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A Man with a Ph.D. - Richard Gayle's Weblog
 Saturday, October 5, 2002
Disease kills 3 million people each year. Electronic Telegraph Oct 5 2002 6:54PM ET [Moreover - moreover...]
You have to really appreciate a news article that tries to humanize a disease that kills millions a year by rattling off some of its victims. Like Alexander the Great, Dante, Oliver Cromwell, Lord Byron. I mean, these guys really have relevance today to what this disease is doing in Africa, much less England. I guess it makes it easier to know that old Alex had the same disease you do ;-) 10:59:13 PM 
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Second-hand sales blamed for bedbugs' comeback. New Scientist Oct 5 2002 12:47PM ET [Moreover - moreover...]
Looks like they are biting. A nasty insect and one that is capable of leaving a nasty bite. Now all I need to find out is if car boot sales are some arcane British term for some normal American activity. I know boot is the same as show, but I have a hard time visualizing a car shoe. Or maybe it refers to shoes sold out of the truncks of cars? Hummm. 10:55:43 PM
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Your Genome on a CD: $500000. Salt Lake Tribune - Mapping and reading J. Craig Venter's genome took 15 years, $5 billion and some of the world's most sophisticated computers.
Your own genetic map - a snip at ' 450000 Guardian
Get Your Red-Hot Genome CD Wired
BBC - Boston Herald - The Daily Texan - and 6 related » [Google Technology News]
Well, I guess Venter has to make a living. But there are several questions I have: What is the verification? I mean, how do I know that it is MY DNA on the CD? How much mis-sequencing is there? What is the error rate? I would guess that at $1000 a genome, there will not be a lot of error checking. This could have very important ramifications. WHat sorts of second opinions are there? What is the liability for the company if it says someone has the gene for Huntington's and they really don't? People believe that we have really sequenced the entire human genome We haven't. We've only sequenced the pparts that can be cloned and sequenced. We currently feel that the rest is not important but I would not bet that is a certainty. There are still many things to learn. 10:47:24 PM
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Friday, October 4, 2002
The Media Got it Wrong. The Salt Lake Tribune this morning has a story on a "blond extinction hoax." Seems that the media (including the major outlets like ABC and CNN) got taken by a hoax that claimed a World Health Organization (WHO) study found that true blonds were becoming extinct. Turns out not one journalist bothered to call WHO. If you've never dealt much with the media, this may come as a shock to you. It doesn't surprise me. Since every story that's been written about me (good and bad) has contained major factual errors, I have to believe that most stories contain factual errors. Journalists are frequently sloppy with the facts, not bothering to investigate or verify them---just reporting on other reports. They're like everyone else---in a hurry to make a deadline, overloaded with information, and trying to impress their boss. That's a recipe for errors. [Windley's Enterprise Computing Weblog]
While some in the media are making fun of Streisand for quoting from a hoaxed speech by Caesar, they should be examining themselves. I commented on this topic a few days ago, from a BBC article. It was a bad report on a bad topic. I could look at it and determine that it was bad science. I just figured that the bad science was done by the group at WHO. But no, the media itself was taken in by a hoax. No fact checking at all anymore. Now I do not really have any expectations that a pop singer at a partisan fund raising function would check her facts. Politics often deal with such nonfactual 'facts'. But the public DOES expect that the media WILL check their facts. What I love is the apparent expectation by the media that IF they do produce bogus articles, it is up to the particular group to correct them. Some compained that WHO did not contact them to provide a correction. WHO's response: Honestly, we have better things to spend our time on. I agree with Windley here. Most times when they write about something I know about, there are huge factual mistakes. 11:00:50 AM
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Researchers successfully deliver drugs to the primate brainstem. Current drug treatments of brainstem tumors are largely unsuccessful, because the drugs often fail to bypass the blood vessel lining protecting the brainstem. Now, an NIH study shows that researchers can effectively deliver drugs to the primate brainstem and monitor how the drugs spread inside the brain. The study provides hope for improving treatment of brainstem tumors and other brain diseases. NIH/National Institute of Neurological Disorders and Stroke [EurekAlert - Biology]
This could have some really important uses. Getting drugs across the blood-brain barrier has been problematic. If this procedure pans out with humans, and there are no long term side effects, it would be quite a boon to medicine. 10:52:08 AM
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Scientists at Scripps Research develop new technology to map spread of malarial drug resistance. Scientists at The Scripps Research Institute (TSRI), Harvard University and the Genomics Institute of the Novartis Research Foundation have found a way to use a relatively new but readily available technology to quickly detect markers in the DNA of the most deadly type of malaria pathogen. NIH/National Institutes of Health, Burroughs Wellcome Fund, Ellison Medical Foundation, Program in Career Development, Research and Training in Global Infectious Diseases; et.al [EurekAlert - Biology]
Parasite, mosquito genomes complete malaria picture. Genome sequences of Plasmodium falciparum, the most lethal malaria-causing parasite, and Anopheles gambiae, a mosquito that transmits the parasite to humans, are now complete, two international research teams announced today. The simultaneous publication in Science of the Anopheles genome and in Nature of the Plasmodium genome was marked by press conferences held in Washington, DC, and London. National Institute of Allergy and Infectious Diseases [EurekAlert - Biology]
Sequenced malaria genome exposes novel drug targets. The genectic code of the malaria parasite has been cracked and is already revealing novel drug targets that could lead to effective treatment of the disease. Australian Research Council, National Health and Medical Research Council, Howard Hughes Medical Institute [EurekAlert - Biology]
New discovery in malaria. Scientists at NYU School of Medicine have for the first time identified genes in mosquitoes that reduce the natural transmission of the most lethal malaria parasite. The findings, reported in the October 4 issue of Science, could potentially open new avenues to preventing malaria, one of the world's greatest scourges. National Institutes of Health [EurekAlert - Biology]
It's Malaria Week at Nature and Science. We have the sequencing of both the mosquito and the malarial parasite, Plasmodium. The mosquito may very well be responsible for more human deaths (2.7 million deaths a year) than any other organism (at least multi-cellular ones). Having this information will be extremely helpful in attacking the problem, if we can generate enough funds to do so. 10:48:39 AM
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Amorous ostriches scoop Ig Nobel prize. New Scientist - An investigation into why amorous UK ostriches were failing to breed is just one of the winners of the 2002 Ig Nobel Prizes. The annual awards for achievements that "cannot or should not be reproduced" were presented at Harvard University on 3 October.
Science of belly lint, ostrich love honored CNN
Science's Dubious Distinctions Noted CBS News
BBC - Boston Herald - ABC Regional Online - Minneapolis Star Tribune - and 52 related » [Google Technology News]
I love the Ig Nobels. It demonstrates the playfulness that is found in the 'best' science. And the one on scrotal assymetry was published in Nature!! Looks good on the cv. Most scientists are glad to get recognition of their work, even if it is with a jaundiced eye.Check out the winners in Economics, as well as the citation: The executives, corporate directors, and auditors of Enron, Lernaut & Hausbie [Belgium], Adelphia, Bank of Commerce and Credit International [Pakistan], Cendant, CMS Energy, Duke Energy, Dynegy, Gazprom [Russia], Global Crossing, HIH Insurance [Australia], Informix, Kmart, Maxwell Communications [UK], McKessonHBOC, Merrill Lynch, Merck, Peregrine Systems, Qwest Communications, Reliant Resources, Rent-Way, Rite Aid, Sunbeam, Tyco, Waste Management, WorldCom, Xerox, and Arthur Andersen, for adapting the mathematical concept of imaginary numbers for use in the business world. [NOTE: all companies are US-based unless otherwise noted.]
Hint:in reality, imaginary numbers are those bases on the square root of -1. However, in thie context of the Ig Nobels we know exactly what they mean. Get more info at the Annals of Improbable Research. 10:19:08 AM
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Okay, a new day and hopefully better luck. We had some phone work done yesterday and it made it difficult to stay connected (Yes, I am still on dial-up). The new house we moved into last year is too far from a substation for DSL and does not have digital cable (But the neighborhood makes up for that. And I can get digital satellite). I'll go see what is out, in particular, some new articles in Nature and Science. 9:25:07 AM
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Monday, September 30, 2002
Is Bioinformatics--and Open-Source Software--in ABI[base ']s Future? [GenomeWeb]
ABI is on the right track. It could become the world leader if it can make software that scientists really understand. The problem is not just making it easier for scientists to find information; they must be able to disperse it also. No one person can know what fact could have an explosive effect on another's thought patterns. We publish papers with this hope (Well, it does help our own careers a little ;-). Putting one of my ideas into the hands of someone who can take it even further is really appealing. Technology not only makes this more likely, but it also allows us the ability to verify how the information passed, making it progressively easier to allow more information to flow. I may just have to give Lee a call. 11:13:28 PM
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Molecular machine could develop drugs for bioweapons victims [EurekAlert!]
I am getting to where I trust no press release if it mentions bioweapons or bioterrorism. It has nothing to do with why this work was originated and is simply a post hoc attempt to hype the work. NOw, a complete structure of the ribosome is nince, although there have been pretty good glimpses published before. It is an amazing effort. It would have been nice to see if there are any novel developments in how it works, etc. I guess I'll have to figure out a way to read the article. 11:07:05 PM
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Scientists discover genetic defect responsible for microcephaly [EurekAlert!]
A very nice study. Using a small, non-outbred group like the Amish, they have found a single gene defect that has a devastaing effect on the development of the fetal brain. And, it appears that all the families affected descend from a single Amish couple. The lack of gene flow in the Amish, as in other small, isolated populations, makes finding these mutations easier, simply becuase they are more likely to be seen. What is nice about this study is that everything originated from doctors that wanted to help families deal with this mutation. If they had not leapt in to help, there might be a large number of Amish families dealing with tragedy. Nice work. 11:02:37 PM
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"Can Global Warming Trigger a "Little Ice Age"?" [Daypop Top 40]
I've mentioned this before but it is still quite interesting. Global warming has been envisioned as creating some kind of hell on Earth. But the Earth is a chaotic system and very small changes can have huge effects. It would be ironic if global warming resulted in colder temperatures in the temperate regions. What is amazing is the information indicating that these sorts of changes can happen very quickly (less than 10 years) and last 1000 years. Because one of the main arguments from environmentalists is that plants and animals can not possibly adapt rapidly enough to the global warming we are generating. Yet, this is taking a century. Little Ice Ages take 10 years and have to be just as devastating to some forms of life. How have they adapted in the past to these sorts of rapid climate changes, ones that we DID not cause? That would be a fun research project. 10:41:27 PM
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VCs Flee Genomics Shops in Q3; Bioinformatics Providers Hardest Hit [GenomeWeb]
Not many pure plays in bioinformatics or proteomics anymore. Everyone is a Drug Discovery Company now. Of course, veryone prety much has access to the same information regarding human proteins, right. So how do you create a competitive advantage? If 500 are looking at the same thing, then blind luck might be better than actively searching. My bias: use modern tools to help create knowledge from the information. This will require not only changes in the way software is used, but active training of the scientists involved. The companies that succeed in this will reach decision points faster, increasing the probability that 'luck' will happen. 10:19:23 PM
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Sunday, September 29, 2002
Biotech has been good to Washington; now state needs to be good to it. Seattle Times Sep 29 2002 11:02AM ET [Moreover - moreover...]
This state is making it more and more difficult to make a go of it in biotech. You need a high powered research community but moneys to the UW are dwindling. And it is going to be as difficult to get into the UW as some of the most elite private universities, since the UW can not expand to meet the needs and hot build more universities. Without a continuing input of new research, biotech here will stagnate. Biotech in Seattle happened because scientists at the UW and the Hutch did not want to leave the area. They were not lured here for the biotech, first. If those scientists go elsewhere, so will the industry. People and businesses in Washington are some of the most highly taxed. The state constitution says that education is the pre-emeinant purpose of the state government, yet it refuses to fully fund education. Penny wise and pound foolish, we shall find ourselves in the near future with no Boeing (because the traffic is so bad), no Microsoft (cheaper to program in INdia) and no biotech (lots of states provide similar research opportunities with less taxes and lower living expenses. AIr conditioning can overcome a multitude of sins). 11:48:47 PM
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