Clear as Mud

 
James F. McGrath is still trying to explain what modern sophisticated religion is all about, and why amateur atheists, like me, just don't get it.

His latest attempt is on his blog at Does Being Exist?. The most revealing paragraph is the last one ...

So if you are looking for evidence that ancient deities and angels exist, with or without wings, residing on Mt. Olympus or just beyond the moon, I don't believe that such entities exist. They were ancient explanations for what we today recognize as natural phenomena. But if you are asking about language that can give symbolic expression to the sense of awe many people feel about the "miracle" that anything exists at all, much less that we exist and can ponder the nature of our existence and wonder about these mysteries, then theology has a lot to offer. Not logical arguments for the existence of invisible persons, but metaphors that allow us to give voice to our limited and inadequate perception of life's inexpressable mystery, then theology has a lot to offer. That doesn't mean that amateurs can't do theology, or write poetry, or make music, or even make scientific discoveries. But in every field, there is a body of knowledge and wisdom that has accumulated that allows one to not repeat all the mistakes and positive groundwork done in the past and build on what has gone before, rather than reinventing the wheel. If one wishes to discuss theology at that sort of level of academic sophistication, it involves significant reading and research to inform oneself, and not simply a handful of conversations with fundamentalists.

Translation: You can't say that the Emperor has no clothes because you haven't invested years of study at the best institutes of fashion design in Paris and Milan. There are hundreds of smart people who have written sophisticated, metaphorical books on the Emperor's clothes. Don't talk to me until you've read all of them and can quote mystical passages and scholarly names as easily as I do.

What McGrath is illustrating here is referred to as The Courtier's Reply [The Emperor's New Clothes and the Courtier's Reply]. The term refers to an elaborate justification of a questionable viewpoint. Instead of addressing whether of not the Emperor is clothed, the courtier defends the "sophisticated" rationalization that the sycophants have constructed to preserve the delusion, and avoid admitting that they can't see the clothes either.

McGrath thinks that theology can be justified because it addresses "life's inexpressable mystery." This is reason enough to reject atheism even though he denies the existence of any of the classical gods. Furthermore, this is reason enough to call himself a Christian.

I'd like to discuss why he is impressed by some "inexpressible mystery" and why he thinks it's a "miracle" that anything exists at all. Why does he feel that this is enough to cause him to posit something beyond the natural world? Why are these feelings so powerful that he rejects the label of atheist and adopts theology as a way of knowing? Those are the key points.

But I'm not allowed to discuss those points, according to McGrath. I can't enter into a debate with him until I've read all of the sophisticated theologians who agree with him. I haven't done my homework. Until then, I'm just an amateur who doesn't understand the arguments against atheism and in favor of modern mysticism/theology.

That's not very helpful. It's a way of protecting one's core beliefs from close scrutiny by skeptics.

There's nothing new about McGrath's argument. It's just a version of the Argument from Personal Experience. Those arguments have been dealt with by atheists. There's nothing sophisticated about them.

Perhaps McGrath has been fooled into thinking that the argument from personal experience is valid because there are many scholars who find it convincing? If so, this is evidence of another logical fallacy called Argumentum ad nauseam.

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Steve Paikin Interviews Richard Dawkins

 
Last week I went to a talk at the Centre for Inquiry by Wodek Szemberg, one of the producers of TVO's The Agenda. The topic was Why So Few Atheists in the Media?.

It was a horrible talk. Wodek Szemberg spend most of his alloted time criticizing atheists and proclaiming that facts and evidence are not important on television shows. Szemberg is an atheist and he claims that most producers, writes, directors, etc. are atheists. They don't need to hear the atheist point of view on television because they are already familiar with it.

The host of The Agenda is Steve Paikin. Paikin is not an atheist. He has made this very clear on numerous shows where his bias against non-believers is patently obvious. He is one of those people who are overly respectful of believers no matter how silly their arguments.

Last year The Agenda ran a series on religion that was, to say the least, quite embarrassing. Near the end of the series the producers were pressured to bring on some atheists for balance. When I asked Wodek Szemberg about this he avoided the topic—it didn't fit into his theme that atheists have nothing to say.

Shortly after that, on May 10, 2007, the producers of the show broadcast an interview with Richard Dawkins [Richard Dawkins: Can We Live by Reason Alone?]. (The producer was Sandra Gionas, not Wodek Szemberg.) Videos of the show have just now been posted on YouTube ...
Part 1, Part 2, Part 2, Part 4, Part 5

If you listen to the opening remarks on the first episode you will hear Steve Paikin admitting that they have Richard Dawkins on the show in response to viewers who requested it. This is a direct refutation of what Wodek Szemberg was telling us last Friday night when he tried to make us believe that nobody wants to hear atheists on television.

Here's part 4 where Steve Paikin tries to argue that religion deserves much more respect and deference than Dawkins is willing to grant.

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[Hat Tip: RichardDawkins.net]

The Toronto Star Reviews "Darwin: The Evolution Revolution"

 
Darwin: The Evolution Revolution is currently on at the Royal Ontario Museum (until August 4, 2008). There was a review of the exhibit by Peter Calamai in yesterday's Toronto Star [Darwin still battling creationists]. It seems like an excellent review. I haven't yet seen the exhibit so I can't comment on the details but everything that Peter Calamai says rings true.

One of the criticisms of the exhibit is that there are too many things to read. Calamai estimates that it would take five hours to read all the explanatory panels. Another criticism is that the written information tilts heavily toward defending Darwin's ideas, and that sometimes this zeal trumps the truth ...

For make no mistake about it, parts of "Darwin: The Evolution Revolution" are an exercise in anti-creationist persuasion, usually subtle but often blatant.

Take this statement from a panel headed "Creationism" at the close of the exhibit:

"For 150 years since the publication of Darwin's Origin of Species, the theory of evolution by natural selection has not been seriously challenged by any other scientific explanation."

The weasel word here is "seriously," since that's very much a qualitative judgment. Yet, even setting Creationism aside, well-respected historians of science such as Peter Bowler (The Non-Darwinian Revolution) have maintained that alternate scientific theories of evolution, such as mutation and Lamarckism, were resolutely championed by mainstream scientists until after World War I.

Evolution through the mechanism of natural selection, the core of Darwin's approach, was simply not a "slam-dunk" scientific revolution after On the Origin of Species was published in 1859, as the ROM exhibit repeatedly implies.

Yet Darwin's thesis is widely accepted by today's scientific community. So why all the defensive proselytizing, as though his ideas were under siege?

Calamai makes a good point. The statement on the exhibit is clearly incorrect and that's embarrassing.

Why is there such an emphasis on defending Darwin when such a defense is serious overkill in Canada?

Because they are – at least in the United States, where this "show-in-a-box" originates. ROM officials acknowledge that they had minimal input on the thematic level to the travelling exhibit from the American Museum of Natural History in New York.

Where evolution is concerned, a chasm yawns between the U.S. and Canada. Polling by Angus Reid published two years ago found that one in five Canadians surveyed agreed with the statement that God created human beings in their present form within the last 10,000 years. Nearly half the Americans surveyed chose this option.

The resulting anti-creationist mindset, while at times annoying, cannot ruin an exhibit that will reward multiple visits at several different levels.

Finally, I'm glad that Peter Calamai closed his article by mentioning the problem of funding.

Perhaps we haven't progressed as far from such times as we'd like to believe. The Darwin exhibit opened without an outside sponsor, although several groups have since rallied to the cause, including the Humanist Association of Canada.

But there's still no major corporate sponsor. They're all too spooked by the prospect of the one-in-five minority of Canadians who believe – despite an Everest of evidence to the contrary – that human beings sprang upon the Earth in their current form a mere 10,000 years ago.

I know the members of the Humanist group who put up the money. Thank God goodness we have some wealthy atheists in town! But that's no excuse for the cowardly behavior of the usual sponsors. Where are the SikKids Foundation, The Gairdiner Foundation, the University of Toronto, and the leading biotech companies in Toronto?

Is it true that some of these potential sponsors have declined because evolution is too controversial? Yes, in some cases that's true. There are members of the Gairdiner family, for example, who have doubts about evolution.

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Atheists Behaving Badly

 
A reader has used the Conservapedia article on Atheism to support his/her belief in supernatural beings.

I thought it might be fun to post some quotes from that article for your Friday amusement. Are these examples of "sophisticated" arguments against religion or do they fall into another category?

In regards to atheism and morality, the Barna Group also found that those who hold to the worldviews of atheism or agnosticism in America were more likely, than theists in America, to look upon the following behaviors as morally acceptable: illegal drug use; excessive drinking; sexual relationships outside of marriage; abortion; cohabitating with someone of opposite sex outside of marriage; obscene language; gambling; pornography and obscene sexual behavior; and engaging in homosexuality/bisexuality.

Moral depravity has been demonstrated in the atheist community through history and through various studies.[61][62][63][64] The Bible asserts that "The fool has said in his heart, 'There is no God.' They are corrupt, they have done abominable works, there is none that doeth good." (Psalms 14:1 (KJV)). The biblical fool is said to be lacking in sound judgment and the biblical fool is also associated with moral depravity. For example, the biblical book of Proverbs states: "A wise man is cautious and turns away from evil, But a fool is arrogant and careless. A quick-tempered man acts foolishly, And a man of evil devices is hated. The naive inherit foolishness, But the sensible are crowned with knowledge."(Proverbs 14:16-18 (NASB)). The book of Proverbs also has strong words regarding the depravity of biblical fools: "The desire accomplished is sweet to the soul: but [it is] abomination to fools to depart from evil." (Proverbs 13:9 (KJV)). Regarding the deceitfulness of fools Proverbs states: "The wisdom of the sensible is to understand his way, But the foolishness of fools is deceit." (Proverbs 14:8 (KJV)). Noted Bible commentator and clergyman Matthew Henry wrote regarding atheism: "A man that is endued with the powers of reason, by which he is capable of knowing, serving, glorifying, and enjoying his Maker, and yet lives without God in the world, is certainly the most despicable and the most miserable animal under the sun."

Rates of atheism are much higher in countries with a state sanctioned religion (such as many European countries), and lower in states without a sanctioned religion (such as the United States). Some argue this is because state churches become bloated, corrupt, and/or out of touch with the religious intuitions of the population, while churches independent of the state are leaner and more adaptable.

Some argue that a troubled/non-existent relationship with a father may influence one towards holding the position of atheism.[69] Dr. Paul Vitz wrote a book entitled Faith of the Fatherless in which he points out that after studying the lives of more than a dozen leading atheists he found that a large majority of them had a father who was present but weak, present but abusive, or absent.[66][70] Dr. Vitz also examined the lives of prominent theists who were contemporaneous to their atheist counterparts and from the same culture and in every instance these prominent theists had a good relationship with his father.[66] Dr. Vitz has also stated other common factors he observed in the leading atheists he profiled: they were all intelligent and arrogant.

Although atheists claim there are reasonable arguments for atheism, the quality of atheist debate has been quite poor from the proponents of atheism. Below are some examples which demonstrate the unreasonableness of atheist debaters.

Doug Jesseph: In October of 1997, atheist Jeffrey Jay Lowder, a founder of Internet Infidels, stated that he believed that in regards to atheism "the most impressive debater to date" was Doug Jesseph.[85] Yet Doug Jesseph claimed in a debate with William Lane Craig in 1996 that the origin of life had a detailed atheistic explanation(s).[86] In 1996, John Horgan wrote the following regarding what the highly respected origin of life researcher Stanley Miller believed to the case regarding naturalistic explanations of the origin of life: "Miller seemed unimpressed with any of the current proposals on the origin of life, referring to them as “nonsense” or “paper chemistry.”"[87] In addition, in 1996, John Horgan wrote the following in Scientific American: "The origin of life is a science writer's dream. It abounds with exotic scientists and exotic theories, which are never entirely abandoned or accepted, but merely go in and out of fashion."[88]

Gordon Stein: In 1985, Christian apologist Dr. Greg Bahnsen and prominent proponent of atheism Gordon Stein had a debate at the University of California, Irvine regarding the positions of atheism and theism. John Frame wrote regarding the debate in which Dr. Bahnsen used the transcendental argument for the existence of God that "In the end, Stein walked and talked like a broken man."[89] The Greg Bahnsen-Gordon Stein debate was recorded and transcribed and was dubbed "The Great Debate"

Atheism and its Decline as a Theoretical Position

According to Munich theologian Wolfhart Pannenberg "Atheism as a theoretical position is in decline worldwide."[103] Oxford scholar Alister McGrath agrees and has stated that atheism's "future seems increasingly to lie in the private beliefs of individuals rather than in the great public domain it once regarded as its habitat."

Atheism in Academia

In 2001 atheist and philosopher Quentin Smith stated the following in respect to atheism: "Naturalists [atheists] passively watched as realist versions of theism … began to sweep through the philosophical community, until today perhaps one-quarter or one-third of philosophy professors are theists, with most being orthodox Christians…. God is not 'dead' in academia; he returned to life in the 1960's and is now alive and well in his last academic stronghold, philosophy departments."

Some have asserted that atheists do not exist. In regards to a biblical statement on atheism Sir Francis Bacon stated in his essay Of Atheism the following regarding atheism: "The Scripture saith, The fool hath said in his heart, there is no God; it is not said, The fool hath thought in his heart; so as he rather saith it, by rote to himself, as that he would have, than that he can thoroughly believe it, or be persuaded of it....It appeareth in nothing more, that atheism is rather in the lip, than in the heart of man.[82]"

In addition, Christian philosophers and apologists Dr. Cornelius Van Til and Dr. Greg Bahnsen argued there are no atheists and that atheists are actively suppressing their belief and knowledge of God and enigmatically engage in self-deception.

Charles Darwin wrote in his private notebooks that he was a materialist which is a type of atheist.[11][12] The Stanford Encyclopedia of Philosophy states the following:

In 1885, the Duke of Argyll recounted a conversation he had had with Charles Darwin the year before Darwin's death:

In the course of that conversation I said to Mr. Darwin, with reference to some of his own remarkable works on the Fertilization of Orchids, and upon The Earthworms, and various other observations he made of the wonderful contrivances for certain purposes in nature — I said it was impossible to look at these without seeing that they were the effect and the expression of Mind. I shall never forget Mr. Darwin's answer. He looked at me very hard and said, “Well, that often comes over me with overwhelming force; but at other times,” and he shook his head vaguely, adding, “it seems to go away. ”(Argyll 1885, 244)

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[Photo Credit: God is for Suckers!]

Pretty Flower

 
Nick sent me this picture of a beautiful flower.¹ I hope it makes your Friday more pleasant.

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1. The Best Flowering Plant.

ORFans

 
ORFans are putative genes that are only found in a single species or in a small number of closely related species. They are interesting examples of evolution. Creationists have focused on the large number of putative ORFans that have been reported in the scientific literature in order to cast doubt on evolutionary theory.

In today's Panda's Thumb Ian Musgrave has posted a long and excellent article on ORFans [Inordinately Fond of Viruses: ORFans and Intelligent Design]. It's a perfect example of how to refute a creationist ... in this case Paul Nelson.¹

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1. I know. It's usually about as difficult as shooting fish in a barrel. But in this case Ian is making a number of important points that also challenge some scientists who are confused about ORFans.

It Happens to All of Us Eventually

 
We all make mistakes from time to time. Some of us make way more than others.

John Dennehy is not one of those people. His blog is excellent and he almost always comes up with wonderful citation classics that truly deserve the attention he gives them.

Today's citation classic is not one of those classics. John seems to have slipped up this time. I hope it's only temporary [This Week's Citation Classic].

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Sophisticated Believers

The sophisticated believers have risen to the challenge. They are attempting to present reasons for believing ... reasons for not being an atheist.

One of the responses comes from Andrew Tatusko (Drew) on Notes from Off Center [God and Supernaturalism].

Drew is well qualified to represent the sophisticated view of religion ...

Andrew Tatusko is a graduate of Princeton Theological Seminary (1999, 2000) from which he earned an M.Div. and Th.M. There he focused on philosophical theology, philosophy of education, and postmodern theory. From there he was a senior instructional designer at Seton Hall University where he worked on initiatives to integrate technology into teaching and learning. Currently he is the program activity director for a Title III grant to integrate technology into teaching, learning, retention and advising at Mount Aloysius College in Cresson, PA.

He currently lives in Duncansville, PA with wife Brenna, sons Alexander and Evan, Stella (Rhodesian Ridgeback mix) and Sophie (Rhodesian Ridgeback) and two cats Digit and Kit Kat. Drew has published articles on postmodern theory, theology, and education. He is working on his dissertation in an effort to complete the Ph.D. in Higher Education Leadership, Management and Policy at Seton Hall University. The focus of the dissertation in on the influence of theological tradition on policy development in religiously-affiliated higher education since the 1970’s.

I'm looking forward to hearing his best arguments against atheism. I assume he's just getting started.

The other sophisticated believer is James F. McGrath on Exploring Our Matrix. McGrath is also well qualified to represent the sophisticated believer position. He is an Associate Professor of Religion at Butler University in Indianapolis (USA). He is the author of John's Apologetic Christology: Legitimation and Development in Johannine Christology [Amazon.com].

James is having trouble explaining his position and his frustration is showing at Not Geting Through.

If you are interested in this discussion then please read their blogs to learn more about how modern sophisticated believers refute Richard Dawkins and the other "new atheists."

See Sophisticated Religion for more discussion.

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Nobel Laureates: George Beadle and Edward Tatum

 

The Nobel Prize in Physiology or Medicine 1958.

"for their discovery that genes act by regulating definite chemical events"

George Wells Beadle (1903 - 1989) and Edward Lawrie Tatum (1909 - 1975) received the Nobel Prize in Physiology or Medicine for their work on the relationship between genes and enzymes—the "one-gene-one-enzyme" concept. They showed that single mutations usually affected production of a single enzyme in a pathway. This lead to the idea that genes encode proteins (enzymes). The concept of one-gene-one-enzyme was not meant to exclude the possibility that genes could encode RNAs or something else, in spite of the fact that this interpretation has become widely believed. The point of Beadle and Tatum's work was to show that there was a one-to-one correspondence between a gene and a protein.

THEME:Nobel LaureatesJoshua Lederberg, a former student of Beadle and Tatum's, shared the Nobel Prize with them in 1958.

The presentation speech was given by Professor T. Caspersson, member of the Staff of Professors of the Royal Caroline Institute.

Your Majesties, Your Royal Highnesses, Ladies and Gentlemen.

One of the most striking features in the development of science during the past two decades is the rapid advance in the diverse fields of biology. Here the tempo of progress continues to quicken. The research contains a vast and complex material whose major portion remains the business of specialists. The observations they make in the laboratories of basic research are apparently distant from the needs of the everyday world. But again and again we discover how short the step is from these basic findings to advances in medical therapy or diagnosis that are of importance to all of us in our daily lives.

For an example we need turn only to the previous Nobel Prize in Genetics, awarded to H.J. Muller for his discovery that X-ray irradiation can change the genetic material in living organisms. The discovery was made, and the detailed analysis carried out, in a type of small fruit fly, and at the time that the prize was awarded, perhaps gave the impression that its greatest interest was in its contribution to basic principles. Now, with the era of atomic energy upon us, we all know that the genetic risks from the high-energy radiation threatening man, belong to the things I just mentioned, of vital and immediate importance to us all.

Experimental genetics is a branch of modern biology in which progress has been especially rapid. The methods and points of view of this and its allied disciplines are indispensable for many fields of medicine today. This rapidly increasing importance of experimental genetics and cell research is easily understood. The research is now reaching towards the very elements of heredity, the structures within each cell that control its life and its behavior, and thus ultimately determine the development of the whole organism. Now we begin to see what the fundamental biological processes may be. That discoveries in this field have consequences in many others is surely no surprise to any of us.

The work of all three winners of the prize lies on this plane. Their studies are concerned with the very basis of heredity and the manner in which the genes function. That hereditary characters are transmitted from parents to offspring via special elements in the ovum and spermatozoon, the so-called genes, has long been known. The organism that develops from the fertilized ovum receives certain of the parents' characters through these genes, and the genetic material in the fertilized egg, that is to say, all these genes combined, determines the development of the organism.

The cells that together constitute an organism as a rule contain a complete set of genes characteristic of the species. In ordinary cell division these are divided and subsequently distributed equally between the two daughter cells. At fertilization, the different genetic materials from two individuals unite in the fusion of the egg and the sperm. The result of the sexual reproduction is to provide offspring with genes from both of their parents. In this way, individuals with differing combinations of characters originate. And just herein lies the biologic value of the sexual process, which can be traced throughout practically the entire animal and plant kingdoms. Without the renewal such a constant recombination of characters involves, an animal or plant species would not be able to survive the struggle for existence.

The characters, which are transmitted by the genes from generation to generation, present a picture of bewildering multiplicity. This very multiplicity of the genes' effects made it difficult to attack experimentally the problem of their structure and manner of functioning; it was impossible to trace straightforward lines that could serve as a background for an experimental study.

The situation was radically changed by Beadle and Tatum, who, through a daring and astute selection of experimental material, created a possibility for a chemical attack upon the field. Circumstantial evidence pointed to a similarity of the genetic mechanisms throughout the entire plant and animal kingdoms. Beadle and Tatum selected as object for their investigations an organism with very simple structure, a bread mold, Neurospora crassa, which is far easier to work with, in many respects, than the objects usually studied in genetics. It is able to synthesize its body substances from a very simple culture medium: sugar, salts, and a growth factor. When cultures of the mold are exposed to X-ray irradiation, mutations - that is, changes in individual genes - result as they do in other organisms. By producing a large number of such mutations and by means of an analysis of the material, which should serve as a model for analytic research, Beadle and Tatum succeeded in demonstrating that the body substances are synthesized in the individual cell step by step in long chains of chemical reactions, and that genes control these processes by individually regulating definite steps in the synthesis chain. This regulation takes place through formation by the gene of special enzymes. If a gene is damaged, for example through irradiation-induced mutation, the chain is broken, the cell becomes defective - and may possibly be unable to survive. Even in the formation of comparatively simple substances the steps in the synthetic chain are many, and consequently the number of collaborating genes large. This explains simply why gene function appeared to be so impossibly complex. The discovery provides our best means of penetrating into the manner in which the genes work and has now become one of the foundations of modern genetics. Its importance extends over other fields as well, however.

Especially valuable is the possibility it affords for detailed study of the processes of chemical synthesis in the living organism. In Neurospora material it is easy by means of X-ray irradiation to produce quickly a large number of strains in which the function of different individual genes has been disturbed. By comparing these strains we are able to determine in detail how the different stages of synthesis succeed one another when the cell's substances are formed. Beadle and Tatum's technique has become one of our most important tools for the study of cell metabolism and has already yielded results of significance to various problems in the fields of medicine and general biology.

The successful results with Neurospora also provided an incentive to continued efforts to probe the basic processes further with the aid of even simpler organisms. The bacteria are even more primitive than Neurospora. The bacterial genetic mechanism was little known; many even doubted that they had one comparable with that of the higher forms of life. Tatum extended the approaches worked out in Neurospora to the bacteria. When Lederberg came to Tatum's laboratory as a young student, they discovered that different bacterial strains could be crossed to produce an offspring containing a new combination of genetic factors. This is the counterpart of the normal sexual fertilization in higher organism; it is usually considered preferable here, however, to speak of «genetic recombination». Bacterial genetics has been developed, primarily through the efforts of Lederberg and his coworkers, into an extensive research field in recent years. He also contributed further evidence that the genetic mechanism of the bacteria corresponds to that of the higher organisms. Moreover, thanks to their simple structure and extraordinarily rapid growth, bacteria provided new and excellent possibilities for a more profound study of the genetic mechanisms. Lederberg has made many contributions in this field. Particularly important is his discovery that sexual fertilization is not the only process leading to recombination of characters in bacteria. Bits of genetic material can, if they are introduced into the bacterial body, become part of the genetic material of the bacterial cell and thus change its constitution. This is usually termed «transduction», and it is the first example demonstrating that it is possible experimentally to manipulate an organism's genetic material and to introduce new genes into it and, the organism new characters. Studies in this are now being carried out in many laboratories in different parts of the world.

The transduction process and certain other related phenomena have greatly improved our means of penetrating experimentally into the basic processes of cell function and cell growth. In all probability they will also prove to have great significance in the study of the function of the higher organisms under normal and pathologic conditions. Work in this field, carried out in laboratories throughout the world, has already greatly expanded our knowledge of the basic processes in bacteriophage infection and of the mechanism of virus infection. The observations also have opened the way to a more profound understanding of certain growth problems. Certainly cancer research will be increasingly influenced by the evolution of our knowledge of the organization of the genetic material and its manner of functioning, that has been made possible by the discoveries of this year's three winners of the Nobel Prize in Physiology or Medicine.

Doctor Beadle and Doctor Tatum. In consequence of an exemplary collaboration in which each has complemented the other to unusual advantage, it has been given to you to make discoveries of fundamental importance to our understanding of the mechanism of Life's processes.

Doctor Lederberg. At first in collaboration with your co-winners of this year's Nobel Prize, and subsequently, along ever-broadening independent lines, you have made possible the advance of research to the structure of the actual genetic material.

Gentlemen. In recognition of your outstanding contributions to science the Karolinska Institute has awarded you this year's Nobel Prize in Physiology or Medicine. On behalf of the Institute I wish to extend the warmest congratulations from your colleagues on your brilliant achievements.

It is my honoured privilege now to invite you to receive your awards from the hands of His Majesty the King.

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Who's Afraid of Bisphenol A?

 
The latest issue of the Tangled Bank points to an article on Giovanna Di Sauro about the dangers of bisphenol A. Recall that bisphenol A is a chemical found in polycarbonate drinking bottles [see Is Your Water Bottle Killing You?].

The first article outlines the chemistry of bisphenol A and its effect on mammalina cells. It refers to the latest papers that have prompted a ban on bisphenol A [Who's Afraid of Bisphenol A: (Part 1)].

The second article discusses whether bisphenol A is dangerous to humans. Can it cause cancer? [Who's Afraid of Bisphenol A: (Part 1)].

I won't tell you the conclusion because, if I did, you wouldn't read the excellent articles on Giovanna Di Sauro. But here's a teaser ...

Making decision in relation to BPA is made even more complicated by the fact that there are many estrogen-like compounds in our environment which are already in the food chain, and which we can absorb by consuming both animal and vegetable products: BPA absorption might only be the tip of the iceberg when it comes to xenoestrogen intake. It would be useful to see what the "total xenoestrogen insult" is in an average adult who consumes meat, vegetables and dairy, and to see what role BPA is playing to increase this insult. Only then we will be able to assess whether cancer risk arising from BPA ingestion is significant, or whether we would do better to worry about different sources of xenoestrogen.

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Tangled Bank #105

 
The latest issue of Tangled Bank is #105. It's hosted at The Beagle Project Blog [Tangled Bank #105].

Welcome, readers, to this tag-teamed edition of the Tangled Bank blog carnival.

In the left-justified corner, all the way from the north Yorkshire coast, not far from where Darwin 'took the waters' in Ilkley, it's Peter McGrath.

And in the right-justified corner, coming to you from London, just a few miles away from Downe Bank, Darwin's inspiration for the tangled bank where "endless forms most beautiful and most wonderful have been, and are being, evolved", it's Karen James.

Well, you glorious swine. Speaking for myself, my blogreading life was full enough without discovering some of the new delights carnivalled here. The long evening reading all these posts has been a 'mental riot' (Darwin's description of the intellectual ferment when he was incubating The Origin), for which many thanks and the RSS has a slew of new entries. A tangled bank is not a monoculture, and I think we can offer something for all here.

I would never call our dear readers much less our prolific bank-tanglers 'swine', however glorious, but I certainly do share Peter's admiration for this fortnight's entries.

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If you want to submit an article to Tangled Bank send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.

I Don't Care

 
There's been a lot of talk in the past two days about the true beliefs of Albert Einstein. A new letter has come to light suggesting that he was a pantheist at best. Richard Dawkins discusses it at Richard Dawkins discusses Einstein's new letters.

Albert Einstein died in 1955. I don't care whether he believed in a personal God, or a Spinoza God, or no God at all. What he believed has no bearing on whether supernatural beings exist or not. The beliefs of Francis Collins and Ken Miller are equally irrelevant.

What counts is the arguments they advance to bolster their beliefs and in the case of Albert Einstein we don't have a very good record of what those arguments are. This isn't true of some other scientists (Collins, Miller) where we can examine the claims to see if they are rational.

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Bertrand Russell's Teapot

 
Here's the original version of Bertrand Russell's argument, quoted from Russell's teapot on Wikipedia.

If I were to suggest that between the Earth and Mars there is a china teapot revolving about the sun in an elliptical orbit, nobody would be able to disprove my assertion provided I were careful to add that the teapot is too small to be revealed even by our most powerful telescopes. But if I were to go on to say that, since my assertion cannot be disproved, it is an intolerable presumption on the part of human reason to doubt it, I should rightly be thought to be talking nonsense. If, however, the existence of such a teapot were affirmed in ancient books, taught as the sacred truth every Sunday, and instilled into the minds of children at school, hesitation to believe in its existence would become a mark of eccentricity and entitle the doubter to the attentions of the psychiatrist in an enlightened age or of the Inquisitor in an earlier time.

This is a very powerful argument; however, it relies on one important bit of information, namely that we could not detect Russell's teapot if it really were orbiting the sun.

This important assumption is about to be put to the test now that the teapot has been located and we have the Hubble telescope in orbit. See The Wedgewood Document on Sneer Review for all the details about the experiment.

We atheists could be in big trouble if this pans out ....

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[See A Teapot in Space for the connection between Russell's teapot and The Hitchhiker's Guide to the Galaxy.]

Monday's Molecule #71

 
Today is Tuesday so it must be time for Monday's Molecule. (Oops! I was traveling yesterday and didn't get around to posting. It doesn't matter since today is a much more important day anyway—it's my birthday.)

Today's molecule is essential for all life as we know it. You need to identify the molecule and give its correct common name as well as the formal IUPAC name. Pay attention to the correct common name—some trivial names just won't do.

There's an indirect connection between today's molecule and a Nobel Prize. The prize I have in mind was not awarded for working out the structure of the molecule. We've already covered that prize. Instead, the prize was for learning something very important about the pathway for synthesis of the molecule. Something genetic.

The first person to correctly identify the molecule and name the Nobel Laureate(s) wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are three ineligible candidates for this week's reward.

THEME:

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

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

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

UPDATE: The molecule is pyridoxine (3- hydroxy-4,5 -bis (hydroxymethyl) -2-methylpyridine) also known as vitamin B₆. (Pyridoxal and pyridoxamine, along with pyridoxine, make up the members of the B₆ family.)

The Nobel Laureates are George Beadle and Edward Tatum who discovered that mutations in Neurospora affected single enzymes in a pathway. Mutants that were unable to grow on vitamin B₆ were among the first mutants they isolated in the 1940's.

The winner this week is Bill Chaney from the University of Nebraska.

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White Water

 
These photos were taken near the Champlain Bridge on the Ottawa river not far from where I grew up. This is right in the heart of Ottawa (Canada).

We never saw anything like this when we were children. The most exciting thing on the Champlain rapids was the occasional log and, rarely, a canoe shooting the rapids.

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The Dandelion Festival in Ottawa

 
Every year in May there's a famous dandelion festival in Ottawa (Canada). People come from all over the world to see the millions of dandelions along the parkways and walkways throughout the city.


Dandelion lovers are very tolerant and generous with their praise of lesser flowers. Here's a small group of dandelion fans admiring some other kind of yellow flower.


The various governments in Ottawa take advantage of the dandelion festival to promote other festivals that are scheduled in early May. The tulip festival is a prime example. Being ecumenical chaps, the tourists who come to see the dandelions will naturally drop by to look at the tulip beds, if they have time. Tulips are pretty picky about where they grow so the flowers are clustered in only a few spots in the city. (Dandelions are everywhere.)

Today was a very nice day in Ottawa. Here's a group of flower lovers who are taking a brief look at the tulips around Dow's Lake. There were about 20,000 people there when we drove by on our way back from seeing the dandelions.



Some tulips are almost as pretty as dandelions ....


I said almost.

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The Best Flowering Plant

 
Tulips are the best flower according to Jane and Michael on Beer with Chocolate. Jane and Michael may have been slightly influenced by their Birthday Adventure in Holland.

Much as I hate to disagree with my offspring (), tulips are not the best flowering plant. Dandelions (from the French dent de lion - lion's teeth) are the best plant.

Not only are dandelions beautiful, they are hardy and ubiquitous. They can grow almost anywhere with a minimum of care. In fact, you have to make special efforts to get rid of them—something you would only do if you have an extreme anti-dandelion prejudice. These days, civic governments throughout Canada are banning herbicides in order to save the dandelion. (You don't see anyone doing that for tulips, do you Jane?)

The most common species of dandelion is Taraxacum officinale.

The flowers are pretty. You can eat the leaves. The leaves will cure many diseases. You can make wine with dandelions. A company in Belgium called Brasserie Fantôme even makes a dandelion beer called Fantôme Pissenlit. (= wet the bed, from dendelion's medicinal properties).

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DNA Replication in E. coli: The Solution

In an earlier posting I described a problem that we often use to encourage critical thinking in our undergraduates. The problem is how can E. coli divide faster that the time it takes to replicate it's chromosome? [DNA Replication in E. coli: The Problem]

Recall that DNA replication always begins at an origin of replication. In bacteria there is usually one origin per chromosome or plasmid. (Eukaryotic chromsomes have multiple origins.)

The replisomes assemble at the origin and then move in opposite directions around the chromomome until the meet at the termination region. Each replisome moves at a rate of 1000 nucleotides per second and it takes about 38 minutes to complete one round of replication. But E. coli can divide every 20 minutes. That's the problem.

The firing of an origin is controlled by regulatory proteins. These proteins trigger the assembly of replisomes at the origin sequences. When most of us are first presented with this problem we think in terms of the events occurring sequentially. Thus, a chromosome is copied, the daughter chromosomes segregate, and a new round of replication begins.

This isn't what happens when the cells are dividing rapidly. Instead, a new round of replication begins at the "future origin" before the current round of replication is completed. At any given instant, there can be six or eight replication forks synthesizing DNA simultaneously inside the cell.

In order for the cell to divide every 20 minutes, all that is required is that a round of replication terminate every 20 minutes. This means that origins fire every 20 minutes. When the daughter chromosome segregate into daughter cells, they are already partially replicated in preparation for the next cell division.

Here's how Fossum et al. (2007) describe the solution in a recent paper in EMBO Journal.

The bacterium Escherichia coli has a single chromosome that is replicated from a single origin (oriC), bidirectionally to the terminus, once per division cycle (Kornberg and Baker, 1992). The cell cycle of slowly growing bacteria is quite similar to that of eukaryotic cells (Boye et al, 1996), with the G1, S and G2/M phases of bacteria termed B, C and D, respectively. E. coli (and certain other bacteria) is capable of very rapid growth in rich medium, with doubling times as short as 20 min. The replication time, however, remains long, with approximately 60–90 min required to replicate and segregate the chromosome. Therefore, the cell cycle is more complicated during rapid growth (Figure 1). If the time it takes to synthesize and segregate the daughter chromosomes (C+D) exceeds one generation time, a new round of replication must be initiated before the previous round is completed (Cooper and Helmstetter, 1968). Thus, initiation occurs at two origins in the 'mother' cell. It can even occur in the 'grandmother' cell at four origins if the time it takes to replicate and segregate the chromosome exceeds two generations. These initiations at two or four origins occur simultaneously, as one event per division cycle (Skarstad et al, 1986). While E. coli and Bacillus subtilis are two examples of bacteria capable of performing multifork replication, other bacteria, such as Caulobacter crescentus, are not. Eukaryotic cells do not replicate with overlapping cycles, but do initiate DNA replication at multiple replication origins, and thus perform a different kind of multifork replication, with the multiple forks on the same copy of the genome (Diffley, 2004).

Figure 1:Replication pattern of rapidly growing E. coli wild-type cells. Cells (yellow) with chromosomes (blue lines) and origins (black squares) are drawn schematically to show the number of replication forks and origins at different stages of the cell cycle. In this example, initiation of replication occurs at four origins at the same time as cell division (bottom). A young cell therefore contains four origins and six replication forks (upper left). As replication proceeds, the oldest pair of forks reach the terminus and the two sister chromosomes segregate. The cell then contains four origins and four replication forks (upper right). Initiation then occurs again at 4 origins and generates 8 new forks giving a total of 12 forks, as cell division approaches (bottom). Because there will be cell-to-cell variability, some cells will contain eight origins before they divide, whereas cells that divide before initiation of replication will contain only two origins (not shown). However, the majority of the cells in the culture will contain four origins.

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Fossum, S., Crooke, E. and Skarstad, K. (2007) Organization of sister origins and replisomes during multifork DNA replication in Escherichia coli. EMBO J 26:4514–4522 [doi:10.1038/sj.emboj.7601871]

Gene Genie #31

 
The 31st edition of Gene Genie has been posted at Adaptive Complexity [Capitalists, Genetic Tests and Your DNA].

Everyone knows there is a lot of crazy stuff on the internet, but did you know there is a lot of great writing about genes, genetics, and human diseases? And believe it or not, sometimes these pieces are written by people who know what they're talking about. If you're looking for what's new in human genetics, you've come to the right place.

Welcome to the 31st Gene Genie, a blog carnival dedicated to great blogging about human genes and how they impact our health. This Mother's Day edition includes an in-depth highlight of the growing industry of personalized genetics.

The beautiful logo was created by Ricardo at My Biotech Life.

The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.

Here are all the previous editions .....

1. Scienceroll
2. Sciencesque
3. Genetics and Health
4. Sandwalk
5. Neurophilosophy
6. Scienceroll
7. Gene Sherpa
8. Eye on DNA
9. DNA Direct Talk
10. Genomicron
11. Med Journal Watch
12. My Biotech Life
13. The Genetic Genealogist
14. MicrobiologyBytes
15. Cancer Genetics
16. Neurophilosophy
17. The Gene Sherpa
18. Eye on DNA
19. Scienceroll
20. Bitesize Bio
21. BabyLab
22. Sandwalk
23. Scienceroll
24. biomarker-driven mental health 2.0
25. The Gene Sherpa
26. Sciencebase
27. DNA Direct Talk
28. Greg Laden’s Blog
29. My Biotech Life
30. Gene Expression
31. Adaptive Complexity

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On the Evolution of the Blood Clotting Pathway

Theme

Blood Clotting
Last year I spent some time studying blood clotting. You can read the series of postings by clicking on the "Theme" link.

One of the reasons for reading up on this topic was because the creationists were promoting it as another example of something that could not evolve. Micheal Behe was one of those creationists.

The data is now in. Russel Doolittle has been working on the evolution of the clotting cascade and the latest results incorporate the information from the lamprey genome. Suffice to say, Behe's claims have been decisively refuted.

Ian Musgrave has the scoop in an excellent article on Panda's Thumb [Behe vs Lampreys: A modest proposal]. This should put an end to ignorant speculation about the non-evolvability of the blood clotting pathway. Or, to be more precise, it should put an end to such speculation by any intelligent, rational, person.

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Blogger’s Code of Conduct

 
If you're not going to follow the Blogger's Code of Conduct, this is what you're supposed to put on your blog.

This is an open, uncensored forum. We are not responsible for the comments of any poster, and when discussions get heated, crude language, insults and other "off color" comments may be encountered. Participate in this site at your own risk.

Don't say you haven't been warned.

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Something to look forward to ....

 

ATHEISTS and agnostics are decent people whose tormented souls will burn for all eternity in the scorching fires of hell, Britain's biggest catholic said last night.

Cardinal Cormac Murphy O'Connor said non-believers should be respected, right up to the point of death when they will finally come face to face with Satan and his blood-soaked pitchfork.

He told a conference in London: "Those without faith should not be shunned or abused. Jesus and Beelzebub are already cooking something up for them, don't you worry about that."

Gee, I wonder how he feels about Jews and Muslims?

The one good thing about all of this is that my agnostic friends will be there to keep me company. It will serve them right for not making up their minds about Beelzebub.

(Christianity is supposed to be one of the monotheistic religions. Could someone who is an expert please explain Beelzebub? Is he/she a god or just some minor supernatural being like Gabriel?)

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[Hat Tip: RichardDawkins.net]

Reciting the Lord's Prayer in Ontario's Legislature

 
Premier Dalton McGuinty started the debate in February when he called for a study of the current practice [Lord's Prayer review ordered].

Queen's Park Bureau Chief
In a bid to separate church and state – or, in this case, province – Premier Dalton McGuinty wants to end the practice of reciting the Lord's Prayer in the Ontario Legislature.

McGuinty surprised observers at Queen's Park this morning by appealing for an all-party committee to replace the prayer.

"I believe it is time for Ontario's Legislature to better reflect Ontario's reality and celebrate our diversity," the premier wrote to the leaders of the Progressive Conservatives and New Democrats.

"It is time to move beyond the daily recitation of the Lord's Prayer in the Ontario Legislature to a more inclusive approach that reflects 21st century Ontario," he said, noting the prayer was last updated in 1969.

"Our counterparts in other provinces and the federal government have adjusted their customs to reflect the diversity of the population.

"The members of the Ontario Legislature reflect the diversity of Ontario – be it Christian, Jewish, Hindu, Muslim, Sikh or agnostic. It is time for our practices to do the same. That is the Ontario way," McGuinty wrote.

This sounds pretty enlightened. Later on we learned that McGuinty had in mind multiple prayers and not just abolishing the practice altogether.

The committee has been struck. One of the first things they did was to set up a website. Within days the website crashed from the volume of submissions [Proposal to scrap Lord's Prayer crashes gov't website]. Can you guess who was responding? Yes, that's right, thousands of people who want to keep the Lord's Prayer in the legislature. It doesn't matter to them if we have Jewish, Muslim, Hindu, Buddhist, and atheist MPP's. No sireee. They all have to say the Lord's Prayer before doing any business in the house. That's only fair.

Naturally, it's the Conservatives who are leading the charge to stifle tolerance and promote bigotry. The latest example is a column from one of the editors of The National Post [John Turley-Ewart: Ontario shouldn't ditch the Lord's Prayer]. You won't believe the silliness of his argument ...

Christians across the province see the Premier's move as a sop to those who think saying the prayer is inconsistent with multiculturalism. Those who disapprove of such a move include Premier McGuinty's own mother. But that has not caused the Premier to waver in his position for change. He is on record saying: "We've got a responsibility to ensure that all people feel truly at home here."

But the move has left many Christians in Ontario wondering if the province is still their home; if it is a place that is in tune with the Christian principles that have informed the province's political and economic values — values that underpin Ontario's success story as a democratic, prosperous province. The Lord's Prayer, recited by Catholics and Protestants alike, is more than words that pay homage to God.

It represents a piece of common ground that Catholics and Protestants could agree on -- a daily ritual that helped in whatever small way to break down the intolerance that existed between the majority Protestants and minority Catholics who founded the province.

In its own small but important way, the recital of the Lord's Prayer is a symbol of the tolerance that has made Ontario the great place it is today to live. That Premier McGuinty would consider dropping the prayer in the name of tolerance is, thus, ironic. It would do a disservice to the province's history and its Christian heritage.

Ontario should keep the Lord's Prayer, add other prayers from different faiths if thought appropriate, and avoid the folly of dismissing history for feel good, fuzzy visions of multiculturalism.

Hmmm ... let's see if I understand this correctly. Forcing atheists to recite, or listen to, the Christian prayer every day, is a symbol of "tolerance."

Earth to John Turley-Ewart ... you are promoting bigotry and intolerance. If you want your Christian friends to say the Lord's Prayer then let them say it by themselves in the privacy of their offices before going to the House to do Ontario's business.

Just because a majority of MPP's may be Christians is no reason for the majority to force their religion on everyone else. That's not the Canadian way.

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Amino Acids and the Racemization "Problem"

Amino acids come in two different "flavors" depending on the orientation of atoms bound to the central α-carbon. The two possibilities are L- and D- configurations. In the examples shown here, you can see that the two forms of serine, L-serine and D-serine, are mirror images of each other. These forms are called stereoisomers because they contain the same atoms with different mirror image arrangements.

Stereoisomers cannot be interconverted without breaking covalent bonds. They are distinct molecules. Almost all amino acids in living organisms are L-amino acids. Proteins are almost exclusively composed of L-amino acids and not D-amino acids.

The α-carbon atom of amino acids is chiral, or asymmetric. You need at least one chiral atom in a molecule in order to have stereoisomers. One amino acid (glycine) does not have a chiral α-carbon so there is only one configuration of glycine.

When amino acids are synthesized in a chemistry laboratory, you often end up with a mixture of equal amounts of L- and D- stereoisomers. When you examine the amino acids found in meteorites and in the vicinity of stars, you find a mixture of both stereoisomers. These are called racemic mixtures since the process of converting one stereoisomer into another is called racemization.

Now, the fact that amino acids in living organisms are all L- forms is not a problem since the L-amino acids are the only ones that are synthesized in any appreciable amounts. All of the amino acid biosynthesis pathways produce only L- forms and not D- forms. This is not unusual since enzyme catalyzed reactions are usually sterospecific. It's not a surprise that modern proteins are composed of L-amino acids because those are the only ones available inside the cell.

The "problem" arises when we start to think about how life arose in the first place. The general assumption is that life arose in a warm pond containing a racemic mixture of L- and D- amino acids. If that is true then how did life evolve to select exclusively L-amino acids? Most of the proposed solutions to these questions make assumptions about how the primordial soup could have spontaneously come to have a preference for L-amino acids over D- amino acids.

I'd like to propose another way of thinking about this problem.¹

Let's assume there was a primordial soup where amino acids came together spontaneously to form short peptides. In the beginning, the soup contained racemic mixtures of the D- and L-forms of amino acids. These molecules were formed spontaneously by the kinds of chemical reactions that are simulated in the laboratory.

Some of the random peptides acted as catalysts for chemical reactions. This is observed in modern-day experiments. One kind of reaction, amino acid synthesis, would have been especially favorable since it created more amino acids and led to more peptides.

The simplest pathway to more amino acids is the formation of glycine, probably by adding an amino group to acetate or glycerol. (This pathway no longer exists.) The next simplest is the conversion of pyruvate (a common three carbon organic acid) to alanine—a fairly simple transamination reaction.

In modern cells, this reaction is catalyzed by sophisticated transaminases but in the beginning it would have been catalyzed by short peptides that formed spontaneously in the primordial soup. Such reactions are stereospecific, the modern reaction only produces L-alanine and never D-alanine (well, hardly ever!). Let's assume that a similar reaction in the beginning produced, by chance, L-alanine.

Another simple pathway is from oxaloacetate (a common four carbon organic acid) to aspartate. Both of these reactions require a relatively simple addition of ammonia to a keto group and both reactions could have been catalyzed (inefficiently) by the same peptide.


As I mentioned above, enzyme catalyzed reactions tend to be stereospecific so it's likely that the early products were L-alanine and L-aspartate from the same enzyme. They could have been D-alanine and D-aspartate, but they weren't. As the concentrations of glycine, L-alanine and L-aspartate increased there were more and more peptides formed and the new peptides were enriched in these two particular L-amino acids.

Other simple amino acid synthesis reactions were catalyzed in the primordial soup. The most likely one is the synthesis of serine from glycerol or glycerate (common three carbon organic alcohols or organic acids). Again, the enzyme catalyzed reactions will only produce one isomer of the amino acid and there might have been selection for those parts of the soup that made L-serine (instead of D-serine) because the L-serine could more easily combine with L-alanine and L-aspartate to make many more peptides. In this case, the specificity of the reaction derives from selecting D-glycerate over L-glycerate as the substrate.

L-serine is the precursor to L-cysteine so it's likely that L-cysteine was also one of the early amino acids to accumulate in the primordial soup. This was an important addition to the repertoire since L-cysteine has a sulfur group and that leads to many more possibilities for catalytic active sites in the peptides. Note that once L-serine began to accumulate in the soup it led directly to the stereospecific L-cysteine. You can't make D-cysteine from L-serine so there's no racemization problem once L-serine accumulates.

L-glutarate (from alpha-ketoglutartic acid, a common five-carbon organic acid) is another good candidate for the primitive amino acids. (It's quite possible that L-alanine, L-asparate, and L-glutamate were all made by the same primitive enzyme using very similar 3, 4, and 5-carbon substrates.)


At this point there would have been all kinds of peptides containing various combinations of L-alanine, L-aspartate, L-serine, glycine, L-cysteine, and L-glutamate since these six amino acids have become much more abundant that the ones formed spontaneously by uncatalyzed reactions that produce a racemic mixture. This is probably the time when there was a shift to encoding peptides in a sequence of nucleotides.

This is an important point. The shift to more and more complex peptides did not have to take place in a random mixture of both forms of all 20 amino acids. It could have taken place under conditions where there was already a significant enrichment of a small number of L-amino acids due to catalytic biosynthesis from non-amino acid precursors.

There's some suggestive evidence to indicate that the primitive genetic code was much simpler than the one we see today and may have only had codons for the six initial amino acids. The other L-amino acid synthesis pathways arose later on and the genetic code expanded when codons were "stolen" from the precursors of these new L-amino acids.

One of the primitive codons for aspartate, for example, might have been AXX (any codon beginning with A). L-aspartate is the precursor to: L-lysine (AAA, AAG), L-asparagine (AAU, AAC), L-threonine (ACX), L-methionine (AUG), and L-isoleucine (AUU, AUC, AUA). The idea is that the new amino acids were originally synthesized on L-aspartate that was attached to its tRNA and they were incorporated into proteins at some positions in place of L-asparate. (This hypothesis on the origin of the genetic code was developed by my former colleague Jeff Wong. The idea came to him while teaching an undergraduate course in biochemistry ... but that's another story.)

Note that many amino acids are made from pre-existing amino acids. Once you have a supply of L-aspartate, for example, it follows that the derivatives will also be L- forms. There's no need to postulate that the preferential use of L-asparagine, L-threonine, L-methinione, and L-isoleucence, in contrast to the D- forms, arose independently. This greatly reduces the probability problem that most people are hung up on.

I don't have any good ideas about how the transition to encoded peptides happened but that's not the real point of this speculative posting.

The real points are ....

1. The most primitive catalysts were probably not very big. They were probably composed of mixtures of L- and D-amino acid residues.
2. The first important step was synthesis of new stereospecific amino acids which meant that the process was no longer dependent on the original pool of compounds that formed spontaneously.
3. The first peptides and polypeptides (proteins) probably contained only six amino acids. These are the amino acids that can be easily made from readily available precursors.

If you think about the origin of life in this way it will help you to understand why biochemists don't think the "racemization problem" is a real problem. This scheme will also help you to understand why some *particular* amino acids came to be enriched in proteins and not all of the other amino acids that were in the primordial soup in the very beginning. (There are far more than 20 amino acids.)

The original choice of the first L-amino acids over their D-isomers was probably an accident. It could just as easily have been the D- amino acids.

UPDATE: I now believe that Metabolism First and the Origin of Life is a more likely explanation for the origin of life. Please ignore references to "primordial soup" in the essay above. My conversion doesn't change the point. In the beginning very simple amino acids were spontaneously synthesized in restricted environments around thermal vents. By chance, the first chiral amino acid, alanine?, may have been L-alanine. All other may have been synthesized using L- amino acid precursors and this explains the the racemization problem.

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1. This is a modified version of an article that was originally posted on talk.origins in January, 2004.