Spore and Evolution

 
Spore is a computer game that let's you "evolve" organisms beginning with a simple cell and moving "upwards" to creatures that can build spaceships. The game is designed by Will Wright whose previous credits include SimCity and The Sims.

Wright and his company have been heavily promoting the game as a way of learning about evolution. As part of this promotion they have distributed free copies to many scientists in advance of the opening day of sales in retail stores. Here's how it's described on the Spore Website.

How will you create the universe?

With Spore you can nurture your creature through five stages of evolution: Cell, Creature, Tribe, Civilization, and Space. Or if you prefer, spend as much time as you like making creatures, vehicles, buildings and spaceships with Spore’s unique Creator tools.

CREATE Your Universe from Microscopic to Macrocosmic - From tide pool amoebas to thriving civilizations to intergalactic starships, everything is in your hands.

EVOLVE Your Creature through Five Stages - It’s survival of the funnest as your choices reverberate through generations and ultimately decide the fate of your civilization.

Time for a reality check. Spore is a computer game. It's purpose is to make bundles of money for Will Wright and his company. It may be an excellent game but it is NOT a way of learning about evolution. Evolution does not have a purpose or a direction.

Carl Zimmer has just published an article in The New York Times about Spore and computer simulations [Gaming Evolves]. Some scientists don't think the game reflects evolution.

Unlike the typical shoot-them-till-they’re-all-dead video game, Spore was strongly influenced by science, and in particular by evolutionary biology. Mr. Wright will appear in a documentary next Tuesday on the National Geographic Channel, sharing his new game with leading evolutionary biologists and talking with them about the evolution of complex life.

Evolutionary biologists like Dr. Near and Dr. Prum, who have had a chance to try the game, like it a great deal. But they also have some serious reservations. The step-by-step process by which Spore’s creatures change does not have much to do with real evolution. “The mechanism is severely messed up,” Dr. Prum said.

Nevertheless, Dr. Prum admires the way Spore touches on some of the big questions that evolutionary biologists ask. What is the origin of complexity? How contingent is evolution on flukes and quirks? “If it compels people to ask these questions, that would be great,” he said.

The object of the game is to "evolve" advanced creatures that the player "designs." What are the chances that the average player is going to appreciate the roles of contingency, and quirks? Probably so close to zero that it's not worth discussing.

I have a problem when we talk about games like Spore and real evolution in the same breath. I have a problem when someone like Will Wright is promoted on the National Geographic TV channel. The press release from National Geographic sounds ominous ..

(WASHINGTON, D.C. — AUGUST 21, 2008) In the newest creation from Electronic Arts Inc. (EA) and video game pioneer and "The Sims" mastermind Will Wright, Spore™ enables players to design a virtual galaxy of new life, such as a one-eyed web-footed creature with a snout, and then control their species' evolution. But how much real-world science is behind this groundbreaking new game? And what genetic connections do people share with a universe of strange organisms?

On Tuesday, Sept. 9, at 10:00 p.m. ET/PT, National Geographic Channel (NGC) presents the premiere of How to Build a Better Being, the companion documentary to the highly anticipated new video game Spore, which will be released nationally on Sunday, Sept. 7. The show, which is also included in the limited run of the collectable "Spore Galactic Edition," joins Wright and leading scientists in exploring the genetic information we share with all animals — even creatures we could never have envisioned. From prehistoric fish with wrists to 8-ton elephants with trunks, get powerful new insight into the origin of species and how our prized parts came to be. Then see how evolutionary creature-making is translated into a brave new world of gaming.

"What are the things that evolution has at its disposal to define a creature, to mix and match the parts, and eventually come up with a unique organism that's going to live its life and try to reproduce?" — Will Wright, gaming innovator

Some would argue that anything that promotes evolution is a step in the right direction. It's a valid point.

But why can't we have our cake and eat it too? Why can't we promote evolution but do it in a scientifically accurate manner? It's abundantly clear to all scientists that the general public knows little about evolution and what little they know is mostly wrong. Do we have to cater to those false impressions?

What effect is it going to have in the long run if we misrepresent science by pretending that evolution is progressive and ladder-like and leads eventually to us—or at least leads to intelligent animals? Is anyone else concerned about this?

The video clip below doesn't mention Spore. It looks like the same old evo-devo emphasis on semi-conserved regulatory genes and regulation of animal development as keys to understanding how humans evolved.


The Spore advertisement exploits the National Geographic connection.

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Comment Policy on Sandwalk

 
I think it's time to re-state my policy on comments. I don't like censorship. That's why my policy is close to the one mockingly described at Draft Blogger's Code of Conduct.

We also decided we needed an "anything goes" badge for sites that want to warn possible commenters that they are entering a free-for-all zone. The text to accompany that badge might go something like this:

"This is an open, uncensored forum. We are not responsible for the comments of any poster, and when discussions get heated, crude language, insults and other "off color" comments may be encountered. Participate in this site at your own risk."

As a consequence of this policy, there are several very annoying people making comments on Sandwalk. I don't respond to comments from those people but others are free to do so.

There are two types of comments that will be removed from Sandwalk. These are cases where censorship is justified, in my opinion.

The first is outright spam of the sort that we all have to tolerate from time to time. If your comment serves no other purpose than to direct people to 30 different "free" travel websites, for example, then these comments will be quickly removed.

The second is blatant promotion of commercial products on the pretext that they are relevant to the content of a posting. An example of the second type is the posting of a website for collagen creme in the comments section of an article about the biochemistry of collagen.

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Alternating Generations

 
Check out When Ferns Don't Look Like Ferns by Christopher Taylor on Catalogue of Organisms. The concept of alternating generations is an important concept that everyone should understand.

All plants undergo alternation of generation to a greater or lesser degree. Here's an interesting way to think about the concept from the Biology course notes at the University of Miami.

If animals were to undergo alternation of generations, then imagine that you are the diploid individual (sporophyte). Your mother, the gametophyte, would be haploid, and would look completely different from you (maybe like a SmurfTM). Your grandmother would be diploid, and look like you. Your own offspring would look like your mama the SmurfTM, your grandchildren would look like you, and so on.

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[Image Credit: Lewis & Clark]

Genes and Geography

 
Your DNA tells you who you are related to. This has led to projects that can trace your ancestors. Your DNA can also tell you where you've come from. This is because most of our ancestors didn't get out much. They tended to marry their cousins and close neighbors. Over many generations the people in a particular region came to resemble each other much more closely than they resembled people in other countries.

Razib at Gene Expression has been discussing the evolutionary implications of this kind of population genetics. See his latest posting and learn how to interpret the map shown below [Genetic map of Europe; genes vary as a function of distance].

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Monday's Molecule #86

 
In honor of all those students who are returning to college this week's molecule is another simple one that should be familiar to every undergraduate taking an introductory biochemistry course. Your task is to identify the molecule and give me its correct common name—the one required on an exam—and the complete, correct IUPAC name.

There's a direct connection between today's molecule and a Nobel Prize. We are looking for the single person most responsible for identifying this molecule as an important part of a metabolic pathway. This person didn't know the exact structure but got the basic chemistry correct. Be careful, there are several possible candidates who haven't already been featured on Sandalk. I want the one person who best meets the criterion.

The first person to correctly identify the molecule and name the Nobel Laureate, 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 four 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 no open.

UPDATE: The molecule is ATP of adenosine 5′-triphosphate. Lots of people got the molecule but nobody guessed the Nobel Laureate (Hans von Euler-Chelpin). There are no winners this week.

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What the Heck?

 
Coturnix posted a video on A Blog Around the Clock. His posting, entitled Just replace '9/11' with 'POW'..., was critical of McCain and his running mate Sarah Palin. The main issue in the election, according to Coturnix and others, is race. If true, that's sad.

I tried to watch the video that Coturnix embedded in his blog and this is what I get ...


Isn't that interesting? Is this a joke or has the server at hulu has been set up to recognize and block IP numbers that are registered outside of the USA? Why?

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Why Is Canada in Afghanistan?

 
The Toronto Star asked this question a few days ago. Here's the entire article from Our Man in Afghanistan. I've chosen to accompany it with a photograph of the Prime Minister of Canada shaking hands with Hamid Karzai. This is the same photo that Canadian Cynic used in Sorry ... why exactly are we over there again?.

My words fail. So here's Britain's The Independent:

"The Afghan president, Hamid Karzai, has pardoned three men who had been found guilty of gang raping a woman in the northern province of Samangan.

The woman, Sara, and her family found out about the pardon only when they saw the rapists back in their village.

“Everyone was shocked,” said Sara’s husband, Dilawar, who like many Afghans uses only one name. “These were men who had been sentenced and found guilty by the Supreme Court, walking around freely.”

Sara’s case highlights concerns about the close relationship between the Afghan president and men accused of war crimes and human rights abuses.

The men were freed discreetly but the rape itself was public and brutal. It took place in September 2005, in the run up to Afghanistan’s first democratic parliamentary elections.

The most powerful local commander, Mawlawi Islam, was running for office despite being accused of scores of murders committed while he had been a mujahedeen commander in the 1980s and a Taliban governor in the 1990s, and since the fall of the Taliban in 2001. Sara said one of his sub-commanders and body guards had been looking for young men to help in the election campaign.

“It was evening, around the time for the last prayer, when armed men came and took my son, Islamuddin, by force. I have eye-witness statements from nine people that he was there. From that niGht until now, my son has never been seen.”

Dilawar said his wife publicly harangued the commander twice about their missing son. After the second time, he said, they came for her. “The commander and three of his fighters came and took my wife out of our home and took her to their house about 200 metres away and, in front of these witnesses, raped her.”

Dilawar has a sheaf of legal papers, including a doctors’ report, which said she had a 17mm wound in her private parts cut with a bayonet. Sara was left to stumble home, bleeding and without her trousers."

Remind me again what Canadians are getting killed and mutilated for?

Exactly. All we're doing is propping up a government that's as corrupt as the group we are fighting. We are caught in the middle of a civil war and the best thing to do is to get the heck out and let the Afghans sort it out for themselves.

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Science and Public Relations

 

I have come to this conclusion: the greatest tragedy of public polity, in science and without, in the democratic nations, one that looks very likely to me to be the major proximal cause of the ultimate failure of democracy, is the invention of public relations.

Read more from John Wilkins at Spin versus framing: the tragedy of PR.

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Barack Obama Answers Science Questions

 
An organization called Science Debate 2008 has crafted 14 questions about science for the US Presidential candidates. Barack Obama has submitted his answers [Presidential answers to the top 14 science questions facing America].

1. Innovation. Science and technology have been responsible for half of the growth of the American economy since WWII. But several recent reports question America’s continued leadership in these vital areas. What policies will you support to ensure that America remains the world leader in innovation?

... My administration will increase funding for basic research in physical and life sciences, mathematics, and engineering at a rate that would double basic research budgets over the next decade. We will increase research grants for early-career researchers to keep young scientists entering these fields. We will increase support for high-risk, high-payoff research portfolios at our science agencies. And we will invest in the breakthrough research we need to meet our energy challenges and to transform our defense programs.

I'm a little confused about how the American system of government works. I think the answer means the following: "My administration will submit to Congress a proposal to increase funding ..." Is that correct? Is it just campaign rhetoric when a Presidential candidate talks like this or does the President really have more power to make laws than I imagine?

The second part of his answer suggests that the office of the President will somehow influence the granting agencies to direct more of their funds to early-career researchers and to "high-risk, high-payoff" grant applications. Can the White House make NIH, for example, distribute money differently or does that require legislation to enact?

I don't think anyone believes that Barack Obama wrote these answers, although I'm certain that he approved them. It would be interesting to know who did write the response and how much influence that person(s) will have if Obama wins the election in November. Does anyone know who his advisers are?

The answers don't seem to be much different than those I would have expected from most other Democratic candidates, or from John Kerry in 2004, or Al Gore in 2000. Am I missing something or is there some radical change in the way things are going to be done in Washington that escapes me?¹

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1. Doubling of research funding in 10 years means a yearly increase of 8%. While this is better than an increase that doesn't match inflation, it doesn't strike me as a very radical proposal to fix the funding situation.

[Hat Tip: Jim Lippard]

Genomics and Darwinism!?

 
The scientific research journal Genome Research is proposing to publish a special issue on "Genomics and Darwinism" to coincide with Darwin's 200th birthday [Genome Research].

Genome Research is now accepting submissions for a special issue, entitled Genomics and Darwinism, devoted to comparative and evolutionary genomics, including primary research reporting novel insights in large-scale quantitative and population genetics, genome evolution, and natural and sexual selection.

The deadline for submissions is September 1 and the issue is expected to coordinate with Darwin's 200th birthday (and 150th anniversary of the publication of On the Origin of Species) in February 2009.

The creationists have already jumped on this as evidence that "Darwinism" is the proper terminology when referring to evolution: see DaveScot's post on Uncommon Descent entitled Is “Darwinism” a term only used by creationists?.

I wish that Genome Research had used "Genomics and Evolution" as their theme. Or, even better, "Genomics: Beyond Darwinism." Is this what Carl Zimmer warned us about when he said that he feared an over-emphasis on Darwin [Carl Zimmer at Chautauqua]? I think Carl is right and I think we need to push back. I'll be sending a letter to the editors of Genome Research.

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Dealing With the Controversy

 
Here's an exercise for those of you who are truly interested in teaching accurate science. Go to the recent posting by Casey Luskin on Evolution: News & Views and figure out how to respond to his challenge. He's claiming that a great deal of evolution is "random" but that's not what the "Darwinists" are saying ["Random" Samples of Media and Textbook Descriptions of Darwinian Evolution].

Is he right?¹ What should we teach in school?

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1. Yes, and no. As usual Casey Luskin has only a superficial understanding of evolution and a very weak grasp of reality. However, from time to time he accidentally stumbles onto an important point. Let's set aside the fact that he has no idea what he's talking about and address how we should respond to such criticisms. My view is here: [Evolution by Accident].

Tangled Bank #112

 
The latest issue of Tangled Bank has been published on Science Notes [Tangled Bank #112].

Welcome, science readers, to Tangled Bank 112. It’s a privilege to host so much good science writing. Today’s entries are presented mainly with only the authors’ comments because it’s late and I want to get them published.

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If you want to submit an article to Tangled Bank, send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.

Connie Barlow and Michael Dowd at Chautauqua

 
One of the many highlights of my week at Chautauqua was meeting Connie Barlow and her husband Michael Dowd. Michael is the author of Thank God for Evolution. His blog, The Evolutionary Evangelist promotes the concept of Evolution Theology ....

As I and others are now using the term, Evolution Theology, or Religion 2.0, refers to those whose position on the science vs. religion controversy tends toward reconciliation or synthesis. The term points broadly to those who do not see themselves at either end of the polarized debate as it is currently framed (either anti-evolutionary creationism and intelligent design at one end, or anti-religious atheism at the other). Theistic evolutionists, religious naturalists, evolutionary humanists, emergentists, pantheists, panentheists, theosophists, and the 11,000+ signers of the Clergy Letter Project may differ in how they integrate evolution and theology , but they all do.

The short Wikipedia article on Michael Dowd refers to him as an itinerant Pentecostal preacher. He and his wife travel around America promoting evolution and Christianity. Michael and Connie sat in on a class that I took (Evolution and Christianity). Michael's version of Christianity is very confusing to me, as was the instructor's version. It's part of the so-called "sophisticated" Christianity that seems to deny any scientifically detectable evidence of God's intervention in affairs of the natural world. Undetectable, that is, unless you are a person of faith. People of faith can see the hand of God in events such as the breakup of the Soviet Union and the tearing down of the Berlin wall whereas the rest of us see these as entirely natural events. People who hold this position often go as far as saying that they really don't believe in supernatural beings because God is everywhere in nature.

I had never heard of Michael Dowd before last week but I have been a fan of Connie Barlow for fifteen years. She is the author of two books that I consult frequently when discussing evolution. The first one is From Gaia to Selfish Genes: Selected Writings in the Life Sciences published in 1991 and the second is Evolution Extended: Biological Debates on the Meaning of Life published in 1995.


The books are collections of excerpts from publications by leading thinkers about evolution. The selection is excellent. All the important ideas are there. In some cases this is my primary source because I haven't been able to find the original works; for example, I don't have a copy of The Logic of Life by François Jacob.

It was a delight to finally meet Connie Barlow (and you, too, Michael!). I wish I had known that she would be in Chautatuqua so I could have brought my books for her to sign. As you might have guessed, Connie is the "evolution" part of the team while Michael is the "theology" part. The unusual part of this relationship is that Connie doesn't necessarily buy into religion in the same way as her husband.

Connie published another book in 2002 called The Ghosts Of Evolution Nonsensical Fruit, Missing Partners, And Other Ecological Anachronisms. I'm not familiar with this book but I think I'll buy it.

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Useful RNAs?

The latest issue of Nature contains a news feature by Anna Petherick [Genetics: The production line]. The article is mostly about a new regulatory RNA called HOTAIR but it's the implications of this discovery that bother me.

Let's look at the question being posed ...

If more than 90% of the genome is 'junk' then why do cells make so much RNA from it?

One of the answers being promoted by many molecular biologists is that this RNA is mostly functional and it represents a massive new level of control that has hitherto gone unnoticed. That doesn't mean that we never knew about regulatory RNAs because, in fact, we've known about them for over three decades. The important point of this opinion is that these RNAs are abundant and it "explains" the presence of so much non-coding DNA in eukaryotic genomes.

The other answer to the question is that transcription is sloppy and it frequently makes mistakes. That's why there's a very low level of transcription from all parts of the genome. It's junk RNA. This explanation seems to be widespread in the molecular biology community but it doesn't get much press because there are few papers that discuss this hypothesis [What is a gene, post-ENCODE?] [Junk RNA].

The probem in this field is that it's difficult to publish a paper that proves a negative (but see Brosius (2005)) and it's easy to publish a paper showing that a particular non-coding RNA has a function. The rare examples of those with function get all the publicity and obscure the fact that 99% of these transcripts may not have a function.

The article continues with ...

It is hard to comprehend the upheaval that RNA has been causing in molecular biology over the past few years. Once viewed as a passive intermediary, it was thought to faithfully carry genetic messages from the DNA sequence to the protein-making machinery, where things were made that actually got things done. Biologists were comfortable in the knowledge that only 1–2% of the human genome made protein-coding RNA in this way, and most of the rest was filler. So when, in 2005, geneticist Thomas Gingeras announced that some cells churn out RNA molecules from about 80% of their DNA, he astonished scientists attending the Biology of Genomes meeting at Cold Spring Harbor Laboratory in New York. Why should cells bother with so much manufacturing if, as it seemed, such a tiny fraction was involved in the important business of protein-making?

I wasn't at this meeting but I'd be very surprised if the scientists were "astonished." I'm pretty sure most of them thought that this was an artifact of some kind, probably due to accidental transcription.

This is a case where the author of the article could have benefited from interviewing more of the skeptics.

Over the past three years or so the case for this 'pervasive transcription' has strengthened. The phenomenon has now been ascribed to mice, fruitflies, nematode worms and yeast. These studies, and Gingeras's original reports, came from microarrays — a technology that relies on the tendency of nucleic acids to find their complementary cousins in a solution. Gingeras works for the microarray manufacturer Affymetrix in Santa Clara, California. But not everyone has been persuaded of the extent of pervasive transcription, in part because microarrays are subject to background 'noise'. Even using no RNA, control chips will give off some signals, and results can be a matter of interpretation.

Yes, false positives may account for some of the observations but I think most scientists recognize that the microchips are actually detecting rare transcripts. The question is whether these rare transcripts are biologically significant or whether they are artifacts like most of the alternative splice variants that made all the headlines a few years ago.

If the transcripts are accidental and nonfunctional then the fact that we see this in mice, fruit flies, nematodes, and yeast isn't a surprise. It is not evidence that the transcripts are functional. We would like to see evidence that most of these transcripts are (1) evolutionarily conserved, (2) reproducibly synthesized from a functional promoter, and (3) abundant enough in vivo to make a difference,

John Mattick, the director of the Centre for Molecular Biology and Biotechnology at the University of Queensland in Brisbane, Australia, has no such qualms. He is a long-time advocate of non-coding RNA's importance. The doubters, he says, "keep regressing to the most orthodox explanation [that the long RNAs are junk]. But they can't just sit on their intellectual backsides and tell us to prove it."

John Mattick is one of the most vocal cheerleaders for non-coding RNA. He maintains that huge amounts of it are biologically functional. His statement is a tacit confession that he has no proof of his claims. What in the world is wrong with asking for "proof" (evidence) whether sitting on our backsides or standing?

Is Mattick advocating science by assertion? It certainly seems that way in many of his papers.

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Brosius, J. (2005) Waste not, want not – transcript excess in multicellular eukaryotes. Trends in Genetics 21:287-288 [DOI: 10.1016/j.tig.2005.02.014]

Everyone Must Read this Paper

 
Christopher Taylor writes on Catalogue of Organisms ...

Nearly thirty years ago, a paper was published that almost every student of evolutionary science will end up reading at some point in their career. Despite being only eighteen pages long and containing no original research, many people see it as marking something of a revolution in biology.

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Spencer Wells at Chautauqua

 
Spencer Wells is Explorer in Residence at the National Geographic Society. He has impeccable credentials: Ph.D. with Richard Lewontin, and postdoc with Luigi Luca Cavalli-Sforza and Sir Walter Bodmer. Wells heads the The Genographic Project, a project that collects and analyzes DNA samples from individuals around the world in an attempt to understand human evolution and migration.

Wells spoke last Wednesday morning in the amphitheater. He gave an interesting and informative lecture on "Deep Ancestry: Inside the Genographic Project." Most Sandwalk readers are familiar with the basic results of these studies. They indicate that modern humans originated in Africa and rapidly spread from there to all other continents. The controversy is about timing. Wells promoted the view that the last migration out of Africa took place only about 50,000 years ago.

Before the lecture, I explained to my students that this type of DNA sequence analysis relies on the fact that different human populations are genetically distinguishable. What this means is that scientists are able to tell what group you belong to by looking at your DNA. This establishes that there is a biological difference between races/populations. That's why you can trace migration routes.

Wells explained this very well without using the "race" word. Africans split from the groups on all other continents less than 100,000 years ago. Later on the migrating population subdivided into Europeans, Asians, and native Americans (+ others). In response to a question after the lecture he made the standard politically correct statement ...

Listen, I’m a scientist, and to the extent that people listen to scientists, I would like them to absorb this message, that scientifically speaking, races have no biological basis.

This got the expected round of applause from the audience. (They love that stuff at Chautauqua.) Nobody seemed to notice the discrepancy between what he said in his lecture and the idea that "races have no biological basis."

Aside from that minor glitch, Wells did a fine job of explaining the science behind these studies. The Genographic kits were on sale at the Chautauqua bookstore and I suspect they sold a lot of kits last week. According to Wells, the Genographic Project is the largest DNA typing program in the world and the information it returns to you on your ancestry is much more reliable—and cheaper—than many of the for-profit companies that have sprung up recently.

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[Photo Credit: Chautauquan Daily]

Nobel Laureate: Arthur Harden

 

The Nobel Prize in Chemistry 1929.

"for their investigations on the fermentation of sugar and fermentative enzymes"



Arthur Harden (1865 - 1940) received the 1929 Nobel Prize in Chemistry for his work on the basic metabolic pathway of fermentation. As we now know, this is the glycolytic pathway whereby sugars such as glucose are converted to pyruvate. In yeast extracts the conversion of glucose to alcohol can be studied in vitro and this led to the discovery of enzymes and pathways.

Much of the basic work on biochemical pathways was done in the early part of the 2oth century. It was recognized that proteins (zymogens) were responsible for the conversion. Harden's contribution was the discovery that there were phosphorylated sugar intermediates in the pathway. He characterized two of these sugars; glucose phosphate and fructose diphosphate [Monday's Molecule #85]. This was a big step towards figuring out how the pathway operated.

Harden shared the 1929 Nobel Prize with Hans Karl August Simon von Euler-Chelpin.

THEME:
Nobel LaureatesThe presentation speech was delivered on December 10, 1929 by Professor H.G. Söderbaum, Chairman of the Nobel Committee for Chemistry of the Royal Swedish Academy of Sciences. (All award ceremonies are held on Dec. 10th because Dec. 10, 1896 was the day Alfred Nobel died.)

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.

The fermentation of liquids containing sugar - there we have a chemical reaction older than all chemical science. The point of time when men first began to take this reaction into their service is really lost in the mists of antiquity, before the beginning of history. The peculiar and apparently self-caused process by which an innocent fruit juice is transformed with the active formation of scum, into a drink which is either stimulating or intoxicating according to the quantity partaken, attracted attention in the very earliest times; and to many peoples it appeared so wonderful that nothing less than the cooperation of a divinity seemed to them possible as an explanation.

Our enlightened time has scarcely the right to marvel at this, when we take into consideration how long a time science has since required to obtain an acceptable conception of the nature of fermentation. Here we stand face to face with one of the most complicated and difficult problems of chemical research. Little more than a couple of centuries separate us from the time when men first began to perceive that the fermenting substance was sugar, which under the influence of a certain something was decomposed, with carbonic acid and ethyl alcohol as the final products of the decomposition.

But what this "something" was, and how it worked, still remained unsolved questions, long defying the most penetrating attempts at interpretation. It was not until our own days that it has been vouchsafed to us to have a fairly satisfactory answer to these questions, but even here the process of development has been slow, toilsome, and it took place, so to speak, in several instalments.

In carrying out the provisions of Alfred Nobel's Will, the Swedish Academy of Sciences has already once before had its attention directed to this sphere of research. That was in 1907, when Eduard Buchner was awarded the Nobel Prize in Chemistry for his discovery of non-cellular fermentation. At the time complaints were raised in certain quarters against this award as being insufficiently justified. Seen in the perspective of distance in time, however, Buchner's discovery has more and more stood out as a line of demarcation between two different epochs, pointing the way to a new phase in the history of the chemistry of fermentation.

Buchner's discovery marked the final decision in a long struggle between two distinct schools - one, the older one, represented by Justus von Liebig the other, the younger one, represented by Louis Pasteur. According to the former school, fermentation was a purely chemical process, evoked by an unorganized ferment with unstable properties, which were imparted to the fermenting substance and thereby brought about its decomposition. According to the latter school, it was rather a physiological process, inseparably connected with the vital act of a microorganism known as the "fungus of fermentation". Buchner's discovery made it evident that to some extent both were right, but also to some extent both were wrong, and, consequently, that the truth lay between the two.

But the value of the discovery makes itself known in a still more definite way through the impulse it has given to later research. In fact, during the last three decades that research has made such great advances, has given such an enlarged insight into the mechanism of the process of fermentation, that the Academy of Sciences has found the time ripe once again to award a Nobel Prize in this department. In so doing the Academy has deemed it right to divide equally the Nobel Prize in Chemistry for the present year between Professor Arthur Harden and Professor Hans von Euler.

Buchner assumed in the yeast juice the presence of a uniform ferment or enzyme, known as "zymase".

When, however, Harden and his fellow-workers filtered a quantity of Buchner's yeast-juice through a gelatine filter, known as an "ultrafilter", and thereby split it up into two fractions (a filtrate and a sediment that did not pass through the filter), the curious state of things occurred that neither of these fractions was any longer able to bring about fermentation, but that after being mixed with one another they recovered that capacity.

Harden explained this by saying that a high-molecular enzyme, the zymase proper, was left on the filter, which let through a low-molecular complementary enzyme, which for the sake of brevity was called co-enzyme or co-zymase.

Another no less important advance is made in Harden's demonstration of the hitherto neglected part played by phosphoric acid in the process of fermentation. It has been found that a certain addition of phosphate gives rise to an equivalent amount of carbonic acid and ethyl alcohol. This effect is associated with the formation of one or more definite compounds between sugar and phosphoric acid - known as the "zymo-phosphates", amongst which a glucose monophosphate and a glucose diphosphate are to be regarded as the most important.

In the same measure as research in this department has made new conquests, a clearer and clearer insight has been gained into the importance of this discovery. In particular the work of von Euler and his pupils during the last few years greatly contributed to the unravelling of the mechanism of phosphorization.

The primary function of phosphoric acid in fermentation consists, according to von Euler, in the fact that in cooperation with an enzyme it gives rise to glucose monophosphate, identical with the monophosphate discovered by Harden and Robison. This phosphate afterwards undergoes a mutation in the presence of co-zymase, inasmuch as a glucose diphosphate and an active glucose are formed, after which the latter yields the necessary material for the subsequent stages of the fermentation.

This demonstration of the part of mutase played by the co-zymase, or in other words of the identity of co-zymase and co-mutase, is of fundamental importance, for it has fully revealed the central position in the process of fermentation of the complementary enzyme in question.

The researches of von Euler and his pupils have further led to the concentration of the co-zymase and to a far more exact study of its properties than had been previously possible. They have been able to determine approximately its molecular weight, which has been found to be about 490; and they have also been able to draw certain definite conclusions concerning its chemical nature, which make it highly probable that we have here what the chemists call a pentosenucleoside. The production of a co-zymase with a high activity has also shown in a brilliant manner the character of that enzyme as a specific activator.

Finally, what gives special interest to the study to the complicated reaction mechanism of the fermentation of sugar is that it has been possible to draw from it important conclusions concerning carbohydrate metabolism in general in both the vegetable and the animal organism.

The brief summary which has now been given, and which, in view of the scanty time allowed, has necessarily been extremely fragmentary, will in any case probably have shown that there is an extremely intimate connection between the researches of Harden and von Euler in this field. On the one hand, the fundamental discoveries of Harden have formed the precondition and point of departure for the various work of von Euler; and on the other hand, it is only the work of the latter that has made fully evident the importance of Harden's discovery.

Under such circumstances the Academy of Sciences has not hesitated this time to avail itself of the expedient that is offered by the Statutes of the Nobel Foundation of dividing the prize between two equally meritorious scientists.

Professor Harden. When the Royal Swedish Academy of Sciences resolved to adjudge to you, together with Professor von Euler, this year's Nobel Prize in Chemistry on account of your important contributions to our knowledge of alcoholic fermentation, the Academy had let herself guided by a firm conviction that these contributions had opened indeed a new chapter in the investigation of that very complicated matter.

It is with the most sincere gratification that I have the honour of conveying to you the congratulations of the Academy on this distinction, the outward signs of which you are now about to receive.

Professor von Euler. It is a great pleasure to the Swedish Academy of Sciences to be able to award this time the Alfred Nobel's Prize also to one of her members, and so much more since during a long series of years we have been in the position to follow from nearby your energetic, persevering, and systematic investigations. The Academy is also firmly convinced that the distinction which has fallen upon you today, will not contain for you the temptation to rest on laurels already obtained, but that on the contrary it will mean a stimulus to continued and, as we all hope, successful work in the service of biochemistry.

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Barbara King Replies

 
Barbara King sent me the following email message in response to my posting on her talk at Chautauqua [Barbara King at Chautauqua]. When people take the time to send me an email message my policy is to post such rebuttals without comment.

Hi, Larry Moran.

I think it's not too helpful to your readers to take a definition out of context from my book, and link it to my Chautauqua talk. At Chautauqua, I did not cite or employ Geertz's definition of religion.

Rather, I mentioned that I would focus on two aspects of religion (necessary but not sufficient aspects, as I put it), 1) the expression of empathy and compassion (which exist in balance with violence and cruelty, of course) and 2) symbolic rituals that in some way seem to go beyond the here-and-now, for example, burial rituals that go beyond hygenic disposal of the dead to include grave good and ritual processes that may embrace the sacred. I think the Chautauqua audience was more than capable of following that sort of framework, laced with a lot of examples from primate studies and archaeology that speak to those two particular aspects (of course, explaining too the inevitable risks in using great apes of today to model early human evolution.... that's an enjoyable point to debate, and I do enjoy conversations where people disagree on such things).

I'm not too sure how you could know what "most" of the audience of hundreds thought of my talk, unless you polled them? Your characterization of confused people doesn't fit with my experience of interacting with people there, at all....

I spoke at AAAS in Boston last winter and made a stand: I won't answer questions about my personal beliefs. The reason is really simpler than any you indicated (I surely don't remember saying what you said I said!): I'm a scientist, and want to keep focus on the science. Seems like a reasonable enough point. I don't understand this peculiar drive to know what scientists' personal beliefs might be! I was pleased that the Chautauqua audience applauded (literally) my answer.

I often enjoy your blog (some days more than others, clearly). I'd appreciate your posting this, if you're open to doing so.

Best wishes,

Barbara King

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What Is a Scientist?

 
The question has come up in the discussion of the AAAS video on Panda's Thumb [The AAAS responds to “Expelled”]. The video highlights several people who claim that science and religion are compatible. Since AAAS is a scientific organization, it makes sense that the people being interviewed are scientists. However, many of them are not—at least not by my understanding of what a scientist is.

For example, some of the people being interviewed are high school teachers in Dover. One of them, Jennifer Miller, is participating in the comments. Is she a scientist? Yes, according to some people because she got an undergraduate degree in biology. According to PvM that's all it takes.

Is this sufficient? I don't think so. I think that a scientist has to be an "expert" in some area of science and I think that having an undergraduate degree isn't enough. This doesn't mean that the testimony of high school science teachers is irrelevant to the discussion about compatibility of science and religion. It just means that they aren't really expert enough in science to be called scientists.

This issue also came up last week when I was talking about it to a fellow evolutionist. That person made the claim that Richard Dawkins isn't a scientist any more. That's going too far, in my opinion. Just because he may not have a grant and may not be publishing papers in the scientific literature does not mean that he has lost his claim to scientific expertise. If we try to stick to a definition like that then not only are high school teachers eliminated but also a great many real scientists.

Why do you think? Can you be a scientist if all you have is an undergraduate degree? Can you be a scientist if you don't publish in scientific journals?

Here's a challenging test of your definition of a scientist. The photograph below is from the April 30, 2008 edition of The Daily Mail in the UK [Calamari for 500: Scientists defrost giant squid with 10.8 inch eyes]. The caption reads, "A technician sits in the tank with the carcass as scientists examine the squid."

Surely these people aren't real scientists?

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[Image Credit: The scientist cartoon is from Jacks of Science]

The Colorado Gazette on Atheism.

 
Last week (Aug. 19) The Gazette from Colorado Springs published an opinion piece on atheism [Dems dismiss the atheists: Why rude guests aren't welcome].

Imagine a world with no religion and one sees a world without the Golden Rule, devoid of most charities, hospitals and great universities. One sees hurricane recovery zones, minus all the chartered planes and buses full of churchgoers giving their time and money to rebuild homes. How many children are fed and clothed by atheist charity organizations? Approximately none.

Imagine no religion and one sees a world ruled by atheist tyrants - Pol Pot, Albania's Enver Hoxha, Stalin and Mao, to name a few - who have murdered tens of millions in modern efforts to cleanse society of religion.

American Muslims, Baptists, Jews, Christians, Buddhists, Mormons, Quakers, Amish, etc., don't erect billboards saying "Imagine No Atheists." They don't advocate government force to cleanse atheist expressions and teachings from the public square. They don't imply that atheists are "irrational," even though atheists claim absolute knowledge. They don't advocate theft and desecration of atheist property, even though an atheist hero in Minnesota stole and destroyed the Catholic Eucharist.

Democrats will nominate a Christian gentleman who respects others. It's likely they didn't invite atheists to their faith service because they didn't want embarrassing guests. Atheists might bring pseudointellectual proselytizers, who are intolerant, self-aggrandizing and rude. Atheists should fund universities and hospitals. They should feed and clothe starving kids. They should act more like Christians and Jews. If they do some of that - if they contribute to a diverse humanity - they might get better party invites.

The interesting thing about this article is the bit about atheists not being charitable. Apparently atheists don't contribute money to social causes and public institutions. Hmmm ....

I urge all religious people to give money to The Bill and Melinda Gates Foundation—an organization founded by the two largest philanthropists of the modern age, Bill Gates and Warren Buffett. Who just happen to be non-believers.

Here's an excerpt from the Wikipedia article on Bill Gates.

In 2000, the Gates Foundation endowed the University of Cambridge with $210 million for the Gates Cambridge Scholarships. The Foundation has also pledged over $7 billion to its various causes, including $1 billion to the United Negro College Fund. According to a 2004 Forbes magazine article, Gates gave away over $29 billion to charities from 2000 onwards. These donations are usually cited as sparking a substantial change in attitudes towards philanthropy among the very rich, with philanthropy becoming the norm.[53] Buffett, who was the world's second richest person,[54] announced on June 25, 2006 that he has pledged to give the foundation 10 million Berkshire Hathaway Class B shares, spread over multiple years through annual contributions.[55]

Gates announced on June 15, 2006 that he would move to a part-time role within Microsoft, leaving day-to-day operations management in July 2008 to begin a full-time career in philanthropy, but would remain as chairman and advisor.[38] Gates credited Buffett with influencing his decision to commit himself to charitable causes.[56] Days later, Buffett announced that he would begin matching Gates's contributions to the Gates Foundation of up to $1.5 billion per year in stock.[57] Buffett helped to guide the foundation to give its endowment away quickly. It became one of the few charitable organizations with a lifespan, promising to spend all of its resources and to close within 50 years of the deaths of its founders.[58]

Both Warren Buffet and Bill Gates have been ardent supporters of Planned Parenthood, a non-profit organization that receives financial support from the Buffet and Bill and Melinda Gates Foundations. Planned Parenthood performs approximately 20% of all abortions in the United States. Planned Parenthood receives almost a third of its money in government grants and contracts ($336.7 million in FY 2007) with the rest coming from clinic income and donations from wealthy individuals such as Bill Gates.

Is it possible that the editors of the The Gazette don't know what they're talking about? Or is criticism like that just being rude?¹

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1. The organizations that I contribute to are Médecins Sans Frontières, Greenpeace (when I'm not mad at them), and Mothers Against Drunk Driving. I'm probably not going to give to MADD any more because I disagree with their position on the legal drinking age. I will not give money to any religious charity because they often use to money to support causes that I strongly disagree with.

[Hat Tip: Hemant Mehta at Friendly Atheist]

[Photo Credit: Bill Gates Kicks Ass]

Evidence of Purpose?

 
Read Travelers in Endless Space on Exercise in Futility.

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[Hat Tip: Primordial Blog]

The Trichoplax Genome

 
Trichoplax adherens is a very simple animal that moves about on surfaces like a gigantic amoeba and ingests any food that it flows over. There are thought to be several species of Trichoplax in addition to Trichoplax adherens.

Because this is such a simple and unusual animal it has been assigned its own phylum, Placozoa with Trichoplax as the only genus.¹

The diagram below is copied from Syed and Shierwater (2002). It shows clearly that Trichoplax adhaerens is a true metazoan with an upper (dorsal) epithelial layer, a lower (ventral) epithelial layer, and an internal layer of contractile fiber cells. There are at least four cell types, not counting the egg and sperm cells that have been reported by others.


Where does Trichoplax fit in the evolution of animals? Clearly, the lineage leading to modern Trichoplax must have diverged very early in animal evolution. This is why Trichoplax is often (incorrectly) referred to as a "primitive animal", or a "living fossil." (See Ryan Gregory's discussion of this terminology at: Kudos on the placozoan genome!.)

The exact branch point is hotly disputed. Did the ancestors of Trichoplax split off before or after the sponges (Porifera) or the Cnideria (jelleyfish, hydras, corals)? Is the modern form of Trichoplax the ancestral form or is it a derived and simplified version of a more complex animal?



The complete genome sequence of Trichoplax adherens has just been published in Nature (Srivastava et al. 2008). There's a pretty good press release on Bio News Net [Genome of simplest animal reveals ancient lineage, confounding array of complex capabilities]. In addition to Ryan Gregory's review, there's another by John Timmer at Nobel Intent (Ars Technica) [Sequencing the bizarre: the genome of a living fossil].

Trichoplax adherens has six chromosomes and a total genome size of about 98 × 10⁶ base pairs (98 Mb). The authors identified 11,514 protein-encoding genes. Because the genome sequence is "only" 98% complete, it wasn't possible to reconstruct entire chromosomes and the association between the sequenced genome and particular chromosomes is impossible to establish due to the absence of genetic studies on Trichoplax (no linkage maps).

The genome is smaller than that of the green alga Chlamydomonas reinhardtii with a genome of 121 Mb and about 15,000 genes [The Genome of Chlamydomonas reinhardtii]. On the other hand, the Trichoplax genome is larger than that of other single-cell organisms such as the protist Giardia lamblia (12 Mb, ~6500 genes) [The Giardia lamblia Genome].

The Trichoplax genome is almost the same size as the C. elegans (nematode) genome at 97 Mb but C. elegans is thought to have more than 15,000 genes. Drosophila melanogaster at 180 Mb has ~16,000 genes and mammals have a genome of 3,300 Mb and 20,000 genes.

About 90% of the Trichoplax genes are present in other animals and the intron positions of the Trichoplax are mostly identical to those in other animals [Junk in Your Genome: Intron Size and Distribution]. This is powerful evidence that the phylum Placozoa belongs in the animal kingdom.

Srivastava et al. constructed a phylogenetic tree using 104 highly conserved genes from species whose complete genomes are available in the sequence databases. The tree (below) shows that the Trichoplax lineage branches after sponges (represented by Amphimedon queenslandica) but before cnidarians (Hydra magnipapillata). The result are not compatible with trees constructed using mitochondrial sequences or ribosomal RNA sequences but that's not too surprising. Mitochondrial DNA and ribosomal RNA sequences are often not reliable for this kind of work.


The conclusion is that Placozoa and most metazoans diverged about 600 million years ago but sponges diverged even earlier.

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1. It isn't unusual to create separate phyla for organisms with distinct body plans but you wouldn't know that from the criticisms leveled at Stephen Jay Gould when he published Wonderful Life [Science and Philosophy Book Club: Wonderful Life]. Incidentally, in The Ancestor's Tale Dawkins readily accepts that Trichoplax adherens may be the sole species in the phylum Placozoa.

[Image Credit: The photograph of Trichoplax is from metamorphnet. That website also has some wonderful movies of Trichoplax.

Srivastava, M., Begovic, E., Chapman, J., Putnam, N.H., Hellsten, U., Kawashima, T., Kuo, A., Mitros, T., Salamov, A., Carpenter, M.L., Signorovitch, A.Y., Moreno, M.A., Kamm, K., Grimwood, J., Schmutz, J., Shapiro, H., Grigoriev, I.V., Buss, L.W., Schierwater, B., Dellaporta, S.L., Rokhsar, D.S. (2008) The Trichoplax genome and the nature of placozoans. Nature 454:955-960. [doi:10.1038/nature07191]

Gene Genie #35

 
The 35th edition of Gene Genie has been posted at Microbiology Bytes [Gene Genie 34: Summertime and the blogging is easy]. (This really is the 35th edition in spite of the title.)

Welcome to edition 34 of Gene Genie, the blog carnival of genes and genetic conditions.

It’s high summer, and the internet is a dead as a doornail, but a few diligent bloggers are still slogging away at the keyboard while everyone else is at the beach.

The beautiful logo was created by Ricardo at My Biotech Life.

The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.

Here are all the previous editions .....

1. Scienceroll
2. Sciencesque
3. Genetics and Health
4. Sandwalk
5. Neurophilosophy
6. Scienceroll
7. Gene Sherpa
8. Eye on DNA
9. DNA Direct Talk
10. Genomicron
11. Med Journal Watch
12. My Biotech Life
13. The Genetic Genealogist
14. MicrobiologyBytes
15. Cancer Genetics
16. Neurophilosophy
17. The Gene Sherpa
18. Eye on DNA
19. Scienceroll
20. Bitesize Bio
21. BabyLab
22. Sandwalk
23. Scienceroll
24. biomarker-driven mental health 2.0
25. The Gene Sherpa
26. Sciencebase
27. DNA Direct Talk
28. Greg Laden’s Blog
29. My Biotech Life
30. Gene Expression
31. Adaptive Complexity
32. Highlight Health
33. Neurophilosophy
34. ScienceRoll
35. Microbiology Bytes

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Barbara King at Chautauqua

 
Barbara King is Professor of Anthropology at the College of William and Mary. Her specialty is primate behavior, especially gorillas. She spoke about how the non-human apes relate to each other and suggested that these relationships reveal the origins of religion. Here's how she describes it on her website.

My newest project has taken me in exciting new directions. My latest book (Evolving God, Doubleday, January 2007) explores the deepest roots of the human religious imagination. Although I definitely do not think apes are religious, I do think that the empathy and compassion and meaning-making shown by apes in the wild and in captivity points us towards clues for understanding the precursors of religion in our earliest hominid ancestors. I trace the evidence for religious, symbolic ritual throughout human prehistory, culminating in the burial rites and art of Neandertals and Homo sapiens.

I don't think it's an exaggeration to say that most people found her talk confusing. Her main point wasn't at all clear. Was she really arguing that non-human ape behavior might be a precursor of religion? Was she making a connection between religion and "empathy and compassion"? If so, what is the connection?

I bought her book, Evolving God: A Provocative View on the Origins of Religion but I haven't had a chance to read it. I thought it might be informative to find her definition of religion. Here it is (p. 18); "Almost certainly, the most widely used and cited definition was proposed by Clifford Geertz: religion is 'a system of symbols which acts to establish powerful, persuasive, and long-lasting moods and motivations in men by formulating conceptions of a general order of existence and clothing these conceptions with such an aura of factuality that the moods and motivations seem uniquely realistic.'"

No wonder most people found her talk confusing. Barbara King specifically notes that her definition of religion does not require "faith, belief, God, gods, spirits, eternal life, souls, or sacred texts."

The main beef I have with Barbara King's presentation comes from her response to a question from the audience. She was asked to describe her religious beliefs and she refused to do so, citing her confidence that her personal beliefs do not influence her science. I don't think that's acceptable in most science that make claims about religion but especially the field of anthropology. I think scientists have an obligation to lay their biases on the table and let outside observers judge whether such beliefs influence the work.

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Edward Larson at Chautauqua

 
Edward J. Larson is University Professor and Hugh & Hazel Darling Chair in Law at Pepperdine University. He has a law degree from Harvard and a Ph.D. in history from the University of Wisconsin-Madison.

Larson is a prolific writer. He is the author of seven books including Summer for the Gods: The Scopes Trial and America's Continuing Debate Over Science and Religion (1997) for which he received the 1998 Pulitzer Prize. Many of us know him for his more recent books, including Evolution: The Remarkable History of a Scientific Theory (2004) and The Creation-Evolution Debate: Historical Perspectives (2007).

Larson gave an interesting and informative talk about the evolution-creation controversy in America. His ideas about the real battle in the Scopes trial are very interesting. He claims that the main dispute was about the social implications of evolution and the conflict between science and religion has been overplayed—especially in the movie Inherit the Wind.¹

I've heard this before. William Jennings Bryan was a populist who thought that social Darwinism is what led to the First World War. He was afraid that teaching evolution in the schools would encourage social Darwinism. Of course, he was also religious and feared that evolution was a threat to religion.

For many in the audience the history of the trials was new information and Larson did a good job of explaining both the scientific issues and the legal ones. He cautioned the audience that things could deteriorate rapidly with only one or two changes on the Supreme Court.

Someone from the audience asked what would have happened if the Dover case had been appealed. Larson said he was confident that the decision would have been upheld at the district court but he's not so sure about the current Supreme Court. If he had to bet, he would put his money on the decision being upheld but he's not very confident.

The one thing that troubled me about his lecture was that he always referred to the conflict between creationism and the Theory of Evolution. My students picked up on this since I was emphasizing the differences between evolution as a fact and a theory. As most of you know, creationists are as much opposed to the facts of evolution as they are to evolutionary theory. It would be better, in my opinion, to refer to the conflict as a fight between creationism and the fact of evolution. To use the phrase "Theory of Evolution" seems to be catering to creationist misconceptions.

On Thursday afternoon the schedule called for a discussion with Diane Ackerman, the author of The Zookeeper's Wife. Unfortunately, Ackerman couldn't make it so Edward Larson filled in with a fascinating (according to Ms. Sandwalk) talk about his latest book A Magnificent Catastrophe: The Tumultuous Election of 1800. Apparently religion played an important role in that election with Jefferson being accused of lacking belief.

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1. The theater class took a course on the play Inherit the Wind. Apparently, the staging of the original play is remarkable. That group also discussed the differences between the real trial and the one in the play and the influence of McCarthyism. I wish I could have taken that course last week, and many others.

Monday's Molecule #85

 
This week marks the beginning of a new term at many colleges and universities in the USA. To mark the occasion, I've chosen a simple molecule that should be familiar to every undergraduate taking an introductory biochemistry course. Your task is to indentify the molecule and give me its correct common name—the one required on an exam—and the complete, correct IUPAC name.

There's a direct connection between today's molecule and a Nobel Prize. We are looking for the single person most responsible for identifying this molecule as part of a metabolic pathway. This person didn't know the exact structure but got the basic chemistry correct. Be careful, there are several possible candidates who haven't already been featured on Sandalk. I want the one person who best meets the criterion.

The first person to correctly identify the molecule and name the Nobel Laureate, 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 four 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 Bill Chaney of the University of Nebraska. He correctly identified the molecule as β-D-fructofuranose 1,6- bisphosphate and he chose [(2R,3S,4S,5R) -2,3,4 -trihydroxy-5- (phosphonooxymethyl) oxolan-2-yl] methyl dihydrogen phosphate as the correct IUPAC name [but see IUPAC]. That's probably more information than we needed but Chaney was the first to reply (by several hours). The Noble Laureate is Arthur Harden.

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Check Your Irony Meters

 
John Lynch has a wonderful comment on the train wreck at Uncommon Descent. Read what DaveScot has to say about people who post comments without identifying themselves [Just another day of “discourse” for the peanut gallery].

Don't follow the links from John's postings unless you have a Mark VIII Irony Meter or better.

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Stephen Matheson's Critique of Michael Behe's Edge of Evolution

 
I've been meaning to write up my own critique of Michael Behe's latest book The Edge of Evolution but there always appear to be more important things to do. Stephen Matheson at Quintessence of Dust has posted a number of articles on the topic. You can find the links in his latest posting Why I'm not a Behe fan, Part IIB: abusing genetics.

I'm in complete agreement with Stephen on one thing ...

These clarifications are important, because much of the criticism of EoE has been botched significantly. The book is bad, really bad, but it can't be honestly characterized as an anti-evolution argument.

Many reviews of The Edge of Evolution are not as good as one might expect from scientists who have read the book.

Stephen Matheson gets the essence of Behe's argument so his review is much better than others. However, I'd like to comment on a few things he says ...

I. Behe's assumption of a particular mutation rate is both absurdly oversimplified and inappropriately extrapolated into the entire tree of life.

The basis of all of Behe's calculations is a mutation rate of 1 in 100 million. This is the estimated rate at which misspelling-type mutation occurs in each generation, averaged over the entire genome, in humans. (The number doesn't consider other types of mutation, now known to be more common than previously thought.) Behe uses this number in all of his (flawed) probability calculations. Even if we knew nothing about mutation rates, the notion of extrapolating from an human (or even mammalian) characteristic to the whole of the biosphere (past and present) is ludicrous enough that it would by itself cast doubt on the credibility of the author.

I don't think this is very important. Behe uses a mutation rate of 10^-8 per generation and that's pretty accurate for mammals. A better mutation rate would be 10^-10 nucleotides per DNA replication (cell generation) [Mutation Rates]. Yes, it's true that different species have different numbers of cell divisions per generation, so Behe should have mentioned this. Bacteria, for example, have a mutation rate of 10^-10 per generation because there's only one cell division per generation. (In mammals there are about 100 cell divisions, hence the mutation rate per generation is 100 times greater.)

Stephen argues that mutation rates vary from species to species and over time. I don't think so. I think the rate 10^-10 per nucleotide per replication has probably been pretty constant over several billion years and I doubt that it differs very much in different species. It's a property of the DNA replication machinery and that's always been the main source of mutation over the long term.

III. Behe claims that huge population sizes automatically generate more evolutionary opportunity than smaller ones do. This is incorrect.

It seems so obvious. More organisms means more mutations means more beneficial mutations means more and faster evolution. It's the kind of obvious, simplistic, intuitive claim that forms the bedrock of any folk science. But it's wrong.

On the contrary, very large population sizes lead to a so-called "speed limit" on adaptation that results from competition among beneficial mutations. The phenomenon is called clonal interference and it's particularly well understood in asexual organisms such as bacteria. The basic idea has been around for decades, but measurement and modeling of the phenomenon has been increasing in the last ten years. A very recent report, the subject of an upcoming post here, showed that the beneficial mutation rate in bacteria is 1000 times higher than previously thought – and the underestimation is due entirely to clonal interference.

The effect is not limited to asexual organisms; in fact, the problem of clonal interference is thought to constitute one of the major driving forces behind the evolutionary development and maintenance of sexual reproduction. The idea is that the genetic shuffling that accompanies sexual reproduction can bring beneficial mutations together and increase the effectiveness of selection.

I thought Behe was right about this. There are more mutations, and more variation, in large populations than in small ones. I thought that one of the flaws in Behe's argument is that he doesn't take into account the existence of abundant neutral and nearly-neutral alleles in a large population. Many of these contribute to the double mutations that he requires.

I'm not familiar with this idea of "clonal interference" that seems to increase the number of beneficial mutations and explains the evolution of sex. It sounds fishy to me but I'll have to read up on it—whenever I find the time. Stephen provides the appropriate references.

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