. The law isn't that hard to understand.

Maybe there's something about being religious that clouds the mind?

Listen for the following words from attorney Megan Kelley, "I've never met a non-lawyer who argues the law so confidently, albeit, so wrongly."




[Hat Tip: Friendly Atheist: You Are Wrong! You Are *So* Wrong!]

Wednesday, December 17, 2008

Get a Job

 
Canada Research Chair (Tier I)
in Comparative Genomics and Evolutionary Bioinformatics
at Dalhousie University, Halifax, Canada

The Faculty of Medicine at Dalhousie University is seeking to attract an outstanding individual eligible for nomination for a Tier I Canada Research Chair faculty position in the area of comparative genomics and evolutionary bioinformatics. The successful candidate will be recognized internationally as a leader in this research area and will join the newly formed Centre for Comparative Genomics and Evolutionary Bioinformatics (http://cgeb.dal.ca/), an interdisciplinary research group with diverse and complementary interests in molecular evolution, microbial diversity, protistology, phylogenetics, genomics, proteomics and bioinformatics. Dalhousie is a leading Canadian research-oriented University, located in Halifax on the scenic Atlantic coast of Nova Scotia.

The Canada Research Chairs program was established by the Government of Canada to foster world class centres of research excellence in a global, knowledge-based economy (www.chairs.gc.ca). Applicants should have a Ph.D. in Biochemistry/Molecular Biology or a related discipline, and currently hold the rank of Professor or Associate Professor (with expectation of promotion to Professor within 1-2 years). The successful candidate will be offered a tenured or tenure-track appointment in the Department of Biochemistry & Molecular Biology (www.biochem.dal.ca/) with limited teaching responsibilities. Preference will be given to applicants with interdisciplinary expertise in both laboratory-based biochemical/molecular biological approaches as well as bioinformatics and/or computer science.

To apply send a curriculum vitae, a brief outline of research achievements and goals, and arrange for three letters of reference to be sent, under separate cover, to: Dr. David M. Byers (Chair, Search Committee), Department of Biochemistry & Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, NS, B3H 1X5 Canada. Interviews may commence as early as January 15th, however we will continue to receive applications until a successful candidate has been chosen up to March 1, 2009. All Chairs are subject to review and final approval by the CRC Secretariat.

Dalhousie University is an Employment Equity/Affirmative Action employer. The University encourages applications from qualified Aboriginal people, persons with a disability, racially visible persons and women.


Get a Job

 
Assistant Professor, Tenure Stream
in Cellular and Molecular Biology of Lipids
Department of Pediatrics, Atlantic Research Centre
Dalhousie University
Halifax, Nova Scotia, Canada


The Department of Pediatrics at Dalhousie University invites applications for a probationary tenure-track position at the rank of Assistant Professor. Candidates should have demonstrated potential to develop a nationally and internationally recognized research program in the field of lipid metabolism, signaling or transport, with emphasis on human diseases such as cancer, obesity, diabetes or cardiovascular. The successful candidate will join an established, interactive group of investigators with complementary research interests at the Atlantic Research Centre (ARC). Members of the ARC have ready access to established core research facilities that include: tissue culture and animal care, cellular imaging (confocal and electron microscopy, flow cytometry), mass spectrometry and microarray technology.

Applicants must hold a PhD degree or equivalent and have at least three years post-doctoral training in biomedical sciences. The successful applicant will be expected to compete for external research and salary support, supervise graduate students and contribute to the teaching activities of the Department. Salary will be commensurate with qualifications and experience. Further information concerning this position, the Department and the ARC may be obtained by consulting arc.medicine.dal.ca and associated links.

Dalhousie University is a research-intensive institution located in the historic port city of Halifax, Nova Scotia, which boasts excellent recreational, cultural and lifestyle opportunities (www.halifax.ca/visitors.asp).

Interested applicants should submit a CV as well as send a statement outlining their research and teaching interests. They should have three letters of reference sent under separate cover directly to the Chair of the Search Committee. At least 2 of these references must come from academic referees.

Chair, Search Committee
Atlantic Research Centre
Room C302, CRC Building, 5849 University Avenue,
Dalhousie University
Halifax, Nova Scotia,
Canada B3H 4H7

Closing date for receipt of applications is January 31, 2009. Starting dates are negotiable; the positions may be filled by Sept. 1, 2009.

All qualified candidate are encouraged to apply; however, Canadians and permanent residents will be given priority. Dalhousie University is an Employment Equity/Affirmative Action employer. The University encourages applications from qualified Aboriginal people, persons with a disability, racially visible persons and women.


Get a Job

 
Department of Biochemistry
College of Medicine
University of Saskatchewan
Assistant Professor

The Department of Biochemistry invites applications for a tenure-track position at the level of Assistant Professor. Candidates must have a Ph.D. with at least 2 years of post-doctoral experience. The successful applicant is expected to establish a strong, independent and externally funded research program in biochemistry, preferably in a research area related to metabolism, gene expression, lipid and carbohydrate biochemistry or the biochemical basis of diseases. An interest and/or experience in bioinformatics would be an asset.

In addition, participation in teaching of both the undergraduate medical and biochemistry curricula will be required. The successful applicant will have a broad range of collaborative possibilities on campus with scientists in other departments and colleges, including the Canadian Light Source (www.cls.usask.ca/) and the Saskatchewan Structural Sciences Centre (www.usask.ca/sssc/).

Please submit both electronic and signed hard copies of the application, including curriculum vitae; a detailed statement on research interests and of previous teaching experience in a single PDF document to:

Dr. R.L. Khandelwal
Head, Department of Biochemistry, College of Medicine
University of Saskatchewan
107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada.
E-mail: ramji.khandelwal@usask.ca
Phone:(306) 966-4368
Fax: (306) 966-4390

Applicants should also arrange for three confidential letters of reference to be sent separately to the same address.

The closing date for receipt of applications is February 1, 2009. The effective date for appointment is between April 1, 2009 and July 1, 2009.

All qualified candidates are encouraged to apply. However, Canadian citizens and permanent residents will be given priority. The University of Saskatchewan is committed to Employment Equity. Members of Designated Groups (women, Aboriginal people, people with disabilities and visible minorities) are encouraged to self-identify on their applications.


Nobel Laureate: Fred Sanger

 

The Nobel Prize in Chemistry 1980.

"for their contributions concerning the determination of base sequences in nucleic acids"



Frederick Sanger (1918 - ) was awarded the Nobel Prize for developing the chain termination, or dideoxy, method of sequencing DNA (The Sanger Method of DNA Sequencing). The method relies on synthesis of DNA in vitro using dideoxynucleotides that cause chain termination from time to time. The original method has been adapted to high throughput methods that are fully automated.

Fred Sanger shared the Nobel Prize with Walter Gilbert. It was Sanger's second Nobel Prize, his first was for developing methods to sequence proteins.


The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

[Photo Credit: The photograph show Fred Sanger in front of the Wellcome Trust Sanger Institute.]

Tuesday, December 16, 2008

Testing Natural Selection: Part 1

 
The latest issue of Scientific American has an interesting article by H. Allen Orr entitled Testing Natural Selection.
Biologists working with the most sophisticated genetic tools are demonstrating that natural selection plays a greater role in the evolution of genes than even most evolutionists had thought.
Orr is an adaptationist. His perspective on evolution focuses on natural selection as the predominant mechanism. He tends to dismiss all other mechanisms as either uninteresting or unimportant.

I though it might be interesting to compare what a pluralist might say about some of the things in the article. It's one way of highlighting the difference between the two points of view.

Naturally, as a pluralist, I disagree with some statements. My main beef, however, is with the growing tendency to over-emphasize natural selection as we approach the 200th anniversary of Darwin's birth and the 150th anniversary of publication of On the Origin of Species. I think it's possible to describe the differences between evolution in the eighteenth century and evolution in the 21st century without diminishing Darwin's contributions.

Orr begins his article by describing natural selection. He explains that there are several kinds of mutations ...
Most important, we know something about the effects of mutations on fitness. The overwhelming majority of mutations are harmful—that is, they reduce fitness; only a tiny minority are beneficial, increasing fitness.
That's not exactly how I would put it. I would have added that there's a third type of mutation that is neither harmful nor beneficial—neutral mutations.

Furthermore, I would have explained that the frequency of these three different kinds of mutations can vary considerably from one species to the next depending on the organization of the genome. In animals and plants, for example, most of the DNA does not seem to be essential so that the overwhelming majority of mutations are neutral and a smaller number—those that interfere with an essential function—are deleterious. A few mutations can be beneficial.

Orr goes on to say ....
Most mutations are bad for the same reason that most typos in computer code are bad: in finely tuned systems, random tweaks are far more likely to disrupt function than to improve it.
I would not use this analogy because it emphasizes something that I think is false; namely that organisms are "fine tuned systems." I tend to think of them as sloppy Rube Goldberg machines and not as well-tested computer code.

I would say that most mutations in essential regions of the genome are deleterious because random hits in DNA are more likely to make things worse than to make things better. The distinction is subtle, but important. Many adaptationists use language implying that living organisms are almost perfectly adapted to their present environment.

In the next section, Orr describes the advances of population genetics and its influence on how we understand natural selection. I would have described how population genetics led to an understanding of all type of evolution, and not just natural selection. Here's what Orr says,
Population geneticists have also provided insight into natural selection by describing it mathematically. For example, geneticists have shown that the fitter a given type is within a population, the more rapidly it will increase in frequency; indeed, one can calculate just how quickly the increase will occur. Population geneticists have also discovered the surprising fact that natural selection has unimaginably keen “eyes,” which can detect astonishingly small differences in fitness among genetic types. In a population of a million individuals, natural selection can operate on fitness differences as small as one part in a million.
I would have said that the growth of population genetics in the early part of the 20th century led to the recognition of random genetic drift as an important mechanism of evolution. Models were developed to explain how natural selection affected the increase in frequency of a beneficial allele and how neutral alleles could also increase in frequency even though they were invisible to natural selection.

The population geneticists also discovered that harmful alleles could become fixed by accident, although that turns out to be a rare event. More importantly, they discovered that natural selection has a stochastic component. Beneficial alleles will only become fixed part of the time. The probability depends on the fitness advantage. For example, if an allele has a fitness advantage of 10% then it will only become fixed 20% of the time. In 80% of cases when such an allele arises in a population it will be lost by random genetic drift before it becomes fixed.1

As the fitness advantage diminishes, the probability of fixation becomes lower and lower so that alleles with small fitness advantages (<1%) will hardly ever change the species. That's what population geneticists discovered about natural selection.

The probability of fixation of neutral alleles (or nearly neutral alleles) is very low but since there are so many more of them than beneficial alleles, much of evolution is characterized by changes due to random genetic drift.

The next section is "How Common Is Natural Selection?". This is where Orr asks the key question ...
One of the simplest questions biologists can ask about natural selection has, surprisingly, been one of the hardest to answer: To what degree is it responsible for changes in the overall genetic makeup of a population? No one seriously doubts that natural selection drives the evolution of most physical traits in living creatures—there is no other plausible way to explain such large-scale features as beaks, biceps and brains. But there has been serious doubt about the extent of the role of natural selection in guiding change at the molecular level. Just what proportion of all evolutionary change in DNA is driven, over millions of years, by natural selection—as opposed to some other process?
We've discussed this distinction between molecular changes and physical traits many times. One of the most annoying characteristics of adaptationists is that they insist on relegating other mechanisms of evolution to the level of DNA sequences but refuse to consider anything but natural selection when it comes to visible phenotypes. There is no justification for this assumption. Many physical traits can be neutral or even deleterious. They were not fixed by natural selection.2

What Orr says is simply not true. There are many biologists who seriously doubt that natural selection drives the evolution most physical traits, even though such pluralists readily agree that most adaptions are due to natural selection. Random genetic drift is a plausible way to explain many physical traits.
Until the 1960s biologists had assumed that the answer was “almost all,” but a group of population geneticists led by Japanese investigator Motoo Kimura sharply challenged that view. Kimura argued that molecular evolution is not usually driven by “positive” natural selection—in which the environment increases the frequency of a beneficial type that is initially rare. Rather, he said, nearly all the genetic mutations that persist or reach high frequencies in populations are selectively neutral—they have no appreciable effect on fitness one way or the other. (Of course, harmful mutations continue to appear at a high rate, but they can never reach high frequencies in a population and thus are evolutionary dead ends.) Since neutral mutations are essentially invisible in the present environment, such changes can slip silently through a population, substantially altering its genetic composition over time. The process is called random genetic drift; it is the heart of the neutral theory of molecular evolution.
As I've already pointed out, random genetic drift was discovered in the 1920s and it was incorporated into the first version of the Modern Synthesis in the 1940s. It dropped out of favor when the synthesis hardened at the time of the Darwin centennial in 1959.

Random genetic drift was revived in the late 1960's with the discovery of neutral alleles. Drift is the way in which selectively neutral alleles become fixed in a population. Random genetic drift and neutral theory are not synonyms.

As I indicated above, since the vast majority of animal and plant genomes is non-essential, it stands to reason that the vast majority of alleles will be neutral. Thus at the molecular level, at least, random genetic drift must be the dominant mechanism of evolution.

By the 1980s many evolutionary geneticists had accepted the neutral theory. But the data bearing on it were mostly indirect; more direct, critical tests were lacking. Two developments have helped fix that problem. First, population geneticists have devised simple statistical tests for distinguishing neutral changes in the genome from adaptive ones. Second, new technology has enabled entire genomes from many species to be sequenced, providing voluminous data on which these statistical tests can be applied. The new data suggest that the neutral theory underestimated the importance of natural selection.
Hmmm ... I could see where this was going even before I read it. Orr is about to quote the infamous work of Drosophila geneticists who have devised complicated tests to show that some synonymous mutations might confer a selective advantage in one species but not in another closely related species. Some of the papers claim that many alleles in coding regions are not neutral even thought they don't change the amino acid. There's no question that this is true in some cases.

It's also true that mutations altering the amino acid are sometimes beneficial, and therefore selected. However, if you align the amino acid sequences of a given gene from hundreds of species and map them on to the structure of the protein it becomes readily apparent that most substitutions cannot have a significant effect on the function of the protein. They must be neutral, or nearly neutral. As a matter of fact, in most proteins it is difficult to find any clearly beneficial alleles present in one species and not in the others.
In one study a team led by David J. Begun and Charles H. Langley, both at the University of California, Davis, compared the DNA sequences of two species of fruit fly in the genus Drosophila. They analyzed roughly 6,000 genes in each species, noting which genes had diverged since the two species had split off from a common ancestor. By applying a statistical test, they estimated that they could rule out neutral evolution in at least 19 percent of the 6,000 genes; in other words, natural selection drove the evolutionary divergence of a fifth of all genes studied. (Because the statistical test they employed was conservative, the actual proportion could be much larger.) The result does not suggest that neutral evolution is unimportant—after all, some of the remaining 81 percent of genes may have diverged by genetic drift. But it does prove that natural selection plays a bigger role in the divergence of species than most neutral theorists would have guessed. Similar studies have led most evolutionary geneticists to conclude that natural selection is a common driver of evolutionary change even in the sequences of nucleotides in DNA.
Pluralists disagree. We still think that random genetic drift is by far the dominant mechanism at the molecular level and that it even plays a significant role at the level of visible phenotypes.

In addition, we like to remind adaptationists that most beneficial alleles are eliminated by random genetic drift before they ever become fixed in a population.


1. Many biologists, and most evolutionary psychologists, do not understand this important point. They think that all they have to do is identify some (real or imagined) benefit and it will automatically take over the population no matter how small the benefit.

2. I know that Orr said "most" physical traits and not "all" physical traits. It's a distinction without meaning since the percentage of non-adaptive changes that adaptationists are willing to admit, grudgingly, is not much different than zero.