Intelligent Design Creationists and Lateral Gene Transfer

 
Some of you might recall an article in Nature Physics published a few weeks ago [Collectivist Revolution in Evolution]. In that article, Mark Buchanan, a physicist, mentioned that biologists were questioning the tree of life.

Buchanan gets so many things wrong I hardly knew where to begin. So, when I blogged about it I just mentioned one thing [Lateral Gene Transfer and the Return of Lamarckian Evolution]. I concluded with ...

This kind of hyperbole is not helpful. Shame on Nature Physics for publishing it.

As expected, the creationists—intelligent and otherwise—were delighted with this latest challenge to evolution. I doesn't matter to them whether a physicist knows what he's talking about.

One of the "otherwises" is named Denyse O'Leary. She's happy to promote the idea that evolution¹ is being challenged. It's a special thrill for her to discover that biology is being questioned in a physics journal [The overthrow of Darwinism - in real life, forget the pop science media].

Denyse doesn't do any of the intellectual heavy lifting (surprise!). Instead she links to another Intelligent Design Creationist named David Tylor. Tylor is also mesmerized by the Nature Physics article. He blogged about it at: The collectivist challenge to Darwinism.

Here's part of what he said ...

Talk of unseating Darwinian evolution has not gone down well with some. Larry Moran quotes some of Buchanan's visionary words and declares: "This kind of hyperbole is not helpful. Shame on Nature Physics for publishing it." However, we could do with more substance in arguments against this essay. Darwinism is inherently reductionistic and it can devise ways of framing HGT to fit into its own mental models. But what it cannot easily do is adopt the holistic perspectives that are emerging everywhere. This is why some of us find a framework of design to be compelling. Design provides a coherent context for systems biology, for biomimetics, and for many other contemporary areas of research. Furthermore, although our understanding of HGT is imperfect and in its infancy, design thinking provides a warrant for inferring the origin of genes capable of being transferred, and for understanding the roles played by HGT in populations.

Where to begin?

Horizontal gene transfer (HGT, also known as Lateral Gene Transfer) has been studied for six decades. We have an excellent understanding of the mechanisms; namely, transformation, transduction, conjugation, fusion, and endosymbiosis. There's nothing new there.

"Darwinism" and "Darwinian evolution" are products of the nineteenth century. The only people who are stuck in that century are the creationists. Modern evolutionary biologists have been at the forefront of "holistic" approaches since the recognition that populations evolve, not individuals. For most biologists, this happened in the 1940s. To put this into perspective, that's at least sixty years ago, or 1% of the entire history of Earth!

I'm actually quite happy to promote the "unseating [of] Darwinian evolution" as anyone who reads Sandwalk will attest. David Taylor and Denyse O'Leary are completely incapable of recognizing that legitimate challenges to the old-fashioned way of thinking about evolution are now part of mainstream biology. In fairness, what can we expect from people who think that a 2500 year old book written in Hebrew, Aramaic, and Greek still contains relevant information about science?

"Design" fails to provide a coherent context for anything. I've yet to see anyone explain how and when God intervened to create modern life.

Finally, in case David Tylor is actually interested in learning about the science he criticizes, here's a list of recent postings on the topic. I'd be happy to debate him whenever he feels ready. I'd be happy to do it on The ID Update: News and Commentary Updates for the ID Community but that blog doesn't allow comments. Isn't that strange?

1. The Tree of Life
2. Perspectives on the Tree of Life: Ford Doolittle
3. Perspectives on the Tree of Life: Day One
4. Perspectives on the Tree of Life: Day Two
5. Perspectrives of the Tree of Life: Day Three
6. On the Origins of Eukaryotes

---

1. She calls it "Darwinism," just like all the other IDiots.

Creationists Made Him Do It!

 
A reader¹ alerted me to a letter by Patrick J. Keeling in the latest issue of Science: Creationists Made Me Do It.

He tells a story about hearing creationists speak in his high school biology class. What was the effect of this indoctrination? ...

For at least one sulky teenager in the small town of Owen Sound, Ontario, it took a creationist to make him into an evolutionary biologist.

This is one of the reasons why exposing high school students to the IDiots should be encouraged, not banned. They are their own worst enemy.

---

1. Thank-you Grace.

Anne Wojcicki's Politically Correct View of Race

 
Anne Wojcicki is the co-founder of "23andMe" a company that will analyze your DNA for a fee. She was recently interviewed and the results are posted on the New York Times website [Genetics Entrepreneur Anne Wojcicki Answers Your Questions].

One of the questions asked about "race." Here's her reply.

A lot of the difficulty in talking about race has been a lack of agreement on what “race” means. In the past, the idea of pure races also included an ordering of certain races as inherently superior to others. We reject this idea absolutely. However, that doesn’t mean that there are no genetic differences between populations of different ancestral origin. A few of our features use the genome-wide data of reference populations from around the world to trace the origin of pieces of an individual’s genome. Some customers have complex patterns depending on where their ancestors originated. These reference populations aren’t “races”; they’re representative samples of peoples who have lived in a single place for a very long time and have thus accumulated different sets of genetic variants over time.

John Hawks noticed this and blogged about it: Modern genomics and race. He said exactly what I was thinking ...

That's a tricky piece of wordcraft -- they're not 'races'; "they're representative samples of peoples who have lived in a single place for a very long time and have thus accumulated different sets of genetic variants over time."

Uhh....I'm thinking that's pretty much the definition of race in a lot of textbooks...

Most species are subdivided into races (also called subspecies, or demes).

Humans are not an exception. Races exist. Pretending that they don't isn't going to solve the problems of racism. It just makes you look stupid.

---

The Evolution of Man Scientifically Disproved

 
When David Schuller came to visit me a couple weeks ago he brought me a special present. It was a book he found in a bookstore. Dated 1925, the title is, The Evolution of Man Scientifically Disproved. The author is the Rev. William A. Williams formerly the president of Franklin College. I thought it might be interesting to present one of his “disproofs” of evolution.

You may think it unfair to dredge up a defense of creationism based on a 84 year old book. It’s not unfair because I’m using the same standards that the creationists use when they talk about “Nebraska Man” and the Scopes trial, not to mention Charles Darwin and Ernst Haeckel. It’s clear that 1925 is “modern science” from their perspective.

Furthermore, the arguments of Rev. Williams aren’t any worse than the ones used in 2009! The title page makes it clear that this is the best that creationists have to offer.

Designed. (1) As an up-to-date text book, and a companion to all other text books on evolution; and

(2) As an antidote to books in libraries teaching evolution, infidelity and atheism; and

(3) As an aid to all students, parents, teachers, ministers, lawyers, doctors, and all other lovers of the truth.

Rev. Willimas begins with a discussion of the population of the world.

The population of the world, based upon the Berlin Census reports of 1922, was found to be 1,804,187,000. The human race must double itself 30.75 times to make this number. This result may be approximately ascertained by the following computation:—

At the beginning of the first period of doubling there would just be two human beings; the second, 4; the 8, eight; the fourth, 16; the tenth, 1024; the twentieth, 1,048,576, the thirtieth, 1,073,741,824; and the thirty-first, 2,147,483,648. In other words, if we raise two to the thirtieth power, we have 1,073,741,824; or to the thirty-first power, 2,147,483,648. Therefore, it is evident even to the school boy, that, to have the present population of the globe, the net population must be doubled more than thirty times, and less than thirty-one times. By logarithms, we find it to be 30.75 times. After all allowances are made for natural deaths, wars, catastrophes, and losses of all kinds, if the human race would double its numbers 30.75 times, we would have the present population of the globe.

Now, according to the chronology of Hales, based on the Septuagint text, 5077 years have elapsed since the flood, and 5177 years since the ancestors of man kind numbered only two, Noah and his wife. By dividing 517 7 by 30.75, we find it requires an average of 168.3 years for the human race to double its numbers, in order to make the present population. This is a reasonable average length of time.

Moreover, it is singularly confirmed by the number of Jews, or descendants of Jacob. According to Hales, 3850 years have passed since the marriage of Jacob. By the same method of calculation as above, the Jews, who according to the Jewish yearbook for 1922, number 15,393,815, must have doubled their numbers 23.8758 times, or once every 161.251 years. The whole human race, therefore, on an average has doubled its numbers every 168.3 years; and the Jews, every 161.251 years. What a marvelous agreement! We would not expect the figures to be exactly the same no more be greatly surprised if one period were twice the other. But their correspondence singularly corroborates the age of the human race and of the Jewish people, as gleaned from the word of God by the most proficient chronologists. If the human race is 2,000,000 years old, the period of doubling would be 65,040 years, or 402 times that of the Jews, which, of course, is unthinkable

While the period of doubling may vary slightly in different ages, yet there are few things so stable and certain as general average, where large numbers and many years are considered, as in the present case. No life insurance company, acting on general average statistics, ever failed on that account. The Jews and the whole human race have lived together the same thirty-eight centuries with very little intermarriage, and are affected by similar advantages and disadvantages, making the comparison remarkably fair.

Also the 25,000,000 descendants of Abraham must have doubled their numbers every 162.275 years, during the 3,988 years since the birth of his son Ishmael. These periods of doubling which tally so closely, 168.3 years for the whole race, 161.251 for the Jews, and 162.275 years for the descendants of Abraham, cannot be a mere coincidence, but are a demonstration against the great age of man required by evolution, and in favor of the 5,177 years since Noah. None of the other various chronologies would make any material difference in these calculations. The correspondence of these figures, 168.3, 161.251 and 162.275 is so remarkable that it must bring the conviction to every serious student at the flood destroyed mankind and Noah became the head of the race.

Now the evolutionists claim that the human race is 2,000,000 years old. There is no good reason for believing that, during all these years the developing dominant species would not increase as rapidly as Jews, or the human race in historic times, especially since the restraints of civilization and marriage did not exist. But let us generously suppose that these remote ancestors, beginning with one pair, doubled their numbers in 1612.51 years, one-tenth as rapidly as the Jews, or 1240 times in 2,000,000 years. If we raise 2 to the 1240th power, the result is 18,932,139,737,991 with 360 figures following. The population of the world, therefore, would have been 18,932,139,737,991 decillion, decillion, decillion, decillion, decillion, decillion, decillion, decillion, decillion, decillion, decillion, or 18,932,139,737,991 vigintillion, vigintillion, vigintillion, vigintillion, vigintillion/

Or, let us suppose that man, the dominant species originated from a single pair, only 100,000 years ago, the shortest period suggested by any evolutionists (and much too short for evolution) and that the population doubled in 1612.51 years, one-tenth the Jewish rate of net increase, a most generous estimate. The present population of the globe should be 4,660,210,253,138,204,300 or 2, 527,570,733 for every man, woman and child! In these calculations, we have made greater allowances than any self-respecting evolutionist could ask without blushing. And yet withal, it is as clear as the light of day that the ancestors of man could not possibly have lived 2,000,000 or 1,000,000 or 100,000 years ago, or even 10,000 years ago; for if the population had increased at the Jewish rate for 10,000 years, it would be more than two billion times as great as it is. that has ever been made, or ever can be made, much in excess of 5177 years, can possibly stand as the age of man. The evolutionist cannot sidestep this argument by a new guess. Q. E. D.

All these computations have been made upon the supposition that the human race sprang from one pair. If from many in the distant past, as the evolutionists assert, these bewildering figures must be enormously increased.

Yet we are gravely told that evolution is "science". It is the wildest guess ever made to support an impossible theory.

That their guesses cannot possibly be correct, is proven also by approaching the subject from another angle. If the human race is 2,000,000 years old, and must double its numbers 30.75 times to make the present population, it is plain that each period for doubling would be 65,040 years, since 2,000,000 ÷ 30.75 = 65,040. At that rate, there would be fewer than four Jews! If we suppose the race to have sprung from one pair 100,000 years ago, it would take 3252 years to double the population. At this rate, there would be five Jews!

Do we need any other demonstration that the evolution of man is an absurdity and an impossibility? If the evolutionists endeavor to show that man may have dissented from the brute, the population of the world conclusively shows that MAN CERTAINLY DID NOT DESCEND FROM THE BRUTE. If they ever succeed in showing that all species of animals may have been derived from one primordial germ, it is impossible that man so came. He was created as the Bible declares, by the Almighty Power of God.

The testimony of all the experts in the present Scopes trial in Tennessee (who escaped cross-examination) was to the effect that evolution was in harmony with some facts and therefore possibly true. The above mathematical calculations prove that the evolution of man certainly not true. They fail to make their case even if we grant their claims. These figures prove the Bible story, and scrap every guess of the great age and the brute origin of man. It will be observed at the above calculations point to the unity of the race in the days of Noah, 5177 years ago, rather than in the days of Adam 7333 years ago, according to Hale's chronology. If the race increased at the Jewish rate, not over 16,384 perished by the Flood, fewer then by many a modern catastrophe. This most merciful providence of God started the race anew with a righteous head.

Now, if there had been no flood to destroy the human race, then the descendants of Adam, in the 7333 years, would have been 16,384 times the 1,804,187,000, or 29,559,799,808,000; or computed the Jewish rate of net increase for 7333 years since Adam, the population would have been still greater, or 35,184,372,088,832. These calculations are in perfect accord with the Scripture story of the special creation of man, and the destruction of the race by a flood. Had it not been for the flood, the earth could not have sustained the descendants of Adam. Is not just a demonstration, decisive and final?

---

A List of Banned Words

 
Carl Zimmer is teaching a course on science writing. Here's a picture of his classroom.

It's a tough job, but somebody has to do it.

Carl has banned certain words and phrases and he posted the list on his blog: The Index of Banned Words. We can all agree that "breakthrough" and "paradigm shift" must be on the list. What about the others? Share your opinion on The Loom.

I'd like to add "Darwinism," "cancer" (unless the article is actually about cancer), and "revolutionary."

---

A Science Literacy Test

 
I missed this Scientific Literacy Quiz that appeared in The Toronto Star last week.

Fortunately Postdiluvian, a med student at the University of Toronto, found it and blogged about it on The Unexamined Life: Science literacy quiz. He didn't say how many he got right. I'm not saying either except to reveal that it was fewer than 26.

Most of the questions are pretty good but one of them is wrong and a couple could have been better worded.

---

Tracking a Press Release

 

David Hone recently published a paper on theropod behavior [see: Baby killers: hunting and feeding behaviours of large theropods].

When the paper came out he made up a press release that he distributed to a bunch of people. He tracked the number of articles that picked up on his press release. Initially there was only one report in the media, then five, then twenty [Media tracking].

He was generally satisfied with the articles that appeared but some of his complaints are interesting ...

This leads us onto the next point here. The press release was often regurgitated in very large and near complete chunks. Now that is part of what it is for of course, but equally I would hope that part of their job would be to give it a bit of a literary polish (since they are, you know, writers) and make it a bit more accessible to the public. If not, then the press might as well just publish the press release in full and save themselves a bunch of money on reporters. On the other had, most of them did add in new introductory paragraphs and needless to say this is where the errors mostly came in. So they either copied stuff without writing anything new, or wrote a couple of paragraphs that they got wrong. Really how hard is to check up on a couple of dinosaur facts (one could contact the authors for example) when already 80% of the article is written for you and you don’t have to read the paper itself? Remember that these are supposed to be not just journalists but science reporters and fact checking (especially from a published paper) should be first nature, let alone second nature and is hardly difficult or even especially time consuming, no matter the deadline.

I've never heard of a scientist who makes the effort to personally advertise a paper that's just been published. Usually it's the institution who sends out the press releases and they go directly to the various wire services who specialize in science stories.

I must admit that the concept of publicizing your own work troubles me a bit.

---

[Hat Tip: Panda's Thumb]

Advice for Scientists on How to Communicate

 
Carl Zimmer is an excellent science writer. He reviews three books directed at scientists on how they should communicate science to the general public. Two of the books are by science writers and the third is by a former biologist who is now a filmmaker in Hollywood.

Part of Carl's review is on his blog: Book [P]review: For The Scientist.

Three books are coming out this year directed at these scientists. Unscientific America: How Scientific Illiteracy Threatens our Future, by my fellow Discobloggers Sheril Kirshenbaum and Chris Mooney, was the first. I talked to Chris about the book in this Bloggingheads talk. Cornelia Dean of the New York Times is publishing another, called Am I Making Myself Clear?: A Scientist’s Guide to Talking to the Public. It’s a lean, straightforward tour of the media landscape, led by a journalist who has written about science for many years.

The third is by a scientists–but it’s called Don’t Be Such a Scientist: Talking Substance in an Age of Style. The author is Randy Olson, a biologist who headed to Hollywood. Back in 2006, I wrote about his documentary, Flock of Dodos–which was his own response to the events in Kansas. Rather than post a statement on a web site, Olson made a funny movie that not only demonstrated the flim-flammery of creationists, but also showed how dismally evolutionary biologists communicated to those beyond their guild.

All advice is valuable but I'd just like to make sure that everyone keeps things in perspective.

The major goal of science writers is to communicate science to the general public. That's what their profession is all about. If we have not been successful at communicating science properly over the past few decades then isn't it reasonable to put some of the blame on the professionals?

Just out of curiosity, have there been many books written by science writers where they criticize their profession and give advice to fellow science writers on how to improve their science communication skills? Or, have science writers decided that it should be scientists, and not science writers, who need to correct the failures of the past?

---

Nobel Laureates: Peter Doherty and Rolf Zinkernagel

 

The Nobel Prize in Physiology or Medicine 1966

"for their discoveries concerning the specificity of the cell mediated immune defence"

Peter C. Doherty (1949 - ) and Rolf M. Zinkernagel (1940 - ) won the Noble Prize in 1996 for their work on the mechanism of cellular immunity (cell-mediated immunity). They were the ones who figured out how T-cells can recognize and kill cells that are infected with a virus.

This is part of the modern era of Nobel Prize awards where the Nobel Foundation is doing a wonderful job of explaining the awards to a scientifically literate general public. Here's the 1996 Press ReleaseTHEME:
Nobel Laureates

Summary

Peter Doherty and Rolf Zinkernagel have been awarded this year's Nobel Prize in Physiology or Medicine for the discovery of how the immune system recognizes virus infected cells. Their discovery has, in its turn, laid a foundation for an understanding of general mechanisms used by the cellular immune system to recognize both foreign microorganisms and self molecules. This discovery is therefore highly relevant to clinical medicine. It relates both to efforts to strengthen the immune response against invading microorganisms and certain forms of cancer, and to efforts to diminish the effects of autoimmune reactions in inflammatory diseases, such as rheumatic conditions, multiple sclerosis and diabetes.

The two Nobel Laureates carried out the research for which they have now been awarded the Prize in 1973-75 at the John Curtin School of Medical Research in Canberra, Australia, where Peter Doherty already held his position and to which Rolf Zinkernagel came from Switzerland as a research fellow. During their studies of the response of mice to viruses, they found that white blood cells (lymphocytes) must recognize both the virus and certain self molecules - the so-called major histocompatibility antigens - in order to kill the virus-infected cells. This principle of simultaneous recognition of both self and foreign molecules has since then constituted a foundation for the further understanding of the specificity of the cellular immune system.

The background to the Laureates' research

The immune system consists of different kinds of white blood cells, including T- and B- lymphocytes whose common function is to protect the individual against infections by means of eliminating invading microorganisms and infected cells. At the same time they must avoid damaging the own organism. What is required is a well developed recognition system that enables lymphocytes to distinguish between on the one hand microorganisms and infected cells, and on the other, the individual´s normal cells. In addition, the recognition system must be able to determine when white blood cells with a capacity to kill should be activated.

In the early 1970s when Peter Doherty and Rolf Zinkernagel had begun their scientific work within immunology, it was possible to distinguish between antibody-mediated and cell- mediated immunity. It was known that antibodies that are produced by B-lymphocytes are able to recognize and eliminate certain microorganisms, particularly bacteria. Far less was known about recognition mechanisms in the cellular immune system, for instance in conjunction with the killing of virus-infected cells by T-lymphocytes. One area where cellular immunity had previously been studied in some detail was, however, transplantation biology. It was known that T-lymphocytes could kill cells from a foreign individual after recognition of certain molecules - the major histocompatibility antigens - in the transplant.

The discovery

Rolf Zinkernagel and Peter Doherty used mice to study how the immune system, and particularly T -lymphocytes, could protect animals against infection from a virus able to cause meningitis. Infected mice developed killer T-lymphocytes, which in a test-tube could kill virus- infected cells. But there was an unexpected discovery: the T-lymphocytes, even though they were reactive against that very virus, were not able to kill virus-infected cells from another strain of mice. What decided whether or not a cell was eliminated by these killer lymphocytes was not only if they were infected with the virus, but also if they carried the "correct" variant of histocompatibility antigens, those of the infected mouse itself. Zinkernagel's and Doherty's findings, which were published in Nature in 1974 (1,2), demonstrated conclusively the requirement for the cellular immune system to recognize simultaneously both 'foreign' molecules (in the present case from a virus) and self molecules (major histocompatibility antigens). What also became obvious was the important function of the major histocompatibility antigens (in man called HLA-antigens) in the individual´s normal immune response and not only in conjunction with transplantation.

The discovery has given an impetus to later research

Zinkernagel's and Doherty´s findings had an immediate impact on immunological research. The wide relevance of their observations concerning the specificity of the T-lymphocytes became apparent in many contexts, both in regard to the ability of the immune system to recognize microorganisms other than viruses, and in regard to the ability of the immune system to react against certain kinds of self tissue. To explain their findings, the two scientists subsequently devised two models; one model was based on a single recognition of 'altered self''(when the histocompatibility antigen has been modified through association with a virus), the other on a 'dual recognition' of both foreign and self. (Fig.) Both the experimental findings and the theoretical models became immensely important in later research. Within a few years, it had been demonstrated that the set of the T- lymphocytes that are allowed to mature and survive in an individual is determined by the ability of the cell to recognize the transplantation antigens of the individual. Therefore, the principle of simultaneous recognition is essential for the ability of the immune system to distinguish between 'self' and 'non-self'.

Further molecular research has both confirmed Zinkernagel's and Doherty's models and clarified the structural basis of their discovery - that a small part (a peptide), for example from a virus, is directly bound to a defined variable part of the body´s own histocompatibility antigens, and that this complex is what is recognized by the specific recognition molecules of T- lymphocytes (T-cell receptors). Taken in all, the clarification of the recognition mechanisms of the T-cells within the cellular immune system has fundamentally changed our understanding of the development and normal function of the immune system and, in addition, has also provided new possibilities for the selective modification of immune reactions both to microorganisms, and to self tissues.

Figure legend: The figure describes how a killer T lymphocyte must recognize both the virus antigen and the self histocompatibility antigen molecule in order to kill a virus-infected target cell. The figure is a modification of the figure published by Zinkernagel and Doherty already 1974 (in Nature 251, p 547).

Relevance for clinical medicine

Many common and severe diseases depend on the function of the cellular immune system and consequently on its mechanisms for specific recognition. Although this naturally applies to infectious diseases, this is also true of a number of chronic inflammatory conditions such as rheumatic diseases, diabetes and multiple sclerosis. Where infectious diseases are concerned, the new knowledge provides a better platform for the construction of new vaccines; one can ascertain exactly what parts of a microorganism are recognized by the cellular immune system, and can specifically focus the production of the vaccine on those parts. Furthermore, regard is paid to the fundamental principles formulated by Doherty and Zinkernagel in trials with vaccination against the emergence of metastases in certain forms of cancer. In many chronic inflammatory diseases, better explanations have been provided for the associations between disease susceptibility and the histocompatibility antigen type carried by an individual. The research that followed from the now awarded discovery has also provided openings for selectively diminishing or altering immune reactions that play a central role in inflammatory diseases.

References

1. Zinkernagel RM, Doherty PC. Restriction of in vitro T cell-mediated cytotoxicity in lymphocytic choriomeningitis within a syngenic and semiallogeneic system. Nature 248, 701- 702, 1974.

2. Zinkernagel RM, Doherty PC. Immunological surveillance against altered self components by sensitised T lymphocytes in lymphocytic choriomeningitis. Nature 251, 547-548, 1974.

3. Doherty PC, Zinkernagel RM. A biological role for the major histocompatibility antigens. Lancet, 1406-1409, 1975.

4. Zinkernagel RM, Doherty PC. MHC restricted cytotoxic T cells: Studies on the biological role of polymorphic major transplantation antigens determining T cell restriction specificity. Advances in Immunology 27, 51-177, 1979.

---

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Atheist Radio at the University of Toronto

 
The University of Toronto publishes eBulletin once or twice a week to let people know what's going on. This is the official voice of the university. This week's issue features David Leaman (Godless Dave) and his campus radio show Godless: Atheist radio show at UTSC attracts listeners worldwide.

I was interviewed on the show in May and it was lot's of fun [Godless Radio].

Here's what the university's eBulletin has to say about the show.

The atheist and freethinker movements have been picking up steam nationwide and across the world. There is also growing interest at UTSC, with a noteworthy addition to this outspoken community being a radio show titled Godless, which began airing on UTSC’s Fusion Radio in January 2009. It is the only show of its kind at U of T.

The name Godless evokes a reaction from most who hear it, and that's exactly the purpose behind the chosen moniker. The term, brought to light in popular culture by right-winger and controversial figure Ann Coulter through the titling of one of her books, was initially used as a pejorative label. The hosts of the show, however, wear the term as a badge of pride.

"Atheism is a lack of a religious world view. There's no dogma or ritual that surrounds it. In fact, the only thing that atheists by definition will have in common with one another is the mutual lack of belief in a God," says fourth-year mathematics student David Leaman (known as 'Dave' on the air), co-host and founder of the online show. "My own personal brand of atheism is one that embraces evidence-based and logical reasoning along with the scientific method. Using these tools, I've come to the realization that the evidence for the existence of God just doesn't hold up. The idea that applying modern methods of inquiry to the 'big questions' should be a bad thing is actually pretty laughable."

---

Monday's Molecule #133: Winner?

 
If you look closely at the two molecules (below) you'll see that the one on that left has an extra bit of polypeptide chain compared to the one on the right. Some part of the protein has been removed to create a smaller version.

This should have reminded you of the kinds of reactions that take place when zymogens are cleaved to produce an active enzyme. This is pepsin, the classic example of such a reaction.

Pepsin is a protease—an enzyme that degrades proteins to small peptides in your stomach during digestion. It is initially synthesized as an inactive precursor called pepsinogen (left). When pepsinogen is secreted into the stomach it is inactive until it is cleaved in an autocatalytic reaction stimulated by HCl secretions. The blue bit sticking out on the right of the figure is chopped off, uncovering the active site in the large cleft in the right center of the molecule. This form of activation makes sense since it's not a good idea to have an active protease in the cytoplasm of your cells.

Pepsin—the protein ferment—has been known since the 1830s. At the end of the nineteenth century Ivan Pavlov carried out a series of experiments in an attempt to understand how digestion in the stomach worked. He learned that the initial secretion containing pepsin was inactive until it was combined with a separate secretion.

Pavlov received the Nobel Prize for his work on digestion.

Only one person guessed the molecule but that person did not figure out that Pavlov was the first one to deduce that digestive enzymes were initially produced in an inactive form. There is no winner this week! Even the "regulars" were stumped this time.

---

Here are two different versions of the same enzyme. One of them is the active form and the other is inactive. You should identify the enzyme and briefly explain the difference between the two structures.

This is a famous enzyme whose activity was first detected over one hundred and fifty years ago. The Nobel Laureate associated with the two forms shown above is also very famous. He was the first person to discover that there were active and inactive forms of the enzyme and to provide a reasonable explanation. The Nobel Prize was awarded for many other contributions to the field and not just for this discovery. However, the fact that he is better known for other studies should not detract from his significant contributions to biochemistry.

The first person to identify the molecules and the Nobel Laureate, wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are only six ineligible candidates for this week's reward: Dima Klenchin of the University of Wisconsin at Madison, Dara Gilbert of the University of Waterloo, Anne Johnson of Ryerson University, Cody Cobb, soon to be a graduate student at Rutgers University in New Jersey, Alex Ling of the University of Toronto, and Markus-Frederik Bohn of the Lehrstuhl für Biotechnik in Erlangen, Germany.

I have an extra free lunch for a deserving undergraduate so I'm going to continue to award an additional prize 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(s) 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.

Comments will be blocked for 24 hours.

---

Monday's Molecule #133

 
Here are two different versions of the same enzyme. One of them is the active form and the other is inactive. You should identify the enzyme and briefly explain the difference between the two structures.

This is a famous enzyme whose activity was first detected over one hundred and fifty years ago. The Nobel Laureate associated with the two forms shown above is also very famous. He was the first person to discover that there were active and inactive forms of the enzyme and to provide a reasonable explanation. The Nobel Prize was awarded for many other contributions to the field and not just for this discovery. However, the fact that he is better known for other studies should not detract from his significant contributions to biochemistry.

The first person to identify the molecules and the Nobel Laureate, wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are only six ineligible candidates for this week's reward: Dima Klenchin of the University of Wisconsin at Madison, Dara Gilbert of the University of Waterloo, Anne Johnson of Ryerson University, Cody Cobb, soon to be a graduate student at Rutgers University in New Jersey, Alex Ling of the University of Toronto, and Markus-Frederik Bohn of the Lehrstuhl für Biotechnik in Erlangen, Germany.

I have an extra free lunch for a deserving undergraduate so I'm going to continue to award an additional prize 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(s) 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.

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

---

Canadian Gets Booted Out of the Creation Museum

 
Derek Rogers is a computer science student at Dalhousie University in Halifax, Nova Scotia (Canada). I met him in Washington last April. He has been active in the atheist bus campaign and other events promoting a nonreligious point of view.

Derek was at the Secular Student Alliance meeting in Ohio and went along with the group that visited the creation museum. He was asked to leave. Here's the video of him explaining what happened to PZ Myers, Seanna and Steve Watson, and others who had just toured the museum.

---

[Hat Tip: Friendly Atheist]

Happy Anniversary!

 
Today is our 41st wedding anniversary.

Here's how Ms. Sandwalk looked back when we first started dating. She looks the same to me today as she did back then.

She has posted an old picture of me on her blog and it's clear that I haven't changed very much either!

---

Elaine Morgan and Aquatic Apes

 
The Aquatic Ape Hypothesis of Elaine Morgan is a classic "just-so" story that attempts to explain the evolution of modern humans by claiming that our ancestors once lived in water. It's a typical adaptationist perspective on biology since it begins with the assumption that every phenotype of humans must have been due to natural selection.

Morgan gave a talk last month sponsored by TED. It's posted at: Elaine Morgan says we evolved from aquatic apes. You should watch it if you are interested in the Aquatic Ape Hypothesis. In addition to being a good example of (false) adaptationist thinking, it's a good example of how a skilled journalist makes a "scientific" case to a general audience. The audience loved her. She gets an enthusiastic standing ovation at the end.

I didn't realize that Elaine Morgan was relying so much on attacking scientific conspiracy in order to bolster her beliefs. Many of her arguments sound similar to those of the Intelligent Design Creationists. Judging by the reception she gets, there's a lot of reasonably intelligent people out there who are willing to buy into the idea that scientists suppress knowledge of things they don't like just because they don't like them.

---

[Hat Tip: John Hawks]

The Biologic Institute Expands

 
Posted yesterday on Evolution News & Views: European scientists working in conjunction with Biologic Institute.

The anti-ID crowd has an old canard about there being no serious scientists who doubt Darwin, let alone any that support intelligent design. And they like to say that there is no science being done by ID scientists. Both ideas are not just false, but absurdly so. Note this announcement of new scientific arrivals at Biologic Institute. Professor Matti Leisola, the Dean of Chemistry and Materials Science at Helsinki University of Technology in Finland; Colin Reeves, Professor of Operational Research in the School of Mathematical and Information Sciences at Coventry University; and Professor Stuart Burgess, Head of the Department of Mechanical Engineering at the University of Bristol.

Three "serious scientists", eh? And not a biologist in the bunch. That's what we've come to expect in an institute that's supposed to be studying evolution creationism.

John Pieret has the scoop on these dudes. All three of them are creationists with strong ties to the Young Earth Creationist movement [The "Pros" from Dover]. John had the idea of comparing these guys to the Three Stooges. I thought it was appropriate so I "borrowed" it.¹

---

1. I steal a lot of John's ideas but let's not tell him, OK? It gives him a swelled head.

Teabaggers

 
American politics is so much fun—I love watching it on TV.

But from time to time the subtleties escape me. This is one of those times. The opponents of universal health care are not referred to as "idiots," which would be the appropriate name—instead, they're called "teabaggers."

What the heck is a "teabagger"? I looked it up on the Urban Dictionary. There are several definitions. One of them involves actions that don't seem to apply in this context. (But it sounds like fun.)

For the benefit of all your foreigners out there, here are the definitions that seem to be relevant ...

4) a person who is unaware that they have said or done something foolish, childlike, noobish, lame, or inconvenient.

and ...

A whining fool shouting loudly for liberty but not willing to pay the bill.

"After most American workers saw more money in their paycheck due to the lower tax rate, the teabaggers at Fox News railed against high taxes, but did not discuss how much Jesus hated hypocrisy."

---

On the Origins of Eukaryotes

 
Carl Zimmer has an article in Science with a provocative title: On the Origin of Eukaryotes. This is well-timed since it appears just when I've returned from a meeting on this very topic. [Go here if you can't see the article on the Science website.]

One of the things we learned at the meeting is that the Woose tree of life is almost certainly an over-simplification at best and wrong at worst. It is no longer possible to claim that eukaryotes have a simple vertical descent relationship with any archaebacterium (or any bacterium, for that matter).

Instead, the early history of life is characterized by a web or a net involving multiple gene exchanges between all primitive species. After some time, the major divisions of life emerged from this "soup" and became separate lineages with an semi-independent history. This view dates back ten years or so and it's illustrated by a figure that Ford Doolittle published in the February 2000 issue of Scientific American. I've used this figure several times. Here it is again so you can see how it relates to Carl's article.

In the case of eukaryotes, the history is complicated by an endosymbiotic event where a proteobacterium was engulfed and evolved into mitochondria. That explains many of the eukaryotic genes with a clear bacterial origin. Those genes, can be reliably traced to a particular lineage of proteobacteria. What this shows is that by the time of the endosymbiosis most of the main lineages of prokaryotes had emerged from the soup and become fairly well-defined.

This doesn't explain the origins of the host cell. That cell presumably had some of the features of modern eukaryotes. Where did it come from? Was it part of an ancient lineage that formed during the gene exchange period of evolution suggesting that some eukaryotic features are ancient? Was it formed by a fusion between a primitive bacterial cell and a primitive archaebacterium? (Or, did archaebacterial arise from a fusion of a primitive eukaryotic cell and a primitive bacterium?)

Some people even believe that the ancient host progenitor of eukaryotes arose fairly late in the game and was only related to archaebacteria, either through a recent common ancestor or from an archaebaterial species within the archaebacterial clade. This is not consistent with the tree shown above but that's OK.

These two hypotheses on the archaebacterial origin of the host cell are the ones that Carl Zimmer highlights in his article: the Three Domain Tree and the Eocyte Tree.


I don't think either of these trees comes close to representing the true history of eukaryotic cells. I don't think it's even possible to represent that history by a tree. Zimmer mentions this possibility in passing but I don't think he does justice to the controversy over the tree of life.

The controversy is not just about which branch of the archaebacterial tree the eukaryotes came from. It's about whether they came from the archaebacerial lineage at all or whether it's even appropiate to be talking about lineages and trees at this stage of the history of life.

Shifting gears slightly, I'd like to bring up another subject. Here's what Carl writes near the end of his article.

Whatever the exact series of events turns out to be, eukaryotes triggered a biological revolution. Prokaryotes can generate energy only by pumping charged atoms across their membranes. That constraint helps limit their size. As prokaryotes grow in size, their volume increases much faster than their surface area. They end up with too little energy to power their cells. Eukaryotes, on the other hand, can pack hundreds of energy-generating mitochondria into a single cell. And so they could get big, evolving into an entirely new ecological niche.

This is a widely believed explanation for the adaptive value of mitochondria and internal membranes. But many species of bacteria have internal membranes and, in the case of photosynthetic species, those internal membranes are packed full of energy-producing proteins.

Why couldn't bacteria have evolved internal membranes in order to get around the size limitation if it was that big of a deal? I don't see anything special about mitochondrial that couldn't have just as easily been handled by infolding of the inner membrane.

---

Perspectives of the Tree of Life: Day Three

Day One, Day Two

The third day (Saturday, August 1) began with a presentation by James McInerney of the National University of Ireland in Maynooth (Ireland): LUCA and LECA: Gene genesis in the genome of Eden. He examined genes in yeast cells and assigned them to ancestral homologs in bacteria and archaebacteria.

The majority of yeast genes are bacterial in origin but a significant minority come from archaebacteria. The genes with the archaebacterial origin are more likely to be found in information flow pathways (DNA replication, transcription, translation) and the genes from (eu)bacteria are more likely to be involved in other metabolic pathways.

The results suggest that the last eukaryotic common ancestor (LECA) was a hybrid formed from the fusion of a primitive bacterial cell and a primitive archaebacterial cell. The descendants of this first eukaryote subsequently entered into an endosymbiotic relationship with a proteobacterium giving rise to mitochondria and an influx of additional bacterial genes.

The second talk on day three was by Christophe Malaterre, a philosopher who divides his time between the IHPST at the Université Paris in Paris (France) and the Université Libre in Brussels (Belgium). Christophe is mostly interested in the early events in the history of life before the last universal common ancestor (LUCA) (On the roots of the tree of life). He is trying to define the basic properties of these "protocells."

This leads naturally to a debate about defining "life." During the transition from a bag of chemicals to a true living cell, there will be a zone where it will be very difficult to decide whether the protocell is living or not.

After a short break we returned to hear a presentation by William (Bill) Martin of Heinrich-Heine-Universität in Düsseldorf (Germany). His presentation was Endosymbiosis and gene transfers from endosymbionts, the most glaring insult to the tree. As the title implies, the key point is that a large percentage of nuclear genes in eukaryotes is derived from mitochondrial genes (proteobacteria) or from chloroplast genomes (cyanobacteria).

What this means is that aside from any consideration of the deep phylogeny of nuclear genes (bacterial or archaebacterial), one of the ancestors of eukaryotes is clearly a bacterial cell (proteobacteria). When you add in the bacterial contribution to genes that don't descend from mitochondria, it turns out that 75% of eukaryotic genes are bacterial in origin. No matter how you want to define the roots of the tree of life (tree, net, web) it is absolutely clear that the original Woose tree with eukaryotes on the same branch as archaebacteria is wrong!

Bill proposes that the first eukaryotic cell was formed when a primitive bacterial cell fused with a primitive archaebacterial cell. He would like to convince us that this primitive archaebacterium arose from within the current clade of Archaea. Most of us weren't convinced but none of us would dare say that to his face 'cause Bill is a very imposing man both intellectually and physically.

John Archibald of the Department of Biochemistry and Molecular Biology at Dalhousie University in Halifax, Nova Scotia (Canada) continued the endosymbiotic theme with a talk on Genetic and genomic threads in the tapestry of photosynthetic life: implications for "tree thinking."

The original photosynthetic eukaryote was the result of an endosymbiotic event involving an early eukaryotic host with mitochondria and a cyanobacterium. This gave rise to the three primary lineages: red algae, green algae, and glaucophytes. All photosynthetic eukaryotes have a single common ancestor represented by this unique endosymbiotic event.

The nuclei of modern flowering plants contain about 4500 genes derived from cyanobacteria via chloroplasts. Only half of these are targeted to the chloroplast. The rest contribute to the metabolism of the remaining part of the cell.

Some photosynthetic eukaryotes arise from a secondary endosymbiosis in which a chloroplast-containing algal cell is engulfed by a non-photosynthetic protist. In this case, genes can be transferred from the nucleus of the endosymbiote to the main nucleus, further complicating the ability to construct a treelike phylogeny that accurately reflects the true ancestral relationships of these species.

Frédéric Bouchard is a philosopher from the Université de Montréal in Montréal, Québec (Canada). When we returned from lunch we were treated to a discussion of: Endosymbiosis in light of reflections on symbiosis and the super organism.

Much of this presentation was based on symbiosis—a situation where two separate species cooperate. One or both species may benefit from this interaction and the question is how do we decide on the adaptive advantage, if any?

This was the only talk that seriously addressed the value of adaptationist thinking. Most people at this meeting seemed to assume that (almost) all evolution was due to adaptation. Bouchard even showed a slide of the Spandrels paper before going into a defense of the adaptationist program.

Andrew Roger is a former student of Ford Doolittle. He is now a professor in the Department of Biochemistry and Molecular Biology at Dalhousie University in Halifax, Nova Scotia (Canada). The title of his talk is a challenge to his former mentor: Deconstructing deconstructions of the tree of life: why a tree of microbes might be realizable, meaningful and useful.

The question is whether in light of significant LGT we can still detect the underlying vertical component in the web of life. Roger reminds us that this vertical component is very much a part of the evolutionary history of life. Let's not throw out the baby with the bath water when we question the tree of life.

There are basically two viable models of the early history of life. In the "Serious LGT" model, lateral gene transfer is ubiquitous but some genes may have been transferred less frequently than others. By looking at these genes it may be possible to recover the basic treelike vertical component of evolution.

Andrew looked at four protein encoding genes and found that they are mostly congruent with the ribosomal RNA tree of prokaryotes. The major divisions, such as cyanobacteria and proto-bacteria are confirmed. Thus, as Andrew points out, it's a mistake to assume that the web of life erases all traces of vertical descent as the alternative “Rampant LGT" model might suggest.

Almost everyone at the meeting supported the “Serious LGT" model as determined by a show of hands at the end of the day. Even Ford Doolittle raised his hand in support of his former student! (But he also supports the "Rampant LGT" model—for some reason Ford was allowed to have two votes. )

John Dupré, a philosopher at the University of Exeter in Exeter (UK) summarized the scientific part of the meeting. We are left with some important questions such as: how much does LGT compromise the tree of life? It's still an open question whether treelike thinking has to be abandoned for all of the tree of life or just for the base. The general consensus is that much of the upper regions are still treelike even though LGT may affect certain genes.

Sina Adl of the Department of Biology at Dalhousie University in Halifax. Nova Scotia (Canada) gave a short talk on PhyloCode a new classification scheme in biology. He pointed out that the current international rules of nomenclature don't work very well and need to be replaced.

The meeting closed with a talk by Susan Spath who has been with the National Center for Science Education (NCSE) in Oakland, California (USA). Her title was Cultural politics and the tree of life. Susan cautioned us to be careful when talking to the media. We should emphasize that most of the evolution that people care about (animals) is very treelike. She reminded us that talk of "Darwin was wrong" is very misleading.

As you might imagine, there was quite a good discussion on how much we should be concerned about creationists and how much we should cater to the difficulty journalists have in understanding genuine scientific controversy.

This was an excellent meeting and the organizers deserve a lot of credit for choosing the venue and the participants. It was by far the best meeting that I've attended in several decades. I plan to go to the next one in Exeter if they'll invite me back.

---

[Photo Credit: These photos are from Christina Behme. The bottom one is of me having dinner on the first evening with Ford Doolittle (left), John Dupré (standing), and Andrew Roger (right).]

12:34:56 07/08/09

 
Sometime around midday you could write the exact time and date as 12:34:56 07/08/09 and if you were up early you could have witnessed 04:05:06 07/08/09.

But only in Europe—and a few other countries [Date and time notation by country].

In America you celebrated the big day last month and if your country is unlucky enough to have adopted the international standard notation then you've missed the big day by two years.

In Canada we use all three notations and this leads to a great deal of confusion. The good news is that we get to celebrate the sequential date three times. Tonight there will be a huge celebration in downtown Toronto with parades and fireworks and speeches by famous people.

How many more sequential time/dates will we celebrate in Canada this millennium?

---

On this Day in 1945

(reposted from August 6, 2007)

At 8:15 AM on August 6, 1945 an atomic bomb was detonated over Hiroshima, Japan. Approximately 78,000 civilians were killed on that day. Six months later the death toll had risen to about 140,000 people.

There are many arguments in favor of dropping the bomb just as there are many arguments against it. What's clear is that in the context of 2007 we are not in a good position to judge the actions of countries that had been at war for many years.

The most important lesson of Hiroshima is that war is hell and many innocent people die. It's all very well to enter into a war with the best of intentions—as the Japanese did on December 7, 1941—but it's foolish to pretend that when you start a war there won't be any suffering. When you do that you can really say that the victims of Hiroshima died in vain.

The killing and maiming of civilians is an inevitable outcome of war, no matter how hard you might try to restrict your targets to military objectives. Before going to war you need to take the consequences into account and decide whether the cost is worth it.

One of the many mistakes in Iraq was the naive assumption that it would be a clean war with few casualties and no long-term consequences for the Iraqi people. Yet today, the numbers of innocent lives lost in Iraq is comparable to the numbers lost in Hiroshima and Nagasaki. And what is the benefit for Iraq that outweighs the cost in human lives? Is it "freedom" and "democracy"?

Hiroshima was not a glorious victory. It was ugly, heartbreaking, and avoidable. War is not an end in itself, it is the failure of peace. War is not an instrument of your foreign policy—it is an admission that you don't have a foreign policy.

[The top photograph shows the mushroom cloud over Hiroshima on the morning of August 6, 1945 (Photo from Encyclopedia Britanica: Hiroshima: mushroom cloud over Hiroshima, 1945. [Photograph]. Retrieved August 7, 2007, from Encyclopædia Britannica Online. The bottom image is taken from a Japanese postcard (Horoshima and Nagassaki 1945). It shows victims of the attack on Hiroshima.]

---

Are Miracles Compatible with Science?

 
This is a common question in the debates about science and religion. My answer is "no." A miracle, by definition, must be miraculous, which means it is not explicable by the process we use in science (evidence and rationality).

Philosophers love this kind of question because it gives them loads of opportunities to talk about dead philosophers and how they interpreted the word "miracle." If they can find logical inconsistencies, or slight subtleties of meaning, then they can declare victory for belief in miracles.

Watch Hugh McLachlan perform this "miracle" in an article written for New Scientist: Opinion: Do you believe in miracles?.

THESE days most people think it unscientific to believe in "miracles", and irreligious not to believe in them. But would the occurrence of miracles really violate the principles of science? And would their non-occurrence really undermine religion? David Hume and Richard Dawkins have attempted to answer these questions in their different ways, but I am not convinced by their arguments, and for me they remain open questions.

So, it's an open question whether miracles are compatible with science, eh? I wish Hugh McLachlan had given us some examples of miracles that he thinks would be compatible with science.

He's been known to read Sandwalk [Hugh McLachlan on Cloning Humans] so maybe he'll give us an examples in the comments.

---

Ten Unexplained Human Characteristics

 
New Scientist is at it again. This time they've come up with Ten things we don't understand about humans.

1. Blushing
2. Laughter
3. Pubic Hair
4. Teenagers
5. Dreams
6. Altruism
7. Art
8. Superstition
9. Kissing
10. Nose-picking

It goes without saying that these "problems" are much more of a concern for adaptationists than for pluralists.

---

Decoding the Structure of the HIV Genome

 
The title of the press release on Biology News Net caught my eye: UNC researchers decode structure of an entire HIV genome. I clicked the link on my aggregator and read the first two paragraphs.

The structure of an entire HIV genome has been decoded for the first time by researchers at the University of North Carolina at Chapel Hill. The results have widespread implications for understanding the strategies that viruses, like the one that causes AIDS, use to infect humans.

The study, the cover story in the Aug. 6, 2009, issue of the journal Nature, also opens the door for further research which could accelerate the development of antiviral drugs.

By the time I finished the article I thought I had a pretty good idea of what they were talking about but, just to be sure, I visited the Nature website to read the actual scientific paper.

Watts, J.M., Dang, K.K., Gorelick, R.J., Leonard, C.W., Bess Jr., J.W., Swanstrom, R., Burch, C.L. and Weeks, K.M. (2009) Architecture and secondary structure of an entire HIV-1 RNA genome. Nature 460:705-710 [doi: 10.1038/nature08237]

Single-stranded RNA viruses encompass broad classes of infectious agents and cause the common cold, cancer, AIDS and other serious health threats. Viral replication is regulated at many levels, including the use of conserved genomic RNA structures. Most potential regulatory elements in viral RNA genomes are uncharacterized. Here we report the structure of an entire HIV-1 genome at single nucleotide resolution using SHAPE, a high-throughput RNA analysis technology. The genome encodes protein structure at two levels. In addition to the correspondence between RNA and protein primary sequences, a correlation exists between high levels of RNA structure and sequences that encode inter-domain loops in HIV proteins. This correlation suggests that RNA structure modulates ribosome elongation to promote native protein folding. Some simple genome elements previously shown to be important, including the ribosomal gag-pol frameshift stem-loop, are components of larger RNA motifs. We also identify organizational principles for unstructured RNA regions, including splice site acceptors and hypervariable regions. These results emphasize that the HIV-1 genome and, potentially, many coding RNAs are punctuated by previously unrecognized regulatory motifs and that extensive RNA structure constitutes an important component of the genetic code.

The authors determined the two- and in some cases the three-dimensional structure of the HIV RNA genome. In other words, they figured out the way RNA folds to form regions of secondary structure (double-stranded RNA). This RNA molecule functions as a complex messenger RNA and the secondary structure plays a role in regulating how the molecule is translated.

The press release doesn't really convey this result very well, especially in the opening paragraph. Part of the problem is misue of the word "decode." We're familiar with journalists who use "decode" to mean "nucleotide sequence" as in "Scientists decoded the human genome." This elevates "decode" to an entirely new meaning.

In fairness, this confusion over the word "decode" is exacerbated by the language used by the authors in the paper.

Our discovery that the peptide loops that link independently folded protein domains are encoded by highly structured RNA indicates that these and probably other mRNAs encode protein structure at a second level beyond specifying the amino acid sequence. In this view, higher-order RNA structure directly encodes protein structure, especially at domain junctions. The extraordinary density of information encoded in the structure of large RNA molecules (Figs 1, 2 and 4d) represents another level of the genetic code, one which we understand the least at present. This work makes clear that there is much to be discovered by broad structural analyses of RNA genomes and intact mRNAs.

I'm not sure this language is helpful.

UPDATE: The press release from Scientific American is different: HIV genome structure decoded.

It might not be super high-res, but researchers at the University of North Carolina at Chapel Hill have described the first full structure of the HIV-1 genome.

The paper, published online today in Nature, maps out the virus' genome down to a one-nucleotide resolution with the help of a technique call SHAPE—selective 2'-hydroxyl acylation analyzed by primer extension—to paint the full, previously unknown picture of the virus (Scientific American is part of Nature Publishing Group).

---

Censorship in the Scientific Community

 
Richard Dawkins interviews Wendy Wright of Concerned Women for America. You really have to watch this if you want to understand what science is up against in some parts of the world.

Richard tries very hard to be patient and respectful. I would not have been so kind in the face of such massive stupidity and ad hominem attacks by Wendy Wright. I find it absolutely astonishing that she attacks scientists and accuses them of stupidity and conspiracy then complains about ad hominem attacks when Richard asks why she rejects evolution.








I don't know how much of this you can stand. Parts 5, 6, and 7 are here.

---

Monday's Molecule #132: Winner!

 
This is a complex between parts of the T-cell receptor (green and blue) and the major histocompatibility complex class II molecule (MHC class II) shown in orange and yellow. There's a peptide bound in the presentation site of the class molecule (red).

When a cell becomes infected with a virus, various viral proteins are broken down into peptides and bound to a site on class II molecules. These molecules are then presented on the surface of the cell when they can be recognized by the T-cell receptor. Since the viral peptide will be seen as a foreign antigen, the infected cell will be destroyed.

The Nobel Laureates are Rolf Zinkernagel and Peter Doherty.

There weren't very many correct answers this week¹ but Markus-Frederik Bohn thought it was very easy. He's a graduate student at the Lehrstuhl für Biotechnik in Erlangen, Germany. He has a Canadian connection but I'll let him reveal it in the comments if he wishes.

---

This is a very famous molecular complex. You need to identify this complex by naming all the major components. You will not win if you skip this part. (Don't forget the red bit.)

There is a Nobel Prize associated with the discover of this complex although the work was done long before the structure was solved. The first person to identify the molecules and the Nobel Laureate(s), wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are only five ineligible candidates for this week's reward: Dima Klenchin of the University of Wisconsin at Madison, Dara Gilbert of the University of Waterloo, Anne Johnson of Ryerson University, Cody Cobb, soon to be a graduate student at Rutgers University in New Jersey, and Alex Ling of the University of Toronto.

I have an extra free lunch for a deserving undergraduate so I'm going to continue to award an additional prize 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(s) 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.

Comments will be blocked for 24 hours.

---

1. Because immunology isn't biochemistry and possibly not even a real science.

The figure is from Reinherz et al. (1999).

Reinherz, E.L., Tan, K., Tang, L., Kern, P., Liu, J., Xiong, Y., Hussey, R.E., Smolyar, A., Hare, B., Zhang, R., Joachimiak, A., Chang, H.C., Wagner, G., and Wang, J. (1999) Science 286:1913-1921. [PubMed] [doi: 10.1126/science.286.5446.1913]

Lateral Gene Transfer and the Return of Lamarckian Evolution

 
Mark Buchanan believes that physics has entered a new era where it has gone beyond the fundamental forces into the realm of "collective phenomena". He claims that biology is about to do the same as he explains in an article that was just published in Nature Physics: "Collectivist Revolution in Evolution."

It now seems clear that biology may also have a second act linked to the widespread importance of collective phenomena. The explosion of genetic and genomic data, of course, has ushered in the era of systems biology, as biologists have come to recognize the need to gain a more holistic understanding of the functioning of organisms. But this may not be the most radical transformation in store for biological science. A coming revolution in biology, some suggest, may go so far as to unseat Darwinian evolution (ran in its modern form) from its position as the key explanatory process in biology, and may just bring back some form of Lamarckian evolution—that old idea of the inheritance of acquired characteristics.

No, it's not epigenetics, it's lateral gene transfer (LGT) that's going to unseat Darwinian evolution and bring back Lamarck.

Much of what he writes about LGT is correct. It does, indeed, make interpretation of molecular evolution more difficult, especially at the root. But some of his ideas do not represent the consensus view in biology: for example, the role of lateral gene transfer in the evolution of the genetic code.

The conjecture is that horizontal gene transfer was indeed required for the present genetic code to take the form it has, and that the emergence of life most likely went through a series of stages, with the early stage more Lamarckian in character, and only the latter stages becoming more Darwinian.

Exploring that point in greater detail will be a task for a new kind of biology, one that breaks with many of the presuppositions of traditional evolutionary thinking, and explores the potential for rich and surprising dynamics in a collective setting. It will almost surely benefit from the ideas and experience of physics, which has already experienced its own collectivist revolution.

This kind of hyperbole is not helpful. Shame on Nature Physics for publishing it.¹

---

1. I wonder if Nature Genetics publishes opinion pieces by evolutionary biologists on the overthrow of quantum mechanics?