What Should We Teach About the "Tree of Life"?

As most of you already know, I think the Three Domain Hypothesis is dead. The history of life is better explained as a net with rampant transfer of genes between species [The Web of Life]. This idea has been widely promoted by Ford Doolittle.

The debate over the tree of life has implications concerning the distinction between "prokaryote" and "eukaryote." I was checking some recent papers and came across one by Doolittle and Zhaxybayeva (2013) that seems particularly relevant. They discuss the evidence for and against the division of life into three domains and the attempt by Norm Pace to ban the word "prokaryote."

The authors point out, once again, that eukaryotic genes are most closely related to genes from cyanobacteria, proteobacteria, and archaebacteria, in that order. The majority, by far, have their closest homologs in bacteria, not archaebacteria. The most likely explanation is that euakryotes are chimeras resulting from fusion of an archaebacterium and a eubacterium plus genes transferred from mitochondria and chloroplast to the nuclear genome.

The Three Domain Hypothesis (part 3)

The scientific dispute over The Three Domain Hypothesis is based on the validity of RNA trees, the importance of protein trees that disagree with the rRNA tree, the evidence for fusions, and the frequency of Lateral Gene Transfer (LGT). But, as usual, there’s more to it than just science. The side with the best advocates has a huge advantage in fights like this.

Let's set the stage by quoting from the article by William Martin.

Thus, it seems to me that there is a schisma abrew in cell evolution, with the rRNA tree and proponents of its infallibility on the one side and other forms of evidence, proponents of LGT, or proponents of a symbiotic origin of eukaryotes on the other. The former camp is well organized behind a unified view (be it right or wrong, still a view) and is arguing that we already have the answers to microbial evolution. The latter camp is not organized into castes of recognized leadership and followers, meaning that (if we are lucky) concepts and their merits, not position or power, will determine the outcome of the battle as to what ideas might or might not be worthwhile entertaining as a working hypothesis for the purpose of further scientific endeavour.

The article by Norman Pace represents the side that already has the answers. He is a strong proponent of the Three Domain Hypothesis. These days, the main thrust of his argument is that we should all jump on the bandwagon or risk being left behind. I heard him speak in San Francisco last April and he sounded more like a preacher than a scientist. His article in Nature, ”Time for a Change”, is an example of the way the Three Domain Hypothesis proponents have been arguing for 20 years.

One of the key problems in deep phylogeny is choosing the right gene. Pace argues in favor of ribosomal RNA—not a surprise since he has invested over 20 years in this molecule. Ideally, what kind of gene do we want to examine in order to determine the deepest branches in the tree of life? According to Pace there are three criteria ....

1. The gene must be universal.
2. The gene must have resisted lateral gene transfer.
3. The gene must be large enough to provide useful phylogenetic information.

Only ribosomal RNA meets all three criteria, says Pace.

There’s no question about #1. Ribosomal RNA genes are fond in all species. There are very few other genes that meet this criterion. Almost all other candidates are absent in at least a few species. Ribosomal RNA satisfies #3 as well. Even the small subunit is large enough.

What about #2? Which genes have “resisted” lateral gene transfer? You can’t just declare by fiat that ribosomal RNA genes haven’t been transferred. It’s a debatable question as we’ll see later on.

I would add three other criteria.

4. The gene must be unique, or if it isn’t, paralogues must be easily recognized.
5. The gene must encode a protein because it’s much more accurate to analyze amino acid sequences than nucleic acid sequences. (And easier to align.)
6. The gene must be highly conserved in order to retain significant sequence similarity at the deepest levels.

Ribosomal RNA doesn’t do so well when we add these criteria. Most bacterial genomes have multiple copies of ribosomal RNA genes. They are usually 99% similar but there are known examples of more divergent paralogues. This is not likely to be a serious problem for deep phylogeny, but it has caused problems at the species level.

Ribosomal RNA does not encode protein. That’s a serious problem that Pace never addresses.

Ribosomal RNA genes are well conserved but not as highly conserved as some others. This is why rRNA can be used to distinguish closely related species whereas the sequences of other genes are identical unless the species diverged more than 10-20 million years ago. Part of the problem with using rRNA sequences in deep phylogeny is that they are too divergent.

Having declared that ribosomal RNA genes are the best choice, Pace then goes on to show us the “true”universal tree of life. As you can see, it is divided into three distinct clusters separated by long branches. The clades represent Bacteria, Archaea, and Eukaryotes; the Three Domains. The prokarotes (Bacteria and Archaea) seem to associate and the eukaryotes seem to be more distantly related.

But first impressions can be misleading. Pace puts the root on the branch leading to bacteria and not on the long branch leading to Eukaryotes. This root is based entirely on two old 1989 papers, which he references. Both of these papers have been refuted, but that’s not something you would learn from reading Pace’s article. (There are other, more recent, experiments that root the tree on the bacterial branch and these should have been used. The fact that they weren’t reflects Pace’s degree of critical thinking on this problem. )

To many of us, the large scale structure of the tree of life just doesn’t look right. The long branches leading from the trifurcation point to Bacteria and Eukaryotes smack of artifact. The branching within each of the domains looks too simple. It’s part of the reason why there’s skepticism about the rRNA tree, as we’ll see.

The rest of the article is a passionate defense of the importance of bacteria. I agree with him, for the most part, and so do lots of evolutionary biologists. Bacteria are much more important than eukaryotes! :-)

Pace contributes very little to the debate since he is not willing to entertain any doubts about the Three Domain Hypothesis. For that we have to look at some other papers.

---

Microbobial Phylogeny and Evolution: Concepts and Controversies Jan Sapp, ed., Oxford University Press, Oxford UK (2005)

Jan Sapp The Bacterium’s Place in Nature

Norman Pace The Large-Scale Structure of the Tree of Life.

Woflgang Ludwig and Karl-Heinz Schleifer The Molecular Phylogeny of Bacteria Based on Conserved Genes.

Carl Woese Evolving Biological Organization.

W. Ford Doolittle If the Tree of Life Fell, Would it Make a Sound?.

William Martin Woe Is the Tree of Life.

Radhey Gupta Molecular Sequences and the Early History of Life.

C. G. Kurland Paradigm Lost.

---

Science Doesn't Have All the Answers but Does It Have All the Questions?

Jerry Coyne has been following the debate between Steven Pinker and Leon Wieseltier on the topic of scientism [see The final round: Pinker vs. Wieseltier on scientism]. Jerry seems to agree with both Pinker and Wieseltier that there are "two magisteria" (science and humanities) ...

[Wieseltier] calls for a “two magisteria” solution, with science and humanities kept separate, but with “porous boundaries.” But that is exactly what Pinker called for, too! Wieseltier claims that Pinker and other advocates of scientism advocate “totalistic aspirations,” i.e., the complete takeover of humanities by the sciences (“unified field theories,” Wieseltier calls them), but Pinker explicitly said that he wasn’t calling for that.

...

As you can see above, Steve never argued that science is, or should be, supreme in all the contexts. Indeed, in his earlier piece he noted that art and literature, while they might be informed in some ways by science, nevertheless have benefits independent of science. To me, those benefits include affirming our common humanity, being moved by the plight of others, even if fictional, and luxuriating in the sheer beauty of music, words, or painting. (Note, though, that one day science might at least explain why we apprehend that beauty.)

I'm not sure how Pinker, Wieseltier, and Coyne are defining science but it's clear that they aren't using the same definition I use.

I think that science is a way of knowing based on evidence and logic and healthy skepticism. I think that all disciplines seeking knowledge use the scientific approach. This is the broad definition of science used by many philosophers and scientists.

Maarten Boudry discusses, and accepts, this definition in his chapter on "Loki's Wager and Lauden's Error" in Philosophy of Pseudescience: Reconsidering the Demarcation Problem. Boudry says that the distinction between the ways of knowing used by biologists, philosophers, and historians are meaningless and there's no easy way to distinguish them (territorial demarcation). On the other hand, there is a way to distinguish between good scientific reasoning and bad scientific reasoning like Holocaust denial.

I have expressed little confidence in the viability of the territorial demarcation problem, and even less interest in solving it. Not only is there no clear-cut way to disentangle epistemic domains like science and philosophy, but such a distinction carries little epistemic weight. The demarcation problem that deserves our attention is the one between science and pseudoscience (and the analogous ones between philosophy and pseudophilosophy and between history and pseudohistory).

Sven Ove Hanson is more specific because he actually defines "science in a broad sense" in a way that I have been using it for several decades. This is from his chapter on "Defining Pseudoscience and Science" in Philosophy of Pseudescience: Reconsidering the Demarcation Problem.

Unfortunately neither "science" nor any other established term in the English language covers all the disciplines that are parts of this community of knowledge disciplines. For lack of a better term, I will call them "science(s) in the broad sense." (The German word "Wissenschaft," the closest translation of "science" into that language, has this wider meaning; that is, it includes all the academic specialties, including the humanities. So does the Latin "scientia.") Science in a broad sense seeks knowledge about nature (natural science), about ourselves (psychology and medicine), about our societies (social science and history), about our physical constructions (technological science), and about our thought construction (linguistics, literary studies, mathematics, and philosophy). (Philosophy, of course, is a science in this broad sense of the word.)

If this is what we mean by science" then there's no difference between the ways we try to acquire knowledge in the humanities or the natural sciences and the debate between Pinker and Wieseltier takes on an entirely different meaning.

There aren't "two magisteria" but only one. Unless, of course, someone is willing to propose a successful non-scientific way of knowing. I have asked repeatedly for examples of knowledge ("truth") that have been successfully acquired by any other way of knowing. So far, nobody has come up with an answer so we can tentatively conclude that science (in the broad sense) is the only valid way of acquiring true knowledge.

Clearly we don't have all the answers to everything so it's clear that neither science nor anything else has all the answers. What about the questions? Are there any knowledge questions that science (in the broad sense) can't address? I don't think there are. I think "science" covers all the questions even though it doesn't (yet) have all the answers.

If this is "scientism" then I'm guilty. What is the alternative? Is it revelation (revealed truth)? Or is there some other way of knowing that I haven't heard about?

---

Is "Prokaryote" a Useful Term?

 
Coturnix (Bora Zivkovic) is the Online Community Manager at PLoS-ONE (Public Library of Science). Part of his job is to get people to post comments on the PLoS websites. [New in Science Publishing, etc.]

So when Bora suggested we get involved in a debate on "Is "prokaryotic" an outdated term?" I hopped on over to the PLoS website and read the comments. I discovered that you have to register on PLoS in order to comment so I went ahead and did that and posted a response to the question.

I don't like registering on websites, it's a painful process, especially in this case 'cause you have to answer a lot of questions. It took me about ten minutes to figure out what to do and to convince the program to let me register even though I didn't want to receive email spam from PLoS. I also had to make up a user ID—Larry_Moran, in this case—because, apparently your name isn't good enough. This is not a very open process.

Theme

The Three Domain Hypothesis
Anyway, the question is important. If you think the Three Domain Hypothesis is well established, then you believe there are two non-eukaryotic domains (Bacteria, Archaea). Furthermore, the eukaryotes cluster with the Archaea according to this hypothesis. Thus, the word "prokaryote" encompasses a paraphyletic group and becomes useless.

But we wouldn't be having this discussion if the Three Domain Hypothesis is incorrect. In that case, the root of the tree might well be a split between eukaryotes and prokaryotes. The point is that the discussion about usefulness of "prokaryote" is really a debate about the validity of the Three Domain Hypothesis and we shouldn't forget that. It's wrong to assume that your side has won that debate and then start to solidify your apparent victory by defining your opponent's point of view out of existence!

Territorial demarcation and the meaning of science

Massimo Pigliucci doesn't get enough respect. He's upset by the "New Atheists" who place a great deal of emphasis on the scientific way of knowing and demand evidence that any other way of knowing is successful. These mean New Atheists (I count myself as one of them) use a very broad definition of science that includes most of the admirable activities of philosophers. Pigliucci is mostly a philosopher and he doesn't think that philosophy is getting enough respect from the New Atheists.

Here's the cartoon he published on his blog to illustrate the problem [see Rationally Speaking cartoon: Sam Harris].

Theme: The Three Domain Hypothesis

 
This is a series of postings that describe the Three Domain Hypothesis. The Three Domain Hypothesis is the idea that life is divided into three domains—bacteria, archaebacteria, and eukaryotes—and that the archaebacteria and eukaryotes share a common ancestor. An example of this tree of life is shown on the Dept. of Energy (USA) Joint Genome Initiative website [JGI Microbial Genomes] (left).

The hypothesis was promoted by Carl Woese in the 1980's but the pure form has now been abandoned and replaced with a “net of life” concept of early evolution as shown in the figure below. This figure is taken from Ford Doolittle's Scientific American article "Uprooting the Tree of Life" (February 2000). © Scientific American




The Three Domain Hypothesis (part 1) (Nov. 17, 2006 )

The Three Domain Hypothesis (part 2) (Nov. 22, 2006)

The Three Domain Hypothesis (part 3) (Nov. 26, 2006)

The Three Domain Hypothesis (part 4) (Nov. 29, 2006)

The Three Domain Hypothesis (part 5) (Dec. 8, 2006)

The Three Domain Hypothesis (part 6) Carl Woese (Dec. 31, 2006)

Now the IDiots Don't Get Evolution (Feb. 14, 2007)

The Web of Life (March 15, 2007)

Is "Prokaryote" a Useful Term? (October 4, 2007)

Celebrating the Three Domain Hypothesis (October 18, 2007)

The Tree of Life (May 22, 2008)

Sequence Alignment (June 22, 2008)

On the Origin of Eukaryotes (December 27, 2008)

The Tree of Life (July 29, 2009)

Perspectives on the Tree of Life: Ford Doolittle (July 30, 2009)

Perspectives on the Tree of Life: Day One (July 31, 2009)

Perspectives on the Tree of Life: Day Two (August 1, 2009)

Perspectrives of the Tree of Life: Day Three (August 7, 2009)

3,000 new genes discovered in the human genome - dark matter revealed

Let's look a a recent paper published by a large group of medical researchers at the University of California, Los Angeles (USA). The paper was published online a few days ago (Oct. 26, 2015) in Nature Immunology.

The authors clam to have discoverd 3,000 previously unknown genes in the human genome.

The complete reference is ...

Nobel Laureates: Gerald Edelman and Rodney Porter

 

The Nobel Prize in Physiology or Medicine 1972.

"for their discoveries concerning the chemical structure of antibodies"

Gerald M. Edelman (1929 - ) and Rodney R. Porter (1917 - 1985) received the Nobel Prize in Physiology or Medicine for elucidating the structure of immunoglobulins (antibodies). They determined that immunoglobulins were composed of two heavy chains and two light chains. There are three domains in the molecule. Two of them form binding sites for antigens and the third one links the two heavy chains together.

Edelman and Porter founded the field of molecular immunology, a field that today encompasses hundreds of labs. If you count all the clinical immunologists and cellular immunologists, there are as many immunology labs in the world as there are biochemistry labs. That was not true in the 1950's when Edelman and Porter began their work.

The presentation speech was in Swedish by Professor Sven Gard of the Karolinska Medico-Chirurgical Instit.

THEME:
Nobel Laureates

Your Royal Highnesses, Ladies and Gentlemen,

Immunebodies or antibodies is the designation of a group of proteins in the blood, that play an important part in the defense against infections and in the development of many different diseases. Their perhaps most characteristic property is the capacity to react and combine with substances, foreign to the organism, so-called antigens and to do so in a highly specific manner. There probably exist more than 50,000 different antibodies in the blood, each of them reactive against one particular antigen. Their main features are similar but they show individual characteristics and constitute, therefore, an extremely heterogeneous group. Since, in addition, they appear as very large molecules of a complex structure, it is understandable that the study of their chemistry for a long time offered great difficulties.

Up to 1959 the knowledge about their nature and mechanism of action was rather incomplete. That same year, however, Edelman and Porter separately and independently published their fundamental studies of the molecular structure of antibodies. Both of them had aimed at splitting the giant molecule into smaller, well defined fragments that might be more easily analysed than would the whole complex.

Porter's aim was to separate those parts of the antibody which are responsible for their specific reactivity. He hoped by this means to obtain a preparation lacking most of the biologic functions of the antibody but, on account of its capacity of combination, capable of competing with the antibody for the binding sites of the antigen. He succeeded in achieving this by means of treatment of the antibody, under strictly controlled conditions, with a protein-splitting enzyme called papain. By this treatment the antibody split into three parts. Two of these could combine specifically with the antigen and they were almost identical in other respects as well. The third fragment differed distinctly from the others, lacked binding capacity but possessed certain other biologic characteristics of the intact molecule.

Edelman for his part assumed the molecule, like those of many other proteins, to be composed of two or more separate chain structures held together by cross links of some kind, most probably so-called sulphide bonds. His assumption turned out to be correct. By means of a fairly rough treatment he was able to sever the cross bonds and release a number of separate chain molecules. Both he and Porter could later show that the antibody was in fact composed of four chains, one pair of identical, "light" chains and one pair of like- wise identical, "heavy" chains.

On the basis of the collected evidence Porter built a model of the molecule which has later, with overwhelming probability, been proven correct.

Accordingly the antibody molecule appears in the shape of the letter Y, with a stem and two angled branches. Each branch is composed of one light and one half of a heavy chain in side by side arrangement. The stem is made up of the remaining halves of the heavy chains. The specific combining capacity is accounted for by the structure of the free tips of the branches and in like measure by the light and the heavy chain; separately they are inactive. Porter's papain treatment attacks the molecule exactly at the point of branching and splits off the branches from the stem.

These discoveries incited an intense activity in laboratories in the four corners of the world. Apparently there existed a latent need for immunochemical research that could not be satisfied until today's prize winners had opened the way and provided the means. During the two decades that have since past our knowledge about the processes of immunity has broadened and deepened to an extent that perhaps has not yet been fully appreciated, even by some specialists in closely related fields. Many novel and fascinating aspects on problems in the fields of molecular biology and genetics have grown out of the immunochemical studies. We have now a new and firmer grasp of the question of the role of immunity as defense against and as cause of disease. Our possibilities to make use of immune reactions for diagnostic and therapeutic purposes have improved. It is, thus, a very important pioneer contribution that has been rewarded with this year's prize in physiology or medicine.

Gerald Edelman, Rodney Porter,

By clarifying the principal chemical structure of immunoglobulins you achieved an extremely important break-through in the field of immunochemistry. You, so to speak, opened the sluice-gates and gave impetus to the flood of research that soon started gushing forth, irrigating previously arid land, making it fertile and producing rich harvests. By awarding you the prize in 'physiology or medicine the Karolinska Institute has recognized the great significance of your accomplishments for biology in general and medicine in particular. On behalf of the Institute I wish to express our admiration and extend to you our heart-felt felicitations.

Now I ask you to proceed to receive your prize from the hands of His Royal Highness the Crown Prince.

---

[Image Credit: The cartoon of an immunoglobulin molecule is from the Genetics Home Reference website of the National Institutes of Health (USA).]

John Mattick still claims that most lncRNAs are functional

Most of the human genome is transcribed at some time or another in some tissue or another. The phenomenon is now known as pervasive transcription. Scientists have known about it for almost half a century.

At first the phenomenon seemed really puzzling since it was known that coding regions accounted for less than 1% of the genome and genetic load arguments suggested that only a small percentage of the genome could be functional. It was also known that more than half the genome consists of repetitive sequences that we now know are bits and pieces of defective transposons. It seemed unlikely back then that transcripts of defective transposons could be functional.

Part of the problem was solved with the discovery of RNA processing, especially splicing. It soon became apparent (by the early 1980s) that a typical protein coding gene was stretched out over 37,000 bp of which only 1300 bp were coding region. The rest was introns and intron sequences appeared to be mostly junk.

Nobel Laureate: François Jacob

 

The Nobel Prize in Physiology or Medicine 1965.

"for their discoveries concerning genetic control of enzyme and virus synthesis"

François Jacob (1920 - ) received the Nobel Prize in Physiology or Medicine for his work on gene expression. He shared the prize with André Lwoff and Jacques Monod. The three men worked together at the Institut Pasteur in Paris, France, at a time when it was one of the leading centers of research in this field.

Jacob made major contributions to the discovery of messenger RNA and the regulation of transcription when these processes were just beginning to be understood. His name, and Monod's, are mostly associated with the lac operon in E. coli but the prize was also given for work with bacteriophage. The concepts of operons, operators, and repressors all come from the work of Jacob and Monod.

THEME:

Nobel Laureates
The presentation speech was given by Professor Sven Gard, member of the Nobel Committee for Physiology or Medicine of the Royal Caroline Institute. As you read it, note how much they knew in 1965 after only a few years of intense work in deciphering the genetic code and working out how genes are transcribed. This is only 12 years after Watson & Crick's paper on the structure of DNA. That's the same amount of time that has elapsed between 1996, when Dolly the sheep was cloned, and today.

Your Majesties, Royal Highnesses, Ladies and Gentlemen.

The 1965 Nobel Prize in Physiology or Medicine is shared by Professors Jacob, Lwoff and Monod for «discoveries concerning the genetic regulation of enzyme and virus synthesis».

This particular sphere of research is by no means easy. I heard one of the prize winners, Professor Jacob, forewarn an audience of specialists more or less as follows: «In describing genetic mechanisms, there is a choice between being inexact and incomprehensible». In making this presentation, I shall try to be as inexact as conscience permits.

It has become progressively more apparent that the answer to what has hitherto been romantically termed the secret of life must be sought in the mechanism of action and in the structure of the hereditary material, the genes. This central field of research has naturally been approached from the periphery and in stages. Only in recent years has it been possible to make a serious attack on these fundamental problems.

Several previous Nobel Prize holders: Beadle, Tatum, Crick, Watson, Wilkins, Kornberg and Ochoa have worked in this sphere of research and have formulated certain basic proposals which have enabled the French scholars to continue their efforts. It has been established that one of the principal functions of genes must be to determine the nature and number of enzymes within the cell, the chemical apparatus which controls all the reactions by which the cellular material is formed and the energy necessary for various life processes is released. There is thus a particular gene for each specific enzyme.

In addition, some light has been thrown on the chemical structure of genes. In principle, they have the form of a long double chain consisting of four different components, which can be designated by the letters a, c, g, and t, and with the property of forming pairs with each other. An «a» in one of the chains has to be matched by a «t» in the other, a «g» only by a «c». However, they can be linked along the length of the chain in any order whatsoever, so that the number of possible combinations is virtually unlimited. A chain of genes contains from several hundreds to many thousands of units; such structures can easily carry the specific patterns for the million or more genes which it is estimated that a cell may have.

This model of the genes represents a coded message containing two types of information. If the double chain of a gene is split lengthwise and each half acquires a new partner, then the final result is two double chains identical to the original gene. The model thus contains information relative to the actual structure of the gene, which permits multiplication, in its turn a condition of heredity. When a cell divides, each daughter cell receives an exact copy of the parent gene. The structure of the double chain ensures the stability and permanence required by hereditary material.

But the model can also be read in another way. Along the length of the chain, the letters are grouped in threes in coded words. An alphabet of four letters allows the formation of more than 30 different words and the sequence in the gene of such words provides the structural information for an enzyme or some other protein. Proteins are also chain molecules built up from twenty or so different types of building blocks. To each of these building blocks there corresponds a chemical code word of three letters. The gene thus contains information on the number, nature, and order of the building blocks in a particular protein.

Thus it was already clear that the hereditary blueprint contained the collective structural information for all substances necessary for the functions of the living cell. It was not known how the genetic information was put into effect or transformed into chemical activity. As to the function of the genes, it was thought that they participated in a sort of procreative act when the new cell came into being, producing new substances necessary for the life of the cell, but subsequently lying dormant until the next cell division. It was presumed that the structure and formation of the chemical apparatus determined in this way defined all the regulatory mechanisms necessary for the cell's ability to adapt to changes in the environment and to respond in an adequate manner to stimuli of different types.

To begin with, the group of French workers were able to demonstrate how the structural information of the genes was used chemically. During a process resembling gene multiplication an exact copy of the genetic code is produced, termed a messenger. The latter is then incorporated into the chemical «workshop» of the cell and wound like magnetic tape onto a spool. For each word arriving on the spool, a constructional unit is attracted, which carries a complement to this word and attaches itself there just like a piece of jigsaw puzzle. The building blocks of a protein are selected in this way one by one, aligned, and joined together to form a protein with the appropriate structure.

The messenger substance is, however, short-lived. The tape lasts only for a few recordings. The enzymes are also used up in a similar way. For the cell to maintain its activity, it is thus necessary to have an uninterrupted production of the messenger material, that is to say continuous activity of the corresponding gene.

However, cells can adapt themselves to different external conditions. Thus there must exist some mechanisms controlling the activity of the genes. The research into the nature of these mechanisms is a remarkable achievement which has opened the way for the possible explanation of a series of hitherto mysterious biological phenomena. The discovery of a previously unknown class, the operator genes, which control the structural genes, marks a major breakthrough.

There are two types of operator genes. One type releases chemical signals, which are perceived by a second, receptor, type. The latter controls in its turn one or more structural genes. As long as the signals are being received the receptor remains blocked and the structural genes are inactive. Certain substances coming from outside or formed within the cell can, however, influence the chemical signals in a specific manner, changing their character so that they can no longer influence the receptor. The latter is unblocked and activates the structural genes; messenger material is produced and the synthesis of enzymes or another protein commences.

Control of gene activity is thus of a negative nature; the structural genes are only active if the repressor signals do not arrive. One can speak here of chemical control circuits similar in many ways to electrical circuits, for example in a television set. In the same way, they can be interconnected or arranged in a series to form complicated systems.

With the aid of such control circuits, the free living monocellular organism can produce enzymes when required, or interrupt chemical reactions if they are likely to cause damage; an excitatory stimulus can provoke movement, flight or attack, depending on the nature of the excitation. With such mechanisms it is possible to direct the development of cells into more complicated structures. It is particularly interesting to note that the activity of viruses is controlled, in principle, in the same manner.

Bacteriophages contain a genetic control circuit complete with emitter, receptor, and structural genes. While chemical signals are being sent and received, the virus remains inactive. When incorporated into a cell, it behaves like a normal component of the cell, and can confer on it new properties which may improve its chances of survival in the struggle for existence. However, if the signals are interrupted, the virus is activated, starts to grow rapidly and soon kills the host cell. There is considerable evidence for the view that certain types of tumor virus are incorporated into a normal cell in the same way, thus transforming it into a tumour cell.

We are easily inclined to hold an exaggerated opinion of ourselves in this era of advanced technology. Thus, we are justified in having a great admiration for the achievements in electronics, where, for example, the attempts at miniaturization to reduce component size, to lower the weight, and reduce the volume of apparatus have enabled a rapid development of space science. However, we should bear in mind that, millions of years ago, nature perfected systems far surpassing all that the inventive genius of man has been able to conceive hitherto. A single living cell, measuring several thousandths of a millimetre, contains hundreds of thousands of chemical control circuits, exactly harmonized and functioning infallibly. It is hardly possible to improve on miniaturization further; we are dealing here with a level where the components are single molecules. The group of French workers has opened up a field of research which in the truest sense of the word can be described as molecular biology.

Lwoff represents microbiology, Monod biochemistry, and Jacob cellular genetics. Their decisive discovery would not have been possible without competence and technical knowledge in all these fields, nor without intimate cooperation between the three researchers. But the mystery of life is not resolved simply with knowledge and technical skill. One must also have a gift for observation, a logical intellect, a faculty for the synthesis of ideas, a degree of imagination, and scientific intuition, qualities with which the three workers are liberally endowed.

Research in this field has not yet yielded results that can be used in practice. However, the discoveries have given a strong impetus to research in all domains of biology with far-reaching effects spreading out like ripples in the water. Now that we know the nature of such mechanisms, we have the possibility of learning to master them, with all the consequences which that will surely entail for practical medicine.

François Jacob, André Lwoff, Jacques Monod. Thanks to your technically unimpeachable experiments and your ingenious and logical deductions, you have gained a more intimate familiarity with the nature of vital functions than anyone before you has done. Action, coordination, adaptation, variation - these are the most striking manifestations of living matter. By placing more emphasis on dynamic activity and mechanisms than on structure, you have laid the foundations for the science of molecular biology in the true sense of the term. In the name of the Caroline Institute, I ask you to accept our admiration and our most sincere congratulations. Finally, I invite you to come down from the platform to receive the prize from His Majesty the King.

---

The Three Domain Hypothesis (part 1)

 

The Three domain Hypothesis is dead. It passed away peaceably sometime in the past ten years. Most people didn't notice.

Last year a wake was held. Friends and enemies of the Three Domain Hypothesis were invited. Many gave eulogies and these were published in a book called Microbial Phylogeny and Evolution: Concepts and Controversies. This is a collection of papers by leading scientists in the field. It's edited by Jan Sapp, a Professor of Biology at York University here in Toronto. I've listed the most interesting articles at the bottom of the page and I'll stick to comments on these articles for now.

Surprisingly, some of the guests at the wake did not know the hypothesis had been falsified. They thought the corpse was still breathing!

The Three Domain Hypothesis refers to the proposal by Carl Woese that; (1) archaebacteria form a monophyletic group, (2) this clade is sufficiently different from all other prokaryotes to deserve elevation to a separate Domain called Archaea (the other two Domains are Bacteria and Eukarya), (3) eukaryotes are more closely related to archaebacteria than to other prokaryotes, and (4) the root of the universal tree of life lies in the branch leading to Bacteria.

The "standard" universal tree of life is based on the Three Domain Hypothesis. It is mostly derived from sequences of the small ribosomal RNA subunit (SSU).

In recent years, all four of the major claims of the Three Domain Hypothesis have been challenged. Some would say that two have been falsified. Furthermore, there is growing recognition that SSU-based trees are not as reliable as we once thought. Surprisingly, this skepticism among evolutionary biologists has not reached the ear of the average scientist who continues to act as though the Three Domain Hypothesis is a done deal.

The literature is large, varied, and controversial. I've been following it for twenty years and it's not possible to write a short note covering all the bases. Instead, I'll concentrate on reviewing a few of the papers in the book.

---

Norman Pace The Large-Scale Structure of the Tree of Life.

Woflgang Ludwig and Karl-Heinz Schleifer The Molecular Phylogeny of Bacteria Based on Conserved Genes.

Carl Woese Evolving Biological Organization.

W. Ford Doolittle If the Tree of Life Fell, Would it Make a Sound?.

William Martin Woe Is the Tree of Life.

Radhey Gupta Molecular Sequences and the Early History of Life.

C. G. Kurland Paradigm Lost.

Are most transcription factor binding sites functional?

The ongoing debate over junk DNA often revolves around data collected by ENCODE and others. The idea that most of our genome is transcribed (pervasive transcription) seems to indicate that genes occupy most of the genome. The opposing view is that most of these transcripts are accidental products of spurious transcription. We see the same opposing views when it comes to transcription factor binding sites. ENCODE and their supporters have mapped millions of binding sites throughout the genome and they believe this represent abundant and exquisite regulation. The opposing view is that most of these binding sites are spurious and non-functional.

The messy view is supported by many studies on the biophysical properties of transcription factor binding. These studies show that any DNA binding protein has a low affinity for random sequence DNA. They will also bind with much higher affinity to sequences that resemble, but do not precisely match, the specific binding site [How RNA Polymerase Binds to DNA; DNA Binding Proteins]. If you take a species with a large genome, like us, then a typical DNA protein binding site of 6 bp will be present, by chance alone, at 800,000 sites. Not all of those sites will be bound by the transcription factor in vivo because some of the DNA will be tightly wrapped up in dense chromatin domains. Nevertheless, an appreciable percentage of the genome will be available for binding so that typical ENCODE assays detect thousand of binding sites for each transcription factor.

This information appears in all the best textbooks and it used to be a standard part of undergraduate courses in molecular biology and biochemistry. As far as I can tell, the current generation of new biochemistry researchers wasn't taught this information.

Understanding Mutation Rates and Evolution

The recent article by physician Joseph A. Kuhn contains a lot of errors and misunderstandings [Physicians Can Be IDiots]. Today I want to focus on one paragraph.

The complexity of creating two sequential or simultaneous mutations that would confer improved survival has been studied in the malaria parasite when exposed to chloroquine. The actual incidence of two base-pair mutations leading to two changed amino acids leading to resistance has been shown to be 1 in 10²⁰ cases (42). To better understand this incidence, the likelihood that Homo sapiens would achieve any single mutation of the kind required for malaria to become resistant to chloroquine (a simple shift of two amino acids) would be 100 million times 10 million years (many times the age of the universe). This example has been used to further explain the difficulty in managing more than one mutation to achieve benefit.

The reference is to The Edge of Evolution by Michael Behe. His book was published in 2007 but I never got around to reviewing it thoroughly—partly because it's so difficult to explain where he goes wrong.¹ Here's my take on one part of the book: The Two Binding Sites Rule. This post covers "chloroquine-complexity clusters" (CCC).

Good Science Writers: Jacques Monod

 
Jacques Monod (1910 - 1976) received the Nobel Prize in Physiology or Medicine (1965) for his work on the regulation of the lac operon (with François Jacob). While best known as a biochemist, Monod was also well respected for his many articles on politics and philosophy.

Dawkins didn't select anything from Monod for The Oxford Book of Modern Science Writing because his selections were limited to books written initially in English. Monod's most famous work is Le Hasard et la Nécessité first published in France in 1970. It is well known in the English version: Chance and Necessity: An Essay on the Natural Philosophy of Modern Biology (1971). The excepts below are from the translation by Austryn Wainhouse.

Various mutations have been identified as due to

1. The substitution of a single pair of nucleotides for another pair;
2. The deletion of addition of one or several pairs of nucleotides, and
3. Various kinds of "scrambling" of the genetic text by inversion, duplication, or fusion of more or less extended segments.

We call these events accidental; we say that they are random occurrences. And since they constitute the only possible source of modification in the genetic text, itself the sole repository of the organism's hereditary structures, it necessarily follows that chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, at the very root of the stupendous edifice of evolution: this central concept of modern biology is no longer one among other possible or even conceivable hypotheses. It is today the sole conceivable hypothesis, the only one that squares with observed and tested fact. And nothing warrants the supposition—or the hope—that on this score our position is ever likely to be revised.

I believe we can assert today that a universal theory, however completely successful in other domains, could never encompass the biosphere, its structure, and its evolution as phenomena deducible from first principles....

In a general manner the theory would anticipate the existence, the properties, the interrelations of certain classes of objects or events, but would obviously not be able to foresee the existence or the distinctive characteristics of any particular object or event.

The thesis that I shall present in this book is that the biosphere does not contain a predictable class of objects or of events but constitutes a particular occurrence, compatible indeed with first principles, but not deducible from those principles, and therefore essentially unpredictable.

Let there be no misunderstanding here. In saying that as a class living beings are not predictable upon the basis of first principles, I by no means intend to suggest that they are not explicable through these principles—that they transcend them in some way, and that other principles, applicable to living systems alone, must be invoked. In my view the biosphere is unpredictable for the very same reason—neither more nor less—that the particular configuration of atoms constituting this pebble I have in my hand is unpredictable. No one will find fault with a universal theory for not affirming and foreseeing the existence of this particular configuration of atoms; it is enough for us that this actual object, unique and real, be compatible with the theory. This object, according to the theory, is under no obligation to exist; but it has the right to.

That is enough for us as concerns the pebble, but not as concerns ourselves. We would like to think ourselves necessary, inevitable, ordained from all eternity. All religions, nearly all philosophies, and even a part of science testify to the unwearying, heroic effort of mankind desperately denying its own contingency.

---

Debating alternative splicing (Part III)

Proponents of massive alternative splicing argue that most human genes produce many different protein isoforms. According to these scientists, this means that humans can make about 100,000 different proteins from only ~20,000 protein-coding genes. They tend to believe humans are considerably more complex than other animals even though we have about the same number of genes. They think alternative splicing accounts for this complexity [see The Deflated Ego Problem].

Opponents (I am one) argue that most splice variants are due to splicing errors and most of those predicted protein isoforms don't exist. (We also argue that the differences between humans and other animals can be adequately explained by differential regulation of 20,000 protein-coding genes.) The controversy can only be resolved when proponents of massive alternative splicing provide evidence to support their claim that there are 100,000 functional proteins.

Religion may have evolved because of its ability to help people exercise self-control

 
Here's an example of evolutionary thinking by a psychologist at the University of Miami. Read the press release (below) and watch the video. It's only when you watch the video that you realize where Professor McCullough is coming from on this issue. He uses the word "evolution" to talk about cultural phenomena without necessarily including genetic changes. In other words, he is not talking about biological evolution.

This can be very confusing and I recommend that evolutionary psychologists change their practice. They should refer to "cultural evolution" and distinguish it from "biological evolution" whenever possible.

Religion may have evolved because of its ability to help people exercise self-control

A study by a University of Miami psychologist reveals that religion facilitates the exercise of self-control and attainment of long-term goals

CORAL GABLES, FL (December 30, 2008)—Self-control is critical for success in life, and a new study by University of Miami professor of Psychology Michael McCullough finds that religious people have more self-control than do their less religious counterparts. These findings imply that religious people may be better at pursuing and achieving long-term goals that are important to them and their religious groups. This, in turn, might help explain why religious people tend to have lower rates of substance abuse, better school achievement, less delinquency, better health behaviors, less depression, and longer lives.

In this research project, McCullough evaluated 8 decades worth of research on religion, which has been conducted in diverse samples of people from around the world. He found persuasive evidence from a variety of domains within the social sciences, including neuroscience, economics, psychology, and sociology, that religious beliefs and religious behaviors are capable of encouraging people to exercise self-control and to more effectively regulate their emotions and behaviors, so that they can pursue valued goals. The research paper, which summarizes the results of their review of the existing science, will be published in the January 2009 issue of Psychological Bulletin.

"The importance of self-control and self-regulation for understanding human behavior are well known to social scientists, but the possibility that the links of religiosity to self-control might explain the links of religiosity to health and behavior has not received much explicit attention," said McCullough. "We hope our paper will correct this oversight in the scientific literature." Among the most interesting conclusions that the research team drew were the following:

• Religious rituals such as prayer and meditation affect the parts of the human brain that are most important for self-regulation and self-control;
• When people view their goals as "sacred," they put more energy and effort into pursuing those goals, and therefore, are probably more effective at attaining them;
• Religious lifestyles may contribute to self-control by providing people with clear standards for their behavior, by causing people to monitor their own behavior more closely, and by giving people the sense that God is watching their behavior;
• The fact that religious people tend to be higher in self-control helps explain why religious people are less likely to misuse drugs and alcohol and experience problems with crime and delinquency.

McCullough's review of the research on religion and self-control contributes to a better understanding of "how the same social force that motivates acts of charity and generosity can also motivate people to strap bomb belts around their waists and then blow themselves up in crowded city buses," he explained. "By thinking of religion as a social force that provides people with resources for controlling their impulses (including the impulse for self-preservation, in some cases) in the service of higher goals, religion can motivate people to do just about anything."

Among the study's more practical implications is that religious people may have at their disposal a set of unique psychological resources for adhering to their New Year's Resolutions in the year to come.

I leave it up to you, dear readers, to decide whether non-religious people (atheists) tend to have higher rates of substance abuse, worse school achievement, more delinquency, worse health behaviors, more depression, and shorter lives. It would imply that countries like Sweden, where half the population is non-religious, are in much worse shape than America, where more than 80% is religious. It would imply that extremely religious countries like Saudi Arabia must be near-perfect societies full of very old people.

Incidentally, the idea of "self-control" is not well explained. If you behave in a certain way because you fear punishment from your god or your priests, then this isn't exactly what I think of when I use the term "self-control."

---

Postmodernism and the Two Cultures

John Wilkins at Evolving Thoughts has some comments about the "two cultures" debate [see Cocktail Parties and the Two Cultures].

While most scientists see the problem as a lack of respect for science, John examines the other side of the coin. Noting that the Sokal Affair often comes up in these discussion, John reacts to the criticism of postmodernism implicit in that reference. It's true that most scientists agree with Alan Sokal that the worst form of postmodernism is an embarrassment to all disciplines, not just the humanities. However, it's also true that humanities (e.g. English, Sociology, Psychology) have been far more lax than the sciences when it comes to intellectual rigor. In that sense, the humanities have lost respect.

John attempts to explain the good things about postmodernism. I understand his point, although I think might be protesting just a bit too much. He concludes with,

There is a cultural divide between the humanities and the sciences, but it is not a simple one. It has to do, ultimately, with respect. The division is between those who respect science, and those who respect the humanities (and the other human-related subjects, like social science, political science and so on). Yes, we in the humanities treat science like a text. This is because, as we are not doing science, we interface with that vibrant tradition via the texts of science, mostly. And we are being, as philosophers, very "meta" about science - that is, we are discussing its discussions, and reflecting upon its reflections. Textualisation is impossible to avoid, although one can correct for it. But some of us respect science. We respect it for the same reason that Locke, Hume, Kant and Mill respected science - it is where the knowledge is gathered (or made, or constructed out of data, etc.), so it is the single most important part of human cognition and social organisation to a philosopher.

Anyone who has spent much time wading through the pious, obscurantist, jargon-filled cant that now passes for 'advanced' thought in the humanities knew it was bound to happen sooner or later: some clever academic, armed with the not-so-secret passwords ('hermeneutics,' 'transgressive,' 'Lacanian,' 'hegemony,' to name but a few) would write a completely bogus paper, submit it to an au courant journal, and have it accepted . . . Sokal's piece uses all the right terms. It cites all the best people. It whacks sinners (white men, the 'real world'), applauds the virtuous (women, general metaphysical lunacy) . . . And it is complete, unadulterated bullshit – a fact that somehow escaped the attention of the high-powered editors of Social Text, who must now be experiencing that queasy sensation that afflicted the Trojans the morning after they pulled that nice big gift horse into their city.

Gary KamiyaYes, it's all about respect. However, I still think scientists are feeling more like Rodney Dangerfield¹ than the average sociologist or philosopher. The way I see it, philosophers and others in the humanities often have a very narrow view of science. It's not that they treat science as just another human endeavor, which is bad enough, it's that they treat science as something that's not a part of their disciplines. This exact point is addressed in a lecture Alan Sokal gave earlier this year [What is science and why should we care?]. "Science" is not just about rocket ships and natural selection, it's a way of thinking. A way of thinking that people in the humanities would be wise to adopt. Sokal says,

At a superficial level you could say that my topic is the relation between science and society; but as I hope will become clear, my deeper theme is the importance, not so much of science, but of the scientific worldview—a concept that Ishall define more precisely in a moment, and which goes far beyond the specific disciplines that we usually think of as "science"—in humanity's collective decision making. I want to argue that clear thinking, combined with a respect for evidence—especially inconvenient and unwanted evidence that challenges our preconceptions—are of the utmost importance to the survival of the human race in the twenty-first century.

Of course, you might think that calling for clear thinking and a respect for evidence is a bit like advocating Motherhood and Aple Pie (if you'll pardon this Americanism)—and in a sense you'd be right. Hardly anyone will openly defend muddled thinking or disrespect for evidence. Rather, what people do is to surround these practices with a fog of verbiage designed to conceal from their listeners—and in most cases, I would imagine, from themselves as well—the true implications of their reasoning.

Sokal has it right, as far as I'm concerned. The war between the two cultures is not just about whether you've read Shakespeare or Einstein, it's about how you think. Either you adopt the scientific worldview that values evidence and rationality, or you practice some form of superstition. In this sense, the humanities are just a part of science and not a separate way of knowing.

Sokal emphasizes this point again and again.

I stress that my use of the term "science" is not limited to the natural sciences, but includes investigations aimed at acquiring accurate knowledge of factual matters relating to any aspect of the world by using rational empirical methods analogous to those employed in the natural sciences.

I don't think John Wilkins would agree with this perspective since it makes philosophy—and all other humanties—just a part of a scientific worldview.²

John continues with his analysis of the two cultures problem.

Scientists often do not respect humanists, either. It is a running gag that PZ or Larry Moran will tweak me and others for being mere philosophers, but the gag is that most scientists really do think philosophy is a waste of funds and office space. Likewise they think the same thing about literary studies, history, social sciences, and in fact everything that is not their own speciality. It's not hard to see this as special pleading, but if scientists want respect, they had better show some. It's not impossible: Ed Wilson and Stephen Jay Gould are just two examples of scientists who - for all their faults - respect the humanities. Nobody has the time or energy (or mental capacity) to become experts in both fields; there's barely enough time to become expert in one subspeciality of one discipline of one field); but we can respect those who do learn those limited domains even if they are not our own. This is a plea for respect too, between the analytic and continental styles of philosophy. Neither is totally stupid nor totally on track. Rather than reject the other styles, perhaps what we should do is mutually support each other to do what we do well.

For the record, I'm much closer to Gould on this issue that it appears. I have a great deal of respect for philosophy, provided that it's done correctly. I would strongly support making philosophy and the study of logic a mandatory course in every university. Similarly, there is much to be learned about human behavior—and, let's face it, we are all interested in ourselves even if we know that we are just one species out of ten million—by studying sociology, English literature, and art history. The problem isn't lack of respect for the subject matter as much as lack of respect for the way the subjects are studied.

I'd also like to point out that I'm an equal opportunity curmudgeon—the best kind, in my opinion. While I don't hesitate to point out the muddle-headedness of philosophers like Michael Ruse and Daniel Dennett who pretend to be scientists, I also don't hesitate to make fun of scientists like Ken Miller and Francis Collins who abuse science to support religion.

In the war between rationalism and superstition there are many in the humanities who are on the wrong side. But there are lots of scientists who are wrong as well. I still think that, as a general proposition, there's more respect for the humanities out there than for science. Our society is educating an entire generation of scientific illiterates who are not only unknowledgeable about basic concepts in science but, in most cases, still quite proud of their ignorance.

The next time you hear someone say that science or math is way too hard for them, you should express your sympathy by saying, "Gee, I'm sorry you're too stupid to understand these things. What can I do to help?"

---

1. or Aretha Franklin

2. To put it even more bluntly. All of the humanities is simply concerned with the behavior of one particular species on this planet. It's just one tiny part of life on this planet, which, in turn, is an infinitesimally small part of the universe. Those who think that the philosophy of Plato is more important than understanding evolution have their priorities all screwed up.

The Molecular Basis of Roundup® Resistance

Recall that glyphosate inhibits the enzyme EPSP synthase, an enzyme that catalyzes the following reaction in the chorsimate biosynthesis pathway [How Roundup® Works].

Funke et al. (2006) explored the molecular basis of this inhibition by looking at the structure of EPSP synthase from the C4 strain of Agrobacterium sp. This is the resistant form of the enzyme that has been genetically engineered into Roundup Ready® plants [Roundup Ready® Transgenic Plants].

Note that the structure of glyphosate resembles one of the substrates of the reaction; namely phosphoenolpyruvate (PEP). It was already known that glyphosate binds tightly to the active site of the enzyme and inhibits the reaction by preventing PEP binding. As it turns out, the site for glyphosate binding is exactly the same as the site for PEP binding and this explains the inhibition.

Funke et al. (2006) looked at the C4 EPSP enzyme with and without one of the other substrates: namely, shikimate-3-phosphate (sometimes called shikimate-5-phosphate). The results reveal the precise location of the active site of the enzyme at the base of a cleft between two domains. This form of the enzyme is called class II EPSP synthase because it is distantly related to the class I enzymes in other bacteria and eukaryotes (30% amino acid sequence identity). This is the first paper to examine the structure of a class II enzyme.

As an aside, notice that the enzyme closes up a little bit when the substrate binds—sort of like a Pacman icon. This mechanism of substrate binding is called induced fit and it's proving to be more common than most people realized.

The glyphosate resistant (Roundup Ready®) mutation in C4 EPSP synthase is a substitution of Alanine (A) for Glycine (G) at amino acid position 100. The glyphosate molecule fits nicely into the wild type G100 form of the enzyme (lower image) and it excludes PEP binding completely. Note that glyphosate (green) is in an extended configuration when it is bound. The dotted lines represent non-covalent interactions between the enzyme and the glyphosate molecule. The blue dots are "frozen" water molecules embedded in the active site.

In the mutant form of the enzyme the extra methyl group on alanine is just big enough to cause glyphosate to distort so it can no longer lie in the optimal extended configuration (top image). This means that glyphosate binds much more weakly and doesn't inhibit enzyme activity.

The important point is that the active site can still accommodate phosphoenolpyruvate because it is smaller than glyphosate. What this means is that the overall activity of the enzyme in the absence of glyphosate is unaffected. There are lots of EPSP synthase mutants that don't bind glyphosate but in almost all cases the rate of the reaction is drastically reduced because PEP binding is also weakened. For example, if you mutate the glycine to alanine at the equivalent position in other bacterial or plant enzymes you abolish PEP binding along with glyphosate binding.

What's special about the class II enzymes in general and the Agrobacterium sp. enzyme in particular, is that the amino acids surrounding the PEP binding pocket are positioned just right so that a slight shift can exclude glyphosate without affecting phosphoenolpyruvate. This is mostly due to the positions of the charged amino acid side chains that form weak interactions with the oxygen atoms and the nitrogen of glyphosate; for example, arginines (R) at 128, 357, and 405; lysine (K) at 28; and glutamate (E) at 354.

The results of this study not only shed light on the mechanism of glyphosate resistance but they also help explain the lack of Roundup® resistant plants. Apparently, the class I enzymes in plants have a binding pocket that is difficult to mutate in a way that excludes glyphosate while still allowing PEP binding. Nevertheless, some examples of Roundup® resistant plants are known. I'll describe them tomorrow.

(Funke et al. had to do a bit of sleuthing and reconstruction in order to solve the structure of the C4 EPSP synthase. The C4 strain of Agrobacterium sp. has, naturally enough, not been given out to scientists outside of Monsanto laboratories. So Funke et al. got the amino acid sequence from US Patent 5633435 and reverse engineered the nucleotide sequence of the gene. They synthesized the nucleotide sequence and amplified the fragments by PCR. They then tacked on a promoter and a transcription termination signal and cloned the articfial gene into an E. coli plasmid. The artificially reconstructed protein was then expressed in E. coli, isolated, purified, and crystallized.)

Funke, T., Han, H., Healy-Fried, M,L., Fischer, M., and Schonbrunn, E. (2006) Molecular basis for the herbicide resistance of Roundup Ready crops. Proc. Natl. Acad. Sci. (USA) 103:13010-13015. [PubMed]

The "Mutationism" Myth I. The Monk's Lost Code and the Great Confusion

This is the second in a series of postings by a guest blogger, Arlin Stoltzfus. You can read the first part at: Introduction to "The Curious Disconnect". Arlin is challenging the status quo in modern evolutionary theory. He's not alone in this challenge but it's important to distinguish between kooks who don't know what they're talking about and serious thinkers who have something to say. Arlin is going to explain to you why everything you thought you knew about mutationism is wrong. I'm happy to give him a chance to post on Sandwalk.

This will be on the exam.

---

The Curious Disconnect

The Curious Disconnect is the blog of evolutionary biologist Arlin Stoltzfus, available at www.molevol.org/cdblog. An updated version of the post below will be maintained at www.molevol.org/cdblog/mutationism_myth1 (Arlin Stoltzfus, ©2010)

The "Mutationism" Myth I. The Monk's Lost Code and the Great Confusion

The mutationism myth tells the story of how, just over a century ago, the scientific community responded to the discovery of Mendelian genetics by discarding Darwinism, and how Darwinism subsequently was restored.Our journey to explore The Curious Disconnect-- the gap between how we think about evolution and how we might think if we were freed from historical baggage-- begins with the Mutationism Myth. In this, the first of four parts, we are not going to confront any tough scientific or conceptual issues. Instead, we are just going to review an odd story about our intellectual history.

The Mutationism Story

While "myth" has the connotation of falsehood, the story that a myth tells isn't necessarily a false one. The mutationism myth, at least, is anchored in historical events.¹

The mutationism myth tells the story of how, just over a century ago, the scientific community responded to the discovery of Mendelian genetics by discarding Darwinism, and how Darwinism subsequently was restored. The villains of the story are the influential early geneticists or "Mendelians" who saw genetics as a refutation of Darwinism; the heroes are first, the founders of population genetics, theoreticians who sorted everything out in favor of Darwinism by about 1930, and second, the architects of the Modern Synthesis, activists who popularized and institutionalized what we're calling "Darwinism 2.0".

This story has been re-told in secondary sources for nearly 50 years, though I sense that the frequency is decreasing as this episode passes into ancient history. To find examples, try looking up "mutationism" (sometimes "Mendelism" or even "saltationism") in the index of a book about evolution.

I encourage you to consult whatever sources you have and to share the stories that you find. Note that you won't always be successful. A quick survey of several dozen contemporary books on my shelf reveals that most don't address this episode specifically (a notable absence, in some cases ²); some tell the mutationism myth with varying degrees of panache; and a few provide a historical account rather than a myth. The few historical accounts that I found were in Gould's 2002 The Structure of Evolutionary Theory, Strickberger's 1990 textbook Evolution, and the Wikipedia entry on "Mutationism".

Sample stories

Lets look at a few examples of the mutationism story. Readers who want to check out a freely available online source from the scholarly literature may refer to Ayala and Fitch, 1997 (http://www.ncbi.nlm.nih.gov/pubmed/9223250?dopt=Citation). One example that really caught my eye is not from scientific literature, but from the 2005 obituary for Ernst Mayr in The Economist:

It was not that biologists had given up on evolution by the 1940s-quite the contrary. But they had got very confused about its mechanism. . . . The geneticists of the early 20th century did not help. They rediscovered the laws of inheritance first developed 40 years earlier by Gregor Mendel, an unsung Moravian monk. They also discovered the idea of genetic mutation. But instead of linking these things to natural selection, they came up with the idea of "saltation"-in other words, sudden mutational shifts from one well-adapted species to another. Nor, the geneticists complained, had there been enough time for natural selection to do its work, given what they had discovered about the rate at which mutations occur, and the fact that most mutations are deleterious. It was all a bit of a mess. . .Mr Mayr's advantage over the laboratory-bound biologists who had hijacked and diluted Darwin's legacy was that, like Darwin, he was a naturalist-and a good one. (anonymous, 2005)

Of course, this is a magazine article, written by anonymous staff writers-- typically one doesn't see such florid language in the scholarly literature. But did the staff writers of the Economist (representing elite opinion) really originate this story, based on their own personal recollections of the 1930's? Of course not. Mayr himself popularized the image of geneticists as laboratory-bound geeks lacking the organic insight of "naturalists". This disdain for the geneticists who "hijacked" Darwin's legacy is readily apparent when evolutionary writers depict geneticists as fools holding "beliefs" that have "obvious inadequacies", unable to understand or "grasp" their own scientific findings:

"It is hard for us to comprehend but, in the early years of this century when the phenomenon of mutation was first named, it was regarded not as a necessary part of Darwinian theory but as an alternative theory of evolution! There was a school of geneticists called the mutationists, which included such famous names as Hugo de Vries and William Bateson among the early rediscoverers of Mendel's principles of heredity, Wilhelm Johannsen the inventor of the word gene, and Thomas Hunt Morgan the father of the chromosome theory of heredity. . . Mendelian genetics was thought of, not as the central plank of Darwinism that it is today, but as antithetical to Darwinism. . . It is extremely hard for the modern mind to respond to this idea with anything but mirth" (Dawkins, 1987, p. 305)

"According to mutationism, random changes in the hereditary material are sufficient for adaptation without much, or any, selection at all. Mutations just somehow happen to be adaptive, the right changes simply manage to occur. The inadequacies of this view are obvious" (Cronin, 1991, p. 47).

"Darwin knew nothing of this [i.e., genetics] but as it turned out, his ignorance was sublimely irrelevant to the problem he was really interested in tackling: evolution. This point was not fully grasped by biologists. Many early geneticists at the dawn of the 20th century, thought their discoveries of the fundamental principles of genetics somehow cast doubt [on], or rendered obsolete, the concept of natural selection. It took several decades of experimentation and theoretical (including mathematical) analysis to show not only that there was no conflict inherent between the emerging results of genetics and the older Darwinian notion of natural selection, but that the two operate in different domains." (Eldredge, 2001, p. 67)

"Mendelian particulate inheritance (today, we call the "particles" genes) was originally identified with De Vries's "mutation theory", according to which new variations or species originated in large jumps, or macromutations, and evolution was exclusively explained by mutation pressure. Darwinian naturalists, believing that Mendelism was synonymous with mutation theory, held on to theories of soft inheritance, while they considered selection a weak force at best. They did not know of the new findings in genetics that would have supported Darwinism. (SegerstrŒle, 2002)

Notice how, in every version of the story above, the position taken by early geneticists just doesn't make sense. This isn't a story of theory versus theory, its a story of confusion ultimately yielding to reason.

If de Vries and the other geneticists are playing the role of the pied piper in this story, the "naturalists" are like the children lured away from their Darwinian home. Ultimately the innocents are returned, and order restored, by (oddly enough) mathematicians:

"Between 1918 and 1932 Fisher, Haldane, and Wright showed that Mendelian genetics is consistent with natural selection. Only then, more than 60 years after the publication of The Origin of Species, was the genetic objection to natural selection finally removed. Modern molecular and developmental genetics have confirmed in exquisite chemical detail the key aspects of genetics necessary for Darwin's ideas to work: that the genetic material is DNA, that DNA has a sequence, . . . mutates . . . contains information . . " (p. 16 of Stearns and Hoekstra, 2005)

Anatomy of a Myth

In a subsequent post, we will look at original sources to see what the "mutationists" actually believed, and why. And eventually we will integrate this into the bigger picture of how evolutionary theory developed. But for now, lets just summarize the pattern that is apparent in the literature.

First, the mutationism story is clearly a story or myth, and not an ordinary scientific truth claim. We can see this because the story-tellers are not using ordinary scientific conventions to convince us that the story is true. If you or I were making an ordinary scientific argument (for instance) for an effect of "translational selection" on codon usage, we would mention a correlation between codon frequencies and the abundance of corresponding tRNAs, citing the classic work of Ikemura (1981), and we might even repeat a figure showing this correlation, to impress this point upon the minds of readers (e.g., just as in Ch. 7 of Freeman & Herron, 1998).

When I see instances of the mutationism story, typically I don't find quotations illustrating what the mutationists believed, nor facts & figures to refute their views, but only vague attributions and generalized claims. Apropos, the following quotation from Ernst Mayr never fails to make me laugh:

The genetic work of the last four decades has refuted mutationism (saltationism) so thoroughly that it is not necessary to repeat once more all the genetic evidence against it. (Mayr, 1960)

And the puissant Dr. Mayr proceeds on, not boring the reader with any tiresome "genetic evidence", nor citing sources that might allow the reader to evaluate the truth of his statement. Its a story, after all.

By contrast, the 3 sources that I mentioned above as providing scientific history, rather than myth, all make reference to specific experimental and theoretical results, and reveal knowledge of specific historically important scientific works. For instance, Strickberger's reference list includes Johannsen, 1903, as well as the 1902 paper by Yule that reconciled Mendelian genetics with quantitative variation (in neo-Darwinian mythology, credit for Yule's work is given to little Ronny Fisher, who was 11 at the time).

Second, every story has a plot or "action", and the main action of the mutationism story is a turn of fate in which power is temporarily in the hands of the wrong people or ideas. In archetypal terms, its a story of usurpation and restoration: the throne is usurped, and the kingdom falls into darkness and confusion until the throne is restored to the king's rightful heirs. The mutationism episode didn't have to be told that way: it might have been presented as a period of reform (in which old ideas were abandoned) or discovery (when new territory was mapped out). Instead, its presented as a mistake, an interlude of confusion, a collective delusion.

Indeed, another way to look at the mythic action is that the Mendelians are wizards or false prophets who place the kingdom under a spell, leading folks astray and causing them to believe things that they just shouldn't have believed.

What delusional spell did the Mendelians cast? In the story by Eldredge, or by Stearns & Hoekstra above, the spell is that Mendelian genetics is inconsistent with "the concept of natural selection" (Eldredge). In the story told by SegerstrŒle, Cronin, Mayr and The Economist, the delusional spell is a bit different: the principle of selection is irrelevant because mutational jumps alone explain evolution.

Third, the key to restoring Darwin's kingdom was to add the missing piece of genetics. Ultimately, after the period of darkness ended, the discovery of genetics "provided the missing link in Darwin's theory" (SegerstrŒle, 2002), or "The missing link in Darwin's argument was provided by Mendelian genetics" (Ayala & Fitch, 1997). Darwinism was restored, not by taking away the power of genetics, but by redirecting it to support Darwinism. Clearly, genetics is the key to ruling the kingdom, like the One Ring that Rules them All in Tolkien's world. The ones who have the ring have the power.

The story is made more fascinating by the fact that the key to power is literally a code of rules developed by a monk that remained lost for nearly half a century. The usurpers who discover The Monk's Code misinterpret it, and use it to overthrow the true king, establishing a reign of error. But when The Founders decipher the true meaning of the Monk's Code, The Architects campaign throughout the kingdom, spreading the news: the Monk's Code proves that Darwin is the true king. Darwin's rule is re-established, all opposition ceases, and the kingdom is unified.

Homework

If you would like to contribute a mutationism story, I would be happy to start a collection if you make it easy for me by providing a complete and well formed text item. Be sure to provide a quoted passage with a source, citing exact page numbers. If we get enough stories, lets try to recruit a sociologist or historian to study this further.

Summary

To summarize, the mutationism story is a myth that is retold in secondary sources. The basic story is simple: the discoverers of genetics misinterpreted their discovery, thinking it incompatible with Darwinism; Darwinism went into disfavor; population geneticists came along and showed that genetics was the missing key to Darwinism; Darwinism was restored and once again reigned supreme.

Next time on the The Curious Disconnect, we'll start pulling on some of the loose threads of this story.

For now, note how the writers quoted above are genuinely baffled by our scientific history. It just doesn't make sense to them. A century ago, most of an entire generation of scientists thought of genetics as a contradiction of Darwinism. This is a historical fact, and presumably it has an explanation that rational folks can understand by examining what scientists of the time wrote. But this historical fact mystifies Dawkins, Eldredge, Cronin, and others.

References

Anonymous. 2005. Ernst Mayr, evolutionary biologist, died on February 3rd, aged 100. The Economist, February.

Ayala, F. J., and W. M. Fitch. 1997. Genetics and the origin of species: an introduction. Proc Natl Acad Sci U S A 94:7691-7697.

Cronin, H. 1991. The Ant and the Peacock. Cambridge University Presss, Cambridge.

Dawkins, R. 1987. The Blind Watchmaker. W.W. Norton and Company, New York.

Eldredge, N. 2001. The Triumph of Evolution and the Failure of Creationism. W H Freeman & Co.

Freeman, S., and J. C. Herron. 1998. Evolutionary Analysis. Prentice-Hall, Upper Saddle River, New Jersey.

Gould, S. J. 2002. The Structure of Evolutionary Theory. Harvard University Press, Cambridge, Massachusetts.

Ikemura, T. 1981. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol 151:389-409.

Mayr, E. 1960. The Emergence of Evolutionary Novelties. Pp. 349-380 in S. Tax, and C. Callender, eds. Evolution After Darwin: The University of Chicago Centennial. University of Chicago Press, Chicago.

SegerstrŒle, U. 2002. Neo-Darwinism. Pp. 807-810 inM. Pagel, ed. Encyclopedia of Evolution. Oxford University Press, New York.

Stearns, S. C., and R. F. Hoekstra. 2005. Evolution: an introduction. Oxford University Press, New York.

Strickberger, M.W. 1990. Evolution (1st edition).

Notes
¹ The defining characteristic of a myth is not that it isn't literally true, but that it isn't told for reason of being literally true, but for reason of being meaningful or poignant: a myth is a story with a cultural value, not necessarily a literal-truth value. The connection between myths and untruths, then, has to do with discoverability: when we find a pattern P = { X people are repeating story Y }, where X is a large number, this pattern by itself does not prove that Y is a myth because X people might have all discovered or verified Y independently; but if Y has diverse elements that are untrue (or unverifiable), then we can conclude that its repetition does not signify independent verification, suggesting that its a myth.



²The Oxford Encyclopedia of Evolution does not have an article on mutationism; the article on Morgan says nothing of his views on evolution; there is no article on Bateson; mutationism is only addressed peripherally in Hull's article on the history of evolutionary theory; it is mainly addressed in SegerstrŒle's article on neo-Darwinism.

---