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Monday, December 17, 2007

Monday's Molecule #56

Most students are busy at this time of year so I'm going to give you a break today. This is a very well-known molecule. You have to name it, giving me the common name and the correct systematic IUPAC name.

There's a direct connection between this molecule and Wednesday's Nobel Laureate(s). Your task is to figure out the significance of today's molecule and identify the relevant Nobel Laureate(s). I don't think this one is very difficult.

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous winners are ineligible for one month from the time they first collected the prize. There is only one ineligible candidate for this week's reward because Sandwalk readers have not been very successful in recent weeks. The prize is a free lunch at the Faculty Club.

Send your guess to Sandwalk (sandwalk(at) and I'll pick the first email message that correctly identifies the molecule (with the correct IUPAC name) and the Nobel Laureate(s). Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

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

UPDATE: We have a winner! The molecule is ADP or 5-(6-aminopurin-9-yl)
-3,4-dihydroxy- oxolan-2-yl methoxy-hydroxy- phosphoryl oxyphosphonic acid. The Nobel Laureates are the men who worked out how ATP synthase makes ATP using ADP as a substrate. Alivia Day was the first person to get the right answers.

It's All About Giving

Have you seen the ads on television? The stores want to convince you that the Christmas spirit is all about giving. Of course they do. And it's not just any sort of "giving" that counts; it only counts if it's expensive and new and you can put it under the tree in a pretty box. The more "giving" you do, the better it will be for Wal*Mart and Sears.

How many of you are "trapped" into buying presents for people who don't really need them? How many of you are only "giving" because you know you're going to "get" and you would feel guilty if you didn't reciprocate? Why not tell people that next year you don't need to exchange gifts in order to demonstrate your friendship?

One or two presents for close family members—more for young children—that's all we need for Chritsmas.

[Hat Tip: PZ Myers The atheist marketing failure]

Sandwalk 2007

John Lynch of Stranger Fruit started a trend last year when he posted the first sentence of the first blog of each month for the entire year. He's done it again this year [My year in blogging. I couldn't do it last year for obvious reasons so here's my summary for 2007.

  • January: Brits Losing After American Invasion: According to recent reports red squirrels in Britain are facing extinction.

  • February: Another Canuck Blogger There's a really good blog called Primordial Blog. As far as I can tell the author (Brian) lives in the Yukon—that's part of Canada (barely) so he must be Canadian.

  • March: Evolution Is a Fact DaveScot over at Uncommon Descent writes in "Theory of Evolution as well tested as…"

  • April: Public Scientific Debates Sean Carrol has posted an article about pubic debates over the validity of string theory [String Theory is Losing the Public Debate].

  • May: My Six Months Are Up! I started Sandwalk six months ago. The goal was to give it six months to see how things worked out.

  • June: Matthew Nisbet and Chris Mooney Video on Framing Science Chris Mooney has challenged me to respond to a video (see below the fold) of a talk that he and Matt Nisbet gave on framing. Over on his blog, Chris criticizes PZ Myers who couldn't sit through the whole hour [PZ, You Can Do Better Than This....]. Neither could I, but at least I got to the 50 minute mark which was more than twice as far as PZ.

  • July: Visible Mutations and Evolution by Natural Selection A recent posting [Darwin Still Rules, but Some Biologists Dream of a Paradigm Shift] raised the issue of adaptationism. The controversy is over the main mechanism of genetic change in evolving populations.

  • August: Heme Groups Monday's Molecule #37 is the heme group found in myoglobin and hemoglobin.

  • September: Theories of Speciation In order to understand real evolution you have to understand speciation. This fact usually comes as a great surprise to adaptationists who tend not to think of such things.

  • October: Do You Think Iran Will Get the Messsage? Here's a scary report from the New York Daily News [ Bush eyes 'surgical' strikes vs. Iran, sez mag].

  • November: Can You Smell Isovaleric Acid? Isovaleric acid [3-Methylbutanoic acid] smells like sweat. It is responsible for some of the odor in a locker room, for example.

  • December: Seymour Benzer (1921 - 2007) Seymour Benzer died last Friday. In the 1950's and 1960's Benzer was a prominent member of the 'phage group founded by Max Delbrück and Salvador Luria [The Nobel Prize in Physiology or Medicine 1969.].

Sharon Moalem Exposed

The Unexamined Life is a blog written by a student in one of the Life Sciences Programs here at the University of Toronto.

This student was curious about the strange behavior of "Dr." Sharon Moalem when confronted with scientific errors on Dr. Sharon's Blog. So our student did some digging and posted the results [Sharon Moalem, "medical maverick"].

It turns out that Dr. Sharon isn't a medical doctor—he has a Ph.D. and he's currently a 33 year old finishing his medical degree in New York. While it's perfectly legitimate to call yourself Dr. Sharon if you have a Ph.D., it seems very clear that "Dr." Sharon is strongly implying that he is a medical doctor on his blog and on the cover of his book.

It also turns out that "Dr." Sharon has found God. He now thinks that science is a way of revealing God. (Sharon Moalem is an Orthodox Jew.) The fact that he is a true believer probably explains his unethical behavior since it is typical of believers to censure contrary opinions on their blogs, demonstrate a lack of knowledge about science, and misrepresent their credentials.

UPDATE: "Dr." Sharon doesn't stop at refusing to post critical comments and editing his original postings to remove uncomfortable links. Now our favorite undergraduate blogger has documented him editing comments! [Sharon Moalem, self-destructing before our eyes] He's becoming more and more like a creationist.

UPDATE: PZ Myers has posted a short review of Survival of the Silliest. He doesn't like it. What a surprise! :-)

Sunday, December 16, 2007

Gene Genie #22

This is the 22nd edition of Gene Genie and the second time it has been hosted on Sandwalk. 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. All of the accepted submissions concern humans. Quite often this means looking at how our genes influence our behavior and many of this week's submissions certainly fit that category.

Tali Shapiro at Helium - Where Knowledge Rules asks whether biology or environment have the stronger influence on gender identity. The posting discusses an usual, and ultimately tragic, case of gender switching [Size

Is love in your genes? That's the question Christian Bachmann of Med Journal Watch asks [Love is in the genes when it comes to style].

It's not only love that's in your genes. There's more and more evidence linking all sorts of altruistic behavior to certain genes. Razib posts on the main Gene Exprsssion website. The candidate gene in this case is AVPR1a a polymorphism tied to variation in altruism.

Over on Living the Scientific Life GrrlScientist took note of the fact that a personalized genetics company published a claim that Jim Watson's genome was 1/16th African [Ebony, Meet Irony]. This result has been questioned on other blogs. For example, John Hawks of john hawks weblog wonders if it's a good idea for a private company to engage in this sort of cheap shot [Will the Watson "gotcha" moment bring down public genomics?].

Were you breastfed? Are you smart? Did you know that there might be a correlation between being breastfed as an infant and your IQ as an adult? Caroline Wright of phgfoundation discusses a recent paper on this subject [Correlation between IQ and breastfeeding moderated by genetics].

The confusion about the relative influence of genes and environment has a semantic component. Coturnix at A Blog Around the Clock asks Has the word "gene" outlived its usefulness?.

Did you know that your response to social stress might be determined by a single nucleotide change in your BDNF gene? Check out what John Fossella has to say in rs6265 (A) is my bodyguard. John runs the blog Biomarker driven mental health 2.0, which is dedicated to supporting consumer-driven personalized medicine.

Meanhwhile, the interest in personalized genetic testing prompted a CBC television show about [The DNA Genealogy Scam], which I blogged about on Sandwalk]. Later on I wondered whether science bloggers shouldn't be more cautious about promoting private testing services [23andMe - More Hype from Genetic Testing Services].

George Church is also a bit skeptical about some aspects of personalized genomics [George Church on Personal Genomics]. The posting is on Epidemix.

Bertalan Meskó weighs in with an opinion on ScienceRoll [Personalized Genetics: Back to the Personal Genome Project ].

Maybe we should all be worried since You Can Now Buy a Genetic Test at Rite-Aid.

One of the problems with personalized genetic testing is that it might reveal something you don't want to know. Matt Mealiffe of DNA and You asks Who's your daddy?.

What if you learn that you have a pre-disposition to cancer, or something worse? Does the information from one of these genetic testing companies prompt life altering changes? PredictER Blog wonders whether people really take these tests seriously [To Blog or To Jog? Genetic Tests and "Life-Changing" Decisions].

DNA direct is a genetic testing and educational services company. It has a blog called DNA Direct Talk and they've submitted an article that addresses the competition between their company and the new companies that have just started up [Opinions on 23andMe, deCODEme, Navigenics: Personal Genomics Services]. The posting was written by Lisa E. Lee, director of content at DNA Direct,

If you are interested in submitting a DNA sample to one of these companies then Hsien-Hsien Lei (Eye on DNA) has some advice for you [How to Prepare Yourself for a Genetic Test].

Gene therapy is when patients with genetic problems are cured by inserting a good copy of the defective gene. There have been several successes, but also some failures. Shelley Batts discusses one of the failures, noting that Gene Therapy Patient Wasn't Killed By the Therapy. Shelley blogs at Retrospectacle.

Speaking of gene therapy, can anything be done about hereditary blindness? Ruth has the story on The Biotech Weblog. She reports on clinical trials that are currently underway [Gene therapy for Hereditary Blindness on Phase I Clinical Trials].

Over on Gene Expression Razib brings up the OAC2 gene, once again. The question is how much do alleles of this gene contribute to eye color and skin color? [OCA2, blue eyes and skin color].

The sickle cell allele of the &beta:-globin gene is another favorite that's been discussed many times in Gene Genie submissions. The latest contribution is by Yann Klimentidis over on Yann Klimentidis' Weblog. The question is when was the sickle cell allele introduced into East Africa? [The sickle cell gene's recent introgression into East Africa]

BRCA1 is another popular gene. Mutations in this gene have been linked to many cancers but the biochemistry hasn't been worked out in most cases. A posting on Genetics & Health looks at one of the latest studies [50% BRCA 1 genes have PTEN mutations]. Elaine Warburton posted the summary.

Steve Murphy has a rather graphic description of Toxic epidermal necrolysis (TEN). This disease may be associated with alleles at the HLA locus and this raises questions about the results of genetic tests [Toxic Epidermal Necrolysis and Pharmacogenomics]. The article is on Gene Sherpas, another blog devoted to personalized genetics.

How many diseases can be cured by gene therapy? In order to answer that question you have to know how many genes we have. Most of you know that the number of known genes in our genome has been dropping steadily since the first drafts of the sequence were published. But do you know how far they've dropped? Keith Robison does and he's posted an article about it on OMICS! OMICS!. You might be surprised to hear what the latest number is [The Incredible Shrinking Human Genome].

Other heath-related articles look at the influence of infection and environment on human health. For example, asks What is MRSA? Symptoms and Prevention. I hope I won't be giving too much away if I reveal that MSA is methicillin-resistant Staphylococcus aureus.

Some of us are interested in human evolution and that's fair game on Gene Genie. Greg Laden at Greg Laden's Blog discusses the results in a recent PLoS Genetics paper in Origin of Native America. These latest results suggest a single migration at some indeterminate date that's likely to be more than 10,000 years ago. You can bet this isn't the end of the controversy. Read Greg's summary and comments.

A recent paper in PNAS has stimulated a lot of blogging. Greg Laden submits his view of the peper at [Study Suggests Increased Rate of Human Adaptive Evolution]. My own submissions began with questions about the study at [Are Humans Evolving Faster?] and [Accelerated Human Evolution] and continued with more questions that provoked a discussion with the primary author of the study (John Hawks, see comments) [Is Evolution Linked to Environmental Change?]

The next edition of Gene Genie will be published at ScienceRoll. You can submit articles at Blog Carnival: Gene Genie.

Granville Sewell Needs My Help

Over on Uncommon Descent, one of the IDiots (Granville Sewell) confesses his ignorance and asks for help [Jean Rostand on Evolution].
It is becoming harder and harder to find Darwinists willing to make a serious attempt to defend their theory, and explain how it could account for the complexity of life, they are almost entirely in attack mode. Their three main arguments are 1) ID is not science 2) ID is not science and 3) ID is not science. I believe ID is science, but I can understand the concern many have about it being taught in science classrooms, so I would like to propose a compromise. How about we simply "have the courage to recognise that we know nothing of the mechanism" of evolution, and leave it at that? Each student can decide for himself/herself what the most likely explanation might be.
Maybe I can help. I'm not a Darwinist but I do know a thing or two about the important mechanisms of evolution.

In natural selection the frequency of an allele increases in the population because the presence of the allele confers a selective advantage on the individual who carries it. This individual will survive and reproduce more frequently than individuals possessing the other allele of the gene in question. Over many generations the beneficial allele has a higher than normal probability of becoming fixed in the population

In random genetic drift an allele will increase in frequency due to chance alone and not because it confers a selective benefit. In most cases the allele will be nearly neutral with respect to its phenotype. Over a long period of time, these non-selected alleles will become fixed relative to other similar alleles in the genome.

There are many other things that you need to learn about evolution, Granville, but these two important concepts will do for now. Good descriptions of these mechanisms are easy to find on the internet. I'm surprised that you've never heard of them before. I guess that's why you're an IDiot.

Merry Christmas from the Turtle Creek Chorale

The Turtle Creek Chorale is a men's choir based in Dalls, Texas (USA). Their mission, among other things, is: "Celebrating a positive image of the gay community and partnering with artists and organizations that share our values and mission."

Here's how they celebrate by singing their own special version of the Hallelujah Chorus, from Handel's Messiah. I wish we could have taken our children to see this version instead of the ordinary version.

Taking the Link Out of Dr. Sharon's Blog

Yesterday Dr. Sharon (Sharon Moalem) posted a silly article about junk DNA [Please Take the Junk Out of DNA]. I've already quoted the silly parts and took note of the fact that I had made a comment on his website. That comment never appeared; instead there's now a single comment that happens to be favorable.

In his original posting Sharon Moalem said,
The idea of junk came out of the central dogma (this is not some Politburo manifesto) because some people erroneously believed that if DNA wasn’t used to make a functional protein than it must be like Grandma’s plastic covered couch, junk.
The words "central dogma" (above) liked to my article [The Central Dogma of Molecular Biology]. In that article, I give the correct version of the Central Dogma,
... once (sequential) information has passed into protein it cannot get out again.
                                                                         (F.H.C. Crick, 1958)
Anyone with a brain can see that Sharon Moalem's statement looks very, very silly once you realize what the Central Dogma really means.

What would you do if you were "Dr. Sharon"? I'll tell you what I would do. I would read the comment I left on his blog then re-read the article on the Central Dogma. I would recognize that I made a mistake and modify my article accordingly. Perhaps I would remove the sentence implying that the concept of "junk" came out of the central dogma. That's what I would do. That's what any rational person would do.

What did "Dr. Sharon" do? He removed the link to my article on the Central Dogma.

Oh dear. That looks bad, doesn't it?

UPDATE: (Sept. 2012) Now his entire post has disappeared.

Saturday, December 15, 2007

The Militant Atheists

Last night's talk by Justin Trottier was quite interesting. There were several in the audience who agreed that Dawkins, Dennet, Harris, and Hitchins are rude and offensive. I have two thoughts about this. One the one hand, I don't care if some people find them offensive—that's their problem and they should develop a tougher skin. On the other hand, I agree with the four horsemen that religion does not get a free pass. It's silly to grant it so much protection that any criticism is ruled out of order.

Here's an amazing conversation between Richard Dawkins, Sam Harris, Daniel Dennett, and Christopher Hitchens. They address the question: are they militant atheists?

They also discuss the relationship between frozen water falls and Jesus Christ.

Part 1:

Part 2:

[Hat Tip: The Unexamined Life]

What the Sickest Are Saying

Dr. Sharon Moalem is the lead author of a book called Survival of the Sickest. According to his website, Sharon Moalem got his Ph.D. "in the emerging fields of neurogenetics and evolutionary medicine from the University of Toronto." He now works at Mount Sinai School of Medicine in New York City (USA).

It looks like a fascinating book (not).
This revelatory book explains how, especially when you take the evolutionary long-view, many diseases are really complicated blessings, not simple curses. Survival of the Sickest answers the riddles behind many diseases that seem to be inexplicably wired into our genetic code, starting with the biggest riddle of them all: If natural selection is supposed to get rid of harmful genetic traits, why are hereditary diseases so common?

Through a fresh and engaging examination of our evolutionary history, Dr. Sharon Moalem reveals how many of the conditions that we think of as diseases today actually gave our ancestors a leg up in the survival sweepstakes. When the option is a long life with a disease or a short one without it, evolution opts for the long ball every time.

Survival of the Sickest explores earth, history, and the human genome to discover how environmental, cultural, and genetic differences shaped us through evolution and continue to play an active role in our health today.
Sharon Maolem has a blog and I was attracted to it today when he linked to my article on the Central Dogma of Molecular Biology. Here's what he says today about junk DNA [Please Take the Junk Out of DNA].
I still cringe whenever I see someone refer to parts of genome as junk or junk DNA. What they are talking about really is areas of DNA that we still don’t fully understand what their function might be. The idea of junk came out of the central dogma (this is not some Politburo manifesto) because some people erroneously believed that if DNA wasn’t used to make a functional protein than it must be like Grandma’s plastic covered couch, junk. Turns out that far from being junk, the really interesting part of our genome may be the part no one really thought to look at which is great for anyone interested in antiques since most of our DNA was previously relegated to the trash bin of evolution.
I've started to set him straight over on Dr. Sharon's Blog. In case it doesn't take the first time, some of you might like to continue his education in basic molecular biology. Looks like he'll need it for his second book.

Thinking Like a Plant

Cameron Smith has just published the second article on plants and intelligence. You can find it on page 6 in the "Ideas" section of today's Toronto Star [Can plants think? This slime solved a maze].

In today's article he mentions my criticism of what he said last week. He's referring to the idea that plants have intelligence when he says,
There are critics of such claims, however. For instance professor Laurence Moran of the University of Toronto's biochemistry department took exception to last week's column in his blog, saying systems biology "can be a very useful approach to a problem," but, "turning it into a religion isn't going to help."

He complains about too much rhetoric and not enough "real data." His blog is at Scroll down until you come to "Junk DNA in the Toronto Star."
Here's the link to that posting [Junk DNA in the Toronto Star].

The main point of my article was to point out the scientific inaccuracies in Cameron Smith's description of junk DNA. I explained that Smith was falling into the same trap as many science journalists—he was bamboozled by the hyperbole and self-promotion that scientists (and press officers) engage in to make their work seem far more important than it really is.

My criticism is part of a bigger campaign, one that puts more onus on science writers to sort out the wheat from the chaff and report on real science for a change [See The Benefits of Science Blogging]. Cameron Smith did not do that in his first article but he has taken a small step in the right direction today. At least he mentions that there are some scientists who are skeptical of the idea that plants can think.

It's easy to get confused here. Nobody is questioning the idea that plants can sense and respond to their environment. Bacteria can do that as well. They have chemical sensors in their membranes that detect certain chemicals and these sensors are connected to the flagella that propel bacteria through their liquid environment. The sensors direct the bacterium to move toward higher concentrations of a favorable chemical (and away from dangerous ones).

Bacteria are single cells. If you call that sort of thing "intelligence" then the word intelligence loses all sense of meaning. We could easily rig up a little electric toy car that finds a heat vent in the floor but we would not (I hope) call the car "intelligent."

Admittedly, plants are a bit more complicated than bacteria so their mechanisms of regulation and feedback are sophisticated. But let's not get confused about the difference between sophisticated feedback circuitry and "thought" which is a trait that one usually associates with meaningful properties of intelligence.

That's exactly what Cameron Smith seems to be doing when he says,
It shouldn't come as a surprise that there are reputable scientists making the controversial claim that plants have memories, that they can store and interpret data, that they can integrate information, that they can identify relationships between dissimilar entities, and that they can analyze and even predict – as, for instance, when the mayapple, a simple white flower that is a forest-floor perennial, makes choices about future branch and flower formation years in advance.

A wealth of scientific detail supporting these claims is available in Communication in Plants, published last year by Springer-Verlag in Germany. The book is a collection of scientific papers edited by professors in Germany and Italy. Since it sells for $234.50 in Canada, looking for it in a university library may be a better option than buying it.

It may be stretching language to say these characteristics demonstrate primitive intelligence. Nevertheless, they point toward a capacity to perform tasks typical of what we call intelligence.
It is, indeed, stretching the point to ask "Can plants think?" That is not responsible science journalism, in my opinion. There are plenty of interesting things to write about when it comes to explaining how plants can interact with their environment. I'm sure there's an audience out there who would like to know how the slime mold finds the best route through the maze, for example (see the opening paragraphs in the article).

The original paper referred to in the newspaper article is Nakagaki et al. (2000). In 2001 Nakagaki published a short review paper describing the experiment.

The figure on the right is taken from that second paper (Nakagaki, 2001). The figure shows the slime mold, Physarum polycephalum, spreading out on the surface of an agar plate looking for food (a). In part (b) you see the leading edge of the spreading disk. As you can see, in search mode the cytoplasm is relatively unorganized.

In (c) you see a plasmodium that has found several sources of food. These food sources are oak flakes (white blobs) that are scattered on the surface of the agar plate. When the plasmodium finds an oak flake it surround it and sets up channels to bring nutrients back to the main body. As you can see, the shape of the plasmodium changes as it contracts those unsuccessful extensions in order to make a superhighway of cytoplasm to the food source.

The slime mold will also behave like this in a maze. It spreads out into all possible paths in the maze looking for food. When it finds a food source, it contracts all the dead-end extensions in order to concentrate on a single extension via the shortest distance to the food. This is what is meant by "intelligence" but it's not much more complicated than the bacteria who locate food by connecting their chemosensors to their flagella.

Nakagaki is very impressed with this behaviour. Here's what he says in the abstract to the second paper.
Even for humans it is not easy to solve a maze. But the plasmodium of true slime mold, an amoeba-like unicellular organism, has shown an amazing ability to do so. This implies that an algorithm and a high computing capacity are included in the unicellular organism. In this report, we discuss information processing in the microorganism to focus on the issue as to whether the maze-solving behavior is akin to primitive intelligence.
Nakagaki might be impressed but I don't know very many other scientists who would use this kind of language to describe a simple mechanical property—a property exhibited by most cells. (Incidentally, Physarum polycephalum is not a plant by any stretch of the imagination. Fungi, are not plants. Fungi are more closely related to animals than to plants. Physarum isn't even a fungus, as one of the commenters reminds me, it's a protist.)

There are two ways science journalists could approach this study (and other similar ones). They could reinforce the hyperbole and try to convince the general public that scientists had stumbled upon something new and extraordinary. Of course, in order to do this the science journalist would have to disguise the fact that the vast majority of scientists scoff at this sort of nonsense. That might convince the editors to publish a sensationalist piece that could sell newspapers.

The other approach would be to explain why such claims do not really make it into the mainstream of scientific discourse. There's a good reason why botany textbooks are not being rewritten to include chapters on plant intelligence. This kind of science journalism is much harder but potentially more useful since it teaches the essence of science, namely skepticism. Maybe the newspaper editors won't pay for such articles but that's another problem.

Cameron Smith is interested in the environment and he was written many wonderful articles on that subject. Today's article contains a warning for those who buy the concept of plant awareness. Such a person is Peter Harries-Jones of York University who accepts that plants demonstrate awareness. Harries-Jones is an anthropologist who has developed an interest in systems theory and ecology. This is the kind of "systems theory" promoted by Gregory Bateson. It's not systems biology, it's the religion that bears only a superficial resemblance to the the science.
In a paper delivered to a New Orleans conference in October, he [Harries-Jones] quoted Gregory Bateson, a pioneer in communication among organisms in ecosystems, to make the case that the first step in ecosystem collapse could be a breakdown of communication, "as a result of too much fragmentation of complex interactions ... This means," he said, "we should pay the closest attention to any changes in the response of living organisms to each other."

Paying attention to such changes is something that should interest even non-believers such as Moran – especially since a breakdown in communication may be already happening with bees.
Sorry, but a breakdown in communication is exactly what I'm witnessing here. A wide gap seems to have opened up between rational thinking and whatever passes for rational thinking among those who think like a plant. If that kind of fuzzy thinking continues then we will, indeed, see a collapse—not of ecosystems but of civilization.

Nakagaki, T., Yamada, H. and Tóth, Á. (2000) Intelligence: Maze-solving by an amoeboid organism. Nature 407:470 [Nature] [PubMed]

Nakagaki, T. (2001) Smart behavior of true slime mold in a labyrinth. Res, Microbiol. 152:767-770. [Res. Microbiol.] [PubMed]

Friday, December 14, 2007

The New Atheism and Canada


Just a reminder, Justin Trottier is speaking on The New Atheism and Canada tonight (7 PM) at the Centre for Inquiry. Be there or be square!
Richard Dawkins, Sam Harris, Christopher Hitchens...the litany of assertive atheists whose gloves have come off is ever expanding. Some call them the new militants, others the new fanatics. Many fellow atheists wonder at the effectiveness of their approach, while others are relieved, having witnessed the rising tide of religious violence and intolerance. The unexplored question is, given the very significant differences between Canada, the US, and the rest of the planet, should the New Atheism approach be applied here?

Justin Trottier will summarize the arguments advocated by the New Atheists while reviewing the social and political scene in Canada from the vantage point of a leading atheist/secularist to address this question. He will also provide advice on how Canadians may organize to promote science, reason and free inquiry, whatever their thoughts on the New Atheism.

Justin Trottier is Executive Director of the Centre for Inquiry Ontario. He is co-Founder of the political advocacy group Canadian Secular Alliance, as well as the President of the multimedia outreach group Freethought Association of Canada. Trottier has had television appearances on CBC, CTS, OMNI, CH and CityTV, as well as dozens of radio appearances and coverage in campus, city and national newspapers. He is a contributor to Humanist Perspective and Free Inquiry magazines and is on the editorial board of the Canadian Freethinker.


The Benefits of Science Blogging

In one of the few time that I agreed with Matt Nisbet, I argued earlier that science blogs are good for science journalists, [Scientists Enter the Blogosphere].
But how significant are these discussions if only a minority of scientists read blogs, or write them? "Blogs are important sources for opinion leaders, activists, and journalists. They help create a lot of the discourse out in the world," explains Nisbet. Indeed, many discussions that grab the attention of bloggers have ended up in the pages of The New York Times or in the news sections of science journals. "Blogs are having an impact because newsmakers read them," says Moran. "To some extent we are writing for science journalists. We are saying ‘Here is something getting the wrong kind of coverage’ or ‘Here is something you should be paying attention to.’"
I'm pleased to see that Michael Lemonick of TIME agrees [Why I Hate Scientist-Bloggers].
Now look what's happened. Go to the Science Blogs website and you'll find dozens of actual scientists, commenting in real time on every aspect of science you can imagine. It wouldn't be so bad if they were inarticulate—but most of them aren't! They're eloquent, funny, sarcastic and really smart (the last kind of goes without saying). No sooner does a paper appear in a major (or even a minor journal) than they jump in with knowledgeable reaction.

The truth is that science journalists have always relied on actual scientists to help us understand the implications of some new discovery. Some of us are pretty savvy about some areas of science, but still, we need to get expert perspective. Scientist-bloggers help us do that, only more efficiently. And because there are so many of them, with many more scientists commenting on their posts, the wisdom of crowds distills the essence of the arguments very quickly.
The bad news is that Sandwalk isn't on his list of favorite science blogs. This is one of those times when people aren't making the distinction between "science blogs" and "ScienceBlogsTM."

[Hat Tip: Pharyngula, which is one of the favorites.]

Algorithmic Inelegance

I've both praised SEED magazine and tried to bury it [SEED and the Central Dogma of Molecular Biology - I Take Back My Praise]. This is one of those times when, unlike Mark Anthony, my main goal is to praise Caesar. Caesar in this case is PZ Myers who shows us month after month that there can be real science in SEED magazine.

This month's column is about development in fruit flies. At least that's what it looks like on the surface. The take-home message is telegraphed in the title of the article and the subheading ...
Algorithmic Inelegance

Complexity in living things is a product of the lack of direction in the evolutionary processes, of the accumulation of fortuitous accidents, rather than the product of design.
Bravo PZ! Life isn't designed. It isn't designed by God the intelligent designer and it isn't designed by Richard Dawkins natural selection. It's called Evolution by Accident.

Biology Envy and Quantum Magic

In this week's issue of New Scientist there's a report of a recurring phenomenon—the desire of physicists to become biologists [Was life forged in a quantum crucible?].
AS if they don't have enough on their hands tackling some of the biggest questions about our universe, some physicists are muscling in on biology's greatest endeavour. Life, say the physicists, began with a quantum flutter.

The idea that quantum mechanics is key to explaining the origin of life was first raised as far back as 1944 in Erwin Schrödinger's influential book What is life?.
Seventy years ago, physicists took up biology for two important reasons: (1) they were expecting to find new fundamental laws in biology, (2) they wanted to show biologists how smart they were.

They partially succeeded in the second goal since some of the most important work in molecular biology was done by physicists who started to work on biological problems. However, the biggest lesson from this experience was that you need to learn how to think like a biologist—and not like a physicist—in order to make progress in the messy field of living organisms.

This is a lesson that physicists need to relearn frequently. The latest attempt to understand biology, while thinking like a physicist, comes from Johnjoe McFadden. In this case, McFadden is not a physicist but a genuine molecular bioogist. He thinks that primitive self-replicating RNAs have to spring up out of the primordial ooze in one fell swoop.
Yet even a primitive ribozyme is a complicated structure, McFadden explains, requiring 165 base-pair molecules to be strung together in the right order. In fact, 4165 possible structures - most of which are not self-replicators - could be made with the same starting ingredients. "That's more than the number of electrons in the universe," he says. What's more, life came about relatively soon after the planet formed, he says. "The puzzle is not only how life emerged, but how it emerged so fast."
The creationists are going to love hearing about those kinds of improbable events.

Most biologists don't think that life began with the sudden formation of a 165 bp ribozyme. Instead, they would postulate much more probable scenarios, including scenarios that precede the RNA world.

But such thinking doesn't concern a physicist because physicists are used to dealing with five or six improbable things before having breakfast. McFadden believes that an extremely improbable ribozyme can form spontaneously by invoking a short-cut in the search algorithm.
McFadden believes that nature employed a quantum trick to speed up the process of sorting through and discarding unwanted structures - the same trick quantum computers employ.

Quantum bits, or qubits, can take on many different values simultaneously, since the properties of particles are not set until they are observed. This means that quantum computers can, in theory at least, exploit this ability to whip through their calculations much faster than their classical counterparts.

McFadden thinks a similar process could have occurred in the chemical soup that spawned life. If many different chemical structures could exist simultaneously in multiple, slightly mutated configurations, they could essentially "test" a range of possibilities at once until they hit a self-replicating molecule. This could trigger the act of replication, he says, which could be violent enough to collapse the delicate quantum states, fixing that structure as a self-replicator.
Thanks for your input, Dr. McFadden, but those kinds of hand-waving explanations don't cut the mustard in biology. They may be acceptable in physics but most biologists have higher standards these days.

However, in fairness, there are a few biologists who find the idea of quantum magic quite attractive. Ken Miller writes in Finding Darwin's God (p. 241).
Even the most devout believer would have to say that when God does act in the world, He does so with care and subtlety. At a minimum, the continuing existence of the universe itself can be attributed to God. The existence of the universe is not self-explanatory, and to a believer the existence of every particle, wave, and field is a product of the continuing will of God. That's a start which would keep most of us busy, but the Western understanding of God requires more than universal maintenance. Fortunately, in scientific terms, if there is a God, He has left himself plenty of material to work with. To pick just one example, the indeterminate nature of quantum events would allow a clever and subtle God to influence events in ways that are profound, but scientifically undetectable to us. Those events could include the appearance of mutations, the activation of individual neurons on the brain, and even the survival of individual cells and organisms affected by the chance processes of radioactive decay.
Now you can add the formation of life itself to the list of subtle, scientifically undetectable, processes that can be used by God.

Johnjoe McFadden is the author of Quantum Evolution. As far as I can tell, McFadden is not promoting belief in the supernatural. Nevertheless, some of his writings appear to almost as mystical as those of Ken Miller. Here's a quotation from his website [Quantum Evolution].
We have all been brought up on the neodarwinian synthesis of Darwinian natural selection with Mendelian genetics that states that the only significant lifestyle change to befall any microbe – mutations – are entirely random. The dogma states that mutations provide the raw material for evolution but natural selection provides the direction of evolutionary change. This dogma has been the central plank of evolutionary theory for nearly a century. But is it always true?

The proposal that the genetic code may inhabit the quantum multiverse suggests that in some circumstances, it doesn’t hold. Mutations are the driving force of evolution; it is they that provide the variation that is honed by natural selection into evolutionary paths. Mutations have always been assumed to be random. But mutations are caused by the motion of fundamental particles, electrons and protons – particles that can enter the quantum multiverse – within the double helix.

When Watson and Crick unveiled their double helix more than half a century ago they pointed out that mutations may be caused by a phenomenon known as DNA base tautomerisation.

Tautomerisation is essentially a chemist’s way of describing a quantum mechanical property of fundamental particles: that they can be in two or more places at one. Quantum mechanics tells us that the protons in DNA that form the basis of DNA coding are not specifically localised to certain positions but must be smeared out along the double helix. But these different positions for the coding protons correspond to different DNA codes. At the quantum mechanical level, DNA must exist in a superposition of mutational states.

If these particles can enter quantum states then DNA may be able to slip into the quantum multiverse and sample multiple mutations simultaneously. But what makes it drop out of the quantum world? Most physicists agree that systems enter quantum states when they become isolated from their environment and pop out of the multiverse when they exchange significant amounts of energy with their environment, an interaction that is termed ‘quantum measurement’. Cells may enter quantum states when they are unable to divide and replicate – perhaps they can’t utilise a particular substrate in their environment. They may collapse out of those quantum states when their DNA superposition includes a mutation that allows them to grow and replicate once more. In this way the environment interacts with, and performs a quantum measurement on the cell, to precipitate advantageous mutations. From our viewpoint, inhabiting only one universe, the cell appears to ‘choose’ certain mutations.
Is this one of those times when a little knowledge of physics (and biology) proves to be a really dangerous thing?
"A little learning is a dangerous thing; drink deep, or taste not the Pierian spring: there shallow draughts intoxicate the brain, and drinking largely sobers us again."

Alexander Pope (1688 - 1744) in An Essay on Criticism, 1709