National Academies: Science, Evolution and Creationism

The National Academies (Science, Engineering, Medicine) (USA) have just published their latest book on the evolution/creationism controversy. You can download it for free on their website [Science, Evolution and Creationism].

Like the previous versions, this one is quite well done. It explains evolutionary concepts correctly and gives clear examples of the evidence supporting the fact of evolution. The book—actually a large pamphlet—describes the various forms of creationism and why they are rejected by science.

I was troubled by one part of the book describing the compatibility of science and religion. It's only two paragraphs plus three pages of quotations but it promotes the fallacy of the Doctrine of Joint Belief. This fallacy makes a virtue out of compartmentalization. It says that because scientist X is religious, it follows that religion and science are compatible. Similarly, because religious leader Y, accepts evolution, it follows that science and religion are not in conflict.

While preparing to blog about this fallacy, my daughter Jane alerted me to a piece in today's New York Times [Evolution Book Sees No Science-Religion Gap]. The article in the New York Times is written by Cornelia Dean who has previously written about the compatibility of science and religion [Scientists Speak Up on Mix of God and Science].

In today's article, Cornelia Dean briefly reviews Science, Evolution and Creationism. She says,

But this volume is unusual, people who worked on it say, because it is intended specifically for the lay public and because it devotes much of its space to explaining the differences between science and religion, and asserting that acceptance of evolution does not require abandoning belief in God.

...

The 70-page book, “Science, Evolution and Creationism,” says, among other things, that “attempts to pit science and religion against each other create controversy where none needs to exist.” And it offers statements from several eminent biologists and members of the clergy to support the view.

I think it's unfortunate that the New York Times article places so much emphasis on this part of the book but the authors of the book¹ must have known what they were doing. Too bad they were misguided.

Here's what they wrote in Science, Evolution and Creationism,

Acceptance of the evidence for evolution
can be compatible with religious faith.

Today, many religious denominations accept that biological evolution has produced the diversity of living things over billions of years of Earth’s history. Many have issued statements observing that evolution and the tenets of their faiths are compatible. Scientists and theologians have written eloquently about their awe and wonder at the history of the universe and of life on this planet, explaining that they see no conflict between their faith in God and the evidence for evolution. Religious denominations that do not accept the occurrence of evolution tend to be those that believe in strictly literal interpretations of religious texts.

Science and religion are based on different aspects of human experience. In science, explanations must be based on evidence drawn from examining the natural world. Scientifically based observations or experiments that conflict with an explanation eventually must lead to modification or even abandonment of that explanation. Religious faith, in contrast, does not depend only on empirical evidence, is not necessarily modified in the face of conflicting evidence, and typically involves supernatural forces or entities. Because they are not a part of nature, supernatural entities cannot be investigated by science. In this sense, science and religion are separate and address aspects of human understanding in different ways. Attempts to pit science and religion against each other create controversy where none needs to exist.

There are two fallacies here. The first one is the one I already alluded to (the Doctrine of Joint Belief). Just because you can find scientists and theologians who proclaim that evolution is compatible with religious faith doesn't make it so. You need to examine their understanding of evolution and also what they mean by "religious faith."

As you might have guessed, the book trots out quotations from the usual suspects, Francis Collins and Kenneth Miller². Their words of wisdom appear on a page with the title "Excerpts of Statements by Scientists Who See No Conflict Between Their Faith and Science." The book makes some amends, in my opinion, by including the following statement on that page.

Scientists, like people in other professions, hold a wide range of positions about religion and the role of supernatural forces or entities in the universe. Some adhere to a position known as scientism, which holds that the methods of science alone are sufficient for discovering everything there is to know about the universe. Others ascribe to an idea known as deism, which posits that God created all things and set the universe in motion but no longer actively directs physical phenomena. Others are theists, who believe that God actively intervenes in the world. Many scientists who believe in God, either as a prime mover or as an active force in the universe, have written eloquently about their beliefs.

The good part about that statement is that it mentions deism, which is a form of religion where the conflict between science and religion really is minimized. The bad parts are that theists who promote interventionist Gods are touted as examples of those who see no conflict between science and religion. (The reason why Theistic Evolutionists don't "see" a conflict is because they choose to look the other way [Theistic Evolution: The Fallacy of the Middle Ground].)

The other bad part is that atheists are equated with the philosophical position of scientism. That's an unnecessary complication. It would have been sufficient, and preferable, to state that many scientists do not believe in supernatural beings. They could have gone on to state that many of those non-believers see a conflict between science and the supernatural.

The second fallacy in the two paragraphs quoted above is something I call the Fallacy of the Undetectable Supernatural. The authors of Science, Evolution and Creationism repeat the silly argument that "supernatural entities cannot be investigated by science." Why not? The only kind of supernatural beings that could never be investigated by science are those that exist entirely as figments of the imagination and have absolutely no effect on the real world as we know it. As soon as your God intervenes in the real world his actions become amenable to scientific investigation.

In this, I agree with Stephen Jay Gould's description of Non-Overlapping Magisteria (NOMA). He states very clearly that religion violates NOMA as soon as it makes a claim for an interventionist God (Gould, 1999). In that case religion is no longer compatible with science.

The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.

                                    Stephen Jay Gould (1999) pp. 85-85

The National Academies are violating NOMA unless they specifically refer to belief in Gods that do not perform miracles of any kind. There are very few religions that believe in non-interventionist Gods who never perform miracles. Therefore, it is much more scientifically accurate to say that science conflicts directly with almost all religious beliefs, including those of Ken Miller and Francis Collins.

This is an important error in Science, Evolution and Creationism since Americans have a right to expect that the National Academies can define the proper magisterium of science. Instead, the National Academies, like NCSE, has taken the easy way out by redefining science as that field of study that is not in conflict with the religious views of Francis Collins and Ken Miller.

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1. The book was produced by a committee headed by Fancisco Ayala.

2. Who appointed Collins and Miller to be the flame carriers for evolution?

Gould, S.J. (1999) Rock of Ages: Science and Religion in the fullness of Life The Ballantine Publishing Group, New York (USA).

Direct-to-Consumer Genetic Testing

 
A growing number of for-profit companies are selling genetic testing services directly to customers who pay anywhere from $100 t0 $1000 for their personal genetic profile.

Several blogs have been actively promoting these private companies and encouraging people to sign up for their services. The cheerleader bloggers have been among the first to submit thier DNA for testing. In general, there has been little discussion about the ethical implications of direct to consumer, for-profit, genetic testing and little discussion about scientific issues such as accuracy. There has been a bit of talk about misleading advertising [23andMe - More Hype from Genetic Testing Services].

One of the more responsible bloggers has been Hsien-Hsien Lei. She is very open about her employment with DNA Direct. She recently posted an article outlining the concerns of the American Society of Human Genetics (ASHG) [American Society of Human Genetics (ASHG) Statement on Direct-to-Consumer Genetic Testing].

The ASHG, like many of us, is worried about this trend to commercialization of genetic testing. They've issued some guidelines on direct-to-consumer (DTC) genetic testing (Hudson et al. 2007).

DTC testing has emerged during a period of rapid growth in the number of genetic tests. Today, there are more than 1,100 genetic tests available clinically, and several hundred more are available in research settings. Although most genetic testing is currently available only through a health care provider, an increasing variety of tests are being offered DTC, often without any health care provider involvement or counseling. The range of tests available DTC is broad, from tests for single-gene disorders, such as cystic fibrosis, to tests for predisposition to complex, multifactorial diseases, such as depression and cardiovascular disease. In addition to providing test results DTC, some companies also make recommendations regarding lifestyle changes on the basis of these results, such as changes in diet or use of nutritional supplements.

....

Recommendations

I. Transparency

To promote transparency and to permit providers and consumers to make informed decisions about DTC genetic testing, companies must provide all relevant information about offered tests in a readily accessible and understandable manner.

• Companies offering DTC genetic testing should disclose the sensitivity, specificity, and predictive value of the test, and the populations for which this information is known, in a readily understandable and accessible fashion.
• Companies offering DTC testing should disclose the strength of scientific evidence on which any claims of benefit are based, as well as any limitations to the claimed benefits. For example, if a disease or condition may be caused by many factors, including the presence of a particular genetic variant, the company should disclose that other factors may cause the condition and that absence of the variant does not mean the patient is not at risk for the disease.
• Companies offering DTC testing should clearly disclose all risks associated with testing, including psychological risks and risks to family members.
• Companies offering DTC testing should disclose the CLIA certification status of the laboratory
  performing the genetic testing.
• Companies offering DTC testing should maintain the privacy of all genetic information and disclose their privacy policies,
  including whether they comply with HIPAA.
• Companies offering DTC testing and making lifestyle, nutritional, pharmacologic, or other treatment recommendations on the basis of the results of those tests should disclose the clinical evidence for and against the efficacy of such interventions, with respect to those specific recommendations and indications.

II. Provider Education

To ensure that providers are aware that genetic tests are being provided DTC and that some of these tests may lack analytic or clinical validity, professional organizations should educate their members regarding the types of genetic tests offered DTC, so that providers can counsel their patients about the potential value and limitations of DTC testing.

• Professional organizations should disseminate information to their members explaining what DTC testing is, what tests are offered DTC, and the potential benefits and limitations of such testing for patients.

III. Test and Laboratory Quality

To ensure the analytic and clinical validity of genetic tests offered DTC and to ensure that claims made about these tests are truthful and not misleading, the relevant agencies of the federal government should take appropriate and targeted regulatory action.

• CMS should create a genetic testing specialty under CLIA, to ensure the analytic validity of tests and the quality of genetic-testing laboratories.
• CMS should ensure that all DTC genetic-testing laboratories are certified under CLIA and should maintain a publicly accessible list containing the certification status of laboratories.
• The federal government should take steps to ensure the clinical validity of DTC tests that make health-related or health care-affecting claims.
• The FTC should take action against companies that make false or misleading claims about DTC tests.
• The FDA and the FTC should work together to develop guidelines for DTC testing companies to follow, to ensure that their claims are truthful and not misleading and that they adequately convey the scientific limitations for particular tests.
• The Centers for Disease Control and Prevention (CDC) should conduct a study on the impact of DTC testing on consumers, to assess whether and to what extent consumers are experiencing benefit and/or harm from this method of test delivery. The CDC should also conduct a systematic comparison between the claims made in DTC advertising and the scientific evidence available to support these claims.

Similar controls need to be put in place in other countries since these testing services are marketed on the internet where they are not restricted to American citizens.

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Hudson, K., Javitt, G., Burke, W., Byers, P., with the ASHG Social Issues Committee (2007) ASHG Statement on Direct-to-Consumer Genetic Testing in the United States. Obstetricians and Gynecology 110:1392-1395. [PubMed]

Why biology is harder than physics

 
Rosie Redfield says [Why biology is harder than physics].

Beginning university students in the sciences usually consider biology to be much easier than physics or chemistry. From their experience in high school, physics has math and formulae that must be understood to be applied correctly, but the study of biology relies mainly on memorization. But in reality biology is much more complex than the physical sciences, and understanding it requires more, not less, brain work.

Read the rest over at RRTeaching. Rosie makes a point that I've also tried to make, but she does a better job.

Rosie is a Professor at the second best (in my opinion) university in Canada.

For another perspective, check out the views of a physics-trained graduate student (Philip Johnson) who works here at the best university in Canada [Biology is harder than physics?]. After expressing some skepticism, Philip closes with ...

I hope someone in the social sciences gets wind of this and belittles biologists. Sociology is obviously more complex than biology, so it clearly requires more brainpower to be a social scientist than a biologist, right?

Uh, no Philip. Sociology is the study of the behavior of one particular biological species (Homo sapiens). It's a teeny, tiny subset of biology.

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Changing Your Mind: Are Science and Religion Compatible?

 
Clay Shirky used to think that science and religion were compatible. That doesn't mean all religious beliefs, of course, because some of them like Young Earth Creationism are not compatible with science. He has changed his mind ... [Religion and Science].

Since we couldn't rely on the literal truth of the Bible, we needed a fallback position to guide our views on religion and science. That position was what I'll call the Doctrine of Joint Belief: "Noted Scientist X has accepted Jesus as Lord and Savior. Therefore, religion and science are compatible." (Substitute deity to taste.) You can still see this argument today, where the beliefs of Francis Collins or Freeman Dyson, both accomplished scientists, are held up as evidence of such compatibility.

Belief in compatibility is different from belief in God. Even after I stopped believing, I thought religious dogma, though incorrect, was not directly incompatible with science (a view sketched out by Stephen Gould as "non-overlapping magisteria".) I've now changed my mind, for the obvious reason: I was wrong. The idea that religious scientists prove that religion and science are compatible is ridiculous, and I'm embarrassed that I ever believed it. Having believed for so long, however, I understand its attraction, and its fatal weaknesses.

Read the rest of the article to find out why the "Doctrine of Joint Belief" is not based on logic.

In the war between "arrogant" atheists and accommodationist atheists (formerly called "appeasers"), Clay Shirky has shifted sides.

Saying that the mental lives of a Francis Collins or a Freeman Dyson prove that religion and science are compatible is like saying that the sex lives of Bill Clinton or Ted Haggard prove that marriage and adultery are compatible. The people we need to watch out for in this part of the debate aren't the fundamentalists, they're the moderates, the ones who think that if religious belief is made metaphorical enough, incompatibility with science can be waved away. It can't be, and we need to say so, especially to the people like me, before I changed my mind.

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Changing Your Mind: Are Scientific Theories Falsifiable?

 
Rebecca Goldstein is a philosopher at Havard University (USA). She used to think that Karl Popper's view of how science is done was correct. Now she's changed her mind ... [Falsifiability]

Said Popper: The criterion of the scientific status of a theory is its falsifiability.

For most scientists, this is all they need to know about the philosophy of science. It was bracing to come upon such a clear and precise criterion for identifying scientific theories. And it was gratifying to see how Popper used it to discredit the claims that psychoanalysis and Marxism are scientific theories. It had long seemed to me that the falsifiability test was basically right and enormously useful.

But then I started to read Popper’s work carefully, to teach him in my philosophy of science classes, and to look to scientific practice to see whether his theory survives the test of falsifiability (at least as a description of how successful science gets done). And I’ve changed my mind.

....

...scientists don’t, and shouldn’t, jettison a theory as soon as a disconfirming datum comes in. As Francis Crick once said, “Any theory that can account for all of the facts is wrong, because some of the facts are always wrong.” Scientists rightly question a datum that appears to falsify an elegant and well-supported theory, and they rightly add assumptions and qualifications and complications to a theory as they learn more about the world. As Imre Lakatos, a less-cited (but more subtle) philosopher of science points out, all scientific theories are unfalsifiable. The ones we take seriously are those that lead to “progressive” research programs, where a small change accommodates a large swath of past and future data. And the ones we abandon are those that lead to “degenerate” ones, where the theory gets patched and re-patched at the same rate as new facts come in.

Many people agree with Rebecca Goldstein but I still hear from lots of Popperians. It's very annoying to see my fellow scientists attack Intelligent Design Creationism on the grounds that it doesn't conform to Popper's idea of science—it's not falsifiable. That's true but irrelevant. Much of the best kinds of science also don't conform to Popper's ideas.

Much of evolutionary theory is not falsifiable in the true Popperian sense.

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Changing Your Mind: Are Humans Evolving?

Steven Pinker, a psychologist at Harvard University (USA) used to think that humans had stopped evolving. Now he's changed his mind ... [Have Humans Stopped Evolving?]

Ten years ago, I wrote:

For ninety-nine percent of human existence, people lived as foragers in small nomadic bands. Our brains are adapted to that long-vanished way of life, not to brand-new agricultural and industrial civilizations. They are not wired to cope with anonymous crowds, schooling, written language, government, police, courts, armies, modern medicine, formal social institutions, high technology, and other newcomers to the human experience.

And:

Are we still evolving? Biologically, probably not much. Evolution has no momentum, so we will not turn into the creepy bloat-heads of science fiction. The modern human condition is not conducive to real evolution either. We infest the whole habitable and not-so-habitable earth, migrate at will, and zigzag from lifestyle to lifestyle. This makes us a nebulous, moving target for natural selection. If the species is evolving at all, it is happening too slowly and unpredictably for us to know the direction. (How the Mind Works)

...

New results from the labs of Jonathan Pritchard, Robert Moyzis, Pardis Sabeti, and others have suggested that thousands of genes, perhaps as much as ten percent of the human genome, have been under strong recent selection, and the selection may even have accelerated during the past several thousand years. The numbers are comparable to those for maize, which has been artificially selected beyond recognition during the past few millennia.

If these results hold up, and apply to psychologically relevant brain function (as opposed to disease resistance, skin color, and digestion, which we already know have evolved in recent millennia), then the field of evolutionary psychology might have to reconsider the simplifying assumption that biological evolution was pretty much over and done with 10-000 — 50,000 years ago.

I'm glad he's changed his mind but it's for the wrong reasons.

Evolution, human or otherwise, cannot ever be stopped. Pinker, like the true adaptationist he is, cannot conceive of any evolution mechanism other than natural selection. Even if his original writings were correct, all he said is that natural selection may have stopped. Evolution by random genetic drift—the most frequent form of evolution—never stops.

It's interesting to see Pinker make the connection between the presumed stoppage of human evolution after the shift from hunter-gatherer mode, and evolutionary psychology. I never really thought about it before but that connection is a basic assumption in most of the the just-so stories promoted by evolutionary psychologists. If there has been lots of recent selection in human populations then it becomes more difficult to attribute our current "primitive" behavior to old adaptations that took place 100,000 years ago.

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[Photo Credit: CivilBrights]

Changing Your Mind: Alan Alda Converts from Atheism to Agnosticism

 
Alan Alda has changed his mind. He used to be an atheist but now he prefers to call himself an agnostic [ So far, I've changed my mind twice about God].

But, slowly I realized that in the popular mind the word atheist was coming to mean something more: a statement that there couldn't be a God. God was, in this formulation, not possible, and this was something that could be proved. But I had been changed by eleven years of interviewing six or seven hundred scientists around the world on the television program Scientific American Frontiers. And that change was reflected in how I would now identify myself.

The most striking thing about the scientists I met was their complete dedication to evidence. It reminded me of the wonderfully plainspoken words of Richard Feynman who felt it was better not to know than to know something that was wrong. The problem for me was that just as I couldn't find any evidence that there was a god, I couldn't find any that there wasn't a god. I would have to call myself an agnostic. At first, this seemed a little wimpy, but after a while I began to hope it might be an example of Feynman's heroic willingness to accept, even glory in, uncertainty.

I think he's dead wrong about the meaning of the word atheism. I think it means that you have not accepted theism and therefore you are "without a belief in God." I see the word atheism as similar to words like "a-toothfairyism" or "a-SantaClausism." You don't believe in Santa Claus so you are an "a-SantaClausist." It does not mean you are committed to the concept that there could not possibly be a Santa Claus.

It would be silly to label yourself an agnostic with respect to belief in Santa Claus. Nobody, especially Christians, goes around announcing that they are agnostic about the existence of the Greek Gods. You don't believe in them, full stop.

There is a version of agnosticism that's perfectly acceptable. John Wilkins, among others, promotes this definition of agnosticism. True agnostics claim that it is impossible to prove one way or the other whether God exists, just as it's impossible to prove one way or the other whether the tooth fairly exists. All rational people are agnostics in this sense. Some of them are also atheists. Alan Alda appears to be both an atheist and an agnostic, just like Richard Dawkins. Alan Alda is a wimp for letting non-atheists redefine atheism and then abandoning his position because of that incorrect definition.

It's not an either/or situation, in my opinion (Wilkins disagrees). You can, and should, be both an atheist and an agnostic.

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[Photo Credit: M*A*S*H]

Changing Your Mind: The Limits Of Darwinian Reasoning

 
Marc D. Hauser is a biologist and psychologist at Harvard University (USA). He is beginning to see the error of his adaptationist ways [The Limits Of Darwinian Reasoning].

Let me be clear about the claim here. I am not rejecting Darwin’s emphasis on comparative approaches, that is, the use of phylogenetic or historical data. I still practice this approach, contrasting the abilities of humans and animals in the service of understanding what is uniquely human and what is shared. And I still think our cognitive prowess evolved, and that the human brain and mind can be studied in some of the same ways that we study other bits of anatomy and behavior. But where I have lost the faith, so to speak, is in the power of the adaptive program to explain or predict particular design features of human thought.

Although it is certainly reasonable to say that language, morality and music have design features that are adaptive, that would enhance reproduction and survival, evidence for such claims is sorely missing. Further, for those who wish to argue that the evidence comes from the complexity of the behavior itself, and the absurdly low odds of constructing such complexity by chance, these arguments just don’t cut it with respect to explaining or predicting the intricacies of language, morality, music or many other domains of knowledge.

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Changing Your Mind: The Obligations and Responsibilities of The Scientist

 
Leon Lederman is a physicist and a Nobel Laureate. He has changed his mind about the The Obligations and Responsibilities of The Scientist.

The role of the Professor, reflecting the mission of the University, is research and dissemination of the knowledge gained. However, the Professor has many citizenship obligations: to his community, State and Nation, to his University, to his field of research, e.g. physics, to his students. In the latter case, one must add to the content knowledge transferred, the moral and ethical concerns that science brings to society. So scientists have an obligation to communicate their knowledge, popularize, and whenever relevant, bring his knowledge to bear on the issues of the time. However, additionally, scientists play a large role in advisory boards and systems from the President's Advisory system all the way to local school boards and PTAs. I have always believed that the above menu more or less covered all the obligations and responsibilities of the scientist. His most sacred obligation is to continue to do science. Now I know that I was dead wrong.

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Changing Your Mind: Maybe Human Races Do Exist After All

 
Mark Pagel is an evolutionary biologist who used to buy into the idea that human races did not exist [We Differ More Than We Thought].

The last thirty to forty years of social science has brought an overbearing censorship to the way we are allowed to think and talk about the diversity of people on Earth. People of Siberian descent, New Guinean Highlanders, those from the Indian sub-continent, Caucasians, Australian aborigines, Polynesians, Africans — we are, officially, all the same: there are no races.

Now, in 2007, he changed his mind ...

What this all means is that, like it or not, there may be many genetic differences among human populations — including differences that may even correspond to old categories of 'race' — that are real differences in the sense of making one group better than another at responding to some particular environmental problem. This in no way says one group is in general 'superior' to another, or that one group should be preferred over another. But it warns us that we must be prepared to discuss genetic differences among human populations.

Good for him. Better late than never, I say.

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Changing Your Mind: The Fallacy of Hypothesis Testing

 
The Edge has asked people to describe whether they have changed their mind about anything and if so, why? It's the Annual Question for 2008.

Some of the replies are worth discussing. For example, Irene Pepperbreg has changed her mind about the meaning of the scientific method [The Fallacy of Hypothesis Testing]. I think she makes some good points, notably ....

Third, I've learned that the scientific community's emphasis on hypothesis-based research leads too many scientists to devise experiments to prove, rather than test, their hypotheses. Many journal submissions lack any discussion of alternative competing hypotheses: Researchers don't seem to realize that collecting data that are consistent with their original hypothesis doesn't mean that it is unconditionally true. Alternatively, they buy into the fallacy that absence of evidence for something is always evidence of its absence.

I'm all for rigor in scientific research — but let's emphasize the gathering of knowledge rather than the proving of a point.

I think this is a serious problem in science today. There are too many papers being published without any serious discussion of competing explanations. There are too many papers that fail to critically examine their own basic assumptions or the possible flaws in their experiments.

There may be a reason for this behavior—scientists don't want to draw attention to possible flaws in their work for fear that the granting agency will find out—but that doesn't excuse it. Scientific rigor demands that you present both sides of a scientific debate in a fair and unbiased manner. The failure to address the arguments of your opponents is nothing less than failing to be a good scientist.

Similarly, the failure to recognize the possible flaws in one's own explanation is the mark of a bad scientist.

While Irene Pepperbreg may be right about the flaws in today's method of doing science, I'm not prepared to throw out the baby with the bathwater. Hypothesis-based science is still important. You just have to form the right hypotheses and put your work in context. The problem, in my opinion, isn't that hypothesis testing is a fallacy: the problem is that it's not being done properly.

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Open Lab 2007

 
Open Lab 2007 is about to be published. The book contains the best articles from science blogs in 2007.

There were 486 articles nominated and the judges selected 53 for publication [Open Lab 2007 - the winning entries for you to see!]. The winners come from a wide selection of science blogs; 20 of them are part of the SEED group (ScienceBlogs^TM) and 33 are from other science blogs.

For the second year in a row there won't be any of my Sandwalk postings in the Open Lab anthology.

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Oops! The Rapture Didn't Happen

 
There was supposed to be a rapture last month but the prediction didn't come true. Either that or it did come true and only a small number of people were raptured, not including the prophet.

In case anyone is interested, here's how our prophet explains his little mistake [Are You Rapture Ready]. I assume he's apologizing to all those people who gave away everything in the expectation that they would soon be in heaven.

I offered to take some of those worldly goods off their hands but I couldn't find anyone who was expecting to be raptured. I guess I don't hang out with the right kinds of people.

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Iowa Caucuses

 
In a few days about 100,000 people will get together in Iowa to elect the next President of the United States. At least I think that's what the caucuses are all about. It's all very confusing. Apparently there are some other states like New Hampshire and South Carolina that have to confirm the Iowa result before it becomes official.

American politics is so confusing. None of this stuff is in the Constitution so I can't check the rules.

Anyway, since those few Iowa citizens are going to have such an important role in choosing the new leader of the free world (sic) I thought you might be interested in seeing how one of them is struggling to make up his mind. John Logsdon of Sex, genes & evolution has written about his quandary [Caucus Conundrum: Considering Compelling Candidates]. Why not pay him a visit and help him decide?

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You Think *You* Have a Tough Job? ....

 

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[Hat Tip: Canadian Cynic]

Airport Security and Liquid Contraband

 
The other day I saw a photograph of an airport security guard standing in front of dozens of large plastic bags full of confiscated liquids. The bags were stacked in a corridor and passengers were streaming by.

"Isn't this strange," I thought. Those bags are full of potentially dangerous chemicals that could destroy an aircraft yet the security guard seems unconcerned about the potential threat. As it turns out, there are lots of people who think that airport security is a farce. Patrick Smith has written about it in today's New York Times [The Airport Security Follies].

“I would not hesitate to allow that liquid explosives can pose a danger,” Greene added, recalling Ramzi Yousef’s 1994 detonation of a small nitroglycerine bomb aboard Philippine Airlines Flight 434. The explosion was a test run for the so-called “Project Bojinka,” an Al Qaeda scheme to simultaneously destroy a dozen widebody airliners over the Pacific Ocean. “But the idea that confiscating someone’s toothpaste is going to keep us safe is too ridiculous to entertain.”

Yet that’s exactly what we’ve been doing. The three-ounce container rule is silly enough — after all, what’s to stop somebody from carrying several small bottles each full of the same substance — but consider for a moment the hypocrisy of T.S.A.’s confiscation policy. At every concourse checkpoint you’ll see a bin or barrel brimming with contraband containers taken from passengers for having exceeded the volume limit. Now, the assumption has to be that the materials in those containers are potentially hazardous. If not, why were they seized in the first place? But if so, why are they dumped unceremoniously into the trash? They are not quarantined or handed over to the bomb squad; they are simply thrown away. The agency seems to be saying that it knows these things are harmless. But it’s going to steal them anyway, and either you accept it or you don’t fly.

It's about time that we started to protest against the waste of time and effort at airport security lines. This is a huge over-reaction to 9/11 and the fear of terrorism.

Read what John Wilkins has to say on Evolving Thoughts [Follies d'Air]. He puts things into historical perspective and points out that we are not only being inconvenienced by such folly but also surrendering considerable rights and freedoms in the name of "security." You'll appreciate John's ability to link airport security measures with Julius Caesar and the Prussians.

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[Photo Credit: Tim Boyle/Getty Images from the MSNBC website (Where will all that liquid contraband go?)]

Atheists Are Intolerant and Militant

 
Here's a video from "TheismBeatsAtheism." It's quite well done but still reflects the hollowness of the typical theist. Note that there's a lot of complaining about the "intolerance" and "militancy" of the atheists but very little defense of theism. The best proof they can offer for God's existence is the fact that 80-90% of American believe in him.

The theists are going to have to do better than this. If there is evidence of a supernatural being then let's hear it. I'm sick of those theists who claim that we have to read some "sophisticated" Christian apologetics in order to understand the arguments for God's existence. Those arguments have been around for 2000 years or more and none of them stand up to rational examination. (Note that they never recommend any Hindu books. Why is that? Every religion has their share of "sophisticated" books proving that their particular religion is correct. What does that tell you?)

I like the part where they complain about the universities. Apparently, getting a college education and learning how to think is detrimental to one's belief in a supernatural being. Do they have solutions to this problem, other than promoting ignorance? Yes, they do—more effort on brainwashing young children ought to work. What's interesting is that these theist dudes would complain about brainwashing by other religions¹ but see nothing wrong with Christians doing it.

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1. Especially the Muslim bogeyman. You might be surprised to learn than all Muslims are intolerant and would kill any atheist who lectured to them. I guess it's okay for Christians to be militant and intolerant toward other religions but not okay for atheists. I loathe hypocrisy.

[Hat Tip: Hemant Mehta at Friendly Atheist (These Atheists… They’re Everywhere!)]

DNA Denaturation and Renaturation and the Role of Hydrogen Bonds and Stacking Interactions

 
Several students have written to me with questions about the structure of DNA. The most troubling questions are from students who have read the article I wrote about a paper that measures the stacking interactions in polynucleotides [Measuring Stacking Interactions]. In that posting I wrote ...

The two strands of double- stranded DNA are held together by a number of weak interactions such as hydrogen bonds, stacking interactions, and hydrophobic effects [The Three-Dimensional Structure of DNA].

Of these, the stacking interactions between base pairs are the most significant. The strength of base stacking interactions depends on the bases. It is strongest for stacks of G/C base pairs and weakest for stacks of A/T base pairs and that's why it's easier to melt A/T rich DNA at high temperature. (It is often incorrectly assumed that this is due to having only two hydrogen bonds between A/T base pairs and three between G/C base pairs.)

THEME

Deoxyribonucleic Acid (DNA)Many students have written to say that my statements contradict their Professors and their textbooks. I'm not surprised. The old-fashioned view of DNA denaturation (pre-1990) supposed that the differences between A/T rich DNA and G/C rich DNA were due to the extra hydrogen bond in G/C base pairs. Many of the Professors who teach introductory biochemistry aren't aware of the fact that this view is incorrect. Even more surprising, some of the current textbooks have not bothered to update their material on the structure of DNA.

Here's the story as we know it today. For those students who have written to me, I repeat the caution I mentioned in my reply to you—be sure to check with your Professor before you write any tests. Make sure he/she understands why you are contradicting what was said in class so you don't get marks taken off. It's always better to do this in advance instead of arguing your case after you have lost marks on the test.

Let's look first at what happens when DNA is denatured by raising the temperature.

As the temperature increases, you start to get local unwinding of the double-stranded DNA. This unwinding occurs preferentially in regions where the two strand are held together less strongly. In these regions the strands separate to form bubbles of single-stranded regions. The DNA sequence in these regions is enriched in A/T base pairs because the interactions between the two strands are weaker in A/T rich regions. In G/C rich regions strands are held together more strongly so they don't unwind until higher temperatures.

Incidentally, even at normal cell temperatures the DNA "breathes" and local regions become temporarily unwound. As you might expect, A/T rich regions are more likely to open up than G/C rich regions. This is one of the reasons why transcription initiation bubbles and DNA replication origins are often A/T rich. It's easier for the proteins (RNA polymerase, and origin binding proteins) to create the locally unwound regions.

When all of the base interactions are broken, the two strands separate. This is called denaturation. (Local unwinding is not denaturation.)

The base are now exposed to the aqueous environment. Single-stranded DNA is more stable than double-stranded DNA at higher temperature. Note that the edges of the bases will still form hydrogen bonds in this situation. They form hydrogen bonds with water molecules. In fact, they will form many more hydrogen bonds with water than they would form with complementary bases in double-stranded DNA.

As the temperature is lowered, the double-stranded form becomes more stable than the single strand in solution, and the DNA renatures. The first step is a nucleation event where two complementary regions come into contact. Nucleation is the rate-limiting step in renaturation. Once nucleation occurs, the rest of the molecule zips up pretty quickly.

It's easy to follow the denaturation of DNA because there's a difference in the absorbance of ultraviolet light between single- and double-stranded DNA. Single-stranded DNA absorbs more strongly.

In a typical melting curve, you measure the increase in UV absorbance as the temperature increases. This tracks the unwinding and denaturation of DNA. The melting point (T_m) is the temperature at which half the DNA is unwound.

DNA that consists entirely of AT base pairs melts at about 70° and DNA that has only G/C base pairs melts at over 100°. You can calculate the T_m of any DNA molecule if you know the base composition. The simplest formulas just take the overall composition into account and they are not very accurate. More accurate formula will use the stacking interactions of each base pair to predict the melting temperature [Wikipedia: DNA melting].

The question is why is there a relationship between the base composition of DNA and the stability of the double-stranded regions?

The first people to think about this question didn't really understand the role of stacking interactions between base pairs in the middle of double-stranded DNA. They also didn't really appreciate hydrogen bonds. They naively assumed that the differences between G/C rich DNA and A/T rich DNA was due to the fact that G/C base pairs have three hydrogen bonds and A/T base pairs have only two [The Chemical Structure of Double-stranded DNA].

We now know that this explanation doesn't make sense. There is no net loss of hydrogen bonds when DNA is denatured, quite the reverse in fact. There are more hydrogen bonds formed between the bases in single-stranded DNA and water molecules than between base pairs in DNA. There's no reason why single-stranded DNA would renature if formation of double-stranded DNA was driven by the creation of hydrogen bonds between base pairs. For every hydrogen bond between bases you would have to break almost two hydrogen bonds to water molecules.

The most important interactions in double-stranded DNA are the stacking interactions between adjacent base pairs. You can think of this as the interactions of electrons on the upper and lower surfaces of the rings that form the bases.

There are ten possible interactions between adjacent base pairs. The energies of these interactions are shown in the table on the left. The arrows indicate the direction of the DNA stand from 3′→5′ [The Chemical Structure of Double-Stranded DNA].

Note first of all that the strength of these stacking interactions (about 30 kJ mol^-1 on average) are greater than the strength of stability conferred by hydrogen bonds (about 3 4 kJ mol^-1)¹. Assuming there are on average six three hydrogen bonds per in two stacked G/C base pair, the total strength of the hydrogen bonds (18 12 kJ mol^-1) is still much less than the stacking interactions.

Secondly, note that stacking interactions involving G/C base pairs are stronger (more negative) than those involving A/T base pairs. This is why the melting temperature of DNA depends on the base composition. It's not because G/C base pairs have one more hydrogen bond than A/T base pairs, it's because G/C base pairs form stronger stacking interactions.

This is why you can calculate a more accurate melting temperature for oligonucleotides if you use the stacking interactions. It's stacking interactions that determine the stability of double-stranded DNA and it's stacking interactions that are disrupted as the temperature increases and more thermal energy is added to the molecule.

Finally, the paper that I discussed in July [Measuring Stacking Interactions] measured the stacking interactions in single-stranded DNA (poly A). As it turns out, the stacking interactions between single bases are, in some cases, strong enough to force single-stranded DNA into a helical structure. This is further evidence of the importance of stacking interactions in conferring stability to the double helix.

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1. The stability conferred by each hydrogen bond is the difference between the strength of the bond in double-stranded DNA and its strength in when bonded to water. Hydrogen bonds between bases and water molecules typically have strengths of about 25 kJ mol^-1 and hydrogen bonds between base pairs are a bit higher.

Do Fundamentalist Christians Actively Resist Learning?

 
Last summer Tom Bozzo, an economist in Madison Wisconsin, played around with the latest data on science education in America [Scientific Knowledge in the US by Religion]. He was interested in any correlations between religion and the understanding of basic scientific concepts.

A reader reminded me of this data. It was discussed on several blogs last summer but I had forgotten the details. There's one pair of graphs that are particularly interesting. The first one shows that fundamentalist Protestants, as expected, do not believe that humans evolved whereas atheists—and most other groups—accept the scientific facts.
Tom wanted to know what these results would look like if he only included those respondents with some college education. He cautions us that the numbers are small.
There are several cautions that need to be emphasized. For one thing, there's a relationship between the amount of education one has and the strength of their religious beliefs. Getting an education tends to drive you away from the most fundamentalist religions. That's probably why there's a smaller percentage of college educated fundamentalists (27%) compared to moderates (39%) and liberals (51%). Another problem is that the numbers are small and the associated error bars are large.

Keeping all these cautions in mind, it is still quite remarkable that some significant percentage of fundamentalist Protestants can go to college and still reject the basic scientific fact that humans evolved. Note that in all of the other groups the college educated subset are more inclined to accept evolution. (Do most of those "college" educated fundamentalists go to some cheap reproduction of a college run by a religious organization?)

As we've seen time and time again on the blogs (and elsewhere), the Christian fundamentalists have erected very strong barriers against learning. It really doesn't matter how much they are exposed to rational thinking and basic scientific evidence. They still refuse to listen.

This is one of the reasons why I would flunk them if they took biology and still rejected the core scientific principles. It's not good enough to just be able to mouth the "acceptable" version of the truth that the Professor wants. You actually have to open your mind to the possibility that science is correct and get an education. That's what university is all about.

Of course, we all recognize the problem here. How do you distinguish between a good Christian who is lying for Jesus and one who has actually come to understand science? It seems really unfair to flunk the honest students who admit that they still reject science and pass the dishonest ones who hide their true beliefs.

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"The Twelve Days of Christmas" Is a Secret Catholic Catechism

 
Friday's Urban Legend: FALSE

Today is the fourth day of Christmas (four calling birds). There's a persistent urban legend floating around the internet that the popular song "Twelve Days of Christmas" is actually a secret message about Christianity, made up by persecuted Roman Catholics in England. The story even made it into our local paper (Toronto Star) a few days ago, albeit with a hint that it might not be true.

Here's the 1998 version of the email message.

You're all familiar with the Christmas song, "The Twelve Days of Christmas" I think. To most it's a delightful nonsense rhyme set to music. But it had a quite serious purpose when it was written.

It is a good deal more than just a repetitious melody with pretty phrases and a list of strange gifts.

Catholics in England during the period 1558 to 1829, when Parliament finally emancipated Catholics in England, were prohibited from ANY practice of their faith by law - private OR public. It was a crime to BE a Catholic.

"The Twelve Days of Christmas" was written in England as one of the "catechism songs" to help young Catholics learn the tenets of their faith - a memory aid, when to be caught with anything in writing indicating adherence to the Catholic faith could not only get you imprisoned, it could get you hanged, or shortened by a head - or hanged, drawn and quartered, a rather peculiar and ghastly punishment I'm not aware was ever practiced anywhere else. Hanging, drawing and quartering involved hanging a person by the neck until they had almost, but not quite, suffocated to death; then the party was taken down from the gallows, and disembowelled while still alive; and while the entrails were still lying on the street, where the executioners stomped all over them, the victim was tied to four large farm horses, and literally torn into five parts - one to each limb and the remaining torso.

The songs gifts are hidden meanings to the teachings of the faith. The "true love" mentioned in the song doesn't refer to an earthly suitor, it refers to God Himself. The "me" who receives the presents refers to every baptized person. The partridge in a pear tree is Jesus Christ, the Son of God. In the song, Christ is symbolically presented as a mother partridge which feigns injury to decoy predators from her helpless nestlings, much in memory of the expression of Christ's sadness over the fate of Jerusalem: "Jerusalem! Jerusalem! How often would I have sheltered thee under my wings, as a hen does her chicks, but thou wouldst not have it so..."

The other symbols mean the following:

2 Turtle Doves = The Old and New Testaments
3 French Hens = Faith, Hope and Charity, the Theological Virtues
4 Calling Birds = the Four Gospels and/or the Four Evangelists
5 Golden Rings = The first Five Books of the Old Testament, the "Pentateuch", which gives the history of man's fall from grace.
6 Geese A-laying = the six days of creation
7 Swans A-swimming = the seven gifts of the Holy Spirit, the seven sacraments
8 Maids A-milking = the eight beatitudes
9 Ladies Dancing = the nine Fruits of the Holy Spirit
10 Lords A-leaping = the ten commandments
11 Pipers Piping = the eleven faithful apostles
12 Drummers Drumming = the twelve points of doctrine in the Apostle's Creed

Snopes.com is all over this one [The Twelve Days of Christmas].

There is no substantive evidence to demonstrate that the song "The Twelve Days of Christmas" was created or used as a secret means of preserving tenets of the Catholic faith, or that this claim is anything but a fanciful modern day speculation, similar to the many apocryphal "hidden meanings" of various nursery rhymes. Moreover, several flaws in the explanation argue compellingly against it:

What's interesting about the Snopes.com article is that it explores the real origins of the song and reveals some interesting facts about the corrupted English version.

What we do know is that the twelve days of Christmas in the song are the twelve days between the birth of Christ (Christmas, December 25) and the coming of the Magi (Epiphany, January 6). Although the specific origins of the song "The Twelve Days of Christmas" are not known, it possibly began as a Twelfth Night "memory-and-forfeits" game in which the leader recited a verse, each of the players repeated the verse, the leader added another verse, and so on until one of the players made a mistake, with the player who erred having to pay a penalty, such as a offering up a kiss or a sweet. This is how the song was presented in its earliest known printed version, in the 1780 children's book Mirth Without Mischief. (The song is apparently much older than this printed version, but we do not currently know how much older.) Textual evidence indicates that the song "The Twelve Days of Christmas" was not English in origin, but French. Three French versions of the song are known, and items mentioned in the song itself (the partridge, for example, which was not introduced to England from France until the late 1770s) are indicative of a French origin.

In the original version, the gift on the fourth day was "colly" birds, not "calling" birds. Apparently, "colly" meant black as coal and a "colly bird" was a blackbird. The five "golden rings" refers to ring-necked pheasants. Thus, the first seven gifts are all birds.

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[Image Credit: Cafepres.com]

The Second Grapevine Genome Is Published

 
A second version of the grapevine genome was published at PLoS ONE last week (Velasco et al. 2007). As I began to collect information on that paper I learned that another genome sequence of grapevine had been published independently last September in Nature (Jaillon et al. 2007). Before discussing the PLoS ONE paper I decided to write up a report of that August genome sequence trying to not let the second sequence influence me [The Grapevine Genome].

This gives us an opportunity to evaluate the state of genome biology and genome evolution by comparing two competing analyses of the same genome. Keep in mind that the authors of the second paper were aware of the first study when they published in PLoS ONE so they had an opportunity to correct or modify their own work in light of the previous paper. Thus, the second group is able to point out "errors" in the first sequence and correct "errors" in their own sequence before publication.

Keep this in mind as you read the second paper because it often seems as though the first group to publish did a very sloppy job. What we don't see in the published work is the evidence of sloppiness in the second study that was fixed by referring to the earlier work.

Velasco et al. (2007) also sequenced the Pinot Noir cultivar of Vitis vinifera but unlike the previous study they used a heterogeneous strain. Recall that in the September paper the sequencing team used an inbred line in order to reduce the extreme heterogeneity seen in normal wine-making strains.

The genome size is 505 Mb (505 × 10⁶ bp). This is larger than the earlier published sequence (487 Mb). The extra DNA is almost entirely due to inclusion of ribosomal RNA clusters. Velasco et al. (2007) identified 29,585 genes—only slightly fewer than the 30,434 genes reported by Jaillon et al. (2007). Both teams used fairly strict criteria for identifying and annotating genes. The number of genes in the grapevine genome is comparable to the number in Arabidopsis (26,819) but fewer than the number in poplar (45,555) and rice (41,046). We can expect this number to fall as false positives are eliminated.

There are 719 tRNA genes (including 163 pseudogenes), 89 snRNA genes, and about 1500 copies of the 18S + 5.8S + 28S ribosomal RNA repeat. There are about 175 copies of the 5S RNA gene.

The authors report 166 copies of snoRNA and 143 copies of microRNAs based on known examples in other plant genomes.

Many plants exhibit very high heterogeneity between homologous chromosomes. Sister chromosomes in the Pinot Noir cultivar differ by as much as 11% in DNA sequence, including large gaps. This gives rise to regions that are hemizygous—they contain only one copy of a DNA sequence in a diploid genome. An example of this heterogeneity is shown below.

Two almost contiguous regions of chromosome 1 are depicted. The red regions are transposons of various kinds (c=Copia, a=Gypsy/athila, etc.). You can see that many of the deletions/insertions are at transposon positions indicating that much of the heterogeneity between sister chromosomes is due to the insertion and excision of active transposons. This level of transposon activity is rare in mammalian genomes but common in flowering plants.

In order to study the evolution of the grapevine genome, Velasco et al. (2007) compared the sequences of paralogous genes. These are genes that belong to a gene family that diverged from a common ancestor. By comparing the differences in sequence between any two genes it is possible to estimate the time of divergence. In order to avoid any bias due to selection, it is preferable to only compare nucleotide substitutions that do not change the amino acid sequence (synonymous substitutions, K_s).

The results are shown in the figure above. Most of the pairs of genes are very similar with 0 or 0.1 substitutions. These genes arose from a very recent duplication event. There is a secondary peak at about 0.9 substitutions indicating that a large number of genes were duplicated at some particular time in the past. If this is evidence of a genome-wide duplication event then these pairs of genes should be clustered in syntenic regions. (Large segments of the chromosome that have the same order of genes.)

The insert (E) shows the distribution of those pairs from syntenic regions. It looks like most of the pairs have accumulated similar numbers of substitutions suggesting strongly that there was a genome-wide duplication event.

It is well known that flowering plant genomes have undergone polyploidization and/or hybridization during their evolution from a common ancestor about 200-300 million years ago. In their September paper in Nature, Jaillon et al. (2007) proposed that the grapevine genome was closer to the common ancestor of dicotyledenous plants. Their analysis suggested that all dicots arose from a hexaploid ancestor (three haploid genome equivalents). Further duplications occurred in the lineages leading to poplar and Arabidospis, according to Jaillon et al. (2007) [The Grapevine Genome].

Velasco et al. (2007) disagree. In the second genome study they claim that the ancestral dicot genome was tetraploid (one round of duplication) and that a second round of duplication (2R) occurred in the grapevine lineage after it diverged from poplar and Arabidopsis (see below). Note that in this study Arabidopsis and poplar are assumed to more closely related to each other than they are to grapevine whereas in the previous study grapevine was clustered with poplar.



A third duplication (3R) took place independently in the lineages leading to Arabidopsis and polar, according to Velasco et al. (2007).

At present, it isn't possible to say who is correct. In fact, they might both be wrong. The significance of these two studies is that it gives us some idea of the level of confidence we can place on speculations about genome evolution. How you interpret your data depends very much on how you compare sequences both within a species and between species. The data does not seem to be good enough to make confident predictions as judged by the differing opinions of these two groups.

The take-home lesson is that we need to take studies of this sort with a large grain of salt. In most cases we won't be lucky enough to have competing labs to analyze the same data and point out differing interpretations.

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Jaillon, O., Aury, J.M., Noel, B., Policriti, A., Clepet, C., Casagrande, A., Choisne, N., Aubourg, S., Vitulo, N., Jubin, C., Vezzi, A., Legeai, F., Hugueney, P., Dasilva, C., Horner, D., Mica, E., Jublot, D., Poulain, J., Bruyère, C., Billault, A., Segurens, B., Gouyvenoux, M., Ugarte, E., Cattonaro, F., Anthouard, V., Vico, V., Del Fabbro, C., Alaux, M., Di Gaspero, G., Dumas, V., Felice, N., Paillard, S., Juman, I., Moroldo, M., Scalabrin, S., Canaguier, A., Le Clainche, I., Malacrida, G., Durand, E., Pesole, G., Laucou, V., Chatelet, P., Merdinoglu, D., Delledonne, M., Pezzotti, M., Lecharny, A., Scarpelli, C., Artiguenave, F., Pè, M.E., Valle, G., Morgante, M., Caboche, M., Adam-Blondon, A.F., Weissenbach, J., Quétier, F., Wincker, P.; French-Italian Public Consortium for Grapevine Genome Characterization (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463-467. [PubMed] [Nature]

Velasco, R., Zharkikh, A., Troggio, M., Cartwright, D.A., Cestaro, A., Pruss, D., Pindo, M., Fitzgerald, L.M., Vezzulli, S., Reid, J., Malacarne, G., Iliev, D., Coppola, G., Wardell, B., Micheletti, D., Macalma, T., Facci, M., Mitchell, J.T., Perazzolli, M., Eldredge, G., Gatto, P., Oyzerski, R., Moretto, M., Gutin, N., Stefanini, M., Chen, Y., Segala, C., Davenport, C., Demattè, L., Mraz, A., Battilana, J., Stormo, K., Costa, F., Tao, Q., Si-Ammour, A., Harkins, T., Lackey, A., Perbost, C., Taillon, B., Stella, A., Solovyev, V., Fawcett, J.A., Sterck, L., Vandepoele, K., Grando, S.M., Toppo, S., Moser, C., Lanchbury, J., Bogden, R., Skolnick, M., Sgaramella, V., Bhatnagar, S.K., Fontana, P., Gutin, A., Van de Peer, Y., Salamini, F., Viola, R. (2007) A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2(12): e1326. doi:10.1371/journal.pone.0001326 [PubMed] [PLoS]

The Grapevine Genome

 
The sequence of the grapevine genome was reported in Nature last September (Jaillon et al. 2007). The 56 authors are all members of the French-Italian Public Consortium for Grapevine Genome Characterization [International Grape Genome Program].

The species is the dicotyledonous plant Vitis vinifera and the variety is cultivar Pinot Noir. In this case, the line was a special inbred variety that was about 93% homogeneous. It was necessary to use a selfed line of plants because most field varieties are very heterogeneous and this would have made it more difficult to assemble the sequence using the shotgun strategy.

The genome has 19 chromosomes amounting to 487 Mb of DNA (487 × 10⁶ base pairs). This is comparable in size to the three other plant genomes that have been sequenced; rice, poplar, and Arabidopsis.

The published sequence is referred to as a "high-quality draft" by the authors. They report 30,434 protein-encoding genes and 600 tRNA genes. (Ribosomal RNA genes aren't included in the paper.) This is somewhat fewer genes than poplar (45,555) and rice (37,544) but more than Arabidopsis (27,029). However, this might be deceptive since the total number of identified genes tends to decrease as annotation proceeds and annotation of the Arabidopsis genome is much further along than annotation of the other genomes.

About 41% of the genome is composed of transposons—most of which are non-functional pseudogenes. Genes make up 46% of the genome (7% exons, 37% introns). This is a much lower percentage of junk DNA than typical mammalian genomes.

Vitis vinefera is a dicotyledonous plant like the poplar tree and the small flowering plant Arabidopsis. Rice is a monocot and monocots and dicots are thought to have diverged about 200 million years ago. Previous studies have suggested that grapevine should be more closely related to popular than to Arabidoposis and the genomic sequence confirms that relationship.

One of the most interesting problems in plant evolution is the tracking of various genome duplications that have occurred. Most plants show traces of recent polyploidization events and/or more ancient ones. This is most clearly seen when looking at paralogous genes in gene families and the evidence for large scale duplication comes from comparisons of large blocks of sequence. These syntenic regions (or paralogous regions) within a haploid genome are strong evidence of ancient duplications.

The figure below is taken directly from the Nature paper. It shows syntenic regions within the grapevine genome (left). Each colored region corresponds to a stretch of paralogous (homologous) genes. As you can see, chromosome 1, 14, and 17 each contain a large block of similar sequence (light green). Chromosomes 10, 12, and 19 have a different syntenic region (red).



The evidence suggests an ancient hexaploidization in the lineage leading to grapevine. When the syntenic regions of poplar (middle) and Arabidoposis (right) are mapped, you can see that the patterns get much more complicated and the regions become scrambled. The simplest explanation is that the grapevine genome is close to the ancestral genome of all dicots and the poplar and Arabidopsis genomes have undergone additional duplications accompanied by gene loss. The rice genome shows no evidence of the ancient tripling of the genome in dicots.

The phylogenetic tree looks like this—where stars represent duplication events. There has been at least one, and possibly two, duplications in the lineage leading to rice. It will be interesting to see if other monocot genomes show evidence of these duplications or whether they are specific to rice.

It appears that there have been two polyploidy events in the lineage leading to Arabidopsis from the time it diverged from the other two dicots. I don't think anyone has a good explanation for why genome duplications are so frequent in the evolution of vascular plants.¹

Note that the gene duplications give rise to larger gene families in flowering plants but what this means is that there are fewer distinct genes in plant genomes compared to mammalian genomes. Of course, plants have a number of metabolic pathways that aren't found in animals and some of the genes for these pathways are specifically amplified in the grapevine genome.

For example, there are more genes for stilbene synthases in grapevine than in poplar or Aribidopsis Stilbane synthases are essential enzymes in the resveratrol pathway. Resveratrol is the wine chemical associated with presumed health benefits coming from wine consumption.

The grapevine genome also has extra copies of the gene for terpene synthases. These are responsible for synthesis of resins, oils, and aromas that give wine its unique taste. These genes are probably the result of selected breeding over the course of several thousand years.

UPDATE: Read about The Second Grapevine Genome Is Published.

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1. Perhaps the Intelligent Design Creationists can explain this using their "scientific" theories.

Jaillon, O., Aury, J.M., Noel, B., Policriti, A., Clepet, C., Casagrande, A., Choisne, N., Aubourg, S., Vitulo, N., Jubin, C., Vezzi, A., Legeai, F., Hugueney, P., Dasilva, C., Horner, D., Mica, E., Jublot, D., Poulain, J., Bruyère, C., Billault, A., Segurens, B., Gouyvenoux, M., Ugarte, E., Cattonaro, F., Anthouard, V., Vico, V., Del Fabbro, C., Alaux, M., Di Gaspero, G., Dumas, V., Felice, N., Paillard, S., Juman, I., Moroldo, M., Scalabrin, S., Canaguier, A., Le Clainche, I., Malacrida, G., Durand, E., Pesole, G., Laucou, V., Chatelet, P., Merdinoglu, D., Delledonne, M., Pezzotti, M., Lecharny, A., Scarpelli, C., Artiguenave, F., Pè, M.E., Valle, G., Morgante, M., Caboche, M., Adam-Blondon, A.F., Weissenbach, J., Quétier, F., Wincker, P.; French-Italian Public Consortium for Grapevine Genome Characterization (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463-467. [PubMed] [Nature]

[Photo Credit: Nature]

Bon Voyage Charles

 
On this day in 1831 Charles Darwin set sail from Plymouth Sound (England) on the newly refitted brig HMS Beagle. Its mission was to explore South America and survey its coast.

The ship returned to England on October 2, 1836 after circumnavigating the globe.

When the ship left England, Darwin was officially the companion of the captain, Robert FitzRoy, but by the time it returned Darwin was the official naturalist.

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[Image Credit: The HMS Beagle Project]

Happy Holidays from Celebrity Atheists

 
The Daily Telegraph (Sydney, Australia) has a gallery of 15 celebrity atheists [Christ-miss for atheist celebs]. My favorites are Katharine Hepburn and Jodie Foster.

It is cause for billions of people to rejoice. But not these celebrity Grinches - sorry, atheists.

They are the stars who do not believe three wise men followed a star to a baby in a manger more than 2000 years ago.

What's significant about this list is not the fact that there are famous people who don't believe in God. That's been true for hundreds of years. And it's not the fact that some of them are very intelligent either—that's almost a given. (We'll ignore Angelina Jolie.)

No, the important point is that atheism is entering the mainstream. Newspaper articles like this wouldn't have been printed ten years ago. The more people learn about life in the absence of religion, the more it will come to be seen as a perfectly normal way to behave. That's a good thing.

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[Hat Tip: Hemant Mehta at Friendly Atheist (Merry Tuesday to These Celebrities)]

Pray for France!

 
This is a public service announcement for all the creationists who have been visiting Sandwalk lately.

France is in trouble. It needs your help [Pray for France]. The country is almost 30% atheist and less than 1% evangelical Christian. This is a problem because, as everyone knows, France is a very special country.

"The kingdom of France is predestined by God to defend the Church of Christ Our Lord. This kingdom will be great among all the kingdoms of the earth. In as much as it is loyal to its calling, it will be victorious. If it proves unfaithful in this, it will be punished harshly. Nevertheless, it will remain until the end of time."

               -St. Remi at King Clovis' baptism in 498

Your task, should you choose to accept it, is to pray for 40 days.

Rampant secularization has made the spiritual battleground in France difficult. Yet, God is on the move – working through His people and drawing in the French people – one soul at a time.

Did you know that for the past 7 years thousands of French people intercede for France during the 40 days preceding Lent?

Pray for France is your access point to join French believers during these 40 Days of Prayer.

Lent begins on Ash Wednesday, which falls on February 6th in 2008. You should start praying on Feb. 6th—if you have trouble thinking of anything good to say about France the website will sell you a brochure of prayers for $3.50.

Not being religious, I can't really get into this effort to support France but I'd really like to see the rest of you participate. As it turns out, I'm going to be in France for the first half of lent and I'd sure like to think that your prayers will make for good weather, good food, and good wine.

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[Hat Tip: Hemant Mehta at Friendly Atheist]

Oh My God!

 
According to a report in the Toledo Blade a recent survey of 1005 American adults reveals the following astonishing facts [Survey finds most Americans believe Jesus born of virgin].

--75 pecent believe that Jesus was born to a virgin. Mary

--69 percent of adults believed Jesus turned water into wine at the wedding in Cana.

--68 percent believed Jesus used five loaves of bread and two fish to feed a crowd of 5,000.

--64 percent believed the Earth was covered by a flood in which Noah, his family, and numerous animals were spared by living on an Ark.

--56 percent expressed literal belief in the Bible account of the devil, disguised a serpent, tempting Eve to eat forbidden fruit.

--49 percent accepted as accurate the Bible story of Samson losing his legendary strength when Delilah had his hair cut.

Guess what folks? This survey was not taken in 1500 AD. These are the opinions of people today in 2007!

[Photo credit: Zarna (Oh My God!)]
[Hat Tip: RichardDawkins.net]

The Human Genetic Variation "Breakthrough"

 
"Human Genetic Variation" is the scientific "breakthrough" of 2007, according to Science magazine. I have a problem with science journalism when science writers misuse the word "breakthrough" but that's topic for another posting [Breakthrough of the Year in Science].

In this thread I want to discuss the actual choice made by Science editors. Elizabeth Pennisi describes the choice in the lead article of this weeks issue [BREAKTHROUGH OF THE YEAR: Human Genetic Variation].

Equipped with faster, cheaper technologies for sequencing DNA and assessing variation in genomes on scales ranging from one to millions of bases, researchers are finding out how truly different we are from one another.

There is some truth to this statement. It's true that the details or the amount of genome-wide of variation are being added to the databases. But is it true that we only realized for the first time in 2007 that humans are different from one another?

Of course not. We've known about massive variation in populations since the the 1960's [The Cause of Variation in a Population]. We've been using DNA fingerprints to identify criminals for more than 15 years. Think about it. Would DNA fingerprinting work if we weren't all different from one another at the level of genome sequence?

The unveiling of the human genome almost 7 years ago cast the first faint light on our complete genetic makeup. Since then, each new genome sequenced and each new individual studied has illuminated our genomic landscape in ever more detail. In 2007, researchers came to appreciate the extent to which our genomes differ from person to person and the implications of this variation for deciphering the genetics of complex diseases and personal traits.

We're familiar with the writings of Elizabeth Pennisi so it shouldn't come as a big surprise that she makes statements like this. She seems to be remarkably deficient in her knowledge of scientific background and history.

It is simply not true that "In 2007, researchers came to appreciate the extent to which our genomes differ from person to person." Real scientists have known and appreciated that fact for decades. It's part of understanding junk DNA, Neutral Theory, and the importance of random genetic drift.

The true part of the statement is that by mapping more and more specific examples of variation we can do some experiments that we couldn't do before. This is an advance in technology but not an advance in our understanding of the extend of human genetic variation.

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Breakthrough of the Year in Science

 
For the longest time science journalists have been misusing the word "breakthrough." What they usually mean is any scientific discovery that merits a press release by a university or a scientific journal. Both of these sources are biased and it's the role of competent science writers to recognize that bias and report the real significance of a scientific publication.

Science usually advances incrementally, building slowly but surely on the work of others. Real "breakthroughs" are extremely rare.

All scientists know this so it comes as a major disappointment to see the publication of the American Association for the Advancement of Science (AAAS) promoting a "Breakthrough" of the Year [Breakthrough of the Year: Human Genetic Variation]. Why couldn't this be a scientific achievement of the year or a scientific advance of the year? Either of those words gives a better impression than"breakthrough" and allows us to nominate real advances in science that aren't necessarily breakthroughs.

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