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A Man with a Ph.D. - Richard Gayle's Weblog
 Friday, September 20, 2002
Science Slow to Ponder Ills That Linger in Anthrax Victims. Survivors of last year's anthrax attacks are of great scientific interest because in the past nearly everyone with inhalation anthrax died. By William J. Broad and Denise Grady. [New York Times: Science]
Okay, this article pissed me off and I was already writing another missive when I stopped and started over. This article intially ticked me off but I forgot that they always wait until the second page to tell you the real stuff.By the end, it discusses what is being done. It appears that it was a slow start because providing grant money for this takes some time. They don't really have a slush fund to do it. It takes time to get everyone's medical information. Each state has different requirements for releasing medical data. They do have blood samples and are going forward. There are only a small number of people, so it will be hard to do real epidemiological work, separating normal fatigue of aging and special anthrax-related fatigue. But they are starting and I do not think irreplaceable time has been lost. They want you to get pissed off but they failed in my case. I am so proud. 9:49:22 PM 
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The Physics of the Wave, in Stadiums, Not Oceans. The sweeping mass of spectators rising in sequence around a stadium can be quantified just about as well as all those other waves. By Henry Fountain. [New York Times: Science]
So play on the field affcts the stability of the Wave, as does size of the initiating units (i.e people). So, while an Expos vs D-Rays game would have low enough field excitement to permit long running waves, there are not enough units to get it going. Neat. 9:36:03 PM
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In Nature vs. Nurture, a Voice for Nature. Steven Pinker, a psychologist of language, is trying to make it safer for biologists to theorize about the genetics of human behavior. By Nicholas Wade. [New York Times: Science]
Born With It? Author Suggests Yes. There is evidence that some universal human social behaviors and faculties are innate, and presumably shaped in part by the genes. In "The Blank Slate," Dr. Steven Pinker lists some behaviors of political consequence which he considers may fall in this category. [New York Times: Science]
The problem I have with the Naturists is the implicit argument that, since these behaviors are implicitly genetic, there is nothing you can do about it. And anyone who compares himself, and his worldview, to Galileo, and his worldview, is suspect in my book. Check out the list of innate behaviors. The first list would seem to be true for most any social animal, while the latter list describes things seen in our nearest relatives. The argument should not be not whether these are innate but to what degree they are modified by the environment, by society. On one side are those who say you can't modify anything, while there are others who feel you can modify everything. For most of recorded history, great thinkers have believed that human nature could be altered, that the baser instincts could be corralled. That is what society does, it modifies these innate instincts, for the betterment of the group. I firmly believe that human society has gotten better at this as time has progressed. It is the combination of strong natures easily modified by beneficial nurtures that makes humans such formidible creatures. Oh well, sociology is not a real science. It is just an area of research that helps create pundits ;-) 9:33:30 PM
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Physics meets biology: Philately will get you nowhere. Nature Sep 19 2002 8:30PM ET [Moreover - moreover...]
SOme will come because it makes it easier to get grant money. Some will come because they think they are smarter than biologists. But some will come that will revolutionize the field. New knowledge almost always gets created when people with different viewpoints interact. But, I think it will be physicists who can see order in chaos. Check out this article in Nonlinear Dynamics, Psychology, and Life Sciences (vol 6, p 37). It discusses a study where 20% of the people could see the underlying order in a chaotic number series, while the other 80% could not. I would suggest that biology would select for a higher percentage of this than in the normal population, but that physicists of a certain type might also have the faculty. That is a study I would like to see. 9:09:00 PM
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DNA codes own error correction. Nature Sep 20 2002 8:46AM ET [Moreover - moreover...]
Purine and pyrimidines as parity codes? Sometimes I have to wonder. But does this actually tell us anything. I'm not enough of an information technologist but it seems kind of arbitrary. He seems to have just given binary encoding to things that have complex molecular shapes. Just to fit the idea of a parity code. And how do unusually modified nucleotides fit in the scheme? Like the ones in tRNA? It still seems like some for of post-hoc argument. 8:57:44 PM
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Haseltine Says Biopharma, Duped by HGP, Should Turn to Expression Genomics [GenomeWeb]
Haseltine is right about getting duped, although I would not exactly phrase it that way. Some science is worth doing because of the technology it develops, not just for the science being done. We went to the moon because of the Soviet Union, right. Well, we would not have gone if JFK had simply said we would have so many new technologies generated that it would send us forward into a new age, the Information Age. He did not know nor could imagine what the Apollo program, and necessary predecessors, would produce. No, we went to the moon to beat the Russians. We were duped and because we were, we have never gone back. Columbus duped the rulers of Spain. But he lead to a new Age. The Human Genome Project duped pharmas. But, the technology that was developed will allow us to get places we could not get before. Will it send us into a new Age? We shall see. But we will be able to examine arenas in Life's panorama that were unaccessible before. 8:47:23 PM
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Business Shun Biotechnology Seafood [AP Science]
Now, I am for GM foods when they are beneficial to the consumer. These are just beneficial to the manufacturer. Simply being cheaper is not how to enter the market. That is not enough of a rationale to overcome customer's worries. Coupled with the comments of someone who obviously did not watch or read Jurassic Park. To Quote the article: McGonigle said the company's lab-grown salmon all will be infertile females, eliminating the risk of escaped fish crossbreeding with native species. Now this GM fish just overexpresses growth hormone, making it grow larger faster. WIll it make things cheaper? What are the economics? Now, in my opinion, economics will not drive GM-foods. They might initially but it will require something else first to drive the market. If I figure it out, I could make billions!! 8:24:14 PM
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Scientist Concedes Antihydrogen Claim [AP Science]
Hey, you know that egos are involved when the intial response is 'Nope. Not true.' This is then followed by 'Well, it might be true but we showed the same thing 3 years ago'. I wonder if his work got published in Nature. Could be a little jealous ;-) 8:10:23 PM
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Green tea may fight allergies. Allergy sufferers may want to add green tea to their sniffle-fighting arsenal. New evidence suggests that drinking the popular brew may provide some relief. Researchers in Japan identified a compound in green tea that, in laboratory tests, blocks a key cell receptor involved in producing an allergic response. The compound, methylated epigallocatechin gallate (EGCG), may have a similar effect in humans, they say. Program for Promotion of Basic Research Activities for Innovative Biosciences [EurekAlert - Biology]
Does this compound make it through our digestive system? It would be very interesting to find out how it works. 8:08:32 PM
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Structure reveals details of cell[base ']s cargo-carriers. Using x-ray crystallography, Howard Hughes Medical Institute researchers have produced the first images of a large molecular complex that helps shape and load the small, bubble-like vesicles that transport newly formed proteins in the cell. Understanding vesicle "budding" is one of the prerequisites for learning how proteins and other molecules are routed to their correct destinations in the cell [EurekAlert - Biology]
X-Ray crystallopgraphy gets better and better every day, as computing power and better technology arrives. This is a very important pathway, since so many proteins are carried by vessicles. Elucidating it is pretty nice. 3:25:59 PM
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Tiny, magnetic spheres may help overcome gene therapy hurdle. In a July article in Molecular Therapy, UF researchers report attaching the adeno-associated virus, a widely used gene carrier, to the surface of tiny manufactured balls known as microspheres, each containing a miniscule particle of iron oxide. Using a magnet placed under culture dishes, the researchers were able to coax large amounts of the microspheres to target areas of the cultures. Whitaker Foundation [EurekAlert - Biology]
Very nice use of technology. You'd like to make sure that the magnetic spheres had little harmful effects, but it could be a very nice way to target other things, like binary toxins, to a specific organ uding chemo. 3:20:48 PM
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Advances in 'micro' RNA exploring process of life. Researchers at Oregon State University have made an important advance in the understanding of "micro-RNA" molecules, which are tiny bits of genetic material that were literally unknown 10 years ago but now represent one of the most exciting new fields of study in biology. National Science Foundation [EurekAlert - Biology]
People used to think that these micro-RNAs were not important or only breakdown products. To see that they may be active manipulators of gene expression is amazing. Nice story to follow. 3:12:55 PM
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Waist circumference as a predictor of cardiovascular risk. Waist circumference has been proposed as a simpler measurement than body mass index that also more accurately reflects body fat distribution. A study by Zhu et al. closely correlated waist circumference with risk of cardiovascular disease in a large group of overweight men and women. National Institutes of Health [EurekAlert - Biology]
So, anytime anyone buys a 'husky'-sized pair of pants, maybe we should give them a pamplet on obesity and cardiovascular risk? Sounds like an idea ;-) 3:07:32 PM
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Genentech tops Science survey of best biopharma employers. When Science asked life scientists around the world which pharmaceutical and biotechnology companies they most admire, Genentech was the clear stand-out, according to a survey in the 20 September issue of the journal, published by the American Association for the Advancement of Science (AAAS). [EurekAlert - Biology]
I will have to check out the article to get some idea of how this was determined.2:49:14 PM
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Researchers discover new risk factor for colon cancer. Studies in mice and humans have revealed that people who are carriers of the rare disease Bloom syndrome are at increased risk for developing colorectal cancer. The results are the first to show that being a carrier of a recessive cancer syndrome gene can raise the risk of cancer, even if that individual does not have the disease itself. [EurekAlert - Biology]
This mutation appears to be found in many Ashkenazi Jews. Even just producing less protein than normal is enough to increase the prevalence of cancer. Since it seems to be a protein involved in repairing DNA damage this is not surprising. What is surprising is that carriers of this defect, that is they have one normal gene and 1 defective one, were THREE times more likely to develop colon cancer than normal controls. It will be interesting if this is due to the need to have two full functional genes in EVERY cell, or whether there is some variability, with some cells having normal levels and others having none at all. Since all it may take is one cancer cell to be formed, either one is tough, but it may affect how you do some sort of gene therapy approach. 2:47:29 PM
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UT Southwestern researchers find protein that both instigates, inhibits heart growth in mice. Researchers at UT Southwestern Medical Center at Dallas have discovered a protein that regulates growth and development of the heart from its fetal stage to adulthood. National Institutes of Health, Donald W. Reynolds Cardiovascular Clinical Research Center, McGowan Charitable Fund [EurekAlert - Biology]
This sounded really interesting until I got to the last line. 'San Diego-based Collateral Therapeutics Inc., a company working to develop genetic treatments for heart ailments, already has licensed the research in order to explore drug-development possibilities.' What does this mean - that no one can work on these molecules without dealing with Collateral Therapeutics. I hate it when releases mention this stuff. 2:39:30 PM
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When Bad Viruses Go Good. In this article, John Edwards looks at the convergence of two disciplines: using real biological viruses to build nanosize materials. This idea is quite attractive. Here is he has to say.
Most biological viruses have a nasty reputation. But scientist Angela Belcher believes that some viruses can be guided into performing a useful task: building high-tech materials.
Belcher and her University of Texas at Austin colleagues were intrigued by the way viruses can easily produce vast armies of new viruses. The researchers soon discovered that virus replication could also build nanosize materials for next-generation optical, electronic and magnetic devices.
Using genetically engineered viruses that are noninfectious to humans, Belcher and her team created liquid crystal suspensions of viruses and nanoparticles that could be cast into thin liquid crystal films.
Belcher believes that viruses have the potential to become cheap, efficient and environmentally safe nanotechnology building tools. "Biology makes material at moderate temperature using self-assembly and using nontoxic materials," she says.
Can you imagine microscopic semiconductors produced by biological viruses? "Most of this research is still at the basic science stage," says Angela Belcher.
So I guess we will not see any real-world applications before at least five years.
Source: John Edwards, CIO Magazine, September 15, 2002 Issue [Roland Piquepaille's Technology Trends]
Very cool work.However, I am waiting for someone to start making the argument that nanotubes of carbon, or other nano-material are not really non-toxic. I wonder how the human digestive system reacts to these things? Not the viruses but the things they would make. Good science fiction story (excepting its use in Ecks vs. Sever, where it appears to just be a plot device). 2:30:16 PM
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Gathered at Gambling Mecca, Genomics Types Ask Why Pharmas Have Quit Betting on Them [GenomeWeb]
Has the -omics bubble burst? Not if you really had an appreciation for how hard it all is. New technologies allow you to ask new questions. They usually do not just hand you the answer. There is a huge amount of work that will need to be done. I particlularly liked the comments of David O'Reilly, the chief business officer for Iconix Pharmaceuticals: he argued that whether genomics technologies bear fruit for pharma has 'nothing to do with technology and everything to do with organizational change.' To really understand the impact of genomic technologies, he said, ask what's happening inside life sciences organizations. If pharma is anything like other industries, it will be 15 to 20 years before genomics technologies are fully integrated. 'In the US we have a certain amount of technological hubris,' he said. 'Ask senior pharmaceutical executives. They're not evaluating the technologies; they're asking themselves, 'How can we organize ourselves to take advantage of these technologies?
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Tuesday, September 17, 2002
DNA database "should include every citizen" [New Scientist]
This is from the man who invented DNA fingerprinting. The idea that my DNA sequence could reside in a government run database is frightening. Because, databases are not secure. Here is a 'what if' for a future detective story. If you know the DNA sequence for an individual, how difficult would it be to synthesize DNA corresponding to that individual and plant it at a murder site? Since everyone knows that a DNA fingerprint is damning, that individual would be found guilty. See, you really cannot easily fake a real fingerprint, but I bet you could do a reasonable facsimile with DNA, enough to convict someone. Assuming you knew what the sequence is for important regions that labs use to examine DNA. It is much easier to break into a database than to completely sequence someone's DNA yourself. I'm waiting for the movie. I'm sure someone will take my idea and make some sort of Minority Report ripoff. Have fun. 11:42:31 PM
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How to balance a stick on your finger. With practice, most people have no trouble balancing a long stick on the end of their finger. But as the stick gets shorter, the challenge is greater. The biggest problem in balancing the stick is that human reaction times can be slower than the time it takes for the stick to fall. An analysis of stick balancing shows how the human nervous system copes with balancing problems even for 98% of the time when reaction time isn't fast enough. A new model suggests that the nervous system introduces random motions to a person's finger. Surprisingly, these random motions can help stabilize the stick. This idea of introducing randomness to an unstable situation and thereby creating something more stable has been previously recognized and used in human-made technologies such as the design of high performance aircraft but this study shows it naturally at work in the human nervous system. The authors suggest that these techniques may also be applicable to making buildings more earthquake-proof and to making two-legged walking robots.
To appear in Physical Review Letters
(From my physics tip sheet) [David Harris' Science News]
I love the idea of random events helping to stabilize a situation. I have to check the article. 11:19:26 PM
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Monday, September 16, 2002
Spending on alternative therapies four times greater than on conventional pharmaceuticals. Following on from last Friday's snippet on alternative vs conventional medicine, a study of spending on pharmaceuticals and alternative therapies in Australia shows that four times as much is spent on the untested, unproven therapies (AUS$2.3 billion per year) than on prescribed pharmaceuticals.
Furthermore, untested alternative therapies have increased in price by 120% (i.e. more than doubled) since 1993, even allowing for inflation.
The study is published in the American journal Preventive Medicine.
That's a lot of money to spend on things that might be doing nothing at all or could even potentially be doing you more harm than good... [David Harris' Science News]
I wonder what the number is in the US? It is strange that people would rather trust something that is declared to be 'natural' when nothing has actually ever been done to demonstrate efficacy, much less whether it is harmful. I am reminded of the Danny Kaye movie 'The Inspector General' with a great song about Yakov's Miracle elixir that cures everything (mainly because it kills you, but you're cured). 11:45:11 PM
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One gene, two important proteins. James E. Darnell, who discovered the first ever cancer-causing "STAT" gene in humans, has made yet another discovery about its fruit fly counterpart. Reporting in the Sept. 15 issue of Genes and Development, he and colleagues show that the one and only STAT gene in flies, which was also discovered by Darnell's group, actually codes for two -- not one -- important proteins. [EurekAlert - Medicine & Health]
A really well-written press release. It makes me want to go out an read the article. STAT proteins have been know for some time. They control the cell's responses to outside stimuli and are often altered in tumor cells. It turns out that, in fruit flies, a specifc STAT gene is made in 2 forms. One form is missing the portion of the protein responsible for activity. Now, why would a cell make a protein that has no apparent activity? The reason is called a dominant negative effect. This altered protein may not have any activity but it can still bind its substrate every bit as well as the normal protein. By doing so, it ties up the substrate so the normal protein can not perform its duty. The normal protein sees less substrate floating around to bind up, because it is all bound to the altered protein. Since the altered protein performs no action on the bound subtsrate, the overall effect is to inhibit the activity of the normal protein. As this report states, much like a key broken off in a lock, the altered protein prevents a new key from being inserted, effectively stopping the reaction. The report is wrong about one thing. It is DOMINANT not DOMINATE.It is called a dominant negative because the altered protein is not only inactive itself but acts to inhibit the activity of the normal protein. Remember dominant and recessive genes from genetics. When recessive and dominant genes are both present in an organism, you do not see expression of the recessive. Usually, the recessive gene is recessive because it makes less active protein. The dominant gene makes more, active protein, with its resulting effects on the organism. In most cases the expression of the recessive gene has no effect on the expression of the dominant gene. They have no real effect on each other since both act to produce something in a positive fashion. One just produces more or makes a more active form. But, in the case of a dominant negative mutation, the altered gene can dominate the normal gene, acting to inhibit directly the activity of the normal genes. So, not only is the altered gene inactive, but it reduces the activity of the normal gene. Dominant negative mutations are used commonly in recombinant technology but this is a nice example of how Nature was there first. 11:34:12 PM
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Wake Forest-Johns Hopkins team discovers prostate cancer gene. Scientists in the Center for Human Genomics at Wake Forest University School of Medicine and Johns Hopkins Medical Institutions have discovered a gene that "may play an important role in prostate cancer susceptibility in both African-American men and men of European descent." Public Health Service, US Department of Defense [EurekAlert - Medicine & Health]
The statistics indicate this gene might be involved but I think a LOT more work will have to be done. Mutations in this gene were found in only 4.4 % of Caucasians and 12% of African-American men WITH prostrate cancer. That means that 95.6% of the Caucasians with prostate cancer DO NOT have these mutations. Now, lots of things can be happening - the gene may have an effect on severity; other processes besides the mutation may be important in the proteins effect on prostrate cancer; there may be other important genes involved. We are a long time from using this gene for screening all men for susceptibility to prostate cancer. 11:01:04 PM
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One in one hundred babies in the US are involved in a car crash while in the womb. One in 100 babies born in the United States will have been involved in a police-reported car crash while in the womb, according to researchers from the University of Pittsburgh's Center for Injury Research and Control (CIRCL) report, published in today's Injury Prevention, a publication of the British Medical Journal Publishing Group. The study also found that trimester status has only minor bearing on the risk of being injured in a crash. [EurekAlert - Medicine & Health]
This seems awfully high. And I never trust a report that comes up with excuses to explain the data it does not like. They say that the accident rate for pregnant woman is half of that found for non-pregnant woman, but then say to ignore this result. Now, if we are supposed to believe that one conclusion is valid by considering the data, it seems to weaken the argument when we are supposed to ignore another conclusion from the same data. There may be good reasons to do so, but you had better be awfully careful. Physicists work all the time by making certain simplifications that allow them to ignore some data. But social scientists risk real problems when they chose to 'simplify' since the underlying causes are not nearly as quantifiable as in physics. 10:54:19 PM
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Gene therapy promising for preventing restenosis. An experimental gene transfer technique shut down cell re-growth in the arteries' interior lining and reduced the inflammatory response [^] two main causes of re-narrowing of newly opened blood vessels, researchers report in today's rapid access issue of Circulation: Journal of the American Heart Association. [EurekAlert - Medicine & Health]
I worked on a molecule called CD39 that was found on the cells lining the walls of blood vessels. Its main job was to prevent platelets from clumping together and forming blood clots. Now this is a very complicated cascade but it is interesting to note that CD39 activity is greatly reduced following oxidative stress. So, if we have oxidative stress, we have less CD39, with less inhibition of platelets and the increased possibility of clots blocking the vessel.I wonder if CD39 is involved in restonosis, or if adding CD39 would reduce the likelihood of restonosis? 10:42:28 PM
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Infpormation Overload and Scholarly activity. Quote: "A vendor to a large pharmaceutical company says that the firm wasted almost two years trying to isolate a compound, not realizing that fellow colleagues had already obtained a patent for it. University of Minnesota researchers, as many others do, discovered after three years of research that results they were writing up had already been published." [Serious Instructional Technology]
I have seen the same sort of thing happen. Poor communication and information flow often result in duplication of effort. Transparency lessens the likelihood of repetition. Scientists talk of mining the bioinformatics data. Data mining often involves individual efforts with litle interconnections. Different people examine the same data and explore the same paths, but with no tools to easily disperse their information. I prefer data farming, with a collective group to examine the data (Some sort of anarcho-syndicalist commmune). With every decision being ratified at a biweekly meeting. 10:32:14 PM
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