The DNA Network

What Medicine Owes the Beatles [Epidemix]

Posted: 16 Jul 2008 06:59 PM CDT

A factoid I just came across: If not for the Beatles, we wouldn’t have CT scans, aka CAT scans, the advanced medical scanning technology that lets your doctor see how badly your bones are broken or whether your aunt really has emphysema.

Here’s the story: in the 1960s, a middle-aged engineer named Godfrey Hounsfield was working at Eletrical & Musical Instrument Ltd., where he began as a radar researcher in 1951. The company, known as EMI for short, was a typical industrial scientific company at the time, working on military technology and the burgeoning field of electronics. Hounsfield was a skilled but unexceptional scientist, leading a team that built the first all-transitor computer in 1958. Through its work in radar the company began working in broadcasting equipment, which complimented its ownership of several recording studios in London. Specifically, at Abbey Road. In the 50s, the company began releasing LPs, and by the end of that decade, thanks to an acquisition of Capitol Records, the company had become a powerhouse in popular music.

Then, in 1962, on the recommendation of EMI recording engineer George Martin, the company signed the Beatles to a recording contract.

That was the bang - over the next decade (and for years thereafter) the company earned millions of dollars from the fab four. So much money, the company almost didn’t know what to do with it.

Meanwhile, Hounsfield’s success with computers had earned him good standing in the science side of the company. Flush with money broken out of teenagers’ piggy banks worldwide, EMI gave Hounsfield the freedom to pursue independent research. Hounsfield’s breakthrough was combining his work with computers together with an interest in X-rays. Invented in 1908, X-rays were still pretty much used to image bodies in two dimensions from a fixed position. Hounsfield’s idea was to measure in three dimensions, by scanning an object - most dramatically, a human head - from many directions. The result was a cross-sectional, interior image that he called computed tomography, or CT. As the Nobel Prize committee put it, in giving him the Nobel Prize in medicine in 1979, before the CT scanner, ”ordinary X-ray examinations of the head had shown the skull bones, but the brain had remained a gray, undifferentiated fog. Now, suddenly, the fog had cleared.”

First released as a prototype by EMI in 1971 - the year after the Beatles broke up – CT scanners started to appear at hospitals in the mid 1970s; today there are about 30,000 in use worldwide.

Just a bit of trivia, apropos of nothing.

A historical take from somebody who worked with Hounsfield is here.

Hounsfield’s Nobel lecture is here.

How do we educate physicians? [The Gene Sherpa: Personalized Medicine and You]

Posted: 16 Jul 2008 02:41 PM CDT

I want to point you to a brilliantly written post by Carl Wieman While there is still much to be learned, there is enormously more known now than existed when the teaching methods in use in most...

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Laboratory Science: From Penal Colonies to Video Game Arcades [The Personal Genome]

Posted: 16 Jul 2008 02:33 PM CDT

Laboratory science is filled with dull, repetitive tasks. Casting gels, pipetting, streaking plates, and on and on. Did you know adult C. elegan worms have 969 cells? Well they do. We know that because a number of graduate students ~~were locked~~ locked themselves into a room and painstakingly counted, and re-counted all those cells.

It should come as no surprise that laboratories have been compared to penal colonies. Glorified work camps for the technically adept! The root word of laboratory is “labor” after all.

Does the practice of science really need to be this way? Could science and laboratory work be more playful? In Shapiro’s 1991 book, The Human Blueprint, George Church wonders whether the lab could be turned into something more akin to a video game arcade:

“In counter to Sydney Brenner’s comparison of a sequencing laboratory to a penal colony, George Church has offered an analogy to a video game arcade, a place where a basically repetitive operation is so enjoyable that the participants work voluntarily for hours on end and even pay for the privilege. ”

Comparisons of science careers to video games are much more fun than comparisons to labor camps or penal colonies. The quote from George above challenges us to think beyond metaphors. How might the laboratory environment itself be transformed into something more playful, fun, and engaging?

–

Robert Shapiro, The Human Blueprint. St. Martin’s Press, 1991. [quote from page 252]

New Educational Model For A New Century [Genomicron]

Posted: 16 Jul 2008 01:14 PM CDT

Over at the home of Genomicron 2.0 (ScientificBlogging.com), physicist, education expert, and Nobel laureate Carl Wieman has an important post about 21st century post-secondary science education.

Optimizing The University - Why We Need a New Educational Model For A New Century

There are currently great needs and great opportunities for improvement in post-secondary science education. As world education improves, we need to provide more students with complex understanding and problem solving skills in technical subjects to allow them to be responsible and successful citizens in modern society.
Emerging research indicates that our colleges and universities are not achieving this. However, there are great opportunities to improve this situation using advances in the understanding of how people learn science and advances in educational technology.

Genes Influence Antidepressant Effectiveness [A Forum for Improving Drug Safety]

Posted: 16 Jul 2008 11:18 AM CDT

Variations in the serotonin transporter gene SLC6A4 directly affect how patients respond to citalopram according to a Mayo Clinic Study just released in the current issue of the American Journal of Medical Genetics Part B: Neuropsychiatric Genetics.

Researchers examined the serotonin transporter gene, or SLC6A4, in 1,914 study participants. The study showed that two variations in this gene have a direct bearing on how individuals might respond to citalopram. SLC6A4 produces a protein that plays an important role in achieving an antidepressant response.

In this study, researchers evaluated the influence of variations in SLC6A4 in response to citalopram treatment in white, black and Hispanic patients. Researchers found that white patients with two distinct gene variations were more likely to experience remission of symptoms associated with major depression. No associations between the two variations and remission were found in black or Hispanic patients.

According to the Centers for Disease Control and Prevention, antidepressants are the most prescribed medication in the country, but many stop taking their medication early because of negative side effects or lack of response. Pharamcogenetic testing looks at genetic variations like SLC6A4 that affect response so medications can be personalized for the patients to help avoid these treatment failures and side effects.

Dr. Mrazek, director of the Genomic Expression and Neuropsychiatric Evaluation (GENE) Unit at Mayo Clinic, stated "first, we started with trial and error - which feels like flipping a coin to select a medication. The Holy Grail would be to be able to consider the implications of variations in many genes. Ultimately, we hope to be able to determine with great accuracy which patients will respond to specific antidepressants and which patients will almost certainly not respond."

Badass Scientist of the Week [Bayblab]

Posted: 16 Jul 2008 11:03 AM CDT

As with last week's badass scientist of the week, this week's scientist is both a thinker, and a human guinea pig. I present to you, John Paul Stapp - Colonel with the USAF, and fastest man on earth.

Dr Stapp was born in Bahia, Brazil, and joined the USAF just around the end of WWII. He was posted to the Aero Medical Laboratory, where he was placed in a team looking at oxygen delivery at high altitudes, as well as the prevention of the bends as the pilot changes pressures frequently. That work lead to a number of currently used techniques.

He was then moved to the deceleration project in 1947 - where he was looking at deceleration from high speeds using the 'gee whizz' rocket (4-kN acceleration) propelled simulator. One of the earlier innovations to come from this set-up was the safety of having rear-facing seats, which are installed in all USAF transport aircraft.

The wider scientific community believed the human body could not survive more than 18 Gs of deceleration--Stapp hit 35. In 1954 he decelerated from 120 miles per hour to 0 in a little under one-and-a-half seconds, and received two huge black eyes as a payoff. Apparently, he was blinded for two days as an added bonus. By some accounts, and he also broke his back, arm, wrist, lost six fillings and the icing on the cake? He got a hernia, and apparently had his retinas pop off more than once.

In return for these injuries, he then built a bigger rocket, believing that the limits of human deceleration had not been fully tested (what did he think was going to happen at the end of those limits?!), and eventually reached a peak G-force of about 42.6 Gs.

He pioneered work in Murphy's law (named after Major Edward Murphy, an Engineer on the team). He also flew about in a jet aircraft (at 917 Kph) without a canopy to establish that the wind effects at those speeds would not harm a person. Fortunately, he was right on that one.

On the origins of clapping [Bayblab]

Posted: 16 Jul 2008 10:43 AM CDT

This question has been on my mind for a while. I always get chills when I'm in a large group clapping. I find it such a strange behaviour. Whether I clap or not cannot be heard by the performers, because all they hear is the thunderous applause of the group, but I feel compelled to do so. Yet when you add everything up, the loudness gives the performers an indication of how much enjoyment they've provided to the group as a whole. The other thing I find funny is that we do not clap in synchrony: it is totally chaotic. Everyone has their own clapping rhythm, which I assume may change depending on the mood but probably falls within a personal bell curve. The other thing I wonder is who started this tradition. I've seen it in every ethnic group I have encountered while traveling, even remote tribes in the jungle with very little outside contacts. I seems as universal as music. And I suspect it shares common origins, which probably were invented independently multiple times. I have heard that even babies seem to inherently want to clap, in which case it might not need to be invented and could be an innate behavior. However clapping can be substituted with feet stumping, but the idea is the same, a loud noise, with a constant rythm. So does clapping precede music, are they even related? Why the hell do we do it?

Does anybody out there know of a good explanation or theory on the origins of clapping?

Wordle is fun. [Genomicron]

Posted: 16 Jul 2008 10:18 AM CDT

Carl Zimmer has posted a spiffy summary of the word usage in his book Microcosm using the super cool Wordle site. For fun, I put in the text of two recent papers (one in press, one in review). I guess you can kinda see what they are about.

The Woodstock of Evolutionary Biology and eye rolling [Genomicron]

Posted: 16 Jul 2008 10:16 AM CDT

In a recent issue of Science there was a piece by Elizabeth Pennisi on the "Altenberg 16" who will be attending what overhyping journalist Suzan Mazur calls the "Woodstock of Evolutionary Biology", only it "promises to be far more transforming for the world".

Puh-lease. People have been saying that the Modern Synthesis is neither modern nor a synthesis and needs to be expanded for some time. And there are a lot more than 16 people saying it.

Thankfully, Pennisi uses the nonsensical hype to discuss some relevant issues, and even points out that the people involved themselves do not see it as a revolution.

Massimo Pigliucci is no Jimi Hendrix. This soft-spoken evolutionary biologist from Stony Brook University in New York state looks nothing like that radical hard-rock musician whose dramatic guitar solos helped revolutionize rock 'n'roll. But to Suzan Mazur, a veteran journalist who occasionally covers science, Pigliucci is the headliner this week at a small meeting she believes will be the equivalent of Woodstock for evolutionary biology. The invitation-only conference, being held in Altenberg, Austria, "promises to be far more transforming for the world" than the 1969 music festival, Mazur wrote online in March for Scoop.co.nz, an independent news publication in New Zealand.
That hyperbole has reverberated throughout the evolutionary biology community, putting Pigliucci and the 15 other participants at the forefront of a debate over whether ideas about evolution need updating. The mere mention of the "Altenberg 16," as Mazur dubbed the group, causes some evolutionary biologists to roll their eyes. It's a joke, says Jerry Coyne of the University of Chicago in Illinois. "I don't think there's anything that needs fixing." Mazur's attention, Pigliucci admits, "frankly caused me embarrassment."

My eyes have rolled -- and did so again at the sight of this latest report, until I saw that it was much more reasonable.

...no one truly expects a scientific Woodstock. "Woodstock was an immensely popular event celebrating a new musical mainstream," says Newman. "I imagine this will be more like a jam session circa 1962."

I look forward to reading the papers that emerge from the meeting, but I don't expect anything revolutionary -- more like some cool ideas to continue discussing.

Did Darwin delay? [Genomicron]

Posted: 16 Jul 2008 10:14 AM CDT

In my evolution course, I note that "Darwin spent 20 years working out his ideas and gathering evidence" before releasing On the Origin of Species in 1859. I don't say he "delayed" publication purposely, though in many cases this long period from idea to outcome has been attributed to fear of the reaction from the clergy, colleagues, society at large, his wife, etc. On this issue, a few bloggers have pointed to a recent essay by John van Wyhe (2007), in which it is argued that there was no delay based on fear, only a protracted writing period. Other historians do not necessarily agree, though the blogs I saw did not mention this. As Odling-Smee (2007) says,

...several Darwin scholars are not convinced. Kohn and others agree that the way in which cultural and social pressures influenced Darwin's decisions may have been overplayed, particularly in the public arena, with less attention being paid to the involved process of scientific discovery. But the consensus in the field is likely to remain that a multitude of factors underpinned Darwin's delay.
Kohn points out that searching for explicit references to a "delay" is a simplistic approach to the problem, and that other factors should be considered. For example, Darwin often criticized religion in his notebooks, which suggests that he would have been aware of the probable implications of his theory for religion. It is hard to see how the absence of specific references to a delay rules out any influence of cultural and societal factors on Darwin's decisions, agrees David Quammen, author of The Reluctant Mr Darwin.
Kohn also points out that in Darwin's later publication The Descent of Man, which applied the theory of evolution to humans, Darwin specifically states in the opening lines that he delayed publishing this tome until he was convinced that the climate was right. It seems likely, therefore, that he would have been aware of the controversy his theories would cause from the outset, and probably avoided discussing humans in Origin of Species for this reason.

I think "yes or no" to the question of whether Darwin delayed publication out of fear is very simplistic. Anyone who has written anything of substance knows that sometimes the effect of fear of reaction is procrastination and/or excessive desire to include every piece of information available. Both can cause writing to take longer than it otherwise would. Was Darwin thorough? Yes. Is that one reason it took so long? Undoubtedly. Was he so thorough because of a fear of reaction? Probably at least in part.

_______

Odling-Smee, L. 2007. Darwin and the 20-year publication gap. Nature 446: 478-479.

Van Wyhe, J. 2007. Mind the gap: did Darwin avoid publishing his theory for many years? Notes and Records of the Royal Society 61: 177-205.

A few more quotes about non-coding DNA. [Genomicron]

Posted: 16 Jul 2008 10:12 AM CDT

Just for fun, here are some quotes I came across while reading a few sources for a paper I am writing.

Remember, a significant number of creationists, science writers, and molecular biologists want us to believe that non-coding DNA was totally ignored after the term "junk DNA" was published in 1972, that the authors of the "junk DNA" and "selfish DNA" papers denied any possible functions for non-coding elements, and, in the case of creationists, that "Darwinism" is to blame for this oversight. The latter of these is nonsensical as the very ideas of "junk DNA" and "selfish DNA" were postulated as antidotes to excessive adaptationist expectations based on too strong a focus on Darwinian natural selection at the organism level.

For those of you who didn't read the earlier series, see if you can guess when these statements were made.

(A)
There is a strong and widely held belief that all organisms are perfect and that everything within them is there for a function. Believers ascribe to the Darwinian natural selection process a fastidious prescience that it cannot possibly have and some go so far as to think that patently useless features of existing organisms are there as investments for the future.
I have especially encountered this belief in the context of the much larger quantity of DNA in the genomes of humans and other mammals than in the genomes of other species.
Even today, long after the discovery of repetitive sequences and introns, pointing out that 25% of our genome consists of millions of copies of one boring sequence, fails to move audiences. They are all convinced by the argument that if this DNA were totally useless, natural selection would already have removed it. Consequently, it must have a function that still remains to be discovered. Some think that it could even be there for evolution in the future -- that is, to allow the creation of new genes. As this was done in the past, they argue, why not in the future?

(B)
A survey of previous literature reveals two emerging traditions of argument, both based on the selectionist assumption that repetitive DNA must be good for something if so much of it exists. One tradition ... holds that repeated copies are conventional adaptations, selected for an immediate role in regulation (by bringing previously isolated parts of the genome into new and favorable combinations, for example, when repeated copies disperse among several chromosomes). We do not doubt that conventional adaptation explains the preservation of much repeated DNA in this manner.
But many molecular evolutionists now strongly suspect that direct adaptation cannot explain the existence of all repetitive DNA: there is simply too much of it. The second tradition therefore holds that repetitive DNA must exist because evolution needs it so badly for a flexible future--as in the favored argument that "unemployed," redundant copies are free to alter because their necessary product is still being generated by the original copy.

(C)
These considerations suggest that up to 20% of the genome is actively used and the remaining 80+% is junk. But being junk doesn't mean it is entirely useless. Common sense suggests that anything that is completely useless would be discarded. There are several possible functions for junk DNA.

(D)
There is a hierarchy of types of explanations we use in efforts to rationalize, in neo-darwinian terms, DNA sequences which do not code for protein. Untranslated messenger RNA sequences which precede, follow or interrupt protein-coding sequences are often assigned a phenotypic role in regulating messenger RNA maturation, transport or translation. Portions of transcripts discarded in processing are considered to be required for processing. Non-transcribed DNA, and in particular repetitive sequences, are thought of as regulatory or somehow essential to chromosome structure or pairing. When all attempts to assign a given sequence or class of DNA functions of immediate phenotypic benefit to the organism fail, we resort to evolutionary explanations. The DNA is there because it facilitates genetic rearrangements which increase evolutionary versatility (and hence long-term phenotypic benefit), or because it is a repository from which new functional sequences can be recruited or, at worst, because it is the yet-to-be eliminated by-product of past chromosomal rearrangements of evolutionary significance.

(E)

This is what I emphasized earlier, that this DNA must have a functional value since nothing is known so widespread and universal in nature that has proven useless.

(F)

I've stopped using the term ['junk'] ...Think about it the way you think about stuff you keep in your basement. Stuff you might need some time. Go down, rummage around, pull it out if you might need it.

Answers to be provided in the comments.

No such thing as natural selection? [Genomicron]

Posted: 16 Jul 2008 10:05 AM CDT

In reading an interesting article in the New York Times (in part because it quotes my colleague Andrew MacDougall), I came upon this statement that caused a bit of a cough.

"There's no such thing as natural selection," Ziska confides. He is not, he hastens to explain, a creationist. He is merely pointing out that the original 19th-century view of evolution, the one presented by Charles Darwin and Alfred Wallace, is obsolete. Their model presented evolution as a process taking place in a nature independent of human interference. That is almost never the situation today — even at sea, where less than 4 percent of the oceans remain unaffected by human activity, according to a recent article in the journal Science. This interference with nature has set the stage for the success of a growing category of weeds, one exemplified by cheatgrass: invasive plant species.

Yes, humans have some impact on a great portion of the globe, but this is nonsense for at least three reasons. One, just because humans are involved does not make something "artificial selection" and therefore disqualify it as natural selection, even within the formulation of Darwin and Wallace which drew a distinction . Artificial selection is the intentional breeding of organisms on the basis of some characteristic (e.g., sleek body shape in dogs or high yield in crops). If we dump waste in the ocean and this creates new selective pressures on marine animals, this hardly counts as artificial selection. From the point of view of the organisms involved, it is simply a change in the environment, and natural selection will then operate as usual. (As a matter of fact, I don't consider "artificial" and "natural" selection to be fundamentally distinct processes anyhow -- feel free to discuss in the comment section). Two, we may influence environments generally, but there are, as we speak, gazillions of organisms out there struggling for survival and hunting, parasitising, avoiding, mating with, and otherwise interacting with one another independent of human action. Three, natural selection is still occurring both in human populations and indeed within human bodies (among pathogenic agents, for example).

(Hat tip: John Hawks blog)

Stephen Hawking moving to Canada? [Bayblab]

Posted: 16 Jul 2008 09:48 AM CDT

Apparently Hawking is disgruntled with the current science funding cuts in place in Britain and may leave Cambridge to join the famous Perimeter Institute! If you don't know about the perimeter institute it's a Waterloo-based theoretical physics institution founded/funded by the RIM (of blackberry fame) maverick Mike Lazaridis, and it is known for its collegial atmosphere and high profile members. This is quite a coup. No word yet if he'll be back on the bayblab podcast...

Science career as a video game? [The Daily Transcript]

Posted: 16 Jul 2008 08:41 AM CDT

Inspired by a conversation with Awesome Mike.

Your science career, what type of video game is it? At times it might resemble a labyrinth full of demons that you must slay. (Or maybe it's like Grand Theft Auto? Well since I've never played that game nor Halo, I'll stick to the metaphorical game that's running through my head.)

Level 1: Undergraduate

The first level is the easiest. Stay focused and you'll get to the end. Final monster at the end of the round? Those exam finals? Psht.

Level 2: Grad Student

This level bit trickier then the previous one. The first major obstacle is choosing the right lab. Pick a postdoc laden lab full of premadonas and you may end up loosing many bonus lives unnecessarily to all sorts of nasty creatures hiding in each corner. Pick a lab where the work is interesting and where you'll receive a good training and you may gain valuable extra powers that can be useful in higher levels. The last dragon to slay in this level is the thesis. In many ways this is the hardest part of this level but in no way near the most challenging.

Level 3: Postdoctoral fellow

In comparison to the previous level, the choice of lab is even more critical. You want a good environment with good connections that has a history of postdocs moving on to the next level. You also want to have a project that you can bring with you. The final dragon to slay at the end of the round? Surviving the eighteen headed monster that is the job market for academia. Unlike in the previous level this monster is brutal. But if you've laid down the proper ground work and have an interesting (and findable) research plan, you'll slay this monster (hopefully).

I am in the process of slaying the multi headed dragon. (Yes this post is a hint as to what's been happening in my science life besides travelling across Europe). But level 3 is as far as I've reached in this game. You can fill me in as to what is to come in the next. But I can imagine ... Level 4: Assistant Professor, Level 5: Full Professor and Level 6 ... Grand Poobah?

Read the comments on this post...

Cool New Blog Carnival [Bayblab]

Posted: 16 Jul 2008 08:35 AM CDT

The Giant's Shoulders is a brand new blog carnival focusing on the history of science. Bloggers are asked to write posts about classic papers or profiling important people or concepts.

Contributors should not only describe the research involved but also put it in a broader historical/scientific context: why is the work in question important/groundbreaking/revolutionary/nifty? [...] Entries profiling an important person or concept in the history of science are also acceptable.

The inaugural edition has gone up at A Blog Around the Clock and it's a doozy - dozens of entries profiling work as far back as 1543 and covering diverse areas from medical case studies to classic physics to ... Dungeons and Dragons? Check it out.

Personalized Medicine in Video [ScienceRoll]

Posted: 16 Jul 2008 05:13 AM CDT

Deanna Kroetz of UCSF’s School of Pharmacy talks about the promise and the limitations of personalized medicine.

(Hat tip: Medical Quack)

Further reading:

Unnatural Approach to Diabetes [Sciencebase Science Blog]

Posted: 16 Jul 2008 04:15 AM CDT

Mulberry leaf As regular readers will be aware, I’m very skeptical of crank claims. Usually, these will claim to cure everything from premenstrual cramps to cancer by way of motor neurone disease and ingrowing toenails, all of them, with one pill. Forgive my flippancy, but the claims of many of those touting such panaceas usually beggars belief.

But some offer quite convincing claims for treating, but not necessarily curing, a specific illness with something novel. One such email arrived recently from a public relations company representing a company selling a herbal supplement. The release discusses the potential of an extract of mulberry leaf to prevent concentration spikes in the blood sugar of patients with Type 2 diabetes mellitus.

This disorder, which is on the increase in the developed world as obesity incidence rises, is characterised by insulin resistance, relative insulin deficiency and hyperglycemia (raised blood sugar levels). Changes in diet and more exercise can often ameliorate the effects in the early stages, but medication and insulin are usually needed in the long term. The main problem is the sharp rises and falls in the concentration of glucose in the blood, which puts a severe strain on the organs, in particular the heart.

The email I received, had the subject line “Type 2 diabetes: a look at natural alternatives to prescription drugs” and seemed innocuous enough. It mentioned the FDA’s pronouncements on diabetes drugs and the need to tighten up on their safety and then went on to highlight mulberry, a natural product that is now being marketed as Glucocil, which can purportedly help prevent those hazardous blood sugar spikes.

According to the press release, mulberry has been used for generations in Chinese medicine and some Indian foods, is showing great promise for Type 2 diabetes sufferers. After seven years of research and development, a medical researcher and scientist from China, Lee Zhong, has discovered a proprietary mulberry leaf extract that has been shown in numerous clinical trials to markedly lower blood sugar levels in Type 2 diabetics, helping them achieve a healthier diet and lifestyle. I asked Zhong for a few details about his work, the efficacy of this food supplement and possible medical issues associated with its use. You can read more about the study in the latest issue of Reactive Reports.

Zhong explains that, “Mulberry leaf
is
a natural
α-glucosidase inhibitorMulberry leaf is a natural α-glucosidase inhibitor. α-glucosidase
inhibitors do not lower blood sugar levels, they reduce and delay the abrupt elevation of blood sugars after meal, therefore stabilize blood sugar levels. π-glucosidase inhibitor drugs, such as Acarbose, are found to 1) reduce diabetic cardiovascular risks 2) be good for weight management 3)
prevent pre-diabetics to become type 2 diabetics.” Zhong and colleagues have published positive results on pure mulberry extract in the journal Diabetes Care, see reference.

It all sounds reasonable so far. But, what is not clearly mentioned in the press release is that Glucocil is not simply mulberry extract. Rather it is a blend of different ingredients:

Mulberry leaf extract
Cissus sicyoides (Insulina) leaf extract
α-lipoic acid
C. quadrangularis extract
Banaba leaf extract
Chromium polynicotinate
vitamin B1, B6, B9 (folic acid), and B12

I asked Zhong about the presence of that chromium salt, as chromium deficiency has long been suggested to be a factor in the development of diabetes. “Chromium was not included in the extracts that used in our published clinical studies (or the efficacy tests),” he told me, “The ingredients used in the final Glucocil formula have records of many years’ safe human usage.” He adds that, “Glucocil was not developed overnight. We had thousands of tests and have plenty scientific evidence to support the product.”

That’s as maybe, but, I think he missed my point, it’s not the safety of the formulation that concerns me, although chromium picolinate has been linked to liver toxicity (Eur J Intern Med. 2002, 13, 518-520), it’s how it can be marketed as a natural product when it so obviously contains a rather non-natural ingredient in the form of that chromium salt. It seems especially odd given that chromium itself is thought to have an effect on diabetes, although that’s as yet unproven.

Aside from the clinical trials and tests carried out with mulberry in isolation, as far as I know, no double-blind placebo-controlled trials have been carried out on the mixed formulation that includes the chromium salt, which has variously been used as a “natural” slimming aid without serious proof of efficacy. Chris Leonard, Director, Translational Research and Technology at Memory Pharmaceuticals, points Sciencebase readers to what he describes as a “thoughtful and well-referenced discussion on chromium and diabetes.

Pharmacologist and toxicologist Sanjeev Thohan, Research Director at drug discovery company Exelixis, adds that chromium picolinate is quite distinct from the hexavalent form of chromium made infamous by the Erin Brokovich issue. He points out that there have been some clinical trials conducted within the last year that use different derivatives of chromium picolinate and that these are close to finishing and will make their data available in the next year or two. He adds that one must, “Remember that the bioavailability of the picolinate derivative and its action on the beta cells is what will determine if there is a positive effect on insulin. Insulin sensitizer drugs, I believe in some of the clinical trials, are being used with the chromium compounds to see the possibility of synergy.” Thohan highlights an additional UK government PDF resource on chromium. The US government’s PDF document on dietary recommendations for vitamins and trace elements also includes a section on chromium.

Zhong adds that, “This product is being marketed as a dietary supplement (not a food or drug) and is designed to assist those who are trying to manage their condition primarily through changes in lifestyle, primarily diet and exercise.” But, to my mind, something with proven activity in such a potentially debilitating disease should not be marketed as a supplement. Consumers should be made aware of the dangers of diabetes and consult their doctor over possible treatments and outcomes.

Zhong tells me that the marketing does stress that potential users talk to their healthcare workers and that they should monitor their blood sugar carefully. However, one in ten, he concedes, don’t necessarily do so. With diabetes on the rise, one in ten could turn out to be quite large numbers of people using an apparently potent supplement without any clear knowledge of what it might be doing to their bodies and without strictly monitoring the progression of their disease.

“Generally speaking, those who are most interested in this product are those who are newly diagnosed and are not on multiple meds as is the case with those who are more seriously ill,” adds Zhong, “The typical Glucocil consumer is someone who is looking for more natural nutritional support.”

Yes, there are problems with pharmaceutical products. But, maybe its time physiologically active herbal remedies were
brought under
the pharma umbrellamaybe its time physiologically active herbal remedies were brought under the pharma umbrella rather than being sold disguised as food supplements. Indeed, there are calls for this to happen in Europe and elsewhere. This way, not only would they gain acceptance or rejection quickly, but those that are truly effective and worthy, and safe, would reach the patients who really need them and lose the downy feathers of alleged quackery.

Mudra, M., Ercan-Fang, N., Zhong, L., Furne, J., Levitt, M. (2007). Influence of Mulberry Leaf Extract on the Blood Glucose and Breath Hydrogen Response to Ingestion of 75 g Sucrose by Type 2 Diabetic and Control Subjects. Diabetes Care, 30(5), 1272-1274. DOI: 10.2337/dc06-2120

A post from David Bradley Science Writer

Unnatural Approach to Diabetes

What does DNA mean to you? #14 [Eye on DNA]

Posted: 16 Jul 2008 03:04 AM CDT

Andrew Yates of Think Gene is feeling blunt today as he tells us what DNA means to him.

Nothing.

My background is computer science, so to me, DNA is the object code of life. Unlike human-designed languages, DNA is entirely unbounded by intelligibility or elegance —only function.

So we are looking for meaning at the wrong level of abstraction. Our understanding of DNA is tainted by an anthropomorphic misunderstanding of how a language “should” work: “genes” are “sequences of letters” positioned by an “index” like words in a book. One word, one meaning[1]. This is a mistake, as supported by the inconsistent success of genome-wide association studies (GWAS) and the disappointing usefulness of today’s genomic testing.

We don’t try to understand object code in software without abstraction, so why do we try to understand DNA directly in life? Here’s why we shouldn’t try to understand DNA directly —even more so than object code:

* DNA is an implementation, not a map of abstractions. That is, units of DNA have no constraint to “mean” anything. Even object code can usually be interpreted as processor instructions and numbers.
* DNA is a template for amino acids and RNA, not a set of instructions (code) or table of facts (data).
* What DNA “describes” is probabilistic, dynamic, highly context-sensitive. It moves. Its parts move. Its environment moves. It’s chemistry. Object code is discrete and static. It’s math.
* DNA is hard to sequence. Object code is trivial to sequence.

Genomics today is like alchemy: we’re tinkering with a system we don’t understand in hopes of some elixir of longevity —except we call it “the cure for cancer.”

Why? Because we are impatient. Because we vastly over-estimate our ability to understand complex systems without simple abstractions. Because we believe what is difficult must be valuable. Because genomic research today is commercial, and gold must be made.

Well, that’s crap.

In software, we abstract object code with higher-level languages. When that system becomes too complex, we make a new, even higher level interface and abstract again. We continue until surface complexity is low enough to be useful.

In genomics, we label genes with some incomprehensible, ontologically-inconsistent name and then strain to make that gene “mean” some attribute or disease.

There is some use for the black-box, top-down genomic testing, but I believe that this approach alone is wrong. I believe that what we should be doing is creating better abstractions, interfaces, by which DNA can be understood. I believe that the future of genomics —the people who will make DNA mean something— will be the language designers who compile to DNA.

Until then, God laughs. There’s a reason why Window’s object code is everywhere, but the source code is top secret. Bill Gates laughs, too.

Dreaming of a life science Semantic Web platform [business|bytes|genes|molecules]

Posted: 16 Jul 2008 12:01 AM CDT

I have long been intrigued by IO Informatics and their flagship Sentient Suite. Bio-IT World is carrying an article about the company that reminded me of that interest. I have never used it, so I wonder if anyone else out there has?

Now the Sentient Suite doesn’t really sit on the WWW, so it’s not really an optimal Semantic Web product, but it does use RDF, a wonderful data model for the kind of data life scientists use, rich in relationships and metadata, and SPARQL to query the data. So at least within the confines of a company’s data sources, in theory you have a rich graph of data which can be queried. I’ve long felt that we either don’t leverage structured data optimally in much life science software, or over engineer it. The company claims to be smart about how it’s doing this, although given the complexity of data, how well they achieve their goals is something I question.

My ideal would be a life science version of the Talis platform, perhaps with an industry facing side (much the way Talis has its library business), and a public facing side that sits on the web with published APIs and the underlying technology that allows developers to build tools on top of it. I am sure they’d be a ton of takers. IO has one side of this (the enterprise facing side). Would be cool if they, or someone else, made a platform available publicly, with some underlying intelligence that can be leveraged by APIs.

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Conflict of interest and openness [The Tree of Life]

Posted: 15 Jul 2008 11:00 PM CDT

The New York Times had a long and extensive article on conflicts of interest in medicine. See Times article here.

I was pleasantly surprised to see them discuss the concept that open access to data can help correct for bias if it occurs by allowing others to redo analyses. For example:

"Having everyone stand up like a Boy Scout and make a pledge isn't going to quell suspicion," said Dr. Donald Klein, an emeritus professor at Columbia, who has consulted with drug makers himself. "The only hope to rule out bias is to have open access to all data that's produced in studies and know that there are people checking it" who are not on that company's payroll.

Unfortunately the Times does not raise the issue of access to the publications themselves. Clearly having the data is good. But if nobody can read the papers and they can just read the press releases that come from the papers, we are all doomed.

There's a Whole Doubt Industry Aimed At Science [adaptivecomplexity's column]

Posted: 15 Jul 2008 10:03 PM CDT

"Can scientists and journalists learn to beat the doubt industry before our most serious problems beat us all?" This is the question asked in an interesting piece at a news? site I've never heard of - "Miller-McCune: Turning Research Into Solutions." I'm not sure about the research and solutions thing, but they do have some interesting comments about the "Doubt Industy."

"Doubt Industry" means organized interests with a strong motivation to get the public to question science: the link between smoking and cancer, the scientific status of evolution, the health hazards of beryllium (apparently a problem for workers in the atomic industry). Whenever scientific results cause problems for someone, especially someone with a strong financial incentive to not believe the science, the time-tested strategy is to question the certainty of the science. A well-known internal memo from one cigarette company in the 1960's famously claimed(PDF):

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Wednesday, July 16, 2008

The DNA Network

The DNA Network

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