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Sunday, July 08, 2007
Mendel's Garden #16
The 16th version of Mendel's Garden has just been posted on Eye on DNA [Mendel’s Garden Genetics Blog Carnival #16M].
Socialized Medicine Will Make America Vulnerable to Terrorists
Americans are probably confused about socialized medicine after seeing Michael Moore's Sicko. Don't worry. Fox News explains why highly efficient, profit-based. corporate health care will protect America from those Jihadist Muslim doctors who are taking over the anonymous, highly bureaucratic systems in Europe.
Listen for the part about your family doctor. In America you can't have doctors who believe in stupid things because they'll be exposed by their patients and their colleagues. Apparently in socialist countries you don't have family doctors (news to me) so patients never find out what their doctors are really thinking. That's why jihadist doctors can hide out in Europe.
Why isn't there more outrage when idiotic things like this are broadcast on network television?
[Hat Tip: Canadian Cynic]
Friday, July 06, 2007
Close, but no cigar.
Over on Post-Darwinist Denyse O'Leary is whining about the fact that so many scientists are non-believers. She quotes from a poll of evolutionists showing that 78% don't believe in God. Having been sensitized to misuse of the word "evolutionist" she adds this at the end of her blog.
(Note for the record: "Evolutionists" here means scientists who believe that gradual Darwinian processes completely account for every aspect of life and that no design whatever is required. It does not mean scientists who merely accept that evolution occurs or that Earth is billions of years old.)Denyse, it's the word "Darwinian" that's being misused. I'm an evolutionist but I do not believe that "gradual Darwinian processes completely account for every aspect of life." Instead I believe that evolution accounts for life and this evolution includes strict Darwinian processes as well as non-Darwinian processes.
Why do you find this so hard to understand?
I'm a Skeptic
I'm a Skeptic and a member of the Board of Consultants of Skeptics Canada. But it's nice to have confirmation ...
You Are Very Skeptical |
Your personal motto is: "Prove it." While some ideas, like life after death, may seem nice... You aren't going to believe them simply because it feels good. You let science and facts be your guide... Even if it means you don't share the beliefs of those around you. |
[Hat Tip: GrrlScientist]
Thursday, July 05, 2007
Mutation Rates
Each of us was born with at least 350 new mutations that make our DNA different from that of our parents.
Douglas Futuyma (2005) p. 162Let’s think about the number of mutations that could accumulate in a population over time. A few pages ago we looked at the origin of antibiotic resistance in bacteria in order to prove that mutations occur randomly. Now we’ll consider just how frequency those mutations could arise in bacteria. Then we’ll ask how frequently mutations occur in humans.
Our model bacterium is Esherichia coli the common, and mostly benign, intestinal bacterium. The entire genome was sequenced in 1997 (Blattner et al., 1997) and its size is 4,200,000 base pairs (4.2 × 106 bp). Every time a bacterium divides this amount of DNA has to be replicated; that’s 8,400,000 nucleotides (8.4 × 106).
The most common source of mutation is due to mistakes made during DNA replication when an incorrect nucleotide is incorporated into newly synthesized DNA. The mutation rate due to errors made by the DNA polymerase III replisome is one error for every one hundred million bases (nucleotides) that are incorporated into DNA. This is an error rate of 1/100,000,000, commonly written as 10-8 in exponential notation. Technically, these aren't mutations; they count as DNA damage until the problem with mismatched bases in the double-stranded DNA has been resolved. The DNA repair mechanism fixes 99% of this damage but 1% escapes repair and becomes a mutation. The error rate of repair is 10-2 so the overall error rate during DNA replication is 10-10 nucleotides per replication (10-8 × 10-2) (Tago et al., 2005).
Since the overall mutation rate is lower than the size of the E. coli genome, on average there won’t be any mistakes made when the cell divides into two daughter cells. That is, the DNA will usually be replicated error free.
However, one error will occur for every 10 billion nucleotides (10-10) that are incorporated into DNA. This means one mutation, on average, every 1200 replications (8.4 × 106 × 1200 is about ten billion). This may not seem like much even if the average generation time of E. coli is 24 hours. It would seem to take four months for each mutation. But bacteria divide exponentially so the actual rate of mutation in a growing culture is much faster. Each cell produces two daughter cells so that after two generations there are four cells and after three generations there are eight cells. It takes only eleven generations to get 2048 cells (211 = 2048). At that point you have 2048 cells dividing and the amount of DNA that is replication in the entire population is enough to ensure at least one error every generation.
In the laboratory experiment the bacteria divided every half hour so after only a few hours the culture was accumulating mutations every time the bacteria divided. This is an unrealistic rate of growth in the real world but even if bacteria only divide every 24 hours there are still so many of them that mutations are abundant. For example, in your intestine there are billions and billions of bacteria. This means that every day these bacteria accumulate millions of mutations. That’s why there’s a great danger of developing drug resistance in a very short time.
Calculating the rate of evolution in terms of nucleotide substitutions seems to give a value so high that many of the mutations must be neutral ones.
Motoo Kimura (1968)I based my estimate of mutation rate on what we know about the properties of the replisome and repair enzymes. Independent measures of mutation rates in bacteria are consistent with this estimate. For example, the measured value for E. coli is 5.4 × 10-10 per nucleotide per replication (Drake et al., 1998). Many of these mutations are expected to be neutral. The rate of fixation of neutral mutations is equal to the mutation rate so by measuring the accumulation of neutral mutations in various lineages of bacteria you can estimate the mutation rate provided you know the time of divergence and the generation time. (Ochman et al., 1999) have estimated that the mutation rate in bacteria is close to 10-10 assuming that bacteria divide infrequently.
The mutation rate in eukaryotes should be about the same since the properties of the DNA replication machinery are similar to those in eukaryotes. Measured values of mutation rates in yeast, Caenorhabditis elegans, Drosophila melanogaster, mouse and humans are all close to 10-10 (Drake et al., 1998).
The haploid human genome is about 3 × 109 base pairs in size. Every time this genome is replicated about 0.3 mutations, on average, will be passed on to one of the daughter cells. We are interested in knowing how many mutations are passed on to the fertilized egg (zygote) from its parents. In order to calculate this number we need to know how many DNA replications there are between the time that one parental zygote was formed and the time that the egg or sperm cell that unite to form the progeny zygote are produced.
In the case of females, this number is about 30, which means that each female egg is the product of 30 cell divisions from the time the zygote was formed (Vogel and Rathenberg, 1975). Human females have about 500 eggs. In males, the number of cell divisions leading to mature sperm in a 30 year old male is about 400 (Vogel and Motulsky, 1997). This means that about 9 mutations (0.3 × 30) accumulate in the egg and about 120 mutations (0.3 × 400) accumulate in a sperm cell. Thus, each newly formed human zygote has approximately 129 new spontaneous mutations. This value is somewhat less than the number in most textbooks where it's common to see 300-350 mutations per genome. The updated value reflects a better estimate of the overall rate of mutation during DNA replication and a better estimate of the number of cell divisions during gametogenesis.
With a population of 6 billion individuals on the planet, there will be 120 × 6 × 109 = 7.2 × 1011 new mutations in the population every generation. This means that every single nucleotide in our genome will be mutated in the human population every 20 years or so.
Douglas Futuyma (2005) p. 162Let’s think about the number of mutations that could accumulate in a population over time. A few pages ago we looked at the origin of antibiotic resistance in bacteria in order to prove that mutations occur randomly. Now we’ll consider just how frequency those mutations could arise in bacteria. Then we’ll ask how frequently mutations occur in humans.
Our model bacterium is Esherichia coli the common, and mostly benign, intestinal bacterium. The entire genome was sequenced in 1997 (Blattner et al., 1997) and its size is 4,200,000 base pairs (4.2 × 106 bp). Every time a bacterium divides this amount of DNA has to be replicated; that’s 8,400,000 nucleotides (8.4 × 106).
The most common source of mutation is due to mistakes made during DNA replication when an incorrect nucleotide is incorporated into newly synthesized DNA. The mutation rate due to errors made by the DNA polymerase III replisome is one error for every one hundred million bases (nucleotides) that are incorporated into DNA. This is an error rate of 1/100,000,000, commonly written as 10-8 in exponential notation. Technically, these aren't mutations; they count as DNA damage until the problem with mismatched bases in the double-stranded DNA has been resolved. The DNA repair mechanism fixes 99% of this damage but 1% escapes repair and becomes a mutation. The error rate of repair is 10-2 so the overall error rate during DNA replication is 10-10 nucleotides per replication (10-8 × 10-2) (Tago et al., 2005).
Since the overall mutation rate is lower than the size of the E. coli genome, on average there won’t be any mistakes made when the cell divides into two daughter cells. That is, the DNA will usually be replicated error free.
However, one error will occur for every 10 billion nucleotides (10-10) that are incorporated into DNA. This means one mutation, on average, every 1200 replications (8.4 × 106 × 1200 is about ten billion). This may not seem like much even if the average generation time of E. coli is 24 hours. It would seem to take four months for each mutation. But bacteria divide exponentially so the actual rate of mutation in a growing culture is much faster. Each cell produces two daughter cells so that after two generations there are four cells and after three generations there are eight cells. It takes only eleven generations to get 2048 cells (211 = 2048). At that point you have 2048 cells dividing and the amount of DNA that is replication in the entire population is enough to ensure at least one error every generation.
In the laboratory experiment the bacteria divided every half hour so after only a few hours the culture was accumulating mutations every time the bacteria divided. This is an unrealistic rate of growth in the real world but even if bacteria only divide every 24 hours there are still so many of them that mutations are abundant. For example, in your intestine there are billions and billions of bacteria. This means that every day these bacteria accumulate millions of mutations. That’s why there’s a great danger of developing drug resistance in a very short time.
Calculating the rate of evolution in terms of nucleotide substitutions seems to give a value so high that many of the mutations must be neutral ones.
Motoo Kimura (1968)I based my estimate of mutation rate on what we know about the properties of the replisome and repair enzymes. Independent measures of mutation rates in bacteria are consistent with this estimate. For example, the measured value for E. coli is 5.4 × 10-10 per nucleotide per replication (Drake et al., 1998). Many of these mutations are expected to be neutral. The rate of fixation of neutral mutations is equal to the mutation rate so by measuring the accumulation of neutral mutations in various lineages of bacteria you can estimate the mutation rate provided you know the time of divergence and the generation time. (Ochman et al., 1999) have estimated that the mutation rate in bacteria is close to 10-10 assuming that bacteria divide infrequently.
The mutation rate in eukaryotes should be about the same since the properties of the DNA replication machinery are similar to those in eukaryotes. Measured values of mutation rates in yeast, Caenorhabditis elegans, Drosophila melanogaster, mouse and humans are all close to 10-10 (Drake et al., 1998).
The haploid human genome is about 3 × 109 base pairs in size. Every time this genome is replicated about 0.3 mutations, on average, will be passed on to one of the daughter cells. We are interested in knowing how many mutations are passed on to the fertilized egg (zygote) from its parents. In order to calculate this number we need to know how many DNA replications there are between the time that one parental zygote was formed and the time that the egg or sperm cell that unite to form the progeny zygote are produced.
In the case of females, this number is about 30, which means that each female egg is the product of 30 cell divisions from the time the zygote was formed (Vogel and Rathenberg, 1975). Human females have about 500 eggs. In males, the number of cell divisions leading to mature sperm in a 30 year old male is about 400 (Vogel and Motulsky, 1997). This means that about 9 mutations (0.3 × 30) accumulate in the egg and about 120 mutations (0.3 × 400) accumulate in a sperm cell. Thus, each newly formed human zygote has approximately 129 new spontaneous mutations. This value is somewhat less than the number in most textbooks where it's common to see 300-350 mutations per genome. The updated value reflects a better estimate of the overall rate of mutation during DNA replication and a better estimate of the number of cell divisions during gametogenesis.
With a population of 6 billion individuals on the planet, there will be 120 × 6 × 109 = 7.2 × 1011 new mutations in the population every generation. This means that every single nucleotide in our genome will be mutated in the human population every 20 years or so.
Blattner,F.R., Plunkett,G., Bloch,C.A., Perna,N.T., Burland,V., Riley,M., ColladoVides,J., Glasner,J.D., Rode,C.K., Mayhew,G.F., Gregor,J., Davis,N.W., Kirkpatrick,H.A., Goeden,M.A., Rose,D.J., Mau,B., and Shao,Y. (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453-1474.©Laurence A. Moran (2007)
Drake,J.W., Charlesworth,B., Charlesworth,D., and Crow,J.F. (1998) Rates of spontaneous mutation. Genetics 148:1667-1686.
Ochman,H., Elwyn,S., and Moran,N.A. (1999) Calibrating bacterial evolution. Proc. Natl. Acad. Sci. (USA) 96:12638-12643.
Tago,Y., Imai,M., Ihara,M., Atofuji,H., Nagata,Y., and Yamamoto,K. (2005) Escherichia coli mutator Delta polA is defective in base mismatch correction: The nature of in vivo DNA replication errors. J. Mol. Biol. 351:299-308.
Vogel,F. and Motulsky,A. (1997) Human Genetics: Problems and Approaches. (Berlin, New York: Springer-Verlag).
Vogel,F. and Rathenberg,R. (1975) Spontaneous Mutation in Man. Adv. Hum. Genet. 5:223-318.
The Evils of Darwinism in America
Over on the Discovery Institute website there's an important announcement [John West's Forthcoming Book] ...
Next Fall ISI Books will release CSC associate director Dr. John West's important book, Darwin Day in America: How Our Politics and Culture Have Been Dehumanized in the Name of Science.Fascinating. Given that "Darwinism" has been so fiercely resisted in America its success in degrading American culture is all that more remarkable.
Darwin Day in America tells the disturbing story of scientific expertise run amuck, exposing how an ideological interpretation of Darwinian biology and reductionist science have been used to degrade American culture over the past century through their impact on criminal justice, welfare, business, education, and bioethics.
I look forward to Dr. West's exposé of European culture where rationalism has been even more successful than in America. I wonder what he thinks of France?
Wednesday, July 04, 2007
Richard Dawkins on Visible Changes and Adaptationism
On another thread [Visible Mutations and Evolution by Natural Selection] we are discussing a common adaptationist claim that once a mutation has a visible phenotype it is almost certainly subject to selection. Some people have questioned whether there is anyone who actually believes in such a thing. Here's Richard Dawkins writing in The Extended Phenotype (1982).
Contrary to Dawkins, I believe that Neutral Theory has reduced the importance of selection in nature. Prior to 1968 it was common to attribute almost all changes to natural selection and it was common to advocate that the presence of variation in a population was due to balancing selection. Today, one has to consider the evidence for adaptation; you can no longer just assume that it is the only game in town.
Of course it's true that natural selection is the only mechanism that affects allele frequencies once you can demonstrate that a visible change affects survival and reproduction. But Dawkins goes farther than that. He strongly implies that all visible phenotypes are subject to selection and neutral alleles are confined to the molecular level.
The biochemical controversy over neutralism is concerned with the interesting and important question of whether all gene substitutions have phenotypic effects. The adaptationism controversy is quite different. It is concerned with whether, given that we are dealing with a phenotypic effect big enough to see and ask questions about, we should assume that it is the product of natural selection. The biochemist's 'neutral mutations' are more than neutral. As far as those of us who look at gross morphology, physiology and behaviour are concerned, they are not mutations at all. It was in this spirit that Maynard Smith (1976b) wrote: "I interpret 'rate of evolution' as a rate of adaptive change. In this sense, the substitution of a neutral allele would not constitute evolution ..." If a whole-organism biologist sees a genetically determined difference among phenotypes, he already knows he cannot be dealing with neutrality in the sense of the modern controversy among biochemical geneticists.In 2007 Dawkins would probably admit to some neutral examples of "genetically determined differences among phenotypes" but his position hasn't changed very much from 1982. For example, in The Ancestor's Tale (2005) he writes,
Contrary to my rather ludicrous reputation as an "ultra-Darwinist" (a slander I would protest more vigorously if the name sounded less of a compliment than it does), I do not think that the majority of evolutionary change at the molecular level is favoured by natural selection. On the contrary, I have always had a lot of time for the so-called neutral theory associated with the great Japanese geneticist Motoo Kimura, or its extension, the "nearly neutral" theory of his collaborator Tomoko Ohta. The real world has no interest in human tastes, of course, but as it happens I positively want such theories to be true. This is because they give us a separate, independent chronicle of evolution, unlinked to the visible features of the creatures around us., and they hold out the hope that some kind of molecular clock might really work.Pluralists believe that all kinds of alleles are neutral or nearly neutral and are fixed in a population by random genetic drift. This includes alleles that produce a visible phenotype. Pluralists do not believe that there is a major distinction between the mechanisms of evolution at the molecular level and the mechanisms at the morphological level.
Just in case the point is misunderstood, I must emphasize that the neutral theory does not in any way denigrate the importance of selection in nature. Natural selection is all-powerful with respect to those visible changes that affect survival and reproduction. Natural selection is the only explanation we know for the functional beauty and apparently "designed" complexity of living things. But if there are any changes that have no visible effect—changes that pass right under natural selection's radar—they can accumulate in the gene pool with impunity and may supply just what we need for an evolutionary clock.
Contrary to Dawkins, I believe that Neutral Theory has reduced the importance of selection in nature. Prior to 1968 it was common to attribute almost all changes to natural selection and it was common to advocate that the presence of variation in a population was due to balancing selection. Today, one has to consider the evidence for adaptation; you can no longer just assume that it is the only game in town.
Of course it's true that natural selection is the only mechanism that affects allele frequencies once you can demonstrate that a visible change affects survival and reproduction. But Dawkins goes farther than that. He strongly implies that all visible phenotypes are subject to selection and neutral alleles are confined to the molecular level.
Nobel Laureate: Adolf Windaus
The Nobel Prize in Chemistry 1928.
"for the services rendered through his research into the constitution of the sterols and their connection with the vitamins"
Adolf Otto Reinhold Windaus (1876-1959) won the Nobel Prize in 1928 for his work on the structure of sterols and their functions. One of the most common sterols is cholesterol and Windaus was able to show that it is synthesized in many different species although he was not able to determine its function. (We now know that it is an important component of membranes.)
Windaus also worked out the synthesis of vitamin D from the plant sterol ergosterol [Monday's Molecule #33]. The Presentation Speech was given by Professor H.G. Söderbaum of the Royal Swedish Academy of Sciences on December 10, 1928. The speech may seem confusing since it talks about two Nobel Laureates, Wieland and Windaus, but Windaus was the sole recipient of the 1928 Nobel Prize. It turns out that the 1927 Nobel Prize in Chemistry was awarded to Heinrich Otto Wieland at the same time as the 1928 Nobel Prize.
Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.
We hear continually that today science, in particular natural science, is becoming increasingly more specialized, that scientists are delving deeper and deeper into specialized studies difficult to survey, that the deep stream of research is turning into ever-shallower brooks and channels, and that in this way the unity that exists between the different branches of science is in danger of being destroyed. Indeed, most people have wondered with some disquiet where this apparently unrestricted specialization will eventually lead. The answer to this question is that, while the question itself is completely justified, the disquiet is in most cases unjustified or at least unduly great.
A stage is reached sooner or later in the development of every natural science, when research, after dealing with problems of more general importance, has of necessity to apply itself to problems of detail of apparently more limited interest. It is simply that the continuous increase in scientific knowledge necessitates a corresponding continuous increase in the division of work. Many fields of science which could once be handled by a few or even one investigator, may only one generation later provide enough or more than enough work for whole hosts of students and their attendants. However, specialization is, or should be, not an end but a means. Even at the stage of the division of work, for the true investigator the end is, and will remain, that of determining the inner connection between the changing phenomena, and, depending on the extent to which this end is achieved, the special researches will gradually merge into greater units; the detail then ceases to be an isolated thing, more or less unimportant as regards the whole, but becomes a necessary link in a connected chain of knowledge.
The work which has been awarded Alfred Nobel's Chemistry Prizes this year by the Academy of Sciences, provides an instructive example of this process.
We are dealing here with several fields of work, which are separate from the start.
First we have biles. As is well-known, biles and hence their specific constituents, bile acids, are of major importance in the digestion process. Now these bile acids have been for almost a hundred years the object of active study by a large number of prominent investigators. In this way a large amount of material was accumulated from observations, but despite this, little was known concerning the connection between the various bile acids, and almost nothing concerning the details of their structure, when Wieland began his work in this field.
Then we have the cardiac poisons. Of animal cardiac poisons chemists were acquainted in particular with so-called bufotalin, which is present in the skin secretion of certain species of the toad genus Bufo. In therapeutics, on the other hand, vegetable cardiac poisons have long been used, especially those belonging to the glucoside group and obtained from species of the plant genera Digitalis and Strophantus. But the production of these substances in the pure state and the determination of the chemical relationships between them had long remained an unresolved problem.
The so-called sterols are also an extremely interesting group from the physiological viewpoint. They too occur both in vegetation and in animals. Most numerous are the vegetable sterols, the so-called phytosterols, but the best-known is certainly cholesterol, which occurs in the animal organism, and which was first found about 150 years ago in gall stones. This substance occurs not only in bile but also in the brain, in nerve substance, in the egg, in blood, and presumably in all cells. Thus we can conclude that it plays an extremely important part in the life process of man and the animals, just as the phytosterols play an extremely important part in the life process of plants. These sterols were however an isolated group for a long time. The difficulties associated with investigation of their chemical constitution were so great that it is only during the last few decades, above all through Windaus's investigations, that a clearer picture has been obtained thereof.
Finally, we come to a group of compounds which have only been known for a relatively short time, but which during this short time have attracted very considerable attention, both from chemists and from the public at large. Who today is unacquainted with vitamins, these mysterious substances which are of such immense significance for life, vita, itself and which have thus justifiably taken their name from it? But compared with those mentioned above, the difficulties which here confronted the investigator were far greater, and in most cases it had to be regarded as sufficient to characterize these substances on the basis of their physiological effects.
Thanks to the work which this year has been found before others worthy of recognition through the award of the Nobel Prize in Chemistry, the inner connection between all these apparently isolated fields of research has been very strikingly demonstrated. Of course the way in which this took place can only be described very briefly here.
Wieland succeeded in producing from bile a saturated acid which can be regarded as the mother substance or parent acid of the bile acids, and which he studied and characterized in detail. When Windaus then produced this same parent acid, cholanic acid, from cholesterol by means of a complicated and very ingenious series of experiments, this indicated very clearly the close relationship between cholesterol and the bile acids. It should be pointed out in this connection that Wieland's investigations into bile acids themselves gave a deeper insight of the mechanism of the action of the bile in the resorption of food in the intestines.
But this is not all. As a result of patient and skilful work, Windaus succeeded in producing several of the digitalis glucosides and their components in the pure state. In this way it was shown that these vegetable cardiac poisons are directly related on the one hand to cholesterol and the bile acids, and on the other hand to the animal cardiac poison bufotoxin, which Wieland studied with great success.
Another sterol which Windaus has studied in detail, is ergosterol, which occurs partly in ergot and partly in yeast. The research carried out in recent years, in which Windaus himself has also played a leading part, has revealed the very important fact that, on being irradiated with ultraviolet light, this ergosterol assumes exactly the same properties as the antirachitic vitamin, "vitamin D", i.e. it will cure rachitis (rickets). For example, it has been found that 5 mg of irradiated ergosterol has the same action in this respect as 1 litre of good cod-liver oil. It can be considered proved, therefore, that ergosterol, or possibly a sterol, the physiological effects of which correspond completely with those of ergosterol, constitutes the antirachitic provitamin, i.e. the mother substance of vitamin D.
All the investigations which we have had to summarize so briefly here, have one thing in common with each other. They were all designed to explain the internal structure of organic materials, their relationships with one another and their transitions into each other. For this reason they are of fundamental importance for our knowledge of a number of processes occurring both in the healthy and in the diseased organism, and therefore of greatest significance not only for chemistry as such, but also for its sister sciences, physiology and medicine. But in order to reach this vantage point of knowledge, where the dividing walls separating the various special researches no longer obstruct vision, where the connection between extensive parts of organic chemistry can be surveyed and where in fact the fields of three main disciplines appear to connect and merge with each other - all this has taken years of hard, diligent, and resourceful work in the deep mines of detailed research. These are the researches which are to be rewarded here.
Professor Wieland. The decision of the Royal Academy of Sciences to award you the Nobel Prize in Chemistry for your work on bile acids and related substances, is only a just recognition of the solution of a problem which is without doubt one of the most difficult which organic chemistry has had to tackle.
The complex composition of the compounds investigated, the large number of atoms contained in the molecules of these compounds, the fact that the material was often very difficult to produce, even in small quantities, these were obstacles which could only be overcome with such striking success through a remarkable skill in experimentation and a rare capacity for finding new ways and means.
In gratitude for what you have achieved for science in this connection, and with hearty congratulations on your well-deserved distinction, the Academy asks you to accept the Nobel Prize in Chemistry for the year 1927 from the hands of his Majesty the King.
Professor Windaus. If the Royal Academy of Sciences had had only one Nobel Prize in Chemistry to award on this occasion, and had had to present it to one person, it would have been in a very difficult position.
For there is no doubt that your work on sterols, vegetable cardiac poisons and other closely related substances merits in the same high degree such an award as the work which we have just recognized.
Moreover, it is clear that your work and that of your colleague in Munich are so interrelated and supplement each other in such a way that it would have been extremely difficult to award the Prize to the one while passing over the other.
In addition, both researches display the same assiduity, the same remarkable capacity for overcoming even the greatest experimental difficulties, and the same lucidity in interpreting the results obtained, that it would obviously have been impossible to give precedence to one investigator over the other.
The fact that two Prizes were available for award this year, has fortunately freed the Academy from this quandary. For this the Academy congratulates itself no less than you, and asks you now to take the last few steps which separate you from the external symbols of the Prize.
And the Winner Is .......
Posted by Sam Chen on Uncommon Descent [IDURC Announces 2007 Casey Luskin Graduate Award].
The Intelligent Design Undergraduate Research Center (IDURC) is proud to present the 2007 Casey Luskin Graduate Award, presented annually to a deserving college graduate for excellence in student advocacy of intelligent design.I wonder if the winner will list the prestigious award on his/her CV?
The recipient of the 2007 Casey Luskin Graduate Award will remain anonymous for the protection of the recipient.
Bacteria, Bloggers, and Toronto
Chris Condayan is the Manager for Public Outreach at the American Society for Microbiology (ASM). At the recent ASM meeting in Toronto he videotaped a number of bloggers and created a podcast that's posted on the MicrobeWorld website. Here's your chance to see some real live bloggers including; John Logsdon [Sex, Genes & Evolution], Jonathan Badger [T. taxus], Yersinia [Yersinia], Moselio Schaechter [Small Things Considered], Tara Smith [Aetiology], and me [Sandwalk].
Tuesday, July 03, 2007
Who Owns Your Lab Notebooks?
When post-docs and graduate students finish their projects in a research laboratory they leave their notebooks behind. Those belong to the principal investigator who runs the lab. Graduate students often have a hard time understanding this policy so Janet Stemwedel explains it on Adventures in Ethics and Science.
The original article is Lab notebooks and graduate research: what should the policy be? and the followup is Kept all my notebooks; what good are notebooks?.
This is a good example of an ethical problem in science.
Labels:
Biochemistry
,
Ethics
Monday, July 02, 2007
Gene Genie #10
Gene Genie #10 was posted Ryan Gregory on Genomicron [Gene Genie #10 -- The Canada Day Ultraspectacular Edition].
Visible Mutations and Evolution by Natural Selection
A recent posting [Darwin Still Rules, but Some Biologists Dream of a Paradigm Shift] raised the issue of adaptationism. The controversy is over the main mechanism of genetic change in evolving populations. Adaptationists tend to attribute as much as possible to natural selection while pluralists emphasize the important role of other mechanisms of evolution, like random genetic drift.
There seems to be little doubt that most of the fixed alleles at the molecular level are probably neutral in their effect. Thus, they have been fixed by random genetic drift. This includes many amino acid substitutions in proteins. Even though these substitutions change the structure of a protein by a small amount, it does not seem reasonable to assume that they have all been selected.
Most adaptationists are content to concede this point (although there are holdouts). However, they draw the line at more "visible" mutations. According to this group, the vast majority of "visible" mutations are subject to natural selection and therefore most fixed alleles with a "visible" phenotype are adaptations. The argument seems to be that once a mutation produces a "visible" phenotype then it is not appropriate to suggest that it might be neutral with respect to natural selection. The line seems to be drawn somewhere above differences in the amino acid composition of proteins but it's not clear exactly where.
p-ter is one of those who are very reluctant to admit that a visible character could have been fixed by accident. He has posted a short article on Gene Expression [Do phenotypes evolve neutrally?]. I recommend that you read the comments to see examples of the extreme version of adaptationism. Most of these adaptationists will even argue that human blood types are adaptive. The idea that most native North Americans have type O blood is due to some undefined selective advantage and not to accident.
This argument has been going on for several decades. As usual, it's not about the existence of natural selection or random genetic drift. It's about their relative importance in evolution. To reiterate, the adaptationists believe that almost all mutations with a visible phenotype have been fixed by natural selection. The pluralists think that many of them are neutral and have been fixed by accident. The adaptationists make a distinction between what happens at the molecular level and what happens at the "visible" level while the pluralists think the same mechanims are operating at both levels.
Richard Lewontin uses the example of the Indian and African rhinoceros to focus the debate. The African rhinoceros has two horns while the Indian rhinoceros has only one. The question is whether this difference is due to natural selection—is two horns better than one in Africa? Or, is it just an accident of evolution that one species has two horns while the other has only one?
I don't understand why the adaptationist camp is so reluctant to admit that some visible characters can be fixed by random genetic drift. The idea that every feature of an organism has to be an adaptation seems so out of touch with our modern understanding of evolution that I'm really puzzled by the vehemence with which adaptationists defend their orthodoxy. It seems as though admitting that visible phenotypes might be non-adaptive is a major threat to their worldview.
There seems to be little doubt that most of the fixed alleles at the molecular level are probably neutral in their effect. Thus, they have been fixed by random genetic drift. This includes many amino acid substitutions in proteins. Even though these substitutions change the structure of a protein by a small amount, it does not seem reasonable to assume that they have all been selected.
Most adaptationists are content to concede this point (although there are holdouts). However, they draw the line at more "visible" mutations. According to this group, the vast majority of "visible" mutations are subject to natural selection and therefore most fixed alleles with a "visible" phenotype are adaptations. The argument seems to be that once a mutation produces a "visible" phenotype then it is not appropriate to suggest that it might be neutral with respect to natural selection. The line seems to be drawn somewhere above differences in the amino acid composition of proteins but it's not clear exactly where.
p-ter is one of those who are very reluctant to admit that a visible character could have been fixed by accident. He has posted a short article on Gene Expression [Do phenotypes evolve neutrally?]. I recommend that you read the comments to see examples of the extreme version of adaptationism. Most of these adaptationists will even argue that human blood types are adaptive. The idea that most native North Americans have type O blood is due to some undefined selective advantage and not to accident.
This argument has been going on for several decades. As usual, it's not about the existence of natural selection or random genetic drift. It's about their relative importance in evolution. To reiterate, the adaptationists believe that almost all mutations with a visible phenotype have been fixed by natural selection. The pluralists think that many of them are neutral and have been fixed by accident. The adaptationists make a distinction between what happens at the molecular level and what happens at the "visible" level while the pluralists think the same mechanims are operating at both levels.
Richard Lewontin uses the example of the Indian and African rhinoceros to focus the debate. The African rhinoceros has two horns while the Indian rhinoceros has only one. The question is whether this difference is due to natural selection—is two horns better than one in Africa? Or, is it just an accident of evolution that one species has two horns while the other has only one?
I don't understand why the adaptationist camp is so reluctant to admit that some visible characters can be fixed by random genetic drift. The idea that every feature of an organism has to be an adaptation seems so out of touch with our modern understanding of evolution that I'm really puzzled by the vehemence with which adaptationists defend their orthodoxy. It seems as though admitting that visible phenotypes might be non-adaptive is a major threat to their worldview.
Monday's Molecule #33
Today's molecule is complex. The short common name of this molecule is sufficient but you're more than welcome to supply the IUPAC name if you know it. There's a direct connection between this Monday's Molecule and Wednesday's Nobel Laureate. (Hint: this molecule is not mentioned in the description of the award but the class of molecules to which it belongs is mentioned.)
The reward (free lunch) goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous free lunch winners are ineligible for one month from the time they first collected the prize. There's only one (Marc) ineligible candidates for this Wednesday's reward since many recent winners haven't collected their prize. The prize is a free lunch at the Faculty Club.
UPDATE: The molecule is ergosterol, a plant sterol that is a precursor to vitamin D. Ultraviolet irradiation converts ergosterol to vitamin D2.
Happy Canada Day
HAPPY
CANADA
DAY
Canada's official birthday was yesterday, July 1, but everyone gets a holiday today to celebrate.
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