Gene Genie #24

 
The 24th edition of Gene Genie has been posted at origins genome resources [Gene Genie issue #24: Human genetics (Illumnia conspiracies and Eric Roberts too) provide a light in winter].

Welcome to the 24th edition of Gene Genie!! During these grey winter doldrums, it is all too easy to hunker down and withdraw from the blogosphere into the minutiae of grant writing and lab management (brrr- I haven’t posted in weeks). So it is with true delight that I present and thank our contributors for brightening the season.

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.

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Changing Minds Through Science Communication

 
There are lots of things going on at the North Carolina Science Blogging Conference but the session I'd most like to have attended was on "Changing Minds Through Science Communication." The speakers were Jennifer Jacquet, Sheril Kirshenbaum, and Chris Mooney.¹

The next best thing to being there is to watch the videotape of the session (below). I must say I'm somewhat underwhelmed. Most of the presentations seemed to be mouthing the same old unsupported platitudes that we've been seeing for the past year, including a shot at Richard Dawkins.

There's was a great deal of talk about getting US Presidential candidates to engage in a science debate sometime in the next few months [Science Debate 2008]. Chris Mooney and Sheril Kirshenbaum spent a lot of time talking about this. How many people think this is a worthwhile way to spend one's time? What are the chances of it happening? If it does happen, will it advance the goal of effective science communication or is there a chance that it will do the opposite? If it doesn't happen, what message will that send about the importance of science?

The goal of the science debate is to use politics and the media to teach the general public about real science (e.g., evolution, global warming, stem cell research etc.) What if the media and politicians trump the process and use the debate to promote anti-science? Going head-to-head with these groups and trying to beat them at the framing game seems a bit naive to me. Am I the only one who thinks this? Since when have candidate debates stuck to scientific facts?

What if a candidate shows up with a list of ten scientists who think that the effects of global warming have been exaggerated, and has ten scientific papers to prove it? What if a candidate says that opposition to stem cell research is based on morality and not atheistic science? What if several of the candidates advocate teaching the controversy in biology class? Aren't we just begging for trouble? Aren't we just giving the kooks an opportunity to refute science during a "science" debate?

There's a good reason why real scientists avoid public debates with creationists. Perhaps science bloggers and science journalists should think about those reasons before promoting a debate on science. They might not get what they're wishing for.

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1. Would it have been impossible to find an active full-time research scientist to participate on this panel? I find it frustrating that scientists are being criticized in a forum like this without being given a chance to present the other side of the case.

Eating Clones

 
We eat cloned organisms every day, but they're plants (e.g., bananas).

Apparently, some people have a great fear of eating cloned animals. Is this irrational fear an "ethical" problem? The underlying question is how do we define an ethical problem? Just because some people incorrectly see a problem where none exists, are we obliged to bow to their definition of "ethics."

Join the discussion on Balblab [Clonal Discrimination].

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The Cloning of Steve Steve

 
Many of our science blogger friends are having a good time in North Carolina at the second North Carolina Science Blogging Conference. I was at the last one and it was lots of fun.

Joshua Rosenau is there and he breaks the news that Steve Steve has been cloned [Scienceblogging]. It has long been suspected that Reed Cartwright had succeeded in cloning Steve Steve but this is the first photographic proof that I'm aware of. As you can see from the photo, some of the cloning attempts were not successful.

I'm waiting to hear the response from the Vatican.

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This ranks among the most morally illicit acts, ethically speaking ...

 
Researchers from Stemagen a private stem-cell research company in California, have created human clones by the same techniques used to clone other mammals. The clones only went through a few cell divisions before being discarded [Ethical storm as scientist becomes first man to clone HIMSELF].

There's nothing remarkable about the science. It's one step toward cloning humans using standard procedures that have been worked out over the past three decades. What's remarkable is the reaction to this announcement. I'm still having trouble figuring out what is the ethical problem here.

I think it's all related to abortion. If you are opposed to allowing a woman to decide what to do with her own body then you're also against stem cell research. The "ethical issue" is mostly confined to religious people (men?) who oppose abortion. At least that's how it appears to me.

Stemagen isn't doing anything wrong; they make this clear on their webpage.

All research at Stemagen is performed in strict accordance with US Federal Regulations for the ethical treatment and protection of human subjects covered in the 45 CFR Part 46 policy issued by the Office of Human Research Protection (OHRP). More specifically, this requires that all research involving human eggs, embryos or human subjects be approved and carefully monitored by an independent Institutional Review Board (IRB) composed of members of the medical and general community, with additional ethical and legal expertise sought when required.

Those who choose to donate oocytes (eggs) and embryos for this type of research do so through informed consents that follow the guidelines for Human Embryonic Stem Cell Research from the National Academy of Sciences (www.nationalacademies.org).

Stemagen's mission is to maintain exemplary standards in human embryonic stem cell research in accordance with the highest ethical and research principles.

This is an important point in so-called "ethical" debates. The scientists are not being unethical and many observers, like me, don't see any ethical problem. Others see an ethical problem as described in the newspaper article.

John Smeaton, of the Society for the Protection of Unborn Children, said: "We have got scientists wandering around in an ethical wilderness, forgetting about matters of justice relating to our fellow human beings.

"We have people creating human beings with the intention of destroying them. That's appalling."

And the Vatican condemned the cloning of human embryos, calling it the "worst type of exploitation of the human being".

"This ranks among the most morally illicit acts, ethically speaking," said Monsignor Elio Sgreccia, president of the Pontifical Academy for Life, the Vatican department that helps oversee the Church's position on bioethics issues.

Here's the issue. At what point does something become an "ethical" issue for society? How many people have to be against something on "ethical" grounds" in order for it to become an ethical problem?

What if their objections are irrational? For example I imagine that US Presidential candidate Mike Huckabee is against stem cell research but his reasons are likely to be as ridiculous as his reasons for opposing same-sex marriage. Does that still count as an ethical problem? It seems to me that elevating stupidity to the level of "ethics" is not the way we want to go.

Why couldn't the headline have been "No Ethical Problem, According to Most Atheists?" Why do we let religious groups define ethics for us? I don't subscribe to their version of ethics, do you?

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Teaching IDiots About Evolution

 
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].

The book attempts to define evolution and it doesn't do a bad job of describing a minimal definition that would be acceptable—that is if you only look at the actual definition. Here it is from page 5.

Evolution consists of changes in the heritable traits of a population of organisms as successive generations replace one another. It is populations of organisms that evolve, not individual organisms.

Sandwalk readers will know that this is the kind of definition that I prefer as well [What Is Evolution?]. This sort of definition is neutral with respect to mechanisms. It doesn't matter whether evolution occurs by natural selection, random genetic drift, of something else entirely. That's just as it should be because the explanation of how evolution occurs lies properly in the domain of evolutionary theory. Thus, we can say that evolution is a fact because we see it happening and we have overwhelming evidence that has happened in the past. We can be confident that it is a fact even though we may not be as certain about how it happened.

Once we start committing to an explanation we can no longer talk about facts, in many cases, since the exact mechanism of evolution is often disputed. The National Academies book begins with a wonderful description of Tiktaalik, a fossil animal that shares characteristics of both fish and primitive tetrapods. It is strong evidence in support of the evolution of tetrapods from fish and that lineage is now considered to be a well established fact.

However, it would be wrong to use Tiktaalik as support for a particular mechanism of evolution. The fossil suggests that natural selection is playing a role but random genetic drift is not ruled out. We know from other sorts of data that natural selection and random genetic drift are facts, as well as being part of evolutionary theory, but it's a good idea to draw a distinction between evolution, the process, and theories about how it occurs. This is especially true when trying to explain things to IDiots.

Unfortunately, the authors of Science, Evolution, and Creationism don't do as good a job in this regard as they should have. For example, the (reasonably correct) definition that I quoted above is found at the end of a paragraph that weakens it considerably. Here's the entire paragraph ...

If a mutation increases the survivability of an organism, that organism is likely to have more offspring than other members of the population. If the offspring inherit the mutation, the number of organisms with the advantageous trait will increase from one generation to the next. In this way, the trait — and the genetic material (DNA) responsible for the trait — will tend to become more common in a population of organisms over time. In contrast, organisms possessing a harmful or deleterious mutation are less likely to contribute their DNA to future generations, and the trait resulting from the mutation will tend to become less frequent or will be eliminated in a population. Evolution consists of changes in the heritable traits of a population of organisms as successive generations replace one another. It is populations of organisms that evolve, not individual organisms.

The next paragraph then goes on to describe natural selection. There is no mention of random genetic drift anywhere in the book, although there is a passing reference to the fact that neutral mutations can be fixed. This reference is found on page 29 near the end of the book.

The net result is that evolution the process, is intimately connected to the mechanism of natural selection in this book. Readers will assume that scientists equate evolution with natural selection and use the terms interchangeably.

Why is this a problem? Well, for one thing, it's wrong. Normally that should be a good enough reason to avoid such errors, but these days there's a movement afoot to frame evolution in a way that resonates with the general public. Perhaps it's okay to define evolution as natural selection if it helps educate the average person? I object to such reasoning in the strongest possible terms. The essence of science is being honest and accurate and those goals should never be sacrificed for political gain. It may be easier to avoid confusion by not mentioning other mechanisms of evolution but the end result is that the public is not being educated correctly about evolution. You can't then turn around and complain that the public doesn't understand evolution.

The IDiots are upset about this book. They have found many ingenious ways of criticizing the contents. Here's a perfect example from Casey Luskin [The Facts about Intelligent Design: A Response to the National Academy of Sciences’ Science, Evolution, and Creationism].

I don't have the time, or the patience, to correct everything that's wrong with this article but there's one point I'd like to address. Here's what Casey Luskin says about evolution.

The NAS unscientifically elevates evolution to the status of unquestionable dogma.

The NAS defines evolution as evolution by natural selection and claims that “[t]here is no scientific controversy about the basic facts of evolution,” asserting that evolution is “so well established that no new evidence is likely to alter” it. In doing so, the NAS treats Neo-Darwinian evolution like an unquestionable dogma, not like a science. Such proclamations from the NAS are dangerous because they threaten the prestige of the NAS as an objective and trustworthy voice advising society.

Moreover, the NAS’s claim that there is no controversy over evolution is a bluff, for there is significant scientific dissent from the view of evolution by natural selection. Leading biologist Lynn Margulis, who opposes ID, criticizes the standard Darwinian mechanism by stating that the “Darwinian claim to explain all of evolution is a popular half-truth whose lack of explicative power is compensated for only by the religious ferocity of its rhetoric.”[7] She further observes that “new mutations don’t create new species; they create offspring that are impaired.”[8] In 2001, biochemist Franklin Harold admitted in an Oxford University Press monograph that "there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.”[9] Other scientists have gone much further.

Over 700 doctoral scientists have signed a public statement asserting their agreement that they "are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life."[10] But what are these scientists to do when the top scientific organization in the U.S. proclaims that evolution is as unquestionable as the existence of atoms or the heliocentric model of the solar system? Clearly the NAS’s statements threaten the academic freedom of scientists to dissent from Neo-Darwinian evolution.

In the past it has been easy to show that the IDiots are either mistaken or lying when they make comments like this. I've said many times that they deliberately try to confuse people by making it seem as though evolution, the fact, is the same as natural selection, the mechanism. They know full well that there's a difference between controversies over the sufficiency of natural selection and whether evolution, per se, is overwhelmingly support by hard evidence. They know that evolution is not the same as Darwinism and attacks on Darwinism are not the same thing as attacks on evolution.

This rebuttal is now a bit more difficult with the publication of Science, Evolution, and Creationism. Nowhere in the book do the authors deliberately make the distinction between natural selection and evolution and nowhere do they mention any other mechanism of evolution (e.g., random genetic drift). When reading the book, most of us recognize that there are abundant, oblique, references to the fact that the authors are not stupid, but that is only apparent to scientists who know about evolution.

Casey Luskin has taken advantage of this lost opportunity on the part of the National Academies to make it look like they are being dogmatic and forcing everyone to accept Darwinism. When I decided to write about Luskin's silly article, I thought it would be easy to refute what he was saying by referring back to the book. I thought the book would make it clear that evolution is not the same as natural selection. Unfortunately, there's nothing I can quote from the book that explicitly makes that point even though it's there implicitly. That's a missed opportunity that I hope can be remedied in future printings.

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Map That Campus XLII

 
This is one of my favorite challenges in the blogosphere. Can you identify the campus on The Daily Transcript?

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Backwards Bush Countdown Clock

 
Trust me, it's not just Americans who are counting the days.

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Science in an Age of Endarkment

 
Be sure to come to this special event sponsored by the Centre for Inquiry, Toronto. The talk will be given in the auditorium just beside my building. I'll be going to the reception beforehand at CFI—join CFI and you can come too!!!

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SCIENCE IN AN AGE OF ENDARKENMENT: scientific fraud, quackery, religion and university politics

Friday, January 25th, 2008: 7:00 pm - 9:00 pm, MacLeod Auditorium, Medical Sciences Building, University of Toronto (1 King's College Circle, Toronto)

When alternative medicine and academia collide... Featuring a major public symposium with David Colquhoun

Eminent UK scientist and noted skeptic David Colquhoun was recently at the centre of controversy after critiquing the pseudoscientific claims of a homeopathic practitioner. Prof. Colquhoun was asked to remove his site from the UCL server, but after a backlash from the scientific community, his website was revived. He will be speaking about alternative medicine, academia, and the conflicts that arise when the two intersect.

David Colquhoun is professor of pharmacology at University College London and fellow of the Royal Society. He runs a blog called "Improbable Science" (http://www.dcscience.net) dedicated to exposing and debunking pseudoscientific claims.

Dr. Colquhoun will appear at a special reception with food and drinks exclusively for Friends of the Centre from 5:00-6:30pm at CFI Ontario preceding his talk. Contact us at toronto@centerforinquiry.net to find out how you can join.

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[Image Credit: Homeopathy wars in the UK]


[For a short summary of the blogging ban see University College London Restores Professor Colquhoun's Website]

Soybean Genome

 
A preliminary draft of the soybean (Glycine max) genome has been released on the Phytozome website [Glycine max Genome].

The reported size of the genome is 950 Mb (950 × 10⁶ base pairs). This is considerably larger that the genomes of grape (505 Mb), Arabidopsis (157 Mb), rice (389 Mb), and polar (485 Mb).

The larger size suggests a recent polyploidization event in the lineage leading to soybean. The number of genes in the draft sequence is 51,320. This also suggests that many genes are duplicated. (Grape has about 30,000 genes, poplar has about 45,000, rice has 38,000 and Arabidopsis has only 27,029.) Keep in mind that the total number of genes is likely to drop by a considerable amount once detailed annotation gets underway. Nevertheless, it looks like the soybean has a lot more genes than the other flowering plants.

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[Photo Credit: [Photograph]. Retrieved January 18, 2008, from Encyclopædia Britannica Online: bean: soybean]

Brampton Prude

 
Brampton is a city west of Toronto and north of Mississauga, where I live. Heart Lake United Church is trying to attract customers so they put up the sign shown here. I think it's funny.

Nicole Cedrone doesn't agree. She thought it was offensive when she drove by on her way home from the doctor [Church Strips Saucy Sign]. She complained and the sign was removed.

"I have to admit, it is funny, but it's not appropriate for where it is," Cedrone said. "I just think it's offensive."

She said she is glad her 11-year-old wasn't in the car with her to ask, `Mom, what does that mean?'"

Well, the photograph of the "offensive" sign is now prominently featured in The Toronto Star where, hopefully, her 11-year-old son will read it and ask questions like, "Mom, what does 'saucy' mean?" By being such a prude, Nicole Cedrone has ensured that the sign will be viewed by millions and not just a small number of people driving along Sandalwood Parkway. Way to go, Nicole.

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Bobby Fischer

 
Bobby Fischer died yesterday in Reykjavik, Iceland, where he had been living for the past several years [Bobby Fischer, 64: Former chess champion].

Back in 1972, Fischer beat Boris Spassky of the USSR to become world chess champion. The event has been glorified as part of the cold war competition between the USA and the USSR but this was only part of the story. Some of us were just interested in it as a major sporting event featuring a radical new hero who didn't always play by the rules.

I remember following the games live on television—yes, that's right, the moves in each game were broadcast live on a large chessborad, with plenty of color commentary. As an amateur chess player, it was a real insight into the world of high level play.

Go to World Chess Championship 1972 for a brief summary of this extraordinary event. We'll never see anything like it again.

Here's the position at adjournment in the final (21st) game [Spassky vs Fischer Game #21]. Fischer (black) has just played h5. After thinking about the position all night Spassky phoned in the next morning to resign and concede the championship. Can you see why he gave up?

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Why I Like Richard Dawkins

 
Richard Dawkins doesn't pull punches and he doesn't beat around the bush. You always know where he stands on any given issue. This is what I admire about Richard Dawkins.

I don't agree with him on lots of things but whenever you engage him you know you've got a fight on your hands. It's the combination of intelligence and forthrightness that make him such a powerful voice in science. We need more scientists who are both smart, and willing to stand up for their ideas. We need more open controversy in science these days. Scientists need to speak up when they encounter silly ideas in the scientific literature. It is not a scientific virtue to be polite in such cases; in fact, it can be detrimental to science to clog up the scientific literature with scientific nonsense on the grounds that one shouldn't criticize fellow scientists in public. Richard Dawkins does not make that mistake.

Dawkins does not like group selection because it conflicts with his adaptationist, gene-centric, worldview. He's been very clear about this over the years. I admire him for sticking to his guns and standing by the original dismissal of group selection by George Williams.¹

David Sloan and E.O. Wilson have recently been pushing for a revival of group selection. They published a short summary of their new book in the Nov. 3 edition of New Scientist [Evolution: Survival of the selfless] where they said,

The concept of genes as "replicators" and "the fundamental unit of selection" averages the fitness of genes across all contexts to predict what evolves in the total population. The whole point of multilevel selection theory, however, is to ask whether genes can evolve on the strength of between-group selection, despite a selective disadvantage within each group. When this happens, the gene favoured by between-group selection is more fit overall than the gene favoured by within-group selection in the total population.

It is bizarre (in retrospect) to interpret this as an argument against group selection. Both Williams and Dawkins eventually acknowledged their error, but it is still common to find the "gene's-eye view" of evolution presented as a drop-dead argument against group selection.

The old arguments against group selection have all failed. It is theoretically plausible, it happens in reality, and the so-called alternatives actually include the logic of multilevel selection. Had this been known in the 1960s, sociobiology would have taken a very different direction. It is this branch point that must be revisited to put sociobiology back on a firm theoretical foundation.

Dawkins responds to this in a letter published in the Dec. 15 issue [Genes Still Central].

Genes still central

David Sloan Wilson's lifelong quest to redefine "group selection" in such a way as to sow maximum confusion - and even to confuse the normally wise and sensible Edward O. Wilson into joining him - is of no more scientific interest than semantic doubletalk ever is. What goes beyond semantics, however, is his statement (it is safe to assume that E. O. Wilson is blameless) that "Both Williams and Dawkins eventually acknowledged their error..." (3 November, p 42).

I cannot speak for George Williams but, as far as I am concerned, the statement is false: not a semantic confusion; not an exaggeration of a half-truth; not a distortion of a quarter-truth; but a total, unmitigated, barefaced lie. Like many scientists, I am delighted to acknowledge occasions when I have changed my mind, but this is not one of them.

D. S. Wilson should apologise. E. O. Wilson, being the gentleman he is, probably will.

* Richard Dawkins, Oxford UK

Does anyone have any doubts about where Dawkins stands on the issue of group selection?

David Sloan Wilson and E.O. Wilson responed to Dawkins' letter by claiming that they were only referring to one minor aspect of the argument against group selection but I don't think anyone is going to be fooled by that. In their article, they clearly imply that Dawkins has acknowledged his "error" in opposing group selection. This is a case where a simple apology would have worked better.

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1. Ironically, Dawkins is a huge fan of kin selection, which, in my opinion is just about as weak as group selection.

Gerty Cori Biochemist on USA Stamp

Biochemist Gerty Cori is going to be on a new USA stamp to be issued in March. Cori and her husband won the Nobel Prize in 1947 for their work on glycogen metabolism [Nobel Laureates: Carl Ferdinand Cori and Gerty Theresa Cori].

One of the key intermediates in this pathway is the Cori ester [Monday's Molecule #25]. That's the molecule pictured on the stamp. Unfortunately, there's a mistake in the structure. How many can spot it? Why didn't they ask a biochemist to check the design?

UPDATE: Here's the correct structure.

The error was first discovered by a reader of Chemical & Engineering News [Going postal over structural errors]. Here's how C&EN describes the mistake ...

It is a sad state of affairs, because it was precisely the isolation of glucose-1-phosphate, and discovery of the so-called Cori ester, that garnered Cori the Nobel Prize. "Long-dead carbohydrate chemists would roll over in their graves to see this structure after all the effort they made to get it right," one sugar chemist wrote in an e-mail to Newscripts.

The glitch made us rather glum, despondent even, as we considered the squandered opportunity to serve some first-class carbohydrates to the American public. For alas, the suboptimal stamps have already been printed and are still scheduled for release in early March, despite the error.

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[Hat Tip: Living the Scientific Life]

A Junk DNA Quiz

 
Take the junk DNA quiz in the left sidebar to let me know what you think of your genome. How much of it could be removed without affecting our species in any significant¹ way in terms of viability and reproduction? Or even in terms of significant ability to evolve in the future? In other words, how much is junk?

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1. I did not choose the word "significant" in order to be obtuse. I picked it in order to eliminate some trivial possibilities that really don't make any difference. For example, no matter how little DNA you delete you would be able to detect some change, even if it's just a reduction in the time to replicate the genome of the amount of energy used. If you think that such changes are "significant" then you should answer "none" to the question in the quiz.