Idiocy has Consequences – II

For an earlier fulmination on this topic see the post of 29 Oct ‘09. Briefly, it was based on an article by Scott Gottlieb, a former deputy commissioner of the FDA, appearing the day before in the Wall Street Journal. Gottlieb gave 3 reasons why the vaccine against the H1N1 flu was so late. One had to do with the usage of single dose preparations rather than 100 dose vials. The reason given for this decision was that less preservative would be used for a single dose vials, and that there were people who believed that the mercury in the preservative caused autism. Knuckling under to this craziness delayed the vaccine because it takes longer to prepare 100 single doses than 1 one hundred dose vial. For a debunking of the idea that vaccines cause autism with actual data see Nature vol. 427 p. 765 ‘04.

Gottlieb gave two more reasons for the delay, one of which was the decision not to use adjuvants. An adjuvant is an immune stimulant administered with the vaccine, which means that you have to use less inactivated virus in each dose to produce a protective immune response. Since one of the big bottlenecks in producing the vaccine is the speed at which viruses can produced, this produces yet another delay because more virus has to be put in each dose.

Today the NY Times reported on a Senate hearing concerning the delay in producing the vaccine. Some 250,000,000 million doses were ordered last spring (in a very timely and appropriate fashion). 120,000,000 doses were to be ready by October. Presently we’re in mid-November with only 42,000,000 doses available. A week or so ago it was noted by the CDC that 4,000 had died of the H1N1 flu including 560 children.

In testimony, Dr. Nicole Lurie (chief of preparedness and response for the Health and Human Services Department) said that one reason adjuvants were not used was because of vaccine activists, and they feared some people would avoid the shots. So the government (in the form of its experts) knuckled under to these cretins twice (once with single dose to avoid so much thiomersal, and once again with adjuvants). It is unlikely that more than a handful of the 250 less 42 million people eligible for the vaccine would have refused it, had it been available in a timely fashion. If the activists want to win a Darwin award by refusing the vaccine, let them — it would improve the general intelligence of the populace. As HL Mencken said about Prohibition — the humble swineherd will put us all in his pen.

In fairness, it should be noted that, at this point, we don’t have enough data to say that the vaccine is actually protective, but most think it will be. As always, in medicine, there is just no substitute for data.

3 Questions for the Cognoscenti

In my last few years of practice, I did a fair amount of expert witness work. One thing you learn very quickly, is that attorneys at trial never ask a question they don’t already know the answer to. The following questions don’t fall into that category.

Question #1: We’ve been doing perturbation theory for the past week or so in the QM course. The underlying assumption is that a small change in the Hamiltonian (usually in the potential) produces a small effect in the set of wavefunctions and their eigenvalues. This was certainly the state of affairs when I first took QM in the spring of ‘61. Since then we know this isn’t always (or even usually) so for many differential equations. What about chaos? How do we know the perturbation didn’t put us into the chaotic regime? Is it the fact that the derivatives in the Schrodinger equation are to the first power hence linear? I got the following from the QM professor — “Perturbation theory is always approximate and will usually work but sometimes not. If chaos raises its beautiful head, we just have to deal with it.” I asked another computational chemist — the response was “Interesting question”. Any thoughts?

Question #2: Presently we must use perturbation theory and variational principles to do QM on systems too complicated to solve in closed form. Will this always be the case? Could advances in mathematics increase the number of solvable Schrodinger equations? John Gribbin in one of his excellent writings (I don’t recall the actual source) said “It’s important to appreciate, though, that the lack of solutions to the three-body problem is not caused by our human deficiencies as mathematicians; it is built into the laws of mathematics.” Is this correct? If so it’s sort of a Godel’s theorem on equations (and any chemistry more complicated than the hydrogen atom). Is Gribbin correct? Any thoughts?

Question #3: I shudder at bringing this one up. See The Curious Wavefunction’s post of 4 November “A wrong kind of religion, Freeman Dyson, Superfreakonomics, and Global Warming” for just why. Nonetheless, in the 2 October ‘09 Science on pp. 28 – 29 the data that there has been no change whatsoever in global temperatures for the past decade is presented, along with a reply of the climate modelers.

Modelers reran their simulations 10 times for a total of 700 years and found 17 episodes of stagnating temperatures lasting a decade or more. The longest period was 15 years, so we’ll have an idea of how good the present models are in another 5 years. The modelers would have more credibility if they had published this sort of thing 10 years earlier before the data became available (did they publish this sort of thing when the models first saw the light of day? — they would have more credibility if they did).

The press is full of stories about retreating glaciers, diminishing artic sea ice, the march of temperate species northward, endangered polar bears etc. etc. An ice cube will melt given enough time if you set it outside the fridge. Is this what is causing the above — is global temperature already too high and causing these changes? Or are they in fact due to something else? If so what? No polemics please.

Some humility is in order

Sometime this month the 60th anniversary of the publication of “Sickle Cell Anemia, a Molecular Disease” will be celebrated. It’s just one of Linus Pauling’s many chemical achievements — electronegativity, quantum theory of the chemical bond, the alpha helix of protein structure and on and on and on. Unfortunately most docs know of him by his crackpot theory that vitamin C was of use in cancer. The general public knows of him as an activist against the Vietnam war. Too bad, he was one of the greatest chemists of the 20th century.

Just figuring out what was wrong with hemoglobin in Sickle Cell anemia was remarkable. The first actual determination of any 3 dimensional protein structure (myoglobin) didn’t occur until 1957. From then on, hemoglobin became to protein structure what E. Coli was to genetics and molecular biology. We know more about hemoglobin than any other protein. Countless studies of its structure and dynamics have been made.

So why be humble? Because we have essentially no treatment of Sickle Cell anemia based on all this structural work. We do have treatments — transfusion, manipulations to increase the production of a fetal variant of hemoglobin, etc. We don’t have a small molecule which stops hemoglobin from aggregating with itself (polymerizing if you will) under conditions of low oxygen, distorting the red blood cells which carry it, which makes them plug up vessels causing sickle cell crises (or even strokes, a few of which I saw as a neurologist).

Why don’t we have a drug? There are all sorts of molecular dynamics simulations of hemoglobin, and computational chemists use models to figure out how to dock molecules onto proteins. For a very cleareyed view of what the various models can and can’t do and just how good they are, go to “The Curious Wavefunction” and start reading.

If we really understood protein structure and dynamics we’d have such a drug, so some humility is definitely in order.

Why premeds should be required to take (and pass) organic chemistry

This post is to be mentioned in the 2 Nov C&EN. I’m reposting it so people can find it. The original came out 1 Sep.

Back when I was posting on “The Skeptical Chymist”, the editor (Stuart Cantrill), told me that noises were being made about dropping organic chemistry from the pre-med curriculum and asked me to comment. I didn’t because the idea seemed so ridiculous. There is no possibility of really understanding anything about cellular biology, drug action, molecular biology etc. etc. without a firm grounding in organic chemistry. You simply must have some idea what vitamins, proteins, DNA and RNA and the drugs you’ll be using look like and how they chemically interact — which is what organic chemistry gives you the background for. Not that you can stop there — but all medical schools teach biochemistry — which starts at organic chemistry and takes off from there. Organic certainly helped me follow molecular biology as it exploded starting in the 60s.

Cynics might say that docs don’t synthesize things or crystallize the drugs they use. Knowing what’s going on under the hood is just esthetic filigree. Just tell them what ‘best practice’ is, and let them follow it like robots. Who cares if they know the underlying science. People drive cars without really understanding what a carburator or a manifold does (myself included).

It wasn’t until I got about 400 pages into the magnificent textbook of Organic Chemistry by Clayden, Greeves, Warren and Wothers (only 1100 action packed pages to go !) that the real answer became apparent. The stuff is impossible to memorize. Only assimilating principles and applying them to novel situations will get you through — exactly like the practice of medicine.

Let us suppose you have an eidetic memory, and know the best treatment for every condition. You wouldn’t have to know any science at all, would you?

What’s wrong with this picture? First of all, there isn’t a best treatment known for every condition. Second, every doc will see conditions and problems that simply aren’t in the books. When I first started out, I was amazed at how much of this there was. I asked an excellent internist who’d been in practice for 30 years if he’d seen it all. He thought he saw something completely new each week. Third, conditions occur in combinations, and many patients (and nearly all the elderly) have many more than one problem. The conditions and treatments interact in a highly nonlinear fashion. The treatment for one problem might make another much worse (see below).

Here is a concrete example using a familiar person (Sonia Sotomayor) and a disorder which should be known to all (the new Swine Flu which swept America and the world this spring). Let’s say that you’re that lucky soul with the perfect memory who knows all the best treatments (well those that exist anyway) and as such you’ve been given the responsibility of taking care of her.

It is public knowledge (e.g. Wikipedia) that Justice Sotomayor has had diabetes since age 8, requiring insulin since that time. Pictures show, that like many diabetics, she is overweight — depending on how tall she is I’d guess by 25 – 45 pounds. Influenza is usually a disease of the fall and winter, and the new Swine Flu is now down in South America, but it’s likely to sweep back up here this fall. We know it’s extremely infectious, but so far fortunately rather benign. There is no guarantee that it will stay that way. Suppose that while down in S. A. it mutated and has become more virulent (a possibility that the CDC takes extremely seriously).

What if she gets the new Swine flu next month? At this point there is no ‘best treatment’ known. Diabetics don’t do well with infections — they get more of them, and have more complications when they do. Her diabetes is certainly going to get worse. What if some think the ‘best treatment’ is corticosteroids (which is often used for severe lung infections) — which will really raise hell with her diabetes? Should you give it? Recall that corticosteroid use during the Asian SARS epidemic (another serious lung infection) seemed to hurt rather than help (Journal of Infection, Volume 51, Issue 2, Pages 98-102). There is no data to help you here and you and your patient don’t have the luxury of waiting for it. Don’t forget that her father died at 42 of heart disease. That could be relevant to what you do. Suppose, like many overweight diabetics she has high blood pressure and elevated lipids as well. How will that affect her management?

Your perfect eidetic memory of medicine will not be enough to help you with her management — you are going to have to think, and think hard and apply every principle of medicine you know to a new and unfamiliar situation with very little data to help you.

Sounds like Organic Chemistry doesn’t it? Anyone without the particular type of mind that is able absorb and apply multiple and (often) conflicting principles doesn’t belong in medicine. A hardnosed mathematician I audited a course from a few years ago, said that people would come up to him saying that if they couldn’t pass Calculus, they wouldn’t get into medical school. He felt that if they couldn’t, he didn’t want them in medical school (I’m not sure he told them this — probably he did). The same thing holds in spades for Organic Chemistry.

Idiocy has consequences — the risks of risk reduction

An article yesterday in the Wall Street Journal by an MD who was a deputy commissioner at the FDA offered 3 reasons why the flu vaccine is in such short supply. One of the three is totally unnecessary. The government decided to require the vaccine to be produced in single dose syringes. The usual technique is to place the vaccine in large vials, distribute them, and then have the locals remove each dose by a separate (and disposable) syringe. It’s obviously more laborious to put 100 doses in 100 syringes, than into one vial. It also takes a lot longer. Hence, one source of delay. Even though 40, 000,000 doses of flu vaccine were ordered last spring at the first inkling of trouble, they are nowhere in sight (we were supposed to have them by November).

What was the rationale for requiring single dose syringes? Multidose vials hang around a lot longer, and the risk of contamination is greater so more preservatives must be used per dose, one such being thiomersal. Basically the government knuckled under to the unfortunate parents of autistic children who believe that their child’s autism was caused by the mercury in thiomersal. There is excellent epidemiologic evidence that it doesn’t. Similar theories of other vaccines causing autism have been proposed and shot down. See [ Nature vol. 427 p. 765 '04 ] for the sordid details of one example.

The flu is certainly out there (as it is every fall) and one local grade school has 22% of the kids out sick. Now assume (1) the H1N1 flu will become more virulent (it certainly doesn’t have to become any more infectious), (2) the vaccine offers some degree of protection against it. Both assumptions are reasonable (but arguable). Assuming them true, this means that people (and so far in the epidemic this means children) will die because they didn’t get the vaccine in time. Idiocy has consequences.

An even more sordid example of the risks of risk reduction is the following [ Nature vol. 354 p. 255 '91 ]. An amazing article places the blame for the cholera epidemic sweeping South America starting in Peru on a misguided application of an Environmental Protection Agency study implicating water chlorination as a cause of cancer. During the 80’s Peruvian officials, citing the EPA study, stopped chlorinating many of the wells in Lima. However, others say that the decision might have been based on economics than data.

It’s comforting to know that the 3,516 who have died so far have been spared a long bout with cancer.

I can’t find the exact quote, but H. L. Mencken when writing about prohibition said something to the effect that “the humble swineherd will put us all into his pen.”

Vegetarians are wimps: Science now tells us why

Oh, it started innocently enough. Population studies had shown that men who ate lots of cruciferous vegetables (collard greens, cabbage, brussels sprouts, broccoli, cauliflower, bok choy etc. etc.) had less prostate cancer. Some folks in Oregon decided to find out why [ Proc. Natl. Acad. Sci. vol. 106 pp. 16663 - 16668 '09 ]. One of the compounds found in all these veggies is sulforaphane. There are all sorts of places to be found on the web that will sell it to you for your health. Sulforaphane is said to fight cancer, improve diabetes and kill bacteria (if you believe Wikipedia). Hosanna.

Prostate cancer is made worse by male hormones (androgens). They produce their effects in cells by binding to a protein (the androgen receptor) which then goes into the nucleus of the cell and turns on the genes which make males male. If there’s no androgen around the receptor just sits there outside the nucleus (e.g. in the cytoplasm), doing nothing. Some forms of prostate cancer have mutations in the receptor which turn it on whether androgen is present or not. This makes the cancer even worse. So one of the mainstays of prostate cancer therapy is lowering androgen levels by a variety of means, none of them pleasant — such as castration and various pills.

The Oregon work shows that sulforaphane decreases the amount of androgen receptor around resulting in less androgenic effects, and presumably less prostate cancer in the long run. How this is thought to occur is pretty interesting, highly technical and is to be found in subsequent paragraphs. It also explains why vegetarians are such wimps.

The androgen receptor sits in the cytoplasm bound to a protein called HSP90 (heat shock protein of 90 kiloDaltons). This protects the androgen receptor from being destroyed. Sulforaphane is a fairly simple molecule — a straight 4 carbon chain with a methyl sulfoxide group at one end and an isothiocyanate (-N=C=S ) group at the other. It should be pretty lipid soluble, meaning it can go everywhere in the body without much trouble. The authors showed that sulforaphane inhibits an enzyme called histone deacetylase 2 (HDAC2). This results in more acetylation of HSP90 on lysine, inhibiting the association of HSP90 with the androgen receptor, leading to increased destruction of the receptor and less androgenic effects in the cell.

The active site of one histone deacetylase that we know about is a tubular pocket containing a zinc binding site and two aspartic acid histidine charge relay systems. My guess is that the business end of sulforaphane is the isothiocyanate, which could react by nucleophilic attack of either the histidine nitrogen or the aspartic acid oxygen on the carbon of the -N=C=S group. Perhaps one of readers knows how it works.

Histone deacetylase inhibitors are presently very ‘hot’ and one of them, SAHA was approved by the FDA for the treatment of T cell cutaneous lymphoma in 2007, and many others are under active investigation. It’s important to remember that although this class of enzymes was discovered by their ability to remove acetyl groups from histones, they also remove acetyl groups from proteins which are not histones (e.g. HSP90).

So veggies are a two-edged sword.

Recursion relations

Well the QM course is moving along, and we’ve solved the Schrodinger equation (SE) for the harmonic oscillator (and its parabolic potential -kx^2). This involves the creation of 3 new variables from composites of old ones, then transforming the SE to something simpler, which is then solved using an exponential multiplied by a polynomial. To prevent the polynomial from blowing up as q (what we’ve transformed x into) gets large, all powers of the q in the polynomial past a certain point must be zero. Another way of looking at this is that the wavefunction must be zero at infinity (the particle has to be somewhere). This simple fact leads to a recursion relationship among the terms of the polynomial. Very cute, but it didn’t have the impact it did when I first saw recursion relationships used in QM years and years ago (48.5 years ago to be exact).

Back then, budding chemists started out by learning that electrons like to be in filled shells. The first shell has 2 elements, the next 2 + 6 elements etc. etc. It allows the neophyte to make some sense of the periodic table (as long as they deal with low atomic numbers — why the 4s electrons are of lower energy than the 3d electons still seems quite ad hoc to me). Later on we were told that this is because of quantum numbers n, l, m and s. Then we learn that atomic orbitals have shapes, in some wierd way determined by the quantum numbers, etc. etc.

Recursion relations are no stranger to the differential equations course, where you learn to (tediously) find them for a polynomial series solution for the differential equation at hand. I never really understood them, but I could use them (like far too much math that I took back then).

So it wasn’t a shock when the QM instructor back then got to them in the course of solving the hydrogen atom (with it’s radially symmetric potential). First the equation had to be expressed in spherical coordinates (r, theta and phi) which made the Laplacian look rather fierce. Then the equation was split into 3, each involving one of r, theta or phi. The easiest to solve was the one involving phi which involved only a complex exponential. But periodic nature of the solution made the magnetic quantum number fall out. Pretty good, but nothing earthshaking.

Recursion relations made their appearance with the solution of the radial and the theta equations. So it was plug and chug time with series solutions and recursion relations so things wouldn’t blow up (or as Dr. Gouterman put it, the electron has to be somewhere, so the wavefunction must be zero at infinity). MEGO (My Eyes Glazed Over) until all of a sudden there were the main quantum number (n) and the azimuthal quantum number (l) coming directly out of the recursions.

When I first realized what was going on, it really hit me. I can still see the room and the people in it (just as people can remember exactly where they were and what they were doing when they heard about 9/11 or (for the oldsters among you) when Kennedy was shot — I was cutting a physiology class in med school). The realization that what I had considered mathematical diddle, in some way was giving us the quantum numbers and the periodic table, and the shape of orbitals, was a glimpse of incredible and unseen power. For me it was like seeing the face of God.

What is schizophrenia really like ?

“I feel that writing to you there I am writing to the source of a ray of light from within a pit of semi-darkness. It is a strange place where you live, where administration is heaped upon administration, and all tremble with fear or abhorrence (in spite of pious phrases) at symptoms of actual non-local thinking. Up the river, slightly better, but still very strange in a certain area with which we are both familiar. And yet, to see this strangeness, the viewer must be strange.”

“I observed the local Romans show a considerable interest in getting into telephone booths and talking on the telephone and one of their favorite words was pronto. So it’s like ping-pong, pinging back again the bell pinged to me.”

Could you paraphrase this? Neither can I, and when, as a neurologist I had occasion to see schizophrenics, the only way to capture their speech was to transcribe it verbatim. It can’t be paraphrased, because it makes no sense, even though it’s reasonably gramatical.

What is a neurologist doing seeing schizophrenics? That’s for shrinks isn’t it? Sometimes in the early stages, the symptoms suggest something neurological. Epilepsy for example. One lady with funny spells was sent to me with her husband. Family history is important in just about all neurological disorders, particularly epilepsy. I asked if anyone in her family had epilepsy. She thought her nephew might have it. Her husband looked puzzled and asked her why. She said she thought so because they had the same birthday.

It’s time for a little history. The board which certifies neurologists, is called the American Board of Psychiatry and Neurology. This is not an accident as the two fields are joined at the hip. Freud himself started out as a neurologist, wrote papers on cerebral palsy, and studied with a great neurologist of the time, Charcot at la Salpetriere in Paris. 6 months of my 3 year residency were spent in Psychiatry, just as psychiatrists spend time learning neurology (and are tested on it when they take their Boards).

Once a month, a psychiatrist friend and I would go to lunch, discussing cases that were neither psychiatric nor neurologic but a mixture of both. We never lacked for new material.

Mental illness is scary as hell. Society deals with it the same way that kids deal with their fears, by romanticizing it, making it somehow more human and less horrible in the process. My kids were always talking about good monsters and bad monsters when they were little. Look at Sesame street. There are some fairly horrible looking characters on it which turn out actually to be pretty nice. Adults have books like “One flew over the Cuckoo’s nest” etc. etc.

The first quote above is from a letter John Nash wrote to Norbert Weiner in 1959. All this, and much much more, can be found in “A Beatiful Mind” by Sylvia Nasar. It is absolutely the best description of schizophrenia I’ve ever come across. No, I haven’t seen the movie, but there’s no way it can be more accurate than the book.

Unfortunately, the book is about a mathematician, which immediately turns off 95% of the populace. But that is exactly its strength. Nash became ill much later than most schizophrenics — around 30 when he had already done great work. So people saved what he wrote, and could describe what went on decades later. Even better, the mathematicians had no theoretical axe to grind (Freudian or otherwise). So there’s no ego, id, superego or penis envy in the book, just page after page of description from well over 100 people interviewed for the book, who just talked about what they saw. The description of Nash at his sickest covers 120 pages or so in the middle of the book. It’s extremely depressing reading, but you’ll never find a better description of what schizophrenia is actually like — e.g. (p. 242) She recalled that “he kept shifting from station to station. We thought he was just being pesky. But he thought that they were broadcasting messages to him. The things he did were mad, but we didn’t really know it.”

Because of his previous mathematical achievments, people saved what he wrote — the second quote above being from a letter written in 1971 and kept by the recipient for decades, the first quote from a letter written in 12 years before that.

There are a few heartening aspects of the book. His wife Alicia is a true saint, and stood by him and tried to help as best she could. The mathematicians also come off very well, in their attempts to shelter him and to get him treatment (they even took up a collection for this at one point).

I was also very pleased to see rather sympathetic portraits of the docs who took care of him. No 20/20 hindsight is to be found. They are described as doing the best for him that they could given the limited knowledge (and therapies) of the time. This is the way medicine has been and always will be practiced — we never really know enough about the diseases we’re treating, and the therapies are almost never optimal. We just try to do our best with what we know and what we have.

I actually ran into Nash shortly after the book came out. The Princeton University Store had a fabulous collection of math books back then — several hundred at least, most of them over $50, so it was a great place to browse, which I did whenever I was in the area. Afterwards, I stopped in a coffee shop in Nassau Square and there he was, carrying a large disheveled bunch of papers with what appeared to be scribbling on them. I couldn’t bring myself to speak to him. He had the eyes of a hunted animal.

Low socioeconomic status in the first 5 years of life doubles your chance of coronary artery disease at 50 even if you became a doc — or why I hated reading the medical literature when I had to

[ Proc. Natl. Acad. Sci. vol. 106 pp. 14716 - 14721 '09 ] is an interesting paper which performed gene profiling on (easily obtainable) white blood cells in 103 healthy adults ages 25 – 40. Half of them were of low socioeconomic status (SES) in the first 5 years of life (as judged by what their parents did). All were of the same socioeconomic status at the time of testing (again judged by occupation). They found differences in gene expression between the two groups which didn’t correlate with lifestyle or perceived stress at the time of testing.

It took a lot of work (and probably money). People don’t do this sort of thing for fun. Why were they interested in the first place? Because of an even more interesting paper from Johns Hopkins [ Arch. Int. Med. vol. 166 pp. 2356 - 2361 '06 ]. This work followed 1131 male Hopkins medical students for FORTY years. 19% came from backgrounds of low socioeconomic status (again judged by what their parents did). The striking conclusion was that there was a 240% increased risk of coronary artery disease by age 50 if you came from a background of low SES. This, in spite of the fact that for the duration of the study MDs were living a high SES existence. Impressive no?

As a practicing MD, I had to plow through this stuff year after year. Very quickly you begin reading papers in the medical literature with the attitude ‘how are they lying to me’. Well, maybe not actually lying, but drawing conclusions not warranted from the data or, worse, missing the forest for the trees. Some scientific training helps but isn’t necessary. My cousin’s boy wrote an absolutely brilliant article for his high school newspaper dissecting the methodology behind the annual college rankings in US News and World Report and he wants to be a writer.

What’s wrong with this paper? Certainly nothing is amiss with the data, painstakingly acquired year after year. Also, they were quite careful to control for lifestyle issues such as weight, smoking, exercise, alcohol consumption etc. etc. However they plotted two curves of coronary artery disease incidence vs. age (one for the low SES and the other for the 81% of the classes not of low SES) and cherrypicked the age at which the curves separated the most (e.g. 50). Also to be noted is that there wasn’t much coronary artery disease at 50 in either group — 13/218 in the low SES and 23/(1141 – 218) in the rest.

Also stated in the paper is that the mortality at age 70 was the same for both groups, even though the low SES group continued to have more coronary artery disease (and death from it). This implies that low SES in childhood actually protects against other fatal diseases (cancer perhaps?). They had to die of something after all. Which way would you want to go? That could have been the title of the paper, but wasn’t.

Even more interesting is the comparison they didn’t make –e.g. with the expected mortality and morbidity of a group of young men who remained in low SES throughout their working lives. This data is likely available. We are always reading about increased morbidity and mortality in one disadvantaged group or another (usually as a way of slamming the current system). My guess is that it would be much worse. That being the case the paper could have been titled, “A high SES in adult life negates the disadvantage of growing up poor”.

Reading the summary of the paper would have missed all this. What the authors chose to present was certainly an attention getter, and they made no attempt to hide their data. However, what your patients are paying for is your ability to evaluate data like this, think about it, and apply it to them. There’s nothing wrong with thinking, but dissecting paper after paper like this becomes tedious after a time. Chemistry, math and molecular biology are so much cleaner intellectually (but far less immediately important to your patients).

A truly awful example of missing the forest for the trees is the following: [ J. Am. Med. Assoc. vol. 259 p. 3158 '88 ] An overview of the Physicians’ Health study in which 22,000 American physicians took either one adult aspirin or a placebo every other day. It’s pretty old but the study was widely cited and was very well worth doing because it dealt with a potentially simple (and cheap) way of preventing heart attack and stroke.

The study was double blind so identical packets of aspirin or placebo had to be prepared and delivered to all 22,000 docs in a timely fashion. Cardiovascular mortality was cut by aspirin, but overall mortality was not. Severe stroke was increased slightly, and there were 80 strokes in the aspirin group versus 70 in the placebo group. However the group experienced just 88 deaths when 733 would have been expected. The authors noted that low numbers of deaths made the data more difficult to interpret. Their discussion focused on whether the aspirin was adding extra. The conclusion was that this dose of aspirin probably wasn’t doing much.

Where’s the forest?

It’s the EIGHTFOLD reduction in mortality from what was expected. It could be due to a beneficial life style (money, social class) but the paper never discussed it. What we need is to reduce mortality in our patients eightfold and then worry about giving aspirin.

Are Biochemists looking under the lamppost?

There’s an old joke about a drunk who lost his keys coming home from the bar one night. Daybreak found him still crawling around searching under a lamppost. A passerby asked him why he didn’t look elsewhere. Drunk’s answer: “That’s where the light is”

Could biochemists be doing something similar? Have a look at [ Science vol. 325 pp. 1230 - 1234 '09 (4 September 2009) ] where a new type of bond between amino acids was found — a sulfilimine bond ( – S = N – ) which crosslinks hydroxy lysine #211 and methionine #93 of adjoining protomers of type IV collagen. By way of background, collagens account for 25% by mass of all mammalian proteins (Molecular Biology of the Cell 4th Ed. p. 1096). Humans have 25 genes for collagen. Since each collagen contains 3 copies of the protein, we could have 15,625 different collagens — but so far only 20 have been found. Type IV collagen is particularly important medically since it is the main type of collagen found in the basement membranes which surround capillaries and muscle cells. Basement membrane thickening occurs early in diabetes (both human and experimental) and is thought to be one source of the vascular problems that diabetics get. Whether the thickening causes glucose intolerance or is caused by it isn’t known.

The sulfilimine bond had never previously been found in biomolecules. However the crosslink between two protein chains in type IV collagen had been known to exist for 20 years, but no one could figure out what it was. The authors used Fourier transform ion cyclotron resonance (FTICR) which can achieve a mass accurary of 2 parts per million (impressive). All sorts of spectroscopy were used as well with NMR playing a big role. A real tour de force.

One chemical question for the cognoscenti. The structure given in figure 2 p. 1232 shows sulfur attached by a double bond to a the nitrogen of hydroxy lysine, but it is also attached by single bonds to a methyl group and to the rest of the methionine amino acid. No charge is shown on the sulfur atom (or anywhere for that matter). Structures for S-adenosyl methionine (where sulfur is bound by 3 covalent bonds to carbon) always puts a positive charge on the sulfur. Shouldn’t sulfilimine show a charge of +2 on the sulfur atom?

How many other wierdnesses are out there? In this case biochemists were forced to look for the bond because they knew it was there. Are protein biochemists basically looking under the lamppost?

Another example of this might be found in a post of mine on the Skeptical Chymist. Stuart Cantrill tells me that since I wrote it, it’s mine. So here it is (slightly edited). Recall that a Nobel was awarded for making the Green Fluorescent protein available to cellular biology.

Chemiotics: Sherlock Holmes and the Green Fluorescent Protein

Gregory (Scotland Yard): “Is there any other point to which you would wish to draw my attention?”
Holmes: “To the curious incident of the dog in the night-time.”
Gregory: “The dog did nothing in the night-time.”
Holmes: “That was the curious incident.”

The chromophore of green fluorescent protein (GFP) is para-hydroxybenzylidene imidazolinone. It is formed by cyclization of a serine (#65) tyrosine (#66) glycine (#67) sequential tripeptide. It is found in the center of a beta barrel formed by the 238 amino acids of GFP.

What is so curious about this?

Simply put, why don’t things like this happen all the time? Perhaps nothing quite this fancy, but on a more plebeian level consider this: of the twenty amino acids, 2 are carboxylic acids, 2 are amides, 1 is an amine, 3 are alcohols and one is a thiol. One might expect esters, amides, thioesters and sulfides to be formed deep inside proteins. Why deep inside? On the surface of the protein, there is water at 55 molar around to hydrolyze them purely by the law of mass action (releasing about 10 kJ/Avogadro’s number per bond in the process). Some water is present in the X-ray crystallographic structure of proteins, but nothing this concentrated.

The presence of 55 M water bathing the protein surface leads to an even more curious incident, namely why proteins exist at all given that amide hydrolysis is exothermic (as well as entropically favorable). Perhaps this is why proteins contain so many alpha helices and beta sheets — as well as functioning as structural elements they may also serve to hide the amides from water by hydrogen bonding them to each other. Along this line, could this be why the hydrophilic side chains of proteins (arginine, lysine, the acids and the amides) are rather bulky? Perhaps they also function to sterically shield the adjacent amides. After all, why should lysine have 4 methylene groups rather than just one or two?

Now the serine-tyrosine-glycine tripeptide should occur by chance once in every 8000 tripeptides. The SwissProt database of proteins contains 144,041,553 amino acids in 399,749 proteins as of 14 October 2008. Does this tripeptide occur 18,805 times in the database as it should? If it doesn’t, is negative selection preventing it? If the tripeptide does occur this often, have we missed other chromophores? Are there other tripeptides missing from SwissProt? If there are, does this tell us how to build other chromophores? Or does it tell us something important about protein structure?

I don’t have the skills to properly interrogate SwissProt or the Protein Data Bank, but I imagine that some of the readership does. Go to it. These are curious incidents indeed.