The latest version of the Tangled Bank has been posted on from Archaea to Zeaxanthol [Tangled Bank #93].Ahoy me mateys and welcome to the 93rd edition of the Tangled Bank, humbly hosted by yours truly. For those of you returning to from Archaea to Zeaxanthol, welcome back. For those new to my blog, let me give you a quick introduction.
At one point in his talk last night Kirk Durston mentioned the bacterial flagella. He acknowledged that the "Darwinists" have proposed an evolutionary pathway from a Type III secretory structure to flagella. Mira, A., Ochman, H. and Moran N.A. (2000) Deletional bias and the evolution of bacterial genomes. Trends Genet. 17:589-96. [PubMed]I asked Durston what would happen if I called Nancy Moran (no relation, that's her above) and asked her whether she agreed that primitive bacteria were complex and all modern bacterial lineages are losing information. He affirmed that she would and that's what modern evolutionary biologists are saying. There are other papers that say the same thing. He accused me of not being aware of them.
Although bacteria increase their DNA content through horizontal transfer and gene duplication, their genomes remain small and, in particular, lack nonfunctional sequences. This pattern is most readily explained by a pervasive bias towards higher numbers of deletions than insertions. When selection is not strong enough to maintain them, genes are lost in large deletions or inactivated and subsequently eroded. Gene inactivation and loss are particularly apparent in obligate parasites and symbionts, in which dramatic reductions in genome size can result not from selection to lose DNA, but from decreased selection to maintain gene functionality. Here we discuss the evidence showing that deletional bias is a major force that shapes bacterial genomes.I think it's pretty obvious from the abstract that they're discussing a particular problem in bacterial evolution; namely selection for small compact genomes. This point is clear in the paper as well.
I went to the lecture in Denyse O'Leary's course last night [I'm Going to a Lecture on Intelligent Design]. As promised, the guest speaker was Kirk Durston, a graduate student in biophysics at the University of Guelph. This are (at least) two major flaws in this argument and it doesn't take an expert in computer science or biochemistry to detect them.
- By making assumptions A, B, C, and D and constructing equations E and F he is able to predict that no protein will have more than X amount of information.
- By making a few assumptions about protein families it is possible to measure the amount of information in a folded domain by plugging the data into his equations. It turns out that most proteins have more than X information.
- Therefore God exists (i.e., the protein must have been intelligently designed).
Axe, D. (2000) Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors. J. Mol. Biol. 310:585-595.
axe, D. (2004) Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds. J. Mol. Biol. 341:1295-1315.
"for their discoveries concerning the mechanism and regulation of the cholesterol and fatty acid metabolism"
Konrad Bloch (1912-2000) and Feodor Lynen (1911-1979) received the Nobel Prize in Physiology or Medicine for their work in deciphering the cholesterol biosynthesis pathway. 
Your Majesties, Your Royal Highnesses, Ladies and Gentlemen.
Since the start of the Nobel Foundation the professorial staff of the Karolinska Institute has chosen the prizewinners in Physiology or Medicine. This year the Karolinska Institute has been reorganized into a medical university and the duties of the professorial staff have been taken over by the medical faculty of the enlarged Karolinska Institute. As the last item on its agenda the professorial staff was to decide this year's Nobel Prizewinners in Physiology or Medicine and on October 15 Professors Konrad Bloch and Feodor Lynen were awarded the prize for their discoveries concerning the mechanism and regulation of the cholesterol and fatty acid metabolism.
The word cholesterol means gallstone and the reason for this name is that cholesterol was isolated almost 200 years ago from human gallstones. Another connection between cholesterol and human diseases has been established more recently. During the last decade there has been a lively discussion, also in the newspapers, about the correlation between atherosclerosis and the amount of cholesterol and other fats in diet and in blood. This discussion has perhaps concealed from many the fact that cholesterol is a necessary constituent of all our cells and that it fulfills important functions. The elucidation of its chemical structure is one of the foremost achievements in organic chemistry during the 1910's and 1920's. In 1928 the German chemists Windaus and Wieland received Nobel Prizes in Chemistry for their work on the structure of cholesterol and the closely related bile acids. The four-ring carbon skeleton characteristic of cholesterol was later found not only in a number of sterols of plant and animal origin but also in the precursors of vitamin D, in the male and female sex hormones, in the hormones from the adrenal cortex, etc.
Nothing was known about the way they were formed or about their interrelationships. When this year's prizewinners started their scientific career, Professor Hevesy had done his discoveries concerning the use of isotopes as tracers in the living organism. When first the stable and later the radioactive isotopes of hydrogen and carbon became available, they were first extensively used by a group at Columbia University that was headed by the late Rudolph Schoenheimer and in which Bloch played an important role. The work of the group with isotopically labeled compounds has laid the foundation of our general knowledge of the dynamic state in the living cell.
One of the fundamental discoveries was the elucidation of the role of acetic acid as a building block for cholesterol as well as fatty acids. Lynen, working in Wieland's laboratory on the metabolism of acetic acid, succeeded in isolating the so-called activated acetic acid, which is the precursor of all lipids in our body and the common denominator of a number of metabolic processes. With all possible refinements in the utilization of isotope techniques, Bloch and collaborators were able to show in a series of brilliant investigations how the two carbon atoms of acetic acid are used for the synthesis of a long hydrocarbon with thirty carbon atoms, squalene, which in turn is cyclized in a novel type of reaction to a steroid with thirty carbon atoms, lanosterol. This lanosterol is then transformed in a complicated series of reactions into cholesterol, which has twenty-seven carbon atoms. Of special interest are the reactions leading to the formation of the hydrocarbon squalene, and the elucidation of these reactions, which are common for the biosynthesis of many other lipids and natural products, is due not only to Bloch and Lynen and collaborators but also to Popjak and Cornforth in England and Folkers and co-workers in the U.S.A. In connection with this work Lynen made two other discoveries of great importance to our understanding of the mechanisms of cellular metabolism: the elucidation of the mechanism of action of the vitamin biotin and the determination of the structure of cytohemin.
At an early stage Bloch made another discovery of fundamental importance in showing that cholesterol is the precursor of bile acids and of one of the female sex hormones. These discoveries opened up a new field of research that has engaged a great number of scientists in different disciplines. We know now that all substances of steroid nature in our body are formed from cholesterol.
Mainly through the basic biochemical work of this year's prizewinners do we know today in detail how cholesterol and fatty acids are synthesized and metabolized in the body. These processes comprise series of reactions with a great number of individual steps. For instance, the formation of cholesterol from acetic acid is a process involving some thirty different steps. Derangements of this complicated mechanism of formation and metabolism of lipids are in many cases responsible for the genesis of some of our most important diseases, especially in the cardiovascular field. A detailed knowledge of the mechanisms of lipid metabolism is necessary to deal with these medical problems in a rational manner.
The importance of the work of Bloch and Lynen lies in the fact that we now know the reactions which have to be studied in relation to inherited and other factors. We can now predict that we, through further research in this field in the near future, can expect to be able to do individual specific therapy against the diseases that in the developed countries are the most common cause of death.
Professor Bloch, Professor Lynen. You have both started your research in Munich and you have proceeded the proud tradition of this town in a splendid way.
Feodor Lynen, you are now standing with dignity in the array of the earlier Munich Nobel Prizewinners, Adolf von Baeyer, Hans Fischer and Heinrich Wieland.
Konrad Bloch, you have like Emil Fischer and Richard Willstätter left Munich and continued your work in the New World.
I have made a very short summary of your successful research work in the field of lipids. You have provided us with detailed knowledge of many fundamental metabolic reactions. This knowledge forms the necessary basis for the study of the different medical problems in the field of lipid metabolism.
It can now be anticipated that in the near future we will learn how to deal with many of these diseases in a rational and successful way.
On behalf of the Caroline Institute I have the honour to congratulate you on your brilliant work and I now ask you to receive your prizes from the hands of His Majesty the King.
[Photo Credits: Konrad Bloch plaque is from Wikipedia. Restricted photos of Feodor Lynen are available on ViewImages]
New Scientist is running a contest for the best laboratory website. The ten finalists are listed on the New Scientist website [Laboratory Website and Video Awards].[Photo Credit: Gregory Lab: Genomic Diversity]
Stephen Fry has posted a long description of a debate he had with an American aquaintance about global climate change [Getting Overheated]. You should read the whole thing but there's one part that caught my eye.We must begin with a few round truths about myself: when I get into a debate I can get very, very hot under the collar, very impassioned, and I dare say, very maddening, for once the light of battle is in my eye I find it almost impossible to let go and calm down. I like to think I’m never vituperative or too ad hominem but I do know that I fall on ideas as hungry wolves fall on strayed lambs and the result isn’t always pretty. This is especially dangerous in America. I was warned many, many years ago by the great Jonathan Lynn, co-creator of Yes Minister and director of the comic masterpiece My Cousin Vinnie, that Americans are not raised in a tradition of debate and that the adversarial ferocity common around a dinner table in Britain is more or less unheard of in America. When Jonathan first went to live in LA he couldn’t understand the terrible silences that would fall when he trashed an statement he disagreed with and said something like “yes, but that’s just arrant nonsense, isn’t it? It doesn’t make sense. It’s self-contradictory.” To a Briton pointing out that something is nonsense, rubbish, tosh or logically impossible in its own terms is not an attack on the person saying it – it’s often no more than a salvo in what one hopes might become an enjoyable intellectual tussle. Jonathan soon found that most Americans responded with offence, hurt or anger to this order of cut and thrust. Yes, one hesitates ever to make generalizations, but let’s be honest the cultures are different, if they weren’t how much poorer the world would be and Americans really don’t seem to be very good at or very used to the idea of a good no-holds barred verbal scrap. I’m not talking about inter-family ‘discussions’ here, I don’t doubt that within American families and amongst close friends, all kinds of liveliness and hoo-hah is possible, I’m talking about what for good or ill one might as well call dinner-party conversation. Disagreement and energetic debate appears to leave a loud smell in the air.I understand this difference. Here in Canada we're half way between Europe and America in terms of debate tactics. In some cases you can have lots of fun carrying on in a "British" tradition. But from time-to-time you encounter some people from the "American" cultural tradition and they take great offense at such behavior.
[Hat Tip: RichardDawkins.net]
[Photo Credit: stephenfry.com]
In previous postings we learned how cholesterol is made from squalene and squalene is made from the six carbon compound mevalonate [How to Make Cholesterol] [Making Squalene].
Anyone who spoke out against the war in Viet Nam and who knew Jane Fonda would get my vote. Especially if the other choice was someone who didn't even like Jane Fonda.[Hat Tip: Canadian Cynic]
Denyse O'Leary is teaching a course on Intelligent Design at the University of St. Michael's College, University of Toronto [Denyse O'Leary's University Course on Intelligent Design]. Session 5. Intelligent design: What the ID proponents actually say (and don’t say) Tuesday November 20, 2007
Michael Behe, author of Edge of Evolution (2007), sees actual design where, for example, Richard Dawkins, author of The Blind Watchmaker, sees the illusion of design. Who’s right? Are they both wrong?
Guest: Kirk Durston, biophysics PhD candidate at the University of Guelph.
Kirk Durston (right) is the National Director of the New Scholars Society. According to his biography on their website,KIRK DURSTON, B.Sc (Physics), B.Sc. (Mech. Eng.), M.A. (Philosophy), Ph.D. Candidate (Biophysics) at the University of Guelph.What is it about creationists that they always seem to have multiple redundant degrees? In this case he has two Bachelor's degrees. What's with that?
Kirk Durston is the National Director of the New Scholars Society. He is currently a Ph.D. candidate in Biophysics at the University of Guelph, specializing in the application of information to biopolymers. His other interests include amateur astronomy, wilderness canoeing & camping, and landscape photography & art.
The sole basis of our beliefs is the Bible, God's infallible written Word, the 66 books of the Old and New Testaments. We believe that it was uniquely, verbally and fully inspired by the Holy Spirit, and that it was written without error (inerrant) in the original manuscripts. It is the supreme and final authority in all matters on which it speaks.We accept those large areas of doctrinal teaching on which, historically, there has been general agreement among all true Christians. Because of the specialized calling of our movement, we desire to allow for freedom of conviction on other doctrinal matters, provided that any interpretation is based upon the Bible alone, and that no such interpretation shall become an issue which hinders the ministry to which God has called us.Jeffrey Shallit had a few things to say about Kirk Durston on Recursivity [Kirk Durston: Apologist for Genocide]. This is going to be an interesting lecture.
One of the regular contributers to the comments section of Sandwalk has suggested we read Who Was Adam? by Fazale Rana and Hugh Ross. Apparently this is a very good explanation of how evolution is compatible with the Bible.We believe the Bible (the 66 books of the Old and New Testaments) is the Word of God, written. As a "God-breathed" revelation, it is thus verbally inspired and completely without error (historically, scientifically, morally, and spiritually) in its original writings. While God the Holy Spirit supernaturally superintended the writing of the Bible, that writing nevertheless reflects the words and literary styles of its individual human authors. Scripture reveals the being, nature, and character of God, the nature of God's creation, and especially His will for the salvation of human beings through Jesus Christ. The Bible is therefore our supreme and final authority in all matters that it addresses.Fazale (Fuz) Rana is a biochemist who works for Hugh Ross at Reasons to Believe.
Now, surprisingly enough, genetically speaking all races are equal. As a matter of fact, if you took a random sample of someone's DNA, just by looking at it you could not tell whether they were African-American, Caucasian, Asian or any other race.I guess Crystal forgot to tell Price et al. (2007) because this is what they say in the abstract of the paper they just published in PLoS Genetics ...
European Americans are often treated as a homogeneous group, but in fact form a structured population due to historical immigration of diverse source populations. Discerning the ancestry of European Americans genotyped in association studies is important in order to prevent false positive or negative associations due to population stratification and to identify genetic variants whose contribution to disease risk differs across European ancestries. Here, we investigate empirical patterns of population structure in European Americans, analyzing 4,198 samples from four genome-wide association studies to show that components roughly corresponding to northwest European, southeast European and Ashkenazi Jewish ancestry are the main sources of European American population structure. Building on this insight, we constructed a panel of 300 validated markers that are highly informative for distinguishing these ancestries. We demonstrate that this panel of markers can be used to correct for stratification in association studies that do not generate dense genotype data.So, not only can we distinguish Caucasians from Africans and Asians, we can also sort out different groups within Caucasians.
Price, V. et al. (2007) Discerning the ancestry of European Americans in genetic association studies. PLoS Genet. In press. [doi:10.1371/journal.pgen.0030236.eor]
Judgment Day is the PBS Nova show about the Dover trial. You can now watch it online in 12 episodes [Judgment Day].[Hat Tip: Monado at Science notes ( "Intelligent Design on Trial" comes to your computer)]
