A Junk DNA Quiz

 
I'm a little busy right now with real world issues so I thought I'd pass alone this abstract posted by Ryan Gregory on Genomicron [And the junk DNA train rolls on...].

Mallik, M. and Lakhotia, S.C. 2008. Noncoding DNA is not "junk" but a necessity for origin and evolution of biological complexity. Proceedings of the Indian National Science Academy Section B - Biological Sciences 77 (Sp. Iss.): 43-50.

All eukaryotic genomes contain, besides the coding information for amino acids in different proteins, a significant amount of noncoding sequences, which may or may not be transcribed. In general, the more evolved or biologically complex the organisms are, greater is the proportion of the noncoding component in their genomes. The popularity and success of "central dogma of molecular biology" during the last quarter of the 20(th) century relegated the noncoding DNA sequences to a mortifying status of "junk" or "selfish", even though during the pre-"molecular biology" days there were good indications that such regions of the genome may function in as yet unknown ways. A resurgence of studies on the noncoding sequences in various genomes during the past several years makes it clear that the complex biological organization demands much more than a rich proteome. Although the more popularly known noncoding RNAs are the small microRNAs and other similar species, other types of larger noncoding RNAs with critical functions in regulating gene activity at various levels are being increasingly,identified and characterized. Many noncoding RNAs are involved in epigenctic modifications, including imprinting of genes. A comprehensive understanding of the significance of noncoding DNA sequences in eukaryotic genomes is essential for understanding the origin and sustenance of complex biological organization of multicellular organisms.

How many things are wrong with this abstract? Hints: The Deflated Ego Problem, The Central Dogma of Molecular Biology, Epigenetics Revisited, The Difference Between Fishand Humans.

The most important question is, how did such a paper ever get published in a peer reviewed journal?

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Denyse O'Leary Thinks Intelligent Design Creationism Is Winning!

 
Here's what Denyse O'Leary say on Uncommon Descent [Looking back: Why I think ID is winning] ...

Having reported news on the ID scene for about five years now, I could give a number of reasons why I think ID is slowly winning the intellectual battle, but let me focus on just one for now ...

Poor Denyse. There are times when I really feel sorry for her.

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Nobel Laureate: Archibald Hill

 

The Nobel Prize in Physiology or Medicine 1922.

"for his discovery relating to the production of heat in the muscle"

Archibald Vivian Hill (1886 - 1977) received the Nobel Prize in Physiology or Medicine for his work on heat production in muscle. He related the heat produced when glycogen was broken down to lactate to the heat generated in frog muscle. Hill was one of the first scientists to relate chemical thermodynamics to biological work.

Hill shared his Nobel Prize with Otto Fritz Meyerhof.

The presentation speech was delivered by Professor J.E. Johansson, Chairman of the Nobel Committee for Physiology or Medicine of the Royal Caroline Institute on December 10, 1923(Note that the 1922 prize was awarded at the same time as the 1923 prize.)

THEME:
Nobel Laureates

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen,

The object of physiology is to endeavour to recognize in the vital processes well-known physical and chemical processes. Accordingly it has to give answers to such questions as these: what is it that takes place in a muscle that contracts, in a gland that emits a secretion, in a nerve when it transmits an impulse? In former times these processes were explained as being the work of what were called «life spirits» - beings who in their mode of existence possessed an unmistakable resemblance to the person who spoke of them. If the muscles of a recently killed animal were seen to twitch when cut or pierced, this was explained by saying that the life spirits had been irritated. From this way of looking at things there still remains the expression «irritation», which we use to denote the starting - or, as we also put it, the liberation - of an active process in an organ. It is a long time, however, since we learnt to regard living organs, muscles, nerves, etc., as mechanisms; and the expression «muscular machine» will probably not strike any educated person in our days as being strange or offensive.

In order to render clear the working of a mechanism it is customary to give a «simplified model» of it. A schematic drawing or an imaginary model may perform the same service, and is at any rate cheaper. The first model that was made of muscular mechanism had the steam-engine as its prototype. Very soon, however, it was perceived that the adoption of an engine of this type presupposes the existence of substances in the muscular fibres capable of sustaining temperatures far exceeding 100°C. The efficiency of muscular work can in fact amount to 20-30%; and such values cannot be obtained by a heat-engine unless the temperature in certain parts of the engine is raised to a considerable height. Hence the muscular machine cannot be referred to that group of motors that transform heat into mechanical work and that are based on the equalization of different temperatures. Theoretically, however, differences in osmotic pressure, surface tension, electrical potential, and so on, offer the same possibility of developing work; and consequently any chemical process whatever that takes place «spontaneously» and that gives rise to such differences in «potential», might be employed in a model of a muscular machine. Thus there is no lack of material for the construction of such a model. The difficulty is to select. In this case there was also a further difficulty, namely that of being able to emancipate oneself, in the design of such a model, from the old and discarded model of a heat-engine. One need not be a physiologist to recognize that muscular activity is essentially bound up with the development of heat, or even with combustion. Now as it is impossible to regard the muscle as a heat-engine, how is it possible to fit these phenomena into the course of action?

This problem has been successfully solved by the two investigators to each of whom the Professorial Staff of the Caroline Institute has this year resolved to award half of the Nobel Prize for 1922 in Physiology or Medicine, namely Professors Archibald Vivian Hill of London and Otto Meyerhof of Kiel. These two men have each worked independently and to a large extent with different methods. Hill has analysed, by means of an extremely elegant thermoelectrical method, the time relations of the heat production of the muscle; and Meyerhof has investigated by chemical methods the oxygen consumption by the muscle and the conversion of carbohydrates and lactic acid in the muscle. Both have made use of the same kind of experimental material, namely the surviving muscle excised from a frog - in fact, the classical frog muscle preparation.

Such a preparation remains alive for several hours, or even days. A suitable stimulus liberates a contraction or develops a state of tension, both of short duration. The twitch takes only one or two tenths of a second. If the stimulus be repeated, the muscle makes a new twitch, apparently resembling the preceding one; and if the muscle is attached to a suitable connecting lever, the several twitches give the same effect as the strokes of a piston in a steam-engine. What was more natural than to regard the muscular twitch as the expression of a circular process in the muscular elements? This process makes itself known in another way also, namely in the form of a development of heat in the muscle preparation. The amount of heat is very insignificant. It is measured in millionths of the usual unit of heat and is recorded in a thermoelectrical way in the form of readings on a galvanometer. Armed with technical resources for observing both the mechanical process and the development of heat in the twitch of an isolated muscle, investigators tried to penetrate more deeply into the muscular process proper. Our countryman Blix showed that everything that impedes the contraction of a muscle during the twitch - that is to say, impedes the diminution of surface of the muscular elements - increases the formation of heat, and from this concluded that the process sought is localized to the surface of certain structural elements which, owing to changed conditions in surface tension, acquire a tendency to pass from an ellipsoidical to a more spherical form. If the load of the muscle gives way to the tension thus created, external work is done. Hence the muscle is mainly to be regarded as a machine that converts chemical energy into tension energy.

In the first experiments that Hill carried out on this subject in 1910 he made use of a thermo-galvanometer designed by Blix. Here he noticed that the reading not only gives the total amount of heat developed, but also is to some extent affected by the period of time taken in the development of heat. He was able to distinguish between an «initial» and a «delayed» development of heat. A subsequent work contained the starting-point for a new method of investigation, which made it possible to trace the development of heat in muscular movements in their various stages. This technique may be described as having been completely developed by 1920; but some of the results that I shall mention had been obtained as early as 1913, that is to say before the outbreak of the World War.

The development of heat in the contraction of the muscle - which to preceding investigators appeared to be «one and indivisible», that is to say, was lumped together as a single phenomenon - can be divided by Hill's method into several periods, the last of which comes long after the end of the mechanical process, that of the twitch. To this must be added the fact that this delayed development of heat entirely fails to appear if the supply of oxygen to the muscle be cut off, while the development of heat during the actual twitch - tension and relaxation - is completely independent of the presence of oxygen. The process of combustion, which it had been customary to connect immediately with the contraction of the muscle, does not actually take place until afterwards. In the experimental arrangements with which we are now dealing (isometrical work) the development of heat during the actual twitch also includes the amount of energy which under other circumstances appears as external work.

Hill's discovery has had a veritably revolutionizing effect as regards the conception of the muscular process. The ordinary view of this process as divided into two phases, tension and relaxation, can, it is true, be retained with regard to the mechanical process, but with regard to the chemical process another division must be adopted - the working phase proper, independent of the supply of oxygen and corresponding to the whole of the mechanical process, and following it an oxidative phase of recovery. If previously in their speculations as to the muscular process physiologists had mainly shown an interest in the actual twitch, investigations now became directed towards the muscle in rest and especially the muscle after preceding exhaustion. Chemical considerations now attracted attention as well as the physical ones.

The earliest known chemical process in the muscle is the formation of lactic acid. This is mentioned as early as 1859 by Du Bois-Reymond. He had found that an excised muscle becomes acid on repeated stimulation even when the rigor mortis sets in. He supposed the cause of this to be the formation of lactic acid - owing, it is stated, to a communication from Berzelius, who had found great quantities of that acid in the flesh of a deer that had been killed in the chase. Since that time lactic acid has played a very important part in discussions as to rigor mortis and the fatigue of the muscle. Some years before Hill began his investigations, two of his countrymen, Fletcher and Hopkins, had shown that the excised muscle not only forms but also converts lactic acid, this depending on whether the muscle is shut off from oxygen or whether oxygen is supplied to it. Some observations also suggested that when the lactic acid disappears from the muscle, only part of it is burnt up, while the rest is re-transformed into the mother substance of lactic acid. In consequence of this there was reason to surmise that the part played by lactic acid in the muscles is not completely represented by such expressions as «by-product of the metabolism», «fatigue substance», «cause of rigor mortis», etc. In this connection Hill proposed that lactic acid should be included as a part of the actual muscle machine.

The formation of lactic acid in the muscle, according to Fletcher and Hopkins, and this development of heat in the muscle during its working phase, according to Hill, exhibit the striking accordance that they take place independent of the oxygen supply. According to Blix, the twitch came about due to the fact that along the surface of certain structural elements there suddenly appears some substance, the nature of which is not stated. If we suppose this substance to be lactic acid - formed either directly or with some intermediate stage from the muscles' well-known store of glycogen - we have a model which combines in itself the most valuable contributions of the investigations of the last few decades on this question. We make the stage of recovery, accompanied by the supply of oxygen, follow the working phase together with Hill's delayed development of heat and Fletcher's conversion of lactic acid. The fact is that lactic acid, when it has done its work, must be got rid of somehow in order that the machine may be kept going.

By a well-known calculation Hill tried to find support for the recently quoted supposition of Fletcher and Hopkins with regar d to a reversion, in conjunction with the lactic acid combustion, of lactic acid to glycogen during the phase of recovery. It is easy to see that the correctness of this supposition forms a condition that the model cited should be acceptable from the point of view of energetics. But objections were made against the analyses and arguments of Fletcher and Hopkins. Moreover, there were adduced, from what were considered to be extremely competent quarters, direct observations which seemed to show that the lactic acid formed in the working phase was completely used in the process of recovery - a piece of wastefulness on the part of Nature which could only be explained by means of auxiliary hypotheses in the presence of which it would have been the simplest thing to let the whole of the attractive model take part in the combustion.

It is at this stage in the development of the question that Meyerhof's contribution comes in. In his investigations concerning the respiration of the tissues (1918) he came to devote his attention to the things that take place in the surviving muscle, and in this connection also to the objections that had been raised against the conclusions of Fletcher and Hopkins and their interpretation of the «lactic acid maximum» of the muscle. He showed that these objections do not really affect the result of the recently cited calculations of Hill. Most important of all, however, was his parallel determination of the lactic acid metabolism and the oxygen consumption during the recovery of the muscle, which yielded the result that the oxygen consumption does not correspond to more than 1/3 - 1/4 of the simultaneous lactic acid metabolism. Evidently the greater part of the lactic acid disappears in some other way than through combustion. In another parallel determination - the development of heat and the oxygen consumption - the development of heat exhibited a deficit in comparison with what could be calculated from the simultaneously observed oxygen consumption. From this the conclusion may be drawn that the combustion of lactic acid in the muscle is combined with some other process, an endothermic one, in the course of which part of the heat developed in the combustion is used up. Meyerhof also made a parallel determination of the carbohydrates and lactic acid in the resting and in the working muscle, also in the recovery period after fatigue; he found: when lactic acid is stored in the muscle, an equivalent quantity of carbohydrates, chiefly glycogen, disappears, while when lactic acid disappears, the quantity of carbohydrates in the muscle is increased by an amount equivalent to the difference between the total amount of lactic acid that has disappeared and the quantity oxidized corresponding to the oxygen consumption.

Hence the processes which we have to take into account in the muscles are: (1) the formation of lactic acid from carbohydrates; (2) the combustion of lactic acid to carbonic acid and water; and (3) the reversion of lactic acid to carbohydrates. But these processes are not confined to the uninjured muscle. Meyerhof has also traced them in finely chopped muscle substance kept moist in a suitable liquid, and in that case found them take place 10-29 times more rapidly than in the well-known muscle preparation. In such a dilution it is also possible to study the effect of different factors such as the concentration of hydrogen ions, the presence of phosphates, etc.; and in particular it has been possible to make clear to what extent the various processes are connected with one another or can be varied in relation to one another. A matter of extremely great interest is the establishment of the fact that the combustion of lactic acid in the muscle cannot take place without a simultaneous formation of lactic acid from carbohydrates, and that the combustion of lactic acid is connected with the formation of carbohydrates in such a way that out of four molecules of lactic acid one is oxidized, while the three others are reverted to carbohydrates. lt is not inconceivable that the reversion does not always extend so far as to produce carbohydrates; but the ideal course of the process may be regarded as precisely defined by Meyerhof, and it has been represented by him in the form of a scheme of chemical reaction. In this scheme, too, can well be fitted the lactacidogen discovered by Embden as a connecting link between glycogen and lactic acid.

The chemical processes just cited have to be fitted into the model of the muscle machine. Ignoring other considerations than those of energy, we can express the course of action in the following way: the change in the muscle which forms the basis of the mechanical process (the external work) presupposes a certain quantity of lactic acid, which comes from the muscle's store of glycogen. When this lactic acid has done its work, 1/4 is burnt into carbonic acid and water, while 3/4 return to the store of glycogen. The upper limit of the efficiency of the machine, calculated according to this scheme, will be 50%, which fully corresponds to the real state of things.

The combustion of lactic acid demands oxygen. The muscle preparation, however, can work even if the supply of oxygen is cut off. The lactic acid formed at every twitch spreads in the muscle out from the places where it is formed until the muscle substance finally becomes so impregnated with lactic acid that it is not relaxed between the twitches, and the impulses applied do not give rise to any further formation of lactic acid. The muscle is exhausted or, as one might also put it, poisoned with lactic acid. In the body the muscle is transfused with blood, which supplies oxygen in far greater abundance than that which the excised muscle preparation can obtain from its environment. Owing to its store of alkali, moreover, the blood itself provides room for a certain quantity of lactic acid from working muscles - a quantity of lactic acid that the blood can afterwards get rid of during a subsequent interval in the work. The possibility of thus distributing the combustion of lactic acid during a period that is longer than the work itself, provides us with an explanation of the immense amount of work achieved, especially in the sporting competitions of our day. Even with a volume per minute corresponding to the extreme working capacity of the heart there is not obtained in these cases a supply of oxygen corresponding to the formation of lactic acid in the muscles; and consequently the individual exposes himself to an accumulation of lactic acid in the blood and in all the tissues or the body - an accumulation that must be characterized as poisoning. When we are dealing with competitions for children and young people who are not yet grown up, there is good reason to think about this detail with regard to the muscle machine.

Professors Hill and Meyerhof. Your brilliant discoveries concerning the vital phenomena of muscles supplement each other in a most happy manner. It has given a special satisfaction to be able to reward these two series of discoveries at the same time, since it gives a clear expression of one of the ideas upon which the will of Alfred Nobel was founded, that is, the conception that the greatest cultural advances are independent of the splitting-up of mankind into contending nations. I also feel confident that you will be glad to know that the proposition which has led to this award of the Nobel Prize originated from a German scientist who, in spite of all difficulties and disasters, has clearly recognized the main object of Alfred Nobel.

In conferring upon both of you the sincere congratulations of the Caroline Institute, I have the honour of asking you to receive from His Majesty the King the Nobel Prize for 1922 in Physiology or Medicine.

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Science and the Question of Purpose

 
Lawrence Krauss has a column in the Aug. 2 issue of New Scientist [Why God and Science Don't Mix].¹ The article is mostly about why scientists should not support the Templeton Foundation but I want to focus on one particular statement.

Krauss says,

Science must follow nature wherever it leads us. If it turn out to suggest that we are alone in a universe without purpose, we must accept that.

Let's not quibble about the "alone" part. I think that science does, indeed, reveal a universe without purpose. In particular, it strongly indicates that humans have no special place in the universe and no special role to fulfill. This is one of the reasons why science and religion are in conflict.

Theistic evolutionists and soft intelligent design creationists claim that the universe was set up by God in a way that makes intelligent life inevitable. Many of them claim that the goal is to evolve humans—or something like humans—whose purpose is to discover God and worship Him.

Here's the question. Does science really tell us that there's no purpose and humans aren't special? I think it does suggest exactly that and anyone who chooses to think otherwise is in concflict with science. It's one of the reasons why I think that science and religion are in conflict.

Now, I admit that the inference of purposelessness isn't obvious to the average person but I think it's plain to those people who study science for a living. Perhaps it explains why so many scientists are nonbelievers and perhaps it's why religious scientists such as Ken Miller, Francois Collins, and Simon Conway Morris have to develop such convoluted arguments to rationalize the conflict [Does the Univese Have a Purpose?].

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1. It's interesting that the print version of this essay is titled "Let's Listen to What Nature Says." A much better title IMHO.

Horse Thieves, Skeletons and Black Sheep in the Family

My mother does genealogy. She has dozens of binders full of notes about our ancestors—some date back to 450 AD but most lineages can't be traced back much before 1500. It's fun to find out about your ancestors and about the history that they lived.

Sometimes there are surprises. Some of our ancestors were United Empire Loyalists who left New Jersey for Prince Edward Island after the American Revolution. We are descended from Isabella Robins, daughter of Richard Robins of Monmouth Co. in New Jersey (b. 1746). Richard's father was Benjamin Robins (b. 1686) and Benjamin's father (Richard's grandfather) was Daniel Robins who was born in Scotland in 1627 and sent to Connecticut in 1652 as an indentured servant after being captured by Cromwell's army following the battles of Dunbar and Wocester. (Our relatives were frequently on the losing side!)

After serving his eight years as an indentured servant, Daniel Robins married Hope Potter in New Haven Conn. in 1641. Now here's the interesting part. Hope Potter's father was William Potter (b. 1608) who first came to New England in 1635. When searching for information about William Potter, my mother came across this opening paragraph on a listserve.

Every amateur genealogist has in the back of his or her mind that someday an ancestral skeleton will appear, perhaps the legendary "horse thief". For those who are descendants of William Potter, the skeleton has appeared, but he did not steal the horses.

Hmmm ....

Turns out that William Potter, my great- great- great- great- great- great- great- great- grandfather, is pretty well known to genealogists. He had lots of descendants but that's not the only reason he's so famous. He was an animal lover.

William Potter was hung in 1662 for bestiality. By his own admission he had a fondness for horses, dogs, cows, sheep and pigs. His wife and children, having caught him in the act, laid charges before the Court of Magistrates in Newhaven (New Haven) [William Potter's Crime].

The Court haveing considered the case p'ceeded to sentence, & first read the law to him, & then the Governor asked him if he had anything to say why the court should not p'ceede to judge him according to the law.

He answered noe, but his great matter was betweene God & his soule, to desire him to give him repentance.

The Governor then declared, that seeing it is soe, they could doe noe otherwise, and he therefore in the name of the court did declare to William Potter that the law read was the sentence of the court, to be executed upon him, viz: that he be hanged on the gallowes till he be dead, & then cut downe & buried, & the creatures with whome he hath thus sinfully acted to be put to death before his eyes.

Twelve generations ago, I have about 4000 direct ancestors. William Potter was only one of them. All the others, I'm sure, were fine god-fearing, outstanding, citizens and a credit to their communities. Especially the ones that weren't Americans.

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Monday's Molecule #83

 

In honor of the Olympics, today's molecule is one that every athlete is afraid of. None of them want to allow this molecule to accumulate in their tissues during the competition.

Your task if to identify the molecule and its precursor and the enzyme responsible for the reaction. Be as specific as possible, especially when identifying the dangerous molecule on the right.

There's a indirect connection between today's molecule and a Nobel Prize. The Noble Laureate was among the first to identify the relationship between production of the molecule and the activity associated with the athletes. He won the prize for explaining, in part, why athletes get hot.

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

THEME:

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

Correct responses will be posted tomorrow. I reserve the right to pick multiple winners if several people get it right.

Comments will be blocked for 24 hours.

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Nisbet Attacks PZ Myers (again)

 
Mathew Nisbet has unleashed another attack on vocal atheists in general and PZ Myers¹ in particular [Two Images of Atheism: Hate versus Community].

Atheists have a major image problem. There's a reason that when people ask me what I believe I have to say with a smile: "I'm an atheist...but a friendly atheist." For sure, atheists for a long time have been unfairly stereotyped in the mainstream media and in popular culture. But we also have a lot of lousy self-proclaimed spokespeople who do damage to our public image. They're usually angry, grumpy, uncharismatic male loners with a passion for attacking and ridiculing religious believers. Any fellow atheist who disagrees with their Don Imus rhetoric, they label as appeasers.

These "new atheists" are the dark under belly of atheism. In books, blogs, and public statements, they sell us ideological porn, sophomoric rants that feed our dark sides and reinforce our own unfair stereotypes about the "other," i.e. the religious.

Yet all of this does far more harm than good. The addictive nature of their rhetoric radicalizes us and leads us to an ever more closed off conversation about how we are superior and everyone else is delusional.

Nisbet thinks he's an expert on how to deal with the problems of religion. He just doesn't get it. Several decades of being "nice" and "friendly" toward those who believe in superstitious nonsense got us nowhere. We atheists were ignored at best, and denigrated at worst.

Now, just a few years after publication of The God Delusion (and other books), atheism is on the radar and the believers have to deal with the fact that non-believers exist. Not only that, the non-believers are fighting back against the religious bigots. People like PZ Myers have done more to advance the case for rationalism over superstition than all the Nisbets have done in decades of accommodation. That makes Matt really, really mad. He just can't cope with the fact that his version of framing didn't work.

The guest blogger on Pharyngula took note of the attack (PZ is in the Galapagos) [Oh, the Drama]. Needless to say, the comments on that blog are not kind to Nisbet, but, then again, neither are the comments on his own blog. Not too many people like Matt Nisbet these days. I can't imagine why. Could it have something to do with bad framing?

Afarensis recognizes the injustice of Nisbet's attack: Framing Science Embraces the Willie Horton Strategy

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1. The picture that Nisbet posted of PZ Myers is beyond the pale. Whatever remaining credibility Nisbet had (not much) is gone.

What Is the "t-complex" and Why Should You Know About It?

 
I used to know all about it and even taught the underlying concept to undergraduates. That was 25 years ago and I'd forgotten what the t-complex was all about. Anonymous Coward¹ wanted to find out and (s)he posted a description on bayblab [WTF is transmission ratio distortion]. Normally I don't like linking to anonymous blogs but I'll make an exception here because this is cool.

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1. What a good pseudonym!

40 Years Ago Today

 
Today is our 40th wedding anniversary.

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The Genius of Charles Darwin

 
This is a really excellent TV series narrated by Richard Dawkins. I'm very impressed with Dawkins as a TV personality and I agree completely with his view of Darwin as an extraordinary genius. The one thing that bothers me is the adaptationist bias of Dawkins—the same thing I've been complaining about in several other postings.

At the beginning of Part 1, Dawkins says ...

This series is about perhaps the most powerful idea ever to occur to a human mind. The idea is evolution by natural selection and the genius who thought of it was Charles Darwin.... What Darwin achieved was nothing less than the complete explanation of the complexity and diversity of all life. And yet it's one of the simplest ideas that anyone ever had.

This is not correct. The complete explanation requires knowledge of genes, genetics, population genetics, random genetic drift, speciation, horizontal gene transfer, biochemistry, physiology, embryology, developmental biology, molecular drive, mutation, recombination, punctuated equilibria, species selection (possibly), cladistics, mass extinctions, plate tectonics, and much more. Even with all that there are still some things we're unsure about, like how to explain the Cambrian explosion

Part 1


Part 2


Part 3


Part 4


Part 5

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How Do Ligands Bind to Proteins?

When glutamine is bound to glutamine-binding protein, the protein is wrapped around the ligand to form a closed binding site that brings more amino acid side chains into contact with the ligand. The unbound protein has a much more open confromation.

The traditional explanations of binding is that the ligand binds to to open form of the protein and causes it to undergo a conformational change creating a closed pocket. The mechanism is called "induced fit." Now, there is evidence that the protein may transiently adopt the closed conformation in the absence of ligand and the ligand binds directly to the closed conformation.

Discount Thoughts reviews a recent paper [Do conformational changes precede or follow binding?]

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[Figure credit: Okazaki, K., Takada, S. (2008) Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms. Proc. Nat. Acad. Sci. (USA) 105:11182-11187. [DOI: 10.1073/pnas.0802524105]

The End Is Nigh

 

The Large Hadron Collider is due to be activated on September 10th. Estimates on how long it will take to create a black hole vary from microseconds to about 24 hours. Let's be optimistic and assume that it will take until Thursday morning (September 11th).

I figure the airport (Cointrin) will be sucked in before noon and Geneva should be swallowed up by at least 2pm. France will be gone by 4pm and we in Toronto will encounter the event horizon at midnight.

The good news is that I won't have to buy Ms. Sandwalk a birthday present on Friday. The bad news is that we may be spending an infinite amount of time together as we cross the event horizon so I might wish I had.

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nigh: Common Teutonic: OE. néah, néh = OFris. nei, nî, MDutch na, nae (Dutch na), OS. nâh (MLG. nâge, nâ), OHG. nâh adv., nâher adj. (MHG. nâ, nâh-, nâch, G. nah), ONor. ná- (in combs. like ná-búi neighbour; Sw. and Da. na-), Goth. nêhwa (nêhw): the stem appears to be unrepresented outside Teutonic. OHG. is the only one of the older languages in which a fully developed adjectival use of the word exists along with the adverbial. In OE. there are very scanty traces of adjectival inflexion, néah being commonly employed either as a simple adv. or with a dependent dative: in predicative use it may sometimes be taken as an adjective, but it is more probable that in such cases also it is an adverb. It is not till the 14th or 15th cent. that the attributive use becomes common.

The original comparative of néah as an adv. is néar, néor, near adv.1, while the adj. form néarra finally became ner, nar a. The OE. superlative níe(hook)hst(a is latterly represented by next a. and adv. After phonetic changes had obscured the relationship of these forms to the positive, a new compar. and superl., nigher and nighest, were formed, and have been in common use since the 16th cent.

= near adv.2 and a. (which in all senses has taken the place of nigh except in archaic or dialect use). [Oxford English Dictionary]

The Hype About Darwin Continues

 
Let me be clear about one thing. I've said it many times but it bears repeating. In my opinion Charles Darwin is the greatest scientist who ever lived and natural selection is one of the greatest ideas in science.

That should never be an excuse for exaggerating Darwin's contribution to modern evolutionary theory yet that's what we're seeing in the run-up to the 150th anniversary of the publication of On the Origin of Species. I was tremendously disappointed in the Royal Ontario Museum symposium a few weeks ago [Darwinism at the ROM] and in several articles that have been published since then.

I'm going to keep harping on this point until it sinks in. Here's the latest example from TimesOnline in the UK [Darwin's Bulldogs].

Next year marks the 200th anniversary of the birth of Charles Darwin and the 150th anniversary of the publication of his On The Origin of Species. The Natural History Museum and the BBC plan extensive education programmes. Anticipating the anniversaries, Professor Richard Dawkins is presenting a series on Channel 4. These are welcome ventures. On the evidence of its first episode, Professor Dawkins's exposition of Darwinism will be an important public resource.

Darwin founded a branch of learning that has remarkable explanatory power and also grandeur. That the mechanism of evolution is natural selection is one of the great discoveries of science, with implications far beyond evolutionary biology. As Ernst Mayr, the biologist, wrote: “No educated person any longer questions the validity of the so-called theory of evolution, which we now know to be a simple fact.”

It is an unfortunate wonder of the modern age that people who are highly educated in some areas may still be resistant to scientific inquiry. We customarily think of objectors to Darwinism as Protestant fundamentalists. There is in fact a worrying trend for Muslim children to be taught the myths of creation, and the pseudoscience of “intelligent design”, as an explanation of the origins of life.

There are three things wrong with this short article.

First, the statement, "That the mechanism of evolution is natural selection is one of the great discoveries of science ..." is just plain wrong. Natural selection is one of the mechanisms of evolution but it is not the only one. Why can't people grasp this simple concept? It does not denigrate Charles Darwin's contribution to point out that we discovered other mechanisms in the 20th century.

Second, Mayr's statement, taken out of context, is misleading. Evolution is a fact but evolutionary theory is not a fact [Evolution Is a Fact and a Theory].

Third, I object to the term "Darwinism" and I am not a Protestant fundamentalist, a Muslim, or an IDiot. I wish journalists would make the effort to realize that modern evolutionary theory is no longer called "Darwinism." [Why I'm Not a Darwinist]. This does not mean that Charles Darwin was wrong. It simply means that the science of evolutionary biology has advanced a smidgen since 1859.

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[Hat Tip: RichardDawkins.net]

Amazing Catch by Ball Girl

 
Friday's Urban Legend: FALSE

This video is making the rounds. It shows a ball girl making an amazing catch of a fly ball then casually tossing it to the left fielder. Too bad it's a fake [Ballgirl].

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Are You Disappointed in Barack Obama?

 
I've always been a bit skeptical of Obama. It seemed to me that he wasn't as sincere about his "progressive" stance as, say, Dennis Kucinich. I wondered whether he wasn't playing to a particular audience in order to win the nomination.

Apparently I'm not the only one. There are a group of Americans who have become very nervous about Obama's move to the center. They've written an open letter to Barack Obama that's been published in The Nation [Change We Can Believe In].

The authors of the letter make the important point that the progressives who were attracted to the Obama campaign are the very ones who will ensure a victory in November. They are worried that these progressives will not make the effort to work for Obama if he continues to abandon the core principles that attracted them to the primary campaign.

We urge you, then, to listen to the voices of the people who can lift you to the presidency and beyond.

Since your historic victory in the primary, there have been troubling signs that you are moving away from the core commitments shared by many who have supported your campaign, toward a more cautious and centrist stance--including, most notably, your vote for the FISA legislation granting telecom companies immunity from prosecution for illegal wiretapping, which angered and dismayed so many of your supporters.

We recognize that compromise is necessary in any democracy. We understand that the pressures brought to bear on those seeking the highest office are intense. But retreating from the stands that have been the signature of your campaign will weaken the movement whose vigorous backing you need in order to win and then deliver the change you have promised.

I think they have a point but the more interesting question, from my perspective, is which one is the real Obama? Does he really believe in universal health care but is willing to make compromises for the sake of political expediency, or is he lukewarm on socialized medicine? Does he really believe that the USA needs to get out of Iraq because it never should have been there in the first place, or is he willing to compromise on that stance? What does he really think about the death penalty? Is he opposed on principle, in which case there's no compromise, or are his "principles" negotiable? Does he really expect to change the way things are done in Washington, or is that just something he says in order to get votes?

There's a discussion going on about this on Pharyngula [Progressives put pressure on Obama] but most readers are avoiding the real question. One commenter (Amplexus) said,

My fellow godless hedonists,

Obama is totally on our side. He's just hiding some of his feelings to get elected. We cannot take a stand on principle, we cannot afford to. Obama is blurring his position to win over independents that he sure as hell is going to shake off when he gets elected.

In other words, Obama is a liar and a hypocrite but that's okay because we all know that deep down he's a true believer.

Is that the common point of view among liberal Americans? Won't John McCain exploit this hypocrisy during the campaign?

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