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Sunday, December 16, 2007

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 http://sandwalk.blogspot.com. 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.

OPEN TO THE PUBLIC COST: $5 (STUDENTS $3)
FREE FOR FRIENDS OF THE CENTRE



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


Revenge of the Peppered Moth

Seven years ago, the creationists launched a attack on the peppered moth. Jonathan Wells tried hard to prove that this well-known example of natural selection was a fraud.

In recent years, this attack has been blunted by first showing that most of what the creationists said was a misrepresentation of the truth (surprise!) and then showing that the actual problems with the original experiments of Kettlewell did not invalidate the conclusion.

More recently, Michael Majerus has repeated the original work in a seven year study of birds preying on peppered moths. This has resulted in an example of natural selection that is more solid than ever before. Naturally, given that creationists are mostly IDiots, there are some who still cling to the myth that peppered moths don't undergo selection [Peppered Moths and the Confused IDiots].

This week's issue of New Scientist has a four page article on the peppered moth [Reclaiming the peppered moth for science]. The article presents an excellent summary of the issue and it's resolution.

More importantly, the article is accompanied by an editorial that I'm going to reproduce here in full. We need more of this kind of blunt talk in the popular science magazines.

IN 2000, a popular school textbook called Biology reluctantly dropped its prime example of evolution in action - industrial melanism in the peppered moth. Nothing in evolutionary biology had forced the change. The decision was entirely political, made in response to creationist attacks.

The loss of the peppered moth was a blow to science education in the US, as it is one of the easiest to understand examples of evolution by natural selection. So it is heartening to hear that biologists are fighting back ("Reclaiming the peppered moth"). Thanks to their efforts, evidence that the moth is an example of evolution in action is more robust than ever.

This tawdry tale reveals much of what is good about science - and rotten about creationism. Creationists went gunning for the moth after a scientific disagreement over the fine detail of a seminal experiment done in the 1950s. They used the debate to portray the science behind industrial melanism as hopelessly flawed, if not fraudulent.

In response, one scientist patiently redid the experiment - it took him seven years. It is hard to think of another system of thought that is so stringently self-critical and self-correcting. In science, everything is provisional. There are no preordained answers and fresh ideas are always welcome, so long as their proponents are happy for them to be tested.

That is not how creationists work. They already know the answer. They seek only evidence that confirms their conclusion, and distort or ignore the rest. Such an unreasoned approach is worthless. Creationists will keep trying to undermine the theory of evolution. All science can do is continue, with dignity, to stick to its guns. As with the peppered moth, the best testable explanation will win out.


[Photo Credit: The photographs are from bill.srnr.arizona. The original source is unknown.]

Thursday, December 13, 2007

23andMe - More Hype from Genetic Testing Services

 
The Genetic Genealogist promotes another for-profit testing service called 23andMe [The Latest on 23andMe].

Go to their website [23andMe] where you'll find this teaser ...
Connect to the Famous and the Infamous
Are you more closely related to European royalty or American outlawry? Use 23andMe's Ancestry tools to find out whether your maternal lineage links you more closely to Marie Antoinette or Jesse James. Your 23andMe account also connects you genetically to many other celebrities and historical figures, from Bono to Ben Franklin. Read more about 23andMe's celebrity features.
I still find it curious that there are "science bloggers" who promote these for-profit companies without ever mentioning the scam that they're perpetrating by misleading the general public about what the tests can achieve. The kit from 23andMe costs $999.00 (US).

Some of the bloggers are employed by companies in this field (e.g. Eye on DNA). I don't know about The Genetic Genealogist




Killer Pet Food Revisited

 
Do you remember the scandal from last March were pet cats and dogs were dying, allegedly from pet food manufactured by Menu Foods of Mississauga, Ontario (Canada)? At the time I was skeptical of the claims. It didn't seem to me that there were very many confirmed cases and it didn't seem likely that pet food from a reputable supplier could be so poisonous [Killer Pet Food?].

Well, the scientists have returned a verdict. A recent study has confirmed 348 cases of pet food-induced nephrotoxicity (236 cats and 112 dogs) [300 Pets May Have Died From Contaminated Pet Food Due To Lethal Combination Of Contaminants].

Initial reports suggested that the deaths were due to melamine contamination even though melamine is relatively harmless. It turns out that the pet food also contained unusual levels of cyanuric acid and melamine and cyanuric acid together form a very insoluble salt that blocks kidney function, causing death in some animals.

The pet food was contaminated and more than 300 pets died as a result. The study does not say how the food came to be contaminated but other sources attribute it to wheat gluten supplied by ChemNutra Inc. This company imported the wheat gluten from Xuzhou Anying Biologic Technology Development Co. in Wangdien, China.

Here's the original press release that's posted on the Food ad Drug Administration (USA) website [ChemNutra Announces Nationwide Wheat Gluten Recall].

ChemNutra Inc., of Las Vegas, Nevada, yesterday recalled all wheat gluten it had imported from one of its three Chinese wheat gluten suppliers – Xuzhou Anying Biologic Technology Development Co. Ltd.

The wheat gluten ChemNutra recalled was all shipped from China in 25 kg. paper bags, and distributed to customers in the same unopened bags. The bags were all labeled "Wheat Gluten Batch No.: _______ Net Weight: 25 kg Gross Weight: 25.1 kg Made in China". The batch numbers included in the recall are 20061006, 20061027, 20061101, 20061108, 20061122, 20061126, 20061201, 20061202, 20061203, 20061204, 20061205, 20061206, 20061208, 20061221, 20070106, 20070111, 20070116, and 20070126. Each ChemNutra shipment had the certificate of analysis information from the supplier, including batch number and the supplier's content analysis and test results. ChemNutra shipped from its Kansas City warehouse to three pet food manufacturers and one distributor who supplies wheat gluten only to the pet food industry. ChemNutra's shipments commenced November 9, 2006 and ended March 8, 2007. ChemNutra did not ship to facilities that manufacture food for human consumption, and the distributor ChemNutra shipped to supplies wheat gluten only to pet food manufacturers. The total quantity of Xuzhou Anying wheat gluten shipped was 792 metric tons.

ChemNutra learned on March 8 from one pet food manufacturer that the wheat gluten it had sold them – all from the Xuzhou Anying - was among ingredients suspected as a potential cause of pet food problems. ChemNutra immediately quarantined its entire wheat gluten inventory and assisted this customer's investigation.

After that manufacturer issued a pet food recall, the FDA immediately commenced a thorough investigation of ChemNutra's wheat gluten, including documentation analysis, inspection, and laboratory testing. ChemNutra cooperated fully with the FDA and immediately notified its other three wheat gluten customers about the FDA's investigation. Those customers had all purchased smaller amounts of the Xuzhou Anying wheat gluten commencing in January, 2007.

On Friday, March 30, the FDA announced they had found melamine in samples of the wheat gluten ChemNutra had imported from Xuzhou Anying. The FDA did not inform ChemNutra of any other impurities in the Xuzhou Anying wheat gluten, nor of any impurities in the wheat gluten from ChemNutra's other two Chinese suppliers.

The toxicity of melamine is not clear. However, since melamine is not approved by the FDA for pet food, it should absolutely not have been in wheat gluten. ChemNutra is extremely concerned about the purity of all of its products. The company is particularly troubled that the certificates of analysis provided by the above-named supplier did not report the presence of melamine.
The Mississauga company, Menu Foods is selling off assets in order to cover the court costs and the liability settlements. They recently sold a manufacturing plant in South Dakota to Mars, Incorporated.


Wednesday, December 12, 2007

Is Evolution Linked to Environmental Change?

 
As a general rule, adaptationists are mostly interested in the results of natural selection and not very interested in evolution by random genetic drift. They tend to use the word "evolution" when what they really mean is "natural selection" or adaptation.

Most adaptationists see evolution as positive natural selection. They focus mostly on changes where the population is becoming more fit with respect to the environment. Some of them think that this eventually results in populations that stop evolving because they have become optimized to a particular niche. In such cases, "evolution" (i.e., positive natural selection) will only start up again if the environment changes.

Whenever I mention this I'm usually confronted with a storm of denials. Apparently none of the adaptationists who comment on Sandwalk are guilty of such fuzzy thinking.

I'm so happy for them. The idea that species have exhausted all possible adaptations and reached the very tip top of their adaptive peak seems incredibly naive. The idea that "evolution" will have halted—as opposed to adaptation—seems even more naive.

Now that I've got that off my chest, let's turn to the Hawks et al. (2007) paper that's getting so much press [Accelerated Human Evolution]. Remember, this is a paper about human evolution.

I've read the paper and I can't really comment because there's no data in the paper. What I mean is that there are no examples of the 11,439 "selective events" that they found. It would have been nice to see a few examples of their data just to get some feel for it's quality.

The paper is complicated because it consists mostly of a discussion of the data, which we can't see. The first author, John Hawks, has made an attempt to simplify the work by posting an explanation on his blog john hawks weblog.

Here's an excerpt from the article titled Why human evolution accelerated [my emphasis-LAM]. The article explains why he expected to see an big increase in evolution adaptation following the development of agriculture about 10-40,000 years ago.
Still, a very small fraction of the mutations in any given population will be advantageous. And the longer a population has existed, the more likely it will be close to its adaptive optimum -- the point at which positively selected mutations don't happen because there is no possible improvement. This is the most likely explanation for why very large species in nature don't always evolve rapidly.

Instead, it is when a new environment is imposed that natural populations respond. And when the environment changes, larger populations have an intrinsic advantage, as Fisher showed, because they have a faster potential response by new mutations.

From that standpoint, the ecological changes documented in human history and the archaeological record create an exceptional situation. Humans faced new selective pressures during the last 40,000 years, related to disease, agricultural diets, sedentism, city life, greater lifespan, and many other ecological changes. This created a need for selection.

Larger population sizes allowed the rapid response to selection -- more new adaptive mutations. Together, the the two patterns of historical change have placed humans far from an equilibrium. In that case, we expect that the pace of genetic change due to positive selection should recently have been radically higher than at other times in human evolution.
Now, if I understand this correctly, here's the scenario. About 40,000 years ago humans had pretty much stopped accumulating adaptations because they were becoming optimized to their environment. This is reflected in the data, which shows a slow rate of adaptation at that time.

Then humans started to live in larger communities as they abandoned the hunter-gatherer mode of existence for one based on farming. This created a new environment that was less fit than the previous one. The human population responded to this less fit environment by expanding rapidly in numbers. This created more opportunity for beneficial mutations that were required under the new environmental conditions. The result was a huge increase in the rate of adaptive evolution.


Pushing Electrons

 
Most of you remember your first organic chemistry course with great fondness. You recall the thrill and excitement of learning new reaction mechanisms and getting used to pushing electrons using those neat little curved arrows.

I can imagine your sense of pride and anticipation when you started taking your first biochemistry course and realized that you could make use of all that chemical knowledge. Biochemists also like to draw curved arrows to show you where electrons are going.


Well, you can thank this week's Nobel Laureate, Sir Robert Robinson, for those arrows. He was the first chemist to use them back in the late 1920's. The convention didn't become popular until after World War II and it only became common in chemistry textbooks during the 1950's. The curved arrows spread to biochemistry textbooks in the '60's and '70's to the delight of all biochemistry students.

Believe it or not, there are some people who are not big fans of curved arrows (Laszlo, 2002).
This short note reflects upon the widespread practice, in the classroom, of the paper tool of reaction mechanisms, taught with Lewis structural formulas, using curved arrows to denote motions of electrons. It is concluded that this practice, while assuredly improving upon the rational understanding of chemical reactions and their underlying logic, can easily become a modern counterpart to medieval scholastics. It has many of the features of slang with respect to more thoughtful and dignified speech. And it may breed cynicism and skepticism on the part of the students when they see this paper tool turned into a universal explanatory device.
What a spoilsport ..... Today's students aren't cynical—they love organic chemistry. Else why would so many take it at university?


Laszlo, P. (2002) Describing Reactivity with Structural Formulas, or when Push Comes to Shove. Chem. Educ: Res. Prac. Euro. 3:113-118.

Nobel Laureate: Sir Robert Robinson

 

The Nobel Prize in Chemistry 1947.

"for his investigations on plant products of biological importance, especially the alkaloids"



In 1947, Sir Robert Robinson (1886 - 1975) won the Nobel Prize in Chemistry for working out the structure of a number of plant alkaloids, especially morphine and strychnine [Morphine, Heroin, Codeine].

The presentation speech was given by Professor A. Fredga, member of the Nobel Committee for Chemistry of the Royal Swedish Academy of Sciences.
THEME:

Nobel Laureates
Your Majesty, Royal Highnesses, Ladies and Gentlemen.

One of the principal aims of organic chemistry is to make clear the chemical structure of substances found in living nature. Interest has been directed particularly towards substances with vital functions or otherwise obvious qualities. The structure of simpler compounds was largely elucidated during the nineteenth century, the more complicated ones being reserved for our century. Sir Robert Robinson's exceedingly fruitful work treats many groups of such substances. In comprehensive investigations he has dealt with the anthocyans, a group of red, blue, or violet pigments found almost everywhere within the vegetable kingdom, and which we meet with in the cornflower and the lark-spur of the fields as well as in claret and beetroot. He has done important work on sex hormones and synthetic substances of less complicated structure but with similar properties. He has done pioneering work on synthetic drugs against malaria, he has contributed towards the investigation of penicillin and he has successfully attacked fundamental questions concerning the mechanism of organic-chemical reactions. In presenting him with this year's Nobel Prize in Chemistry, the Royal Academy of Sciences has in mind, however, particularly his work on alkaloids.

By alkaloids we understand a numerous group of nitrogenous basic substances from the vegetable kingdom. They usually have striking, sometimes sensational physiological effects. Among them are quinine, cocaine, and atropine, all of which have important medicinal qualities, further morphine, doubtless well-known, and strychnine known for its medicinal value and - in somewhat larger doses - as an exceedingly active poison. Plants containing alkaloids have generally drawn the attention of primitive peoples, and in the cases where they are met with in countries with ancient culture, the knowledge of their properties often goes back to pre-historic age. They have been used as medicines and means of enjoyment, for ritual and criminal purposes. They can carry our thoughts to poetry and romance - it is not only decadent poets who have sung the praise of opium and poppy juice - but they have also been associated with vice, crime and horror.

During the nineteenth century we began to learn how to isolate the active substances themselves, the alkaloids, and investigation of their chemistry still continues with unabated interest. It was soon found that these alkaloids are usually very complicated in structure; the molecule of morphine contains 40 atoms, that of strychnine 47, each of which has its definite place in relation to the others. To reveal the inner architecture of these complicated systems through different chemical operations is a task as difficult as it is fascinating. It requires great experimental skill, creative power and sharp logic. In this sphere of alkaloid research, Sir Robert stands out as our foremost contemporary. He has solved the riddle of the morphine molecule's structure, in connection with which quite 20 different formulae have been under consideration, he has clarified the essential features of the strychnine formula, even though some details are still uncertain, and he has made decisive contributions towards the investigation of many other alkaloids with strangely sounding names like gnoscopine, harmaline, physostigmine, and rutaecarpine.

It has often been asked how plants build up these singular molecules. Here, Sir Robert has formed a theory which rests upon the amino-acids contained in proteins, and which seems to present a satisfactory answer to the question. The theory is illustrated by Sir Robert's famous synthesis of tropinone, a substance closely related to cocaine. We have here a case where three rather simple molecules spontaneously unite into a complicated system, which earlier we could only build up step by step through a long series of reactions. We may suppose that here Sir Robert has found the key to nature's own way of working. This theory has also gained great importance as a guide when determining intricate structures, and it has rendered it possible to trace hidden connections within the multifarious group of alkaloidal substances.

The tendency in natural science tends more and more to the removal of the traditional boundaries between the different sciences. The sum of total knowledge constantly increases, human intellect, however, is limited and cooperation therefore becomes a matter of necessity. For the individual scientist it becomes a difficult task to broaden and deepen his science on its own particular basis without turning his back upon productive collaboration. Perhaps this is felt particularly in chemistry; it is there that the threads of research into life and matter run together, and thus chemistry has acquired a key position within the natural science of to-day. Sir Robert has solved the problem with great success. He has devoted his life to organic chemistry, but the importance and the consequences of his work extend far into the fields of biological and medicinal research.

Professor Sir Robert Robinson. The intricate problems of organic structure are not of a nature to attract the interest of the general public. Our science is an exclusive one. You have not gained your scientific reputation by startling discoveries, which, like the atomic fission, resound in the columns of the daily press.

By your very important and very numerous investigations, you have gradually changed our ideas on fundamental questions. As a student of molecular architecture you have, with eminent success, pursued the line of work emerging from Kekulé and Couper, and you have thrown light upon the formation of complicated structures within the living plant. Among organic chemists, you are to-day acknowledged as a leader and a teacher, second to none. In recognition of your services to Science, the Royal Academy has decided to bestow upon you the Nobel Prize for Chemistry for your investigations on plant products of biological importancc and especially for your outstanding work on the structure and the biogenesis of complicated alkaloids.

Sir Robert. On behalf of the Academy, I request you to receive your prize from the hands of His Majesty the King.