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 Friday, January 10, 2003
Lynx expands genomics collaboration with Takara Bio. InPharm.com Jan 10 2003 11:47PM ET [Moreover - moreover...]
I believe that Lynx is a company that Sydney Brenner helped found that uses some very interesting technology (At least he is on the papers describing the technology as well as on the board). Stuff that I hope makes a big impact on the world. Sydney is one of the giants in biology. He is almost like Forrest Gump, in that he has been present at some of the great moments in molecular biology over the last 40 years, often as the instigator, only think of a Forrest Gump smarter than the brightest person you know. Syndey is smarter than him. Watch what Sydney is doing, because it will be important. 11:40:09 PM 
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Lawrence Lessig on Since1968.com - Interview with Lawrence Lessig on since1968.com. In it, he talks about software piracy, intellectual freedom, and Mickey Mouse. Short, but pretty interesting. I don't know enough about the visionaries myself. I need to find out more. [Matt Brown's Radio Weblog]
Keep an eye out for Larry Lessig whenever you read about copyright, fair use or other conflicts between the digital and the analog world. He is shaping much of the debate on these issues and the people he brings together may have a huge impact on society. He may very well be one of those people our children's children read about when they deal with this part of are history. He is one of the organizers behind the Creative Commons project that is mentioned a few items below. 11:30:21 PM
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Separated before birth: Molecular signals part fetal blood and lymphatic vessels [EurekAlert!]
A very nice paper. Almost everyone knows something about the blood system but not many really know about the lymphatic (except for mothers checking their child's lymph nodes). Now we are narrowing down some of the developmental pathways needed to create separate lymphatic and circulatory systems. It will be fascinating to see what cellular pathways are involved. But what is also apparent from this work is that a set of proteins have a very important part early in development AND also a very important but much different role later in an organism's life. This is something to be very aware of. What a protein does and the effect it has on an organism is time dependant. These proteins do several very different things, depending on how old the orgnism is. Simply examining the effects of the protein in vitro outside an organism will never reveal this. 11:18:03 PM
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A Novelist Who Walks the Walk. Science fiction writer Cory Doctorow, an outspoken advocate of the free publication and copying of digital works, is putting his money where his mouth is. He's giving away his first novel to anyone who wants it. By Paul Boutin. [Wired News]
A very nice experiment and an example of someone putting their beliefs into practice. I think the last comment by Peter Watts is telling. At some point there will be a digital book every bit as useful as a paperback. But I beleive that by that time, there will have been a change in most companies business models, allowing them to make money. In this case, there were more downloads that books published. WHat is the profit per book normally and how is it split up. In the future, the overhead for publishing should be less. The difficulty will be isolating the good books from the noise. Publishers kind of do this now, as do record companies or movie studios. The problem is that they are now too restrictive and are harming the flow. I would expect that there will still be a place for a filterer but their cut of the pie will be smaller. We shall see. People are very creative and I am sure that individuals will come up with creative solutions that corporations will never dream of. 11:10:50 PM
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Whole-body 18F-FDG PET significantly impacts patient management/radiation therapy [EurekAlert!]
Nice new technology that can impact treatment of cnacers. Bet it costs a whole lot. WHat I found very interesting about this is the boilerplate at the end: Copies of the article, accompanying commentary and images related to the study are available to media upon request to Kimberly A. Bennett (202-955-1253). Copies of the current and past issues of The Journal of Nuclear Medicine are available online at jnm.snmjournals.org. Print copies can be obtained at $15 per copy by contacting the SNM Service Center, Society of Nuclear Medicine, 1850 Samuel Morse Drive, Reston, VA 20190-5315; phone: 703-326-1186; fax: 703-708-9015; e-mail: servicecenter@snm.org. A yearly subscription to the journal is $170. A journal subscription is a member benefit of the Society of Nuclear Medicine.
Now it used to be that you would request reprints from the authors of a paper. They would send this to you for free. No one gets reprints anymore because of the internet. This journal says you can order hard copies for $15. But, it takes only a little time to go to the web site and find out that you can get a pdf of this article for only $8.00. Why don't they mention this? I guess it is old boilerplate because they are not makig any money on $15 an article in hard copy. The big change you see in professional journals, particularly ones done by highwire press, is the ability to access articles or entire sites on a temporary basis rather than having to buy an entire subscription. This makes the works much more accessible to a wider group than before.A very nice and novel approach using new technologies in ways unavailable before. 11:03:36 PM
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Wired Tires: RFID Chips in Michelins. The RFID technology allows vital tire identification information-such as tire size, type, serial number, date of manufacture and speed rating-to be stored on a chip the size of a match head. The chip is in the center of two wiggled filaments, which actually constitute the transponder's antenna.
The information on the RFID chip, which can be read by a receiver held or positioned up to 30 inches away from the tire, corresponds to the vehicle identification number. That makes the tire "uniquely identifiable with the vehicle," according to Gettys and his colleagues.
Had that technology existed three years ago, it could have put a lot of lawyers out of business in the Ford Motor Co./Bridgestone-Firestone tire controversy, in which defective Bridgestone tires were blamed for causing scores of deaths on rollover crashes of 1990s-model Ford Explorer sport-utility vehicles.
A large part of that controversy stemmed from arguments over which tires were subject to recall and which tires were okay. RFID technology could have pinpointed the exact batch of tires that had the problem, Michelin officials say.
In its initial form, Michelin's RFID technology will be of use only to technicians in vehicle service bays. But Michelin researchers said the RFID chip eventually could be given enough intelligence to communicate directly with vehicle owners and drivers-telling them if the tires are properly inflated, overheated, overloaded, or if tire tread is dangerously worn. The Goodyear Tire and Rubber Co. has a similar innovation that will be available on tires beginning in 2004, according to company spokesman Dave Russ. [Smart Mobs]
Of course, it does not seem like it would be too difficult to adapt this so someone could keep track of their car (or at least the tires). This might prevent some cars from being stolen but it also invites some awfully powerful 'Big Brother' images. 10:54:19 PM
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Lexmark draws first blood in lawsuit. Court orders SCC to stop making microchip used in printer toner cartridges [InfoWorld: Top News]
I will never buy a printer from a company that uses the DMCA to prevent anyone else from making an ink cartridge for the printer. Lexmark is not quite there yet but they might be at any time if they decided they could get away with it and not lose customers. Auto manufacturers are trying the same thing, using specialized microprocessors that only their dealers can access. If some garage mechanic figured out how to access this information, they could be charged with a crime because of the DMCA. I hope this law gets amended soon but there will be a lot of money thrown at the opposition by the Content Cartel. 10:31:03 PM
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Foot and mouth strategy strengthened [Nature Science Update]
This is potentially a huge development. Using cytokines as adjuvants for vaccines could save a lot of animals from being slaughtered. I just wonder what the added price will be but it is most likely not a whole lot greater than the value of animals that are slaughtered. Pretty spiffy. 10:25:41 PM
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Researchers discover novel function of gene often associated with cancer. Science Blog Jan 10 2003 5:00PM ET [Moreover - moreover...]
Bloom syndrome is one of a number of genetic diseases that appear to increase the incidence of cancer. Not too surprisingly, it is an enzyme that is involved in correcting damage done to the DNA of the chromosomes. Chromosome damage is often the root cause of many cancers usually because the expression of an important gene regulating cell growth eventually gets altered, resulting in a cascade that eventually produces cancerous tissue. Some of the major effects of this genetic disorder are on the immune system. The chromosomes in most cells are static, they do no undergo tremendous rearrangements. Some exceptions are the germ cells (i.e. sperm and eggs). In these cells, segments of DNA will be exchanged between pairs of chromosomes, a process called crossing-over.
Another important cell type is found in the immune system. Many of the cell types in this system must recognize foreign protein from invading organisms. They employ a variety of mechanisms to deal with this. One example are antibodies. Each cell that produces antibodies actually only produces one specific type. If the antibody reacts with a foreign protein, various cellular pathways are switched on, resulting in the proliferation of that specific cell. There will now be more of the reactive antibody which will bind more of the foreign protein, allowing it to be removed from the system.
Now, one of the great problems in immunology over the past 50 years has been how does the body generate reactive antibodies, especially ones to proteins it has never seen? There is a huge diversity in the number of antibodies produced in a human being. Is each one of them coded for by a single gene? This would necessitate billion of copies of similar genes. It turns out that the cells use a much simpler but much more powerful system. They use a set of modules and link them together by gene translocation.
Each antibody is made of two proteins, a heavy chain and a light chain (H and L). The important part of any antibody, the portion that actually binds antigen, is found in the variable region of each chain. This region is coded for on the chromosome by modules (VH, DH and JH from the heavy chain and VL and JL from the light chain). In each cell there are two chromosomes containing the regions coding for the variable regions for the H and L chains. These regions will contain 65 VH genes; 27 DH genes; 6 JH genes; 40 kappa VL genes; 5 kappa VL genes; 40 lambda VL genes; and 4 lambda JL genes.The cell uses a very specific system of gene translocation on the chromosome to rearrange these modules in a random way. The number of combinations can easily run into the billions. There are other systems to increase the diversity (i.e. splicing errors and random mutation).
So, the immune system creates the diversity it needs not by having billions of copies of entire genes but by using the combination of a series of modules to produce billions of cells, each with 1 particular copy. This allows a huge amount of diversity to be created with minimal resources but it opens important problem. The cells in the immune system have 2 things that make them very susceptible to cancer. They are rapidly growing - the proliferation needed to respond to an infection. One way the body prevents cancer is just to prevent the cell fro ever dividing. If it is impossible for it to divide it will not become cancerous. Obviously, this method of control is not fully implemented in immune cells.
The second item is the unique recombination processes that take place in an immune cell. Essentially, the cell damages its own DNA and fixes it. In order to recombine the various modules, the actual DNA strands must be broken and then reformed with DNA from another portion of the chromosome. Genetic rearrangements are often found in cancer cells. Immune cells do this naturally. So, all it takes is one in a billion to do it wrong, and you have a lymphoma. It is amazing that the system is so precise that lymphomas do not develop every time.
So, this paper adds some more evidence that genetic damage is an important part of cancer progression. It also identifies a new function for preventing DNA damage. Mammals have very strong immune systems. It may be because they also have very efficient mechanisms to repair DNA damage. I do not believe you can have one without the other. 6:06:30 PM
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