If Spiders Are Arthropods then Where Are the Segments?

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

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[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?

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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.

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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.

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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.

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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?

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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.

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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.

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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

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Webpages as Graphics for Sandwalk

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

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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.

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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!".

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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

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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.

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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?

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