Happy St. Patrick's Day!

 

Niall Nóigiallach is a very famous man (Nóigiallach is Gaelic for "having Nine Hostages"). He was an Irish King who lived from about 350 to 405 AD. The "nine hostages" refers to hostages that he kept from each of the places that owed him allegiance.

Niall was fond of raiding the coast of Roman Britain and on one of those raids he captured a man named Maewyn Succat, who became a slave in Ireland. Succat eventually escaped, returned to Britain, and became a Christian missionary. He then went back to Ireland to convert the Irish heathens to Christianity. We know Maewyn Succat by his Christian name, Patrick, or Saint Patrick.

Aside from converting the Irish heathens to Christianity, St. Patrick is famous for his skill as a magician. One of his most famous tricks was removing all the snakes from Ireland. At least that's what the legend says.

Connie Barlow describes A St. Patrick's Day Parable.(This is the same Connie Barlow I met last summer—the one who edited Evolution Extended.)

Ireland is a land of no snakes. It has no slithering serpents. There are no rat snakes in Ireland; there are no rattlesnakes; there are no garter snakes. There are no snakes at all.

The absence of snakes in Ireland seems to cry out for an explanation — but only if one regards or ventures to the island from outside: from England, say, or from continental Europe. To the indigenous Celts, there would, of course, have been nothing to explain. The Gaelic peoples no more needed to explain an absence of snakes on their island home than they needed to explain an absence of kangaroos. To those who came to Ireland from abroad, however, a dearth of serpents was a striking anomaly in need of an answer.

We humans must have answers. And so arose the legend of St. Patrick and the snakes. The reason Ireland has no snakes, the story goes, is that Patrick charmed all snakes on the island to come down to the seashore, slither into the water, and drown. So Ireland did once have snakes, but it has them no more. Patrick charmed them all into the sea.

She goes on to explain why there are no snakes in Ireland but I prefer to swtich to the website of the Smithsonian National Zoological Park for their explanation of Why Ireland Has No Snakes.

Now snakes are found in deserts, grasslands, forests, mountains, and even oceans virtually everywhere around the world. Everywhere except Ireland, New Zealand, Iceland, Greenland, and Antarctica, that is.

One thing these few snake-less parts of the world have in common is that they are surrounded by water. New Zealand, for instance, split off from Australia and Asia before snakes ever evolved. So far, no serpent has successfully migrated across the open ocean to a new terrestrial home. As the world's oceans have risen and fallen over the millennia, land bridges have come and gone between Ireland, other parts of Great Britain, and the European mainland, allowing animals and early humans to cross. However, any snake that may have slithered it's way to Ireland would have turned into a popsicle when the ice ages hit.

The most recent ice age began about three million years ago and continues into the present. Between warm periods like the current climate, glaciers have advanced and retreated more than 20 times, often completely blanketing Ireland with ice. Snakes, being cold-blooded animals, simply aren't able to survive in areas where the ground is frozen year round. Ireland thawed out for the last time only 15,000 years ago. Since then, 12 miles of icy-cold water in the Northern Channel have separated Ireland from neighboring Scotland, which does harbor a few species of snakes. There are no snakes in Ireland for the simple reason that they can't get there.

[The book cover is from a book by Sheila MacGill Callahan (Author) and Will Hillenbrand (Illustrator). You can buy it on Amazon.com.]

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Reposted from St. Patrick Banished Snakes from Ireland with a snippet from Niall Nóigiallach - Niall of the Nine Hostages. You find out how Irish I am by clicking here.

You Can Be Good Without God

 
I spotted this ad at the Queen's Park subway station in Toronto.

Kudos to the Humanist Association of Canada.

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NSERC President Praises Gary Goodyear

 
Gary Goodyear is Canada's Minister of State (Science and Technology). His government has just cut funding of basic research grants by $148 million over the next three years. Gary Goodyear is a chiropractor and he may be a creationist.

So, what does the President of NSERC think of this? See the [press release].

OTTAWA — Prime Minister Stephen Harper ventured into the lion's den Monday, defending his government's record on science funding before some of the country's top researchers.

He emerged without a scratch.

Indeed, he actually basked in praise for Gary Goodyear, his minister of state for science and technology.

Goodyear has been much maligned by some scientists who maintain research was shortchanged in the Jan. 27 federal budget. But there was no criticism Monday at an awards ceremony for the winners of prestigious research prizes handed out by the federally funded Natural Sciences and Engineering Research Council.

"It has been a real pleasure for us to work with the Hon. Gary Goodyear," said NSERC president Suzanne Fortier.

"He has already proven himself a champion of the science and technology community."

I know some people who would disagree with Suzanne Fortier. Two representatives of the Canadian Association of University Teachers (CAUT) didn't have such a favorable impression [When Chiropractors Get Angry ....].

Some people would argue that. as a kind of public servant, the President of NSERC should not criticize government policy. Perhaps, but that doesn't mean she has to suck up to the executioner.

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[Photo Credit: NSERC]

Does Canada's Science Minister Accept Evolution?

You might think that's a silly question. How could anyone in Canada become Minister of State (Science and Technology) and not accept the most important scientific fact in biology? Yes, it's true that Gary Goodyear is a chiropractor but he can't also be a creationist, can he?

Apparently he can, according to The Globe and Mail [Minister won't confirm belief in evolution].

Researchers aghast that key figure in funding controversy invokes religion in science discussion

Canada's science minister, the man at the centre of the controversy over federal funding cuts to researchers, won't say if he believes in evolution.

“I'm not going to answer that question. I am a Christian, and I don't think anybody asking a question about my religion is appropriate,” Gary Goodyear, the federal Minister of State for Science and Technology, said in an interview with The Globe and Mail.

A funding crunch, exacerbated by cuts in the January budget, has left many senior researchers across the county scrambling to find the money to continue their experiments.

Some have expressed concern that Mr. Goodyear, a chiropractor from Cambridge, Ont., is suspicious of science, perhaps because he is a creationist.

We are in far worse trouble than I thought. No wonder the Stephen Harper party is cutting back on basic research. They must think most researchers are really stupid for believing in all those silly theories like evolution.

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Monday's Molecule #112

 
You may have noticed that today's molecule isn't a molecule. Your task is to identify what this equation is describing.

There's only one Nobel Laureate whose discovery is relevant.

The first person to identify the equation and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are six ineligible candidates for this week's reward: James Fraser of the University of California, Berkeley, Guy Plunket III from the University of Wisconsin, Deb McKay of Toronto, Maria Altshuler of the University of Toronto, David Schuller of Cornell University and Adam Santoro of the University of Toronto

A previous winner has offered to donate a free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours.

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Casey Luskin on Junk DNA and Junk RNA

 
Intelligent Design Creationists can't abide junk DNA. Its very existence refutes the idea that living things are designed by some intelligent being. This is why the IDiots go out of their way to make up stories "disproving" junk DNA.

The latest attempt is by Casey Luskin [Nature Paper Shows "Junk-RNA" Going the Same Direction as "Junk-DNA"]. Having failed to explain why half of the human genome is composed of defective transposons, he now pins his hope on the idea that most of the genome is transcribed. Luskin seems particularly upset by my statement that most of these transcripts are junk [Junk RNA].

Luskin thinks that a recent paper in Nature supports his view that a large fraction of the genome isn't junk. The paper by Guttman et al. (2009) says no such thing. Here's the important part ...

Genomic projects over the past decade have used shotgun sequencing and microarray hybridization1, 2, 3, 4 to obtain evidence for many thousands of additional non-coding transcripts in mammals. Although the number of transcripts has grown, so too have the doubts as to whether most are biologically functional5, 6, 13. The main concern was raised by the observation that most of the intergenic transcripts show little to no evolutionary conservation5, 13. Strictly speaking, the absence of evolutionary conservation cannot prove the absence of function. But, the markedly low rate of conservation seen in the current catalogues of large non-coding transcripts (<5% of cases) is unprecedented and would require that each mammalian clade evolves its own distinct repertoire of non-coding transcripts. Instead, the data suggest that the current catalogues may consist largely of transcriptional noise, with a minority of bona fide functional lincRNAs hidden amid this background. Thus, to expand our understanding of functional lincRNAs, we are faced with two important challenges: (1) identifying lincRNAs that are most likely to be functional; and (2) inferring putative functions for these lincRNAs that can be tested in hypothesis-driven experiments.

In other words, most of the transcripts are probably transcriptional noise, or junk, just as I said. This is the consensus opinion among informed¹ molecular biologists.

Guttman et al. wanted to identify the small subset that might be functional. They identified 1,675 transcripts that show evidence of conservation. The average transcript has six exons averaging 250 bp. Thus, each transcript has about 1500 bp. of conserved exon sequence.

Even if every single one of these lincRNAs have a biological function they will only account for 1675 × 1500 = 2.5 million bp. This represents less than 0.1% of the genome. Casey Luskin ain't gonna disprove junk DNA using this paper.

Luskin ends his article with ...

As an ID proponent, I'm still waiting for Darwinists to let go of their precious "junk" arguments for blind evolution and common descent and learn the lesson that you can't assume that if we don't yet see function for a biomolecule, then it's probably just "junk."

This is a point of view that creationists share with many scientists who haven't studied the subject. They assume that the only reason for labeling most of our DNA junk is because we don't know what it does. That's just not true. There's plenty of good evidence that most of our genome can't be functional. We know a lot about the part that consists of transposons and defective transposons, for example [Junk in Your Genome: SINES and Junk in your Genome: LINEs]. That's 44% of our genome.

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1. I added the qualifier "informed" after a commenter pointed out that most molecular biologists probably don't know enough about the topic to have an opinion. Thus, according to this commenter, the consensus opinion would be "I don't know."

Science Cannot Fully Describe Reality, Says Templeton Prize Winner

 
Shocking news: the winner of this year's Templeton Prize says that science isn't everything. He proposes a way to reconcile science and religion [Science Cannot Fully Describe Reality, Says Templeton Prize Winner].

The only shocking thing about this is that Science magazine treats it seriously. Don't they know what the Templeton Prize is for? It's for people who advocate reconciliation between science and religion.

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Censorship at Uncommon Descent

 
Barry Arrington posted this message on Uncommon Descent.

The moderation policy does not apply to you; you are held to a higher standard. I expect your posts to have at least some tangential relationship to Darwinism, ID, or the metaphysical or moral implications of each. The purpose of this site is not to provide a place for you to jump up and rant on one of your pet peeves. DaveScot will no longer be posting at UD.

What in the world did DaveScot do to deserve this?

He posted an article pointing out that religious people were often racist. He challenged the current dogma on Uncommon Descent that was trying to link Darwin to racism. You can read it here but you won't find it at Racism Sans Darwin - other inspirations on Uncommon Descent. Here's an excerpt ...

Since we now seem to be focused on racism instead of design detection and my motto is “When in Rome do as the Romans do” in order to balance the picture of the theory of evolution’s role in racist movements let’s look at some of the other modern history where evolution isn’t the banner around which racists rally.

Selected bits from Religious Tolerance on Christian Identity Movements . Timothy McVeigh, for instance, was a card carrying CIM member.

History:

The Christian Identity movement is a movement of many extremely conservative Christian churches and religious organizations, extreme right wing political groups and survival groups. Some are independent; others are loosely interconnected. According to Professor Michael Barkun, one of the leading experts in the Christian Identity movement, “This virulent racist and anti-Semitic theology, which is practiced by over 50,000 people in the United States alone, is prevalent among many right wing extremist groups and has been called the ‘glue’ of the racist right.”

The largest Christian Identity movement has traditionally been the Ku Klux Klan which was reorganized in 1915 by William Simmons, a Christian pastor. He had been inspired by the film The Birth of a Nation which portrayed the KKK as a champion of white civilization. The KKK slid into obscurity by the second World War, but was revitalized in the mid 1950’s as a reaction to enforced racial integration in the southern US.

I guess the IDiots at Uncommon Descent don't want anyone to distract from their "Darwin was a racist" campaign.

DaveScot was a big fan of Expelled I wonder if he'll complain to Ben Stein?

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[Hat Tip: Afarensis]

What's Up with New Scientist?

 
Amanda Gefter wrote a nice article in New Scientist pointing out the sneaky tricks that creationists use to discredit science. You can read the article here.

As a book reviews editor at New Scientist, I often come across so-called science books which after a few pages reveal themselves to be harbouring ulterior motives. I have learned to recognise clues that the author is pushing a religious agenda. As creationists in the US continue to lose court battles over attempts to have intelligent design taught as science in federally funded schools, their strategy has been forced to... well, evolve. That means ensuring that references to pseudoscientific concepts like ID are more heavily veiled. So I thought I'd share a few tips for spotting what may be religion in science's clothing.

Red flag number one: the term "scientific materialism". "Materialism" is most often used in contrast to something else - something non-material, or supernatural. Proponents of ID frequently lament the scientific claim that humans are the product of purely material forces. At the same time, they never define how non-material forces might work. I have yet to find a definition that characterises non-materialism by what it is, rather than by what it is not.

Unfortunately, you can't read this article on the New Scientist website because it has been removed. If you click on How to spot a hidden religious agenda you'll find the following message ....

New Scientist has received a complaint about the contents of this story. It has temporarily been removed while we investigate. Apologies for any inconvenience.

I can't imagine a complaint that would cause a respectable magazine to withdraw that article. It sounds like New Scientist isn't standing behind its writers.

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[Hat Tip: PZ Myers]

Shepherd's Pie

 
John Wilkins knows about Real Meat Pies.

Janet Stemwedel has a recipe for Vegetarian Shepherd's Pie.

VEGETARIAN SHEPHERD'S PIE!!!! Gimme a break.

Janet, what do you think those sheps are herding out there in the fields? Tofu?

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The Profzi Scheme

 
This cartoon is making the rounds. It's from PHD Comics.

I've been associated with four universities in my career and I've never seen anything that even remotely resembles this. In my experience, departments recruit outstanding junior faculty who may, or may not, work in a field similar to current faculty members. Usually not. No single Professor makes the decision to recruit new scholars to the department.

In my experience, when funding gets tight it is often the senior faculty members who lose and the productive junior faculty survive. Is my experience that unusual?

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Is the Media Being Responsible about Health Issues?

 
Ben Goldacre is a physician and he doesn't think the media is being responsible. In fact, he thinks they may be complicit in the needless deaths of children. Visit his blog Bad Science and read why he says ... Christ I need a haircut. Then watch this video.

We have a problem with health literacy and science literacy. Professional health journalists and professional science journalists have a choice. They can continue to do nothing and blame the marketplace—in which case they become part of the problem—or they can speak out on behalf of good science—in which case they can become part of the solution.

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[Thanks to Chris Nedin for the link.]

The Taste of Gouda

 
Dutch Gouda cheese has a unique taste (pronounced HOW-dah in the Netherlands but Goo-dah everywhere else). Most of the chemicals that make up this unique taste have been identified. The bitter taste is due to CaCl₂ and MgCl₂ plus various peptides derived from incomplete digestion of milk protein. The sour taste is due to lactic acid and phosphates. The salty taste comes from sodium chloride, sodium phosphate and the amino acid L-arginine. Monosodium l-glutamate and sodium lactate contribute the umami taste. (The five tastes are sweet, salty, sour, bitter and umami.)

Combinations of all these compounds at the appropriate concentrations mimicked the taste of Gouda cheese but something was missing. The "mouthfulness," and the complexity of the mature cheese was not present in the artificial concoctions. The missing taste is called the kokumi sensation.

Theme
A Sense of Smell
Toelstede et al. (2009) have found the missing chemicals. They mostly consist of various γ-L-glutamyl dipetides such as γ-Glu-Glu, γ-Glu-Gly, γ-Glu-Gln, γ-Glu-Met, γ-Glu-Leu, and γ-Glu-His. The structure of γ-Glu-Glu is shown below.

Most people don't realize that peptides and amino acids can impart very powerful tastes. Monosodiun glutamate (MSG) is an obvious example. So is aspartame, a powerful sweetener that's a modified tripeptide (Asp-Phe-Ala methyl ester).

Isn't biochemistry wonderful?


Here's a tough question. Let's say you could identify, with absolute certainty, all the chemicals that make up the taste of Gouda cheese. Let's say you make them in a lab and mix them with tofu and get something that tastes exactly like Gouda cheese. Would there be some people who want to ban that artificial Gouda cheese because it has chemicals? Would those same people be happy to eat the "natural" cheese because it doesn't have chemicals?

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Toelstede, S., Dunkel, A., and Hofmann. T. (2009) A Series of Kokumi Peptides Impart the Long-Lasting Mouthfulness of Matured Gouda Cheese. J. Agric. Food Chem., 2009, 57 (4), pp 1440–1448. [DOI: 10.1021/jf803376d]

Mitotic Recombination

 
It is widely believed that recombination, or crossing over, only occurs at meiosis in diploid eukaryotes. Most textbooks reinforce this belief by associating crossovers with chiasmata, which are only seen at meiosis.

In spite of the textbook claims, most people are well aware of the fact that recombination takes place in somatic cells. After all, it's the basis of most recombinant DNA technology and underlies many of the mechanisms that cause cancer. Furthermore, some developmental processes, such as immunoglobulin gene rearrangements require recombination in somatic cells.

Mitotic recombination has been known to occur since the 1930s when it was used for fate mapping in Drosophila so it's somewhat surprising that crossing over is so intimately connected with meiosis in the textbooks. The frequency of mitotic crossing over may be lower than that seen during meiosis, although the differences may not be great in most species.

In yeast, the frequency of recombination during meiosis can be 10,000 times greater than the frequency of crossing over in somatic cells but that's partly because meiotic recombination is very high in yeast cells. Perhaps they have been selected in vitro for high rates of recombination.

Why does recombination occur in mitotic cells? Probably for the same reason it occurs during meiosis—it's a form of DNA repair.

There's a short review of mitotic recombination in the lastest issue of PLoS Genetics [Mitotic Recombination: Why? When? How? Where?]. Let's try and put an end to the false idea that recombination and crossing over only takes place during meiosis.

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Levels of Selection

 
There's an interesting article in the latest issue of New Scientist. Bob Holmes writes about The selfless gene: Rethinking Dawkins's doctrine.

Evolutionary success is all about looking out for number one - or so most biologists would tell you. The genes that do the best job of passing themselves along to the next generation, whether by brute selfishness or canny cooperation, are the ones that flourish - a view most memorably championed by Richard Dawkins more than 30 years ago in his bestselling book The Selfish Gene.

This relentless focus on the gene may not tell the whole story, however. A small but growing coterie of evolutionary biologists argue that it leaves us blind to crucial evolutionary processes at higher scales - among groups, species and even whole ecosystem. If they are right, the popular view of evolution and the biological world needs a radical shake-up.

Almost everyone agrees that the gene's-eye view works perfectly well most of the time. "It's dominated the field, and dominated for a long time," says Michael Ruse, a philosopher of science at Florida State University in Tallahassee. Indeed, many biologists think the selfish-gene concept can explain all the intricacies thrown up by evolution, and not just the obviously selfish ones.

The article is better than most. It gives an adequate overview of group selection and species selection (sorting).

However, before reading on you should be aware of two false notions that are being perpetuated. First, there's more to evolution than adaptation and selfish genes. Not all genes are selfish and even at higher levels species sorting may occur in the absence of species selection.

Second, the concept of the selfish gene has been very important in evolutionary theory. Far more important, I think, than most people realize. But it is not correct to say that it has dominated the field, or that it's the current dogma. If you consult any evolutionary biology textbook you'll find that "selfish gene" barely gets mentioned. Almost everything is explained by considering the individual organism as the unit of selection. Dawkins has failed to convince any but a handful of evolutionary biologists that the gene perspective is a better way of looking at evolution.

The article closes with ....

It is still too early to know whether group, species and ecosystem-level selection are major evolutionary forces or merely minor curiosities - baroque ornaments on the central edifice of individual or gene-level selection. But the dominance of the "selfish gene" in evolutionary thought is facing its strongest challenge in many years.

This is a good way of putting it. Hierarchical theory is an interesting development and it is making some headway but it's fair to say that most evolutionary biologists don't think of group selection and species selection as major players.

However, the dominant thinking is that it's the individual and not the gene that forms the proper unit of selection. And the greatest challenge to the dominance of selection at the level of the either the gene or the individual is neither group selection or species selection, it's random genetic drift.

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Note: People get confused about the meaning of The Selfish Gene. Just because we talk about population genetics and changing frequencies of alleles does not mean that we are adopting Dawkins' perspective. He explains what he means by "selfish gene" in the opening chapter of The Extended Phenotype.

The thesis that I shall support is this. It is legitimate to speak of adaptations as being "for the benefit of" something, but that something is best not seen as the individual organism. It is a smaller unit which I call the active germ-line replicator. The most important kind of replicator is the "gene" or small genetic fragment. Replicators are not, of course, selected directly, but by proxy; they are judged by their phenotypic effects. Although for some purposes it is convenient to think of those phenotypic effects as being packaged together in discrete "vehicles" such as individual organisms, this is not fundamentally necessary. Rather, the replicator should be thought of as having extended phenotypic effects, consisting of all its effects on the world at large, not just its effects on the individual body in which it happens to be sitting.

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