Which Animal Phylum Has the Most Species?

 
I bet almost all of you think it's Arthropoda since there are so many insects and especially beetles, which God was very fond of.¹

However, recent advances in taxonomy have suggested that there are one million species of nematode. This is about the same number of species as arthropods so the primacy of insects has been challenged.

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1. This is a reference to a famous quip by J.B.S. Haldane. When asked to name the most important thing he has learned about God from studying biology he reportedy said, "I'm not sure, but He seems to be inordinately fond of beetles."

[Photo Credit: Iowa State University Plant Disease]

Happy Autumnal Equinox

 
If I've got this right then today at 11:44 AM EST (i.e. right now!) is the Autumnal Equinox. Have a very happy one!



Most people think that the Spring and Fall equinoxes are the days when there are equal amounts of daylight and night. If that's true then why is the Autumnal Equinox at 11:44 in the morning?

Here's the answer from Wikipedia. It's the sort of thing I would have expected to find on Bad Astronomy but, if it's there, I couldn't find it.

An equinox in astronomy is the moment in time (not a whole day) when the centre of the Sun can be observed to be directly above the Earth's equator, occurring around March 20 and September 23 each year.

More technically, at an equinox, the Sun is at one of two opposite points on the celestial sphere where the celestial equator (i.e., declination 0) and ecliptic intersect. These points of intersection are called equinoctial points—the vernal point and the autumnal point. By extension, the term equinox may be used to denote an equinoctial point.

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[Image Credit: eSky]

Monday's Molecule #89

 

You may have noticed that this week's "molecule" isn't exactly a molecule. It's something else entirely. In order to win the fabulous prize you need to tell me what the figure represents and what species it refers to.

There's a direct connection between today's "molecule" and a Nobel Prize. I'm looking for the people who contributed to the work shown in the figure. One of them could have won a Nobel Prize for several other key discoveries but this is the one the Nobel Prize committee decided to pick. A wise choice, in my opinion.

The first one to correctly identify the molecule and name the Nobel Laureates, wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are three ineligible candidates for this week's reward. You know who you are.

THEME:

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

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: This week's winner is Brad Hersh of Clemsen University. The figure is the cell lineage of the nematode Caenorhabditis elegans and the Nobel Laureates are Sulston, Horvitz, and Brenner (2002). Congratulations Brad!

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Joseph Mallord William Turner (1775–1851)

 
Turner was an English artist who did most of his work in the first half of the nineteenth century. I'm a fan of most of Turner's paintings but I particularly like the seascapes that show Napoleonic era battleships.

John Pieret visited the Turner exhibition at the Metropolitan Museum of Art in some big city south of the border. He was mean kind enough to post pictures on his blog at Page Turner. It's hard to imagine how someone can have such good taste in art and such a bad

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Yes, Virginia, there is a Santa Claus

 
Yesterday was 111th anniversary of an editorial published in The New York Sun. The author was Francis Pharcellus Church. See the article on Wikipedia for the complete history of Yes, Virginia, there is a Santa Claus.

Most people don't know what Frances Pharcellus Church actually wrote so here it is ...

Virginia,

Your little friends are wrong. They have been affected by the skepticism of a skeptical age. They do not believe except they see. They think that nothing can be which is not comprehensible by their little minds. All minds, Virginia, whether they be men’s or children’s, are little. In this great universe of ours, man is a mere insect, an ant, in his intellect as compared with the boundless world about him, as measured by the intelligence capable of grasping the whole of truth and knowledge. Yes, Virginia, there is a Santa Claus. He exists as certainly as love and generosity and devotion exist, and you know that they abound and give to your life its highest beauty and joy. Alas! how dreary would be the world if there were no Santa Claus! It would be as dreary as if there were no Virginias. There would be no childlike faith then, no poetry, no romance to make tolerable this existence. We should have no enjoyment, except in sense and sight. The eternal light with which childhood fills the world would be extinguished. Not believe in Santa Claus! You might as well not believe in fairies. You might get your papa to hire men to watch in all the chimneys on Christmas eve to catch Santa Claus, but even if you did not see Santa Claus coming down, what would that prove? Nobody sees Santa Claus, but that is no sign that there is no Santa Claus. The most real things in the world are those that neither children nor men can see. Did you ever see fairies dancing on the lawn? Of course not, but that’s no proof that they are not there. Nobody can conceive or imagine all the wonders there are unseen and unseeable in the world. You tear apart the baby’s rattle and see what makes the noise inside, but there is a veil covering the unseen world which not the strongest man, nor even the united strength of all the strongest men that ever lived could tear apart. Only faith, poetry, love, romance, can push aside that curtain and view and picture the supernal beauty and glory beyond. Is it all real? Ah, Virginia, in all this world there is nothing else real and abiding. No Santa Claus! Thank God! he lives and lives forever. A thousand years from now, Virginia, nay 10 times 10,000 years from now, he will continue to make glad the heart of childhood.

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Does Science Need Religion?

 
That's the question asked by Scott Hatfield on Monkey Trials. He discusses a recent statement by Malcolm Brown who is Director of Mission and Public Affairs for the Church of England. Scott also responds to criticisms of Brown's position from Jason Rosenhouse. You can find all the links at GOOD SCIENCE, GOOD RELIGION along with an excellent analysis by Scot.

For what it's worth, I agree with much of Scot's analysis and with Jason Rosenhouse. Malcolm Brown is expressing a position that's very common among theists even though it is often denied. For the believer, science has to make room for God and accommodate religion because the two working together are superior to either one on its own. Brown is worried about those who claim to compartmentalize religion and science and keep them separate.

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Fideism

"Fideism" is a new word for me. It cropped up on Friendly Atheist in one of the comment threads [Impromptu Religious Debate on Real Time]. I had to look it up. Here's the description of fideism on Wikepedia ...

Alvin Plantinga defines "fideism" as "the exclusive or basic reliance upon faith alone, accompanied by a consequent disparagement of reason and utilized especially in the pursuit of philosophical or religious truth." The fideist therefore "urges reliance on faith rather than reason, in matters philosophical and religious," and therefore may go on to disparage the claims of reason.[3] The fideist seeks truth, above all: and affirms that reason cannot achieve certain kinds of truth, which must instead be accepted only by faith.[4] Plantinga's definition might be revised to say that what the fideist objects to is not so much "reason" per se — it seems excessive to call Blaise Pascal anti-rational — but evidentialism: the notion that no belief should be held unless it is supported by evidence.

The fideist notes that religions that are founded on revelation call their faithful to believe in a transcendent deity even if believers cannot fully understand the object of their faith. Some fideists also contend that human rational faculties are themselves untrustworthy, because the entire human nature has been corrupted by sin, and as such the conclusions reached by human reason are therefore untrustworthy: the truths affirmed by divine revelation must be believed even if they find no support in human reason. Fideism, of a sort which has been called naive fideism, is frequently found in response to anti-religious arguments; the fideist resolves to hold to what has been revealed as true in his faith, in the face of contrary lines of reasoning.

Specifically, fideism teaches that rational or scientific arguments for the existence of God are fallacious and irrelevant, and have nothing to do with the truth of Christian theology.

I wonder if this belief is widespread? I always thought that Christians wanted their religious beliefs to be rational and certainly the Intelligent Design Creationists are among those who think that God's existence has been demonstrated.

Nevertheless, when discussing the existence of God with most Christians I've discovered that the "faith" argument is eventually trotted out as their main defense. It's another way of saying that science and religion are different ways of knowing. Science relies on evidence and rationality and religion relies on something else.

Maybe this is why religion gets special privileges in our society? It's because religion doesn't play by the same rules that we use to demonstrate stupidity in politics and economics. I doubt that most religious people could define fideism and I doubt that they could defend it as well as Alvin Plantinga, but I bet it's what they really believe; namely, that faith cannot be criticized using rational arguments and evidence.

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Is There a Difference Between Being Angry About Right-wing Politics and Being Angry About Religious Superstitions?

 
This is an interesting show where Andrew Sullivan argues strongly that the left should attack Sarah Palin but then he turns on Bill Maher when he (Maher) criticizes silly religious superstition (guardian angels). It's a good insight into the thinking of people like Sullivan. It's exactly what's wrong with our society— religion has special privileges that protect it from the kind of critical thinking that we apply everywhere else and otherwise intelligent people like Sullivan don't see the inconsistency.

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[Hat Tip: Friendly Atheist]

Jed Bartlet Advises Barack Obama

 
The West Wing was one of my favorite TV shows during its time. Maureen Dowd thinks so too 'cause she asked its creator, Aaron Sorkin, to imagine what President Jed Bartlet might say to Barack Obama if given the chance. Her op-ed piece was published in yesterday's New York Times [Seeking a President Who Gives Goose Bumps? So’s Obama].

Here's the best bit of advice from Bartlet to Obama ...

OBAMA The problem is we can’t appear angry. Bush called us the angry left. Did you see anyone in Denver who was angry?

BARTLET Well ... let me think. ...We went to war against the wrong country, Osama bin Laden just celebrated his seventh anniversary of not being caught either dead or alive, my family’s less safe than it was eight years ago, we’ve lost trillions of dollars, millions of jobs, thousands of lives and we lost an entire city due to bad weather. So, you know ... I’m a little angry.

OBAMA What would you do?

BARTLET GET ANGRIER! Call them liars, because that’s what they are. Sarah Palin didn’t say “thanks but no thanks” to the Bridge to Nowhere. She just said “Thanks.” You were raised by a single mother on food stamps — where does a guy with eight houses who was legacied into Annapolis get off calling you an elitist? And by the way, if you do nothing else, take that word back. Elite is a good word, it means well above average. I’d ask them what their problem is with excellence. While you’re at it, I want the word “patriot” back. McCain can say that the transcendent issue of our time is the spread of Islamic fanaticism or he can choose a running mate who doesn’t know the Bush doctrine from the Monroe Doctrine, but he can’t do both at the same time and call it patriotic. They have to lie — the truth isn’t their friend right now. Get angry. Mock them mercilessly; they’ve earned it. McCain decried agents of intolerance, then chose a running mate who had to ask if she was allowed to ban books from a public library. It’s not bad enough she thinks the planet Earth was created in six days 6,000 years ago complete with a man, a woman and a talking snake, she wants schools to teach the rest of our kids to deny geology, anthropology, archaeology and common sense too? It’s not bad enough she’s forcing her own daughter into a loveless marriage to a teenage hood, she wants the rest of us to guide our daughters in that direction too? It’s not enough that a woman shouldn’t have the right to choose, it should be the law of the land that she has to carry and deliver her rapist’s baby too? I don’t know whether or not Governor Palin has the tenacity of a pit bull, but I know for sure she’s got the qualifications of one. And you’re worried about seeming angry? You could eat their lunch, make them cry and tell their mamas about it and God himself would call it restrained. There are times when you are simply required to be impolite. There are times when condescension is called for!

Whoa! That doesn't sound like bipartisanship to me!

I agree with this approach but, from what I gather, there are millions of American who don't. They seem to think it's a sin to come right out and say what you really think. It's supposed to be much better to lie and pussyfoot around the issues and launch your attacks in a much more devious and underhanded manner. It's supposed to be better to pretend that you will change things in Washington by something called "bipartisanship" where you accommodate the wishes of kooks with crazy ideas about how to run a society. Play to the lowest common denominator—that's how to win an election.

This love for the lowest common denominator is the same attitude that leads to criticism of the vocal atheists (but interestingly enough, not the vocal Christian right wing). It would be nice if the "elite" were admired and respected in America, and in Canada, but is it going to happen in our lifetime? Are we ever going to see the day when people admit that Christopher Hitchens really is smarter than Rush Limbaugh and Bill Clinton really is smarter than George Bush? And so is Al Gore?¹

Jed Bartlett is advocating a different strategy. He says you should pitch our ideas to the top half of the "denominators" and leave the lower half to the other side. Maybe it's not such a bad idea. Maybe Obama will never get the votes of the bottom feeders anyway and it's time to stop trying.

OBAMA Good to get that off your chest?

BARTLET Am I keeping you from something?

OBAMA Well, it’s not as if I didn’t know all of that and it took you like 20 minutes to say.

BARTLET I know, I have a problem, but admitting it is the first step.

OBAMA What’s the second step?

BARTLET I don’t care.

OBAMA So what about hope? Chuck it for outrage and put-downs?

BARTLET No. You’re elite, you can do both. Four weeks ago you had the best week of your campaign, followed — granted, inexplicably — by the worst week of your campaign. And you’re still in a statistical dead heat. You’re a 47-year-old black man with a foreign-sounding name who went to Harvard and thinks devotion to your country and lapel pins aren’t the same thing and you’re in a statistical tie with a war hero and a Cinemax heroine. To these aged eyes, Senator, that’s what progress looks like. You guys got four debates. Get out of my house and go back to work.

Gee, I almost forgot about the lapel pins. It's how you demonstrate that you've sold out to the framers.

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1. And, in Canada, Stéphane Dion really is a whole lot smarter than Stephan Harper or Jack Layton?

[Big Hat Tip to Chance and Necsssity]

How Should Scientists Talk to a Politician?

 
Janet Stemwedel refers us to a video on how scientists should talk to politicians [Retired congresscritter offers communication tips to scientists].

The congresscritter in question being Sherwood Boehlert, who represented New York's 24th Congressional district (1983-2007), and chaired the House Science Committee (2001-2007). Boehlert offers this advice in a video called "Speaking for Science: Bringing Your Message to Policymakers," available for download from the American Chemical Society website.*

The video presents two scenarios in which a group of scientists meets with their Congressional representative (who happens to be a member of the House Science Committee, played by Boehlert). As you might guess, the idea is to contrast the effective meeting with the disastrous one.

As you might guess, the effective way to talk to a politician about science is to be brief and to the point and avoid all that sciency stuff that only confuses everyone. You need to stop trying to explain science to the staff member and concentrate on what's in it for the politician.

I'm not naive. I know that this is the way to be effective when you're asking a politician to do something for science. However, I'm enough of an idealist to dream about a future where scientists would make videos explaining to politicians how they should behave when prominent scientists make an effort to come by their office in an attempt to teach them some science so they can do their jobs better.

Why do politicians always think that everyone has to play by their rules? I thought they were there to serve the people, not the other way around.

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An Example of Faulty Logic from Cold Spring Harbor

A press release from Cold Spring Harbor Laboratory promotes the work of Michael Zhang and Adrian Krainer who work with splicing factors. In a typical attempt to hype the significance of the work, the press release claims that each human gene has many different variants produced by alternative splicing [CSHL team traces extensive networks regulating alternative RNA splicing].

That may or may not be correct—I happen to think it's mostly an artifact of EST cloning—but that's not the point I want to make here. The main point is the rationalization explained thus,

Biologists involved in the Human Genome Project were frankly astonished to discover that everything that makes us human is the product of a set of only 23,000 or so genes.¹ That number in itself, though several times smaller than prior estimates, is not shocking; it is the relative size of other genomes that surprised scientists.

The common fruit fly that hovers over your ripening bananas, for instance, possesses some 14,000 genes. It's perfectly obvious that human beings are vastly more complex, biologically, than a fly. Molecular biologists have demonstrated in recent years that it is not the number of genes that is the key to complexity but rather the number and diversity of gene products that a given set of genes can instruct cells to manufacture.

Rather than a single gene ordering the production of a single kind of protein, as scientists used to assume, it turns out that individual genes can in some cases give rise to dozens or even thousands of different proteins, thanks to a phenomenon called alternative splicing.

This is one version of what I call The Deflated Ego Problem. The "problem" is that some people are really, really, upset about the fact that humans may only have a few thousand genes more than a fruit fly.

So they look for some way to reflate their egos and one of the most common arguments is the one shown above. (It's excuse #1 on the list.) It goes like this.... Humans are so much more complex that fruit flies even though they have only a few thousand more genes because each human gene does double, or triple duty. Each human gene makes several different proteins by alternative splicing of the primary RNA transcript.

Viola! Problem solved.

Except for one little nasty fact. Drosophila genes also show abundant levels of alternative splicing. In fact they produce just as many variants per gene as humans, if you believe the EST data (which I don't).

Oops. There goes that solution. Humans don't have that many more proteins than fruit flies after all.

This is such an obviously bogus argument that I'm surprised it still appears in the scientific literature. Doesn't anyone realize that in order for it to salvage deflated egos there has to be no—or much less— alternative splicing in fruit flies?

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Some people were surprised and embarrassed by the "low" number of genes in the human genome but others were pretty happy that their estimates were close to the mark [Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome].

The Altenberg 16 Make It into Nature

 
Nature News has an article on the recent conference in Altenberg, Austria that brought together 16 biologists who want to change evolutionary theory. The article by John Whitfield covers both sides of the story reasonably well [Biological theory: Postmodern evolution?].

The bottom line is that many of the participants at the conference are advocating changes to evolutionary theory that are either unnecessary or wrong. This is especially true of the evo-devo crowd as Whitfield makes clear from his interview with opponents of evo-devo.

But lost in all the hype is a real need to address some problems with the Modern Synthesis that didn't even come up at the meeting. The problem is very clear from the article. Here's how John Whitfield describes the current version of the Modern Synthesis.

Leaving aside the troublesome adjective, what is the modernism that the Altenburg meeting is meant to move beyond — or to use Pigliucci's preferred term, 'extend'1? Between about 1920 and 1940, researchers such as the American Sewall Wright and the Englishmen Ronald Fisher and J. B. S. Haldane took Charles Darwin's ideas about natural selection and Gregor Mendel's insights into how traits pass from parents to offspring — which many biologists of the time believed antithetical — and fused them into a mathematical description of the genetic makeup of populations and how it changes. That fusion was the modern synthesis. It treats an organism's form, or phenotype, as a readout of its hereditary information, or genotype. Change is explained as one version of a gene being replaced by another. Natural selection acts by changing the frequency of genes in the next generation according to the fitness of phenotypes in this one. In this world view, the gene is a black box, its relationship to phenotype is a one-way street, and the environment, both cellular and external, is a selective filter imposed on the readout of the genes, rather than something that can influence an organism's form directly.

This is a view of evolution that doesn't recognize random genetic drift as an important mechanism of evolution. Surely in 2008, a publication like Nature shouldn't be publishing the old-fashioned adaptationist view of evolution? What's wrong with adding one sentence to say that Sewall Wright also took an idea that Charles Darwin never heard of, random genetic drift, and incorporated that idea into our modern understanding of evolution so that we now recognize that random genetic drift is one of the main mechanisms of evolution?

I think the main reason we don't see such a description is because people like John Whitfield are completely unaware of any mechanism other than natural selection. Or, at least, unaware of the fact that it could be important and needs to be part of modern evolutionary theory.

The Modern Synthesis needs to be updated but updated in the manner described by Stephen Jay Gould and not by the Altenberg 16.

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NCSE on the Michael Reiss Affair

 
The National Center for Science Education has issued a press release on the recent resignation of Michael Reiss from his role as Director of Education for the Royal Society of London (UK) [Royal Society furor over creationism].

The NCSE is highly critical of the way Reiss' remarks were misrepresented in the popular press. NCSE is indirectly critical of those Nobel Laureates who called for Michael Reiss to resign based on those false reports in British newspapers.

Under the circumstances, the press release from NCSE is pretty good but it stops short of taking a position. I would have been happier if NCSE had told us their official stance on: (a) whether creationism should be challenged in British schools, (b) whether Michael Reiss should have resigned, and (c) whether it is appropriate for clergy to play a leading role in deciding policies about science and religion in a scientific organization.

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Alex Palazzo Is in Toronto

 
Alex has temporarily suspended blogging on The Daily Transcript because he is Off to Toronto.

We hope he will consider moving here permanently in the very near future. Please help him make up his mind by posting encouraging comments about the Dept. of Biochemistry, the University of Toronto, Toronto, Ontario, and Canada.

Comments about the wonderful weather, the high quality of our undergraduates, the easy access to the downtown core, the outstanding faculty, the high speed internet connection, free health care, Tim Horton's, fabulous research opportunities, lunch at the Faculty Club and anything else that might occur to you, are especially welcome.

Oh, and don't forget to mention that PZ Myers is coming next month!

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Join the Center for Inquiry

 
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