I'm not sure how well tolerated SWNTs will be in the body, since some studies have shown toxicity (see http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd= Search&db=PubMed&term=toxicity+nanotube+carbon&too l=QuerySuggestion). Also, while it's probably possible to derivatize the ends of nanotubes without greatly affecting their properties, derivatizing the sides (is this what you mean by "surface"?) would likely degrade their conductivity, as it would disrupt the flow of the pi electrons.
A good point, but my impression is that cancers generally become methotrexate resistant because of mutations in DHFR, not changes in folate transport. I could be wrong, though.
A very good reference. Liposomes (also a kind of nanoparticle) carrying cancer drugs have already been approved for use in the clinic. To my knowledge, none of the liposome are as specifically targeted as the dendrimers discussed in the article, but they still have some cancer-specificity due to their size (the blood vessels in tumors tend to be immature and leaky, thus allowing the liposomes to cross into cancerous tissue more easily than normal tissue). See: http://www.jnj.com/news/jnj_news/20050207_122707.h tm http://www.alza.com/alza/pr_ALZA__S_CAELYX__Approv ed_in_Canada_for_Treatment_of_Advanced_
Re:bad article summary from bad article title
on
Photoshop for DNA
·
· Score: 1
Not surprising, since it was a very bad article to start with. I found it impossible to figure out exactly what this company is doing based on the article. It was one of the worst examples of hi tech business journalism I've seen in a long time.
However, if you look at the interested of some of the founders (Jay Keasling http://www.lbl.gov/pbd/about/people/keasling.htm/, and Drew Endy http://web.mit.edu/endy/www/index.html/) my best guess is the the company is working on technologies to make large scale genetic alterations easier. Both of those guys have interests that require the manipulation of lots of genes at once, which is still rather difficult.
Re:$42.6 million grant from the Bill & Melinda
on
Photoshop for DNA
·
· Score: 1
The grant from Gates was *not* given to the company mentioned in the article. It was to a different company (Amyris) that happens to share a founder. Amyris will use the money to try to develop a cheaper source of a naturally occurring antimalarial compound (artemisinin).
I think you're looking for liboil: "Liboil is a library of simple functions that are optimized for various CPUs. These functions are generally loops implementing simple algorithms, such as converting an array of N integers to floating-point numbers or multiplying and summing an array of N numbers. Such functions are candidates for significant optimization using various techniques, especially by using extended instructions provided by modern CPUs (Altivec, MMX, SSE, etc.)." http://www.schleef.org/liboil/. The site seems to be down at the moment, but it's also listed on Freshmeat.
I believe the GStreamer people are looking into using liboil. The license is two-clause BSD.
Lyons may well be a shill for SCO. Enderle certainly is. However, as I understand it, Enderle did not call SCOX a great investment. From what I read on the Yahoo financial boards (sorry, no link) he said that the people who disagreed with him about SCO should buy a clue, which would be the best investment they could make.
Python, which also bears little resemblance to C#, also appears to run very nicely on.NET and pretty well on Mono. http://ironpython.com/. While they aren't all open source, there are also many other languages with compilers directed at the CLI: http://www.gotdotnet.com/team/lang/.
Finally, there seems to be no reason to suppose that Java is somehow more flexible than.NET because Java can be run on Mono via the IKVM project http://www.ikvm.net/.
I'm not advocating the use of Mono (and I'm certainly not advocating the use of Windows), but arguments against it should be technically correct.
First off, let me say that there is really no ambiguity about the structure of DNA anymore. Structures of DNA have been determined by x-ray crystallography, NMR, and to lower resolution, electron microscopic methods. The kinetics of the binding of DNA strands to one another has been studied in detail (and naturally the kinetics would be very sensitive to differences in the number of strands found in the structure).
Most of the x-ray structures which have been solved have used multiple heavy atom derivatives, which relieves the ambiguity of the Bessel function solutions that you referred to IIRC. Also, many of the structures which have been solved show DNA bound to the proteins which bind it in vivo. Since the structure is antiparallel double helical when bound to these proteins (and in general, the structures are consistent with large numbers of biochemical and genetic experiments on the proteins and DNA sequences in question), one has to assume that the Watson-Crick structure is generally correct.
I don't follow your thread-tying experiment, despite a degree in biochemistry. Eukaryotic DNA (which includes the DNA that Franklin, Wilkins, Watson & Crick worked on, I believe) is linear. Thus, you shouldn't be tying *any* of the threads together.
Bacterial DNA and some viral DNAs are circular, but the correct way to model them is to twist a black and white thread together, then tie them, black to black and white to white.
Anyway, you are raising the issue of topological transitions in DNA. This is a well understood and extensively studied issue. In fact, there is even a good mathematical formalism for it. For the math, see (sorry, no full text for these):
So, the need for de-linking enzymes has been appreciated for some time, and enzymes that catalyze that reaction have been identified and characterized. In fact, inhibitors of these enzymes (called topoisomerases) are used in treating cancer and bacterial infections. For more recent references and explanations, see:
Slashdot Mirror
Well, there's BRL-CAD (www.brlcad.org), although I imagine it's a very different beast than AutoCAD.
Actually, if you read the article, they put reconstructed viral chromosomes into cells and *did* make whole (presumably infectious) virus.
But the virus is under lock and key at the CDC and there are no plans to allow it to be shipped elsewhere.
I'm not sure how well tolerated SWNTs will be in the body, since some studies have shown toxicity (see http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd= Search&db=PubMed&term=toxicity+nanotube+carbon&too l=QuerySuggestion). Also, while it's probably possible to derivatize the ends of nanotubes without greatly affecting their properties, derivatizing the sides (is this what you mean by "surface"?) would likely degrade their conductivity, as it would disrupt the flow of the pi electrons.
A good point, but my impression is that cancers generally become methotrexate resistant because of mutations in DHFR, not changes in folate transport. I could be wrong, though.
MOD PARENT UP
h tm v ed_in_Canada_for_Treatment_of_Advanced_
A very good reference. Liposomes (also a kind of nanoparticle) carrying cancer drugs have already been approved for use in the clinic. To my knowledge, none of the liposome are as specifically targeted as the dendrimers discussed in the article, but they still have some cancer-specificity due to their size (the blood vessels in tumors tend to be immature and leaky, thus allowing the liposomes to cross into cancerous tissue more easily than normal tissue). See: http://www.jnj.com/news/jnj_news/20050207_122707.
http://www.alza.com/alza/pr_ALZA__S_CAELYX__Appro
However, if you look at the interested of some of the founders (Jay Keasling http://www.lbl.gov/pbd/about/people/keasling.htm/, and Drew Endy http://web.mit.edu/endy/www/index.html/) my best guess is the the company is working on technologies to make large scale genetic alterations easier. Both of those guys have interests that require the manipulation of lots of genes at once, which is still rather difficult.
The grant from Gates was *not* given to the company mentioned in the article. It was to a different company (Amyris) that happens to share a founder. Amyris will use the money to try to develop a cheaper source of a naturally occurring antimalarial compound (artemisinin).
One problem: diamond, being carbon, will presumably burn in an oxygen atmosphere if the temperature is right.
I believe the GStreamer people are looking into using liboil. The license is two-clause BSD.
Lyons may well be a shill for SCO. Enderle certainly is. However, as I understand it, Enderle did not call SCOX a great investment. From what I read on the Yahoo financial boards (sorry, no link) he said that the people who disagreed with him about SCO should buy a clue, which would be the best investment they could make.
Kluge
Python, which also bears little resemblance to C#, also appears to run very nicely on .NET and pretty well on Mono. http://ironpython.com/. While they aren't all open source, there are also many other languages with compilers directed at the CLI: http://www.gotdotnet.com/team/lang/.
.NET because Java can be run on Mono via the IKVM project http://www.ikvm.net/.
Finally, there seems to be no reason to suppose that Java is somehow more flexible than
I'm not advocating the use of Mono (and I'm certainly not advocating the use of Windows), but arguments against it should be technically correct.
Kluge
First off, let me say that there is really no ambiguity about the structure of DNA anymore. Structures of DNA have been determined by x-ray crystallography, NMR, and to lower resolution, electron microscopic methods. The kinetics of the binding of DNA strands to one another has been studied in detail (and naturally the kinetics would be very sensitive to differences in the number of strands found in the structure).
9
7
t ml o po.html
Most of the x-ray structures which have been solved have used multiple heavy atom derivatives, which relieves the ambiguity of the Bessel function solutions that you referred to IIRC. Also, many of the structures which have been solved show DNA bound to the proteins which bind it in vivo. Since the structure is antiparallel double helical when bound to these proteins (and in general, the structures are consistent with large numbers of biochemical and genetic experiments on the proteins and DNA sequences in question), one has to assume that the Watson-Crick structure is generally correct.
I don't follow your thread-tying experiment, despite a degree in biochemistry. Eukaryotic DNA (which includes the DNA that Franklin, Wilkins, Watson & Crick worked on, I believe) is linear. Thus, you shouldn't be tying *any* of the threads together.
Bacterial DNA and some viral DNAs are circular, but the correct way to model them is to twist a black and white thread together, then tie them, black to black and white to white.
Anyway, you are raising the issue of topological transitions in DNA. This is a well understood and extensively studied issue. In fact, there is even a good mathematical formalism for it. For the math, see (sorry, no full text for these):
FB Fuller, The Writhing Number of a Space Curve, PNAS 68(4) 815-819, 1971
http://www.pnas.org/cgi/content/abstract/68/4/815
FHC Crick, Linking Numbers and Nucleosomes, PNAS 73(8) 2639-2643, 1976
http://www.pnas.org/cgi/content/abstract/73/8/263
FB Fuller, Decomposition of the Linking Number of a Closed Ribbon: A Problem from Molecular Biology, PNAS 75(8) 3557-3561, 1978
http://www.pnas.org/cgi/content/abstract/75/8/355
So, the need for de-linking enzymes has been appreciated for some time, and enzymes that catalyze that reaction have been identified and characterized. In fact, inhibitors of these enzymes (called topoisomerases) are used in treating cancer and bacterial infections. For more recent references and explanations, see:
http://www.maich.gr/natural/staff/sotirios/topo.h
http://cmgm.stanford.edu/biochem201/Handouts/DNAt
http://crab.nyu.edu/~alex/mypapers/MolBiolRev.pdf