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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Examples of Accelerated Human Evolution

Gregory Cochran and Henry Harpending claim that human evolution has accelerated in the last 10,000 years. In one sense this has to be correct since the number of humans is increasing exponentially and that means far more mutations are occurring every generation. Many of those new mutations are contributing to a significant increase in variation.

But that's not what they mean. They claim that adaptations have increased. When they talk about accelerated human evolution they are mostly talking about an increase in natural selection.

For those of you who have not read the book, I thought I'd give you some of the examples that feature prominently in the opening chapter.

... when humans hunted big game 100,000 years ago, they relied on close-in attacks with thrusting spears. Such attacks were highly dangerous and physically taxing, so in those days, hunters had to be heavily muscled and have thick bones. That kind of body had its disadvantages—if nothing else, it required more food—but on the whole, it was the best solution in that situation. But new weapons like the atlatl (a spearthrower) and the bow effectively stored muscle-generated energy, which meant that hunters could kill big game without big biceps and robust skeletons. Once that happened, lightly built people, who were better runners and did not need as much food, became competitively superior. A heavy build was yesterday's solution: expensive, but no longer necessary. (p. 3)

With the invention of nets and harpoons, fish became a more important part of the diet in many parts of the world., and metabolic changes that better suited humans to that diet were favored. (p. 4)

Close-fitting clothing provided better protection against cold, allowing people to venture farther north. In cool areas, people needed fewer physiological defenses against low temperatures, while in the newly settled colder regions they needed more such defenses, such as shorter arms and legs, higher basal metabolism, and smaller noses. (p. 4)

With the advent of new methods of food preparation, such as the use of fire for cooking, teeth began to shrink, and they continued to do so over many generations. Pottery, which allowed storage of liquid foods, accelerated that shrinkage. (p. 4)

As the complexity of human speech approached modern levels, there must have been selection for changes in hearing (both changes in the ear and in how the brain processes sounds) that allowed better discrimination of speech sounds. Think of the potential advantages in being just a bit better at deciphering a hard-to-understand verbal message than other people: Eavesdropping can be a life-or-death affair. (p. 4)

... we believe that the obvious difference between racial groups are linked to gene variants that have recently increased in fitness and had major fitness effects. Blue eyes, found only in Europeans and their near neighbors, are a result of a new version of the DNA that controls the expression of OCA2 that has undergone strong selection, at least in Europe. (p. 18)

Dry earwax is common in China and Korea, rare in Europe, unknown in Africa: The gene variant underlying dry earwax is the product of strong recent selection. (p. 18)

We can confidently predict that many (perhaps most) as yet unexplained racial differences are also the product of recent selection. For example, we argue that the epicanthic eyelid found in the populations of northern Asia is most likely the product of strong and recent selection. (p. 18)

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Atheist Buses Will Run in Ottawa

 
Ottawa city council voted last month to ban the atheist ads from OC Transpo buses.¹ Last night they voted 13-7 to allow the ads after city solicitor Rick O'Connor told them the ban is an unreasonable infringement of free speech [City blesses atheist ads].

Transit officials made the decision after receiving four complaints from the public, but O'Connor said in the end the city's argument may not hold up in court.

"Based on the information available at this time, it appears that the city may not be able to justify its refusal of the proposed advertising on the basis that it is offensive, and consequently, it may be found to be an unreasonable infringement of the association's freedom of expression under Section 2(b) of the Charter," the memo says.

"If the decision to refuse the ads was based solely on the four complaints received from the public, it is likely that this decision will be found to be unreasonable and lacking in proportionality, and therefore not justifiable under Section 1 of the Charter."

Thanks to the Humanist Association of Ottawa for standing up for freedom of expression.

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1. Technically, they did not ban the ads. Instead, they failed, in a tie vote, to overturn the decision of OC Transpo. That decision has now been overturned in a second vote and the ads will run.

Teach Your Children Well

 
Chelsea Juman is one of the Intel Baby Nobelist Finalists on the Scientific American website.

According to her study, if you drank underage as a teenager you should never tell your children 'cause, if you do, they'll think it's OK.

Well, it's too late for me but all you young people out there better pay attention. You need to start lying to your children from a very young age. Whatever you do, pretend you never touched a glass of wine or a bottle of beer before you were 21 years old.¹ Don't even think about drugs. Lie through your teeth. That'll make 'em respect you.

As soon as they turn 21 you can take them out to a bar and have a long talk about responsible drinking.

Better not tell them about sex either. Abstinence is the only answer.

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1. If you're an American. If you live in any other country you can tell them you drank when you were much younger—16 in Italy, Germany, or France, for example.

In the Quality of Heatlh Care Journalism

 
A survey of members of the Association of Health Care Journalists (AHCJ) reaches the following conclusions [U of Minnesota professor authors report the state of health care journalism] ....

• Ninety-four percent of survey respondents say the bottom line pressure in media organizations is seriously hurting the quality of news coverage of health care issues
• Forty percent of staff reporters in the survey say the number of health reporters at their organization has gone down since they've been there, and 11 percent say they personally have been laid off over the past few years due to downsizing.
• Thirty-nine percent of respondents who are still in the business believe it is at least somewhat likely that their position will be eliminated in the next few years
• Nearly nine in ten (88 percent) survey respondents think health care coverage leans too much toward short "quick hit" stories, and two-thirds (64 percent) say the trend toward shorter stories has gotten worse in the past few years
• A majority of respondents (52 percent) say there is too much coverage of consumer or lifestyle health, and too little of health policy (70 percent), health care quality (70 percent) and health disparities (69 percent)

So, the quality of health care journalism has declined. This isn't earth shattering news.

I bet that 100% of health care journalists will say that it's not their fault.¹

"Real" science journalists are different. Most of them say they are doing a terrific job and the bad science reporting is all due to other journalists writing about science.

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1. Of course it's not all their fault but when a bad health care article gets published you can't blame it all on the editors.

On the Demise of Religion

 
Michael Spencer writes about The coming evangelical collapse in The Christian Science Monitor.

We are on the verge – within 10 years – of a major collapse of evangelical Christianity. This breakdown will follow the deterioration of the mainline Protestant world and it will fundamentally alter the religious and cultural environment in the West.

Within two generations, evangelicalism will be a house deserted of half its occupants. (Between 25 and 35 percent of Americans today are Evangelicals.) In the "Protestant" 20th century, Evangelicals flourished. But they will soon be living in a very secular and religiously antagonistic 21st century.

This collapse will herald the arrival of an anti-Christian chapter of the post-Christian West. Intolerance of Christianity will rise to levels many of us have not believed possible in our lifetimes, and public policy will become hostile toward evangelical Christianity, seeing it as the opponent of the common good.

Millions of Evangelicals will quit. Thousands of ministries will end. Christian media will be reduced, if not eliminated. Many Christian schools will go into rapid decline. I'm convinced the grace and mission of God will reach to the ends of the earth. But the end of evangelicalism as we know it is close.

I agree with him but I think he's mistaken if he thinks that belief in God will survive the collapse of the evangelical right.

Evangelical Christianity is in trouble because its very core is being challenged, not because of its association with old-fashioned morality.

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[Hat Tip: RichardDawkins.net]