Re:My reply to Nytmes.org
on
Who Owns Science?
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· Score: 2, Informative
The author makes some very good points, but I have one quibble: "The doctoral students cannot use the text they have written as part of their theses" is not a true statement. My PhD thesis contains three chapters that were previously published, and that's typical for many others I know (in biology, anyway -- is there some other rule in other fields?).
Yes, you are right that samples that are believed to be from this influenza outbreak are already being studied. Samples have been isolated from fixed and frozen samples. Here is one example from Science 1997 Mar 21;275(5307):1793-6:
Initial genetic characterization of the 1918 "Spanish" influenza virus.
The "Spanish" influenza pandemic killed at least 20 million people in 1918-1919, making it the worst infectious pandemic in history. Understanding the origins of the 1918 virus and the basis for its exceptional virulence may aid in the prediction of future influenza pandemics. RNA from a victim of the 1918 pandemic was isolated from a formalin-fixed, paraffin-embedded, lung tissue sample. Nine fragments of viral RNA were sequenced from the coding regions of hemagglutinin, neuraminidase, nucleoprotein, matrix protein 1, and matrix protein 2. The sequences are consistent with a novel H1N1 influenza A virus that belongs to the subgroup of strains that infect humans and swine, not the avian subgroup.
A recombinant strain has also been created (under level 3 biosafety conditions) bearing the 1918 HA, NA, or M segments, and interestingly these strains were blocked in mice by currently available antiviral agents (reference =Proc Natl Acad Sci U S A 2002 Oct 15;99(21):13849-54).
Someone mod up the Anonymous Coward-- s/he is making a good point.
Lott's book has been bitterly attacked by the "antiviolence" groups since its publication (a web search will easily turn up examples) but he has rebutted these criticisms point by point. I'm not sure there are any truly objective observers on the gun control issue, but I consider Lott's research to be some of the closest I've seen.
On the contrary, D. radiodurans has been tested in space. Here is one of several different experiments mentioned on PubMed:
FEMS Microbiol Lett 2002 Sep 24;215(1):163-8
"Microbial survival of space vacuum and extreme ultraviolet irradiation: strain isolation and analysis during a rocket flight."
R Saffary et al.
"We have recovered new isolates from hot springs, in Yellowstone National Park and the Kamchatka Peninsula, after gamma-irradiation and exposure to high vacuum (10(-6) Pa) of the water and sediment samples. The resistance to desiccation and ionizing radiation of one of the isolates, Bacillus sp. strain PS3D, was compared to that of the mesophilic bacterium, Deinococcus radiodurans, a species well known for its extraordinary resistance to desiccation and high doses of ionizing radiation. Survival of these two microorganisms was determined in real and simulated space conditions, including exposure to extreme UV radiation (10-100 nm) during a rocket flight. We found that up to 15 days of desiccation alone had little effect on the viability of either bacterium. In contrast, exposure to space vacuum ( approximately 10(-6) Pa) decreased cell survival by two and four orders of magnitude for Bacillus sp. strain PS3D and D. radiodurans, respectively. Simultaneous exposure to space vacuum and extreme UV radiation further decreased the survival of both organisms, compared to unirradiated controls. This is the first report on the isolated effect of extreme UV at 30 nm on cell survival. Extreme UV can only be transmitted through high vacuum, therefore its penetration into the cells may only be superficial, suggesting that in contrast to near UV, membrane proteins rather than DNA were damaged by the radiation."
If you are interested in bacteria that can live in extremely hostile environments, D. radiodurans is a great example to read up on... it is being bioengineered for bioremediation of radioactive waste.
An aside for the "radiation causes mutations and hey then there's evolution" crowd, D. radiodurans is believed to have developed its extraordinary radiation-resistance as a side of effect of desiccation resistance. There is no evidence that there is any natural environment that would have led to direct selection of such extreme resistance to radiation. (Although humans have now such created such environments at nuclear reactors or in food irradiation facilities.)
One thing that is not being made clear by the newspapers is just how crippled M. genitalium (the bug whose genetic material they plan to use) is to begin with. The "wild type" strain that causes infections in nature was not even able to be grown in petri dishes for many years because its genome is so streamlined, that it has to rely on host cells to get some very basic building blocks of life. One has to give M.g. media (food) much much more complex than the media that E.coli needs just to get it to grow in the lab at all. It's barely more alive than a virus. Biologically, it would be incredibly surprising if this engineered bug could grow outside of a very pampered environment, and it would have to pick up a significant fraction of E.coli's ~4000 genes to even have a decent metabolism, let alone any "dangerous" qualities.
There are NOT eukaryotic bacteria. That is a contradiction in terms.
Re:Awesome if it pans out.
on
Helpful Handicap
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· Score: 3, Informative
>If this works, we should definitely re-introduce it to the games
That would be cool, but we'd have to re-introduce the standing long jump; apparently the modern Olympic event is a long jump with a running start, so it's not clear that the halteres make any difference with that.
For the visually oriented, there's pictures of halteres in the commentary in Nature along with another brief article. The technical description and data to support this theory about how the halteres were beneficial is here, but I think this is only accessible to Nature subscribers.
I agree: dubious seems to be the correct attitude for now. The authors have a manuscript on line, linked from the Indians' UK collaborators at Cardiff Centre for Astrobiology but I can't find any indication any of this has been published in a peer reviewed journal.
The evidence in the mss is:
1) some electron micrographs showing some clumpy things (putatively cells) and
2) the fact that some clumpy things in their samples can be dyed with flourscent dyes that stain the membranes of viable Earth bacteria.
While I might accept this as weak evidence there are some unknown organisms at high altitude, it is far from proving they are extraterrestial! Besides, why do they assume that an extraterrestial organism would have the same type of cell membrane as an Earth bacterial cell?
No, you are way off base. They are not trying to make pigs that genetically match individual humans.
As a biology PhD, my understanding is that they are trying to engineer pigs whose organs will be less likely to be attacked as "alien" (leading to organ rejection) by human immune systems *in general*. This involves making multiple genetic changes in the pigs' DNA to make their genetic markers more compatible with humans'. This article is about a new method for making the genetic changes that may be quicker and less expensive... the technical details are in PNAS.
It's true that non-paternity (finding out the supposed father isn't really the father) is a well-known side effect of genetic testing. But, according to my Medical Genetics book the estimated rate is 5-10%.
I know a guy who had his flap disturbed a couple months after LASIK, when playiing football. Probably not the best decision on his part, but now he needs a cornea transplant. Yikes.
Interesting to read your message-- I'm at 20/60 and 20/400 uncorrected and I've had 3 optometrists tell me I was the most unbalanced vision they'd ever treated. It is hard to explain not having depth perception to people who take it for granted. (My eyes have always been unbalanced so they don't really work together-- yes, I am the person with no dominant eye.) Don't get why you can't wear glasses though?
Since we're sharing anecdotes.... I have been considering having this surgery for a couple years now. I have about 8 friends who had the surgery and are happy; one who has severely dry eyes, haloing, and trouble seeing well enough to drive at night; and one who disturbed the flap before it healed and is effectively blind in that eye. So far, I think I'm going to keep waiting.
A number of things I have read suggest that the "success rates" quoted by those selling LASIK ignore problems including dry eyes, poorer night vision or haloing in some patients. Those patients will still be counted as "successful" if they had improvement by other measurements (20/60 to 20/30 or whatever). For some people this is worth the risk, but I think it's very important to go beyond the advertising hype, get the best information you can find and decide for yourself.
It is absolutely true that opticians only measure certain characteristics of vision. An example of this is a friend of mine, who had his vision dramatically improved from near-legal-blindness to 20/20, but he has noticed a large decrease in his ability to resolve contrast under some conditions. Doesn't sound too bad if you can just adjust your monitor, but try skiing down a snow-covered hill on an overcast day....
Speaking of ignorance, someone who states
"I just can't say enough about it," [Brad Hill said] "I get at least 30 albums a month or so at 10 bucks a month. That's 10 cents each." does not really impress me with his keen judgement. I will be careful not to run out and read any of his books or articles.
This is a really thought-provoking idea. I don't think it could be implemented, but thanks for the idea.
I do wonder if any one has checked out the prevelance of antibiotic resistant bacteria in a situation like an isolated, war-torn country that has not had a drug supply available (or outside visitors) for some time. In theory the bacteria would have lost unneccessary resistance genes, but it only takes one cell with the resistance gene to restart the cycle....
>you could then know what to expect not only in your life
Several points here--
1) I'm not convinced this would be great!
2) that's not how DNA works. For argument, let's assume that it becomes cheap to sequence all your DNA. The information you would have is your genotype. However, this only -suggests- what your physical and personality characteristics (phenotypes) will be, and only gives a probability that you may get some disease if exposed to correct environmental trigger/health conditions, etc.
3) For most diseases, which are complex and involve many genes, there's a long way to go between identifying some disease genes, and knowing what to change to "fix" them. (The cases like SCID or cystic fibrosis where something could theoretically be fixed by changing a single gene are very rare). This may happen, but I'm not sure if it will be in "our time".
Well, actually,if you read the details, the worms do survive the spin. They don't have any bones to break and their structure is simple enough that it adapts to being squished.
Slashdot Mirror
The author makes some very good points, but I have one quibble: "The doctoral students cannot use the text they have written as part of their theses" is not a true statement. My PhD thesis contains three chapters that were previously published, and that's typical for many others I know (in biology, anyway -- is there some other rule in other fields?).
A recombinant strain has also been created (under level 3 biosafety conditions) bearing the 1918 HA, NA, or M segments, and interestingly these strains were blocked in mice by currently available antiviral agents (reference =Proc Natl Acad Sci U S A 2002 Oct 15;99(21):13849-54).
Lott's book has been bitterly attacked by the "antiviolence" groups since its publication (a web search will easily turn up examples) but he has rebutted these criticisms point by point. I'm not sure there are any truly objective observers on the gun control issue, but I consider Lott's research to be some of the closest I've seen.
Here's a fairly non-technical article if you want to learn more about this bug: ScienceNews
FEMS Microbiol Lett 2002 Sep 24;215(1):163-8 "Microbial survival of space vacuum and extreme ultraviolet irradiation: strain isolation and analysis during a rocket flight." R Saffary et al.
"We have recovered new isolates from hot springs, in Yellowstone National Park and the Kamchatka Peninsula, after gamma-irradiation and exposure to high vacuum (10(-6) Pa) of the water and sediment samples. The resistance to desiccation and ionizing radiation of one of the isolates, Bacillus sp. strain PS3D, was compared to that of the mesophilic bacterium, Deinococcus radiodurans, a species well known for its extraordinary resistance to desiccation and high doses of ionizing radiation. Survival of these two microorganisms was determined in real and simulated space conditions, including exposure to extreme UV radiation (10-100 nm) during a rocket flight. We found that up to 15 days of desiccation alone had little effect on the viability of either bacterium. In contrast, exposure to space vacuum ( approximately 10(-6) Pa) decreased cell survival by two and four orders of magnitude for Bacillus sp. strain PS3D and D. radiodurans, respectively. Simultaneous exposure to space vacuum and extreme UV radiation further decreased the survival of both organisms, compared to unirradiated controls. This is the first report on the isolated effect of extreme UV at 30 nm on cell survival. Extreme UV can only be transmitted through high vacuum, therefore its penetration into the cells may only be superficial, suggesting that in contrast to near UV, membrane proteins rather than DNA were damaged by the radiation."
If you are interested in bacteria that can live in extremely hostile environments, D. radiodurans is a great example to read up on... it is being bioengineered for bioremediation of radioactive waste.
An aside for the "radiation causes mutations and hey then there's evolution" crowd, D. radiodurans is believed to have developed its extraordinary radiation-resistance as a side of effect of desiccation resistance. There is no evidence that there is any natural environment that would have led to direct selection of such extreme resistance to radiation. (Although humans have now such created such environments at nuclear reactors or in food irradiation facilities.)
One thing that is not being made clear by the newspapers is just how crippled M. genitalium (the bug whose genetic material they plan to use) is to begin with. The "wild type" strain that causes infections in nature was not even able to be grown in petri dishes for many years because its genome is so streamlined, that it has to rely on host cells to get some very basic building blocks of life. One has to give M.g. media (food) much much more complex than the media that E.coli needs just to get it to grow in the lab at all. It's barely more alive than a virus. Biologically, it would be incredibly surprising if this engineered bug could grow outside of a very pampered environment, and it would have to pick up a significant fraction of E.coli's ~4000 genes to even have a decent metabolism, let alone any "dangerous" qualities.
>It seems an important ethical question whether it's morally right to create a human who might have major medical problems somewhere down the road
ANY human baby that is currently created is at risk for major medical problems (due to genetics OR environmental influences)....
There are NOT eukaryotic bacteria. That is a contradiction in terms.
That would be cool, but we'd have to re-introduce the standing long jump; apparently the modern Olympic event is a long jump with a running start, so it's not clear that the halteres make any difference with that.
For the visually oriented, there's pictures of halteres in the commentary in Nature along with another brief article. The technical description and data to support this theory about how the halteres were beneficial is here, but I think this is only accessible to Nature subscribers.
1) some electron micrographs showing some clumpy things (putatively cells) and
2) the fact that some clumpy things in their samples can be dyed with flourscent dyes that stain the membranes of viable Earth bacteria.
While I might accept this as weak evidence there are some unknown organisms at high altitude, it is far from proving they are extraterrestial! Besides, why do they assume that an extraterrestial organism would have the same type of cell membrane as an Earth bacterial cell?
No, you are way off base. They are not trying to make pigs that genetically match individual humans. As a biology PhD, my understanding is that they are trying to engineer pigs whose organs will be less likely to be attacked as "alien" (leading to organ rejection) by human immune systems *in general*. This involves making multiple genetic changes in the pigs' DNA to make their genetic markers more compatible with humans'. This article is about a new method for making the genetic changes that may be quicker and less expensive... the technical details are in PNAS.
It's true that non-paternity (finding out the supposed father isn't really the father) is a well-known side effect of genetic testing. But, according to my Medical Genetics book the estimated rate is 5-10%.
Have you never heard of academic research? The NIH? University medical centers?
I know a guy who had his flap disturbed a couple months after LASIK, when playiing football. Probably not the best decision on his part, but now he needs a cornea transplant. Yikes.
Interesting to read your message-- I'm at 20/60 and 20/400 uncorrected and I've had 3 optometrists tell me I was the most unbalanced vision they'd ever treated. It is hard to explain not having depth perception to people who take it for granted. (My eyes have always been unbalanced so they don't really work together-- yes, I am the person with no dominant eye.) Don't get why you can't wear glasses though?
Since we're sharing anecdotes.... I have been considering having this surgery for a couple years now. I have about 8 friends who had the surgery and are happy; one who has severely dry eyes, haloing, and trouble seeing well enough to drive at night; and one who disturbed the flap before it healed and is effectively blind in that eye. So far, I think I'm going to keep waiting.
A number of things I have read suggest that the "success rates" quoted by those selling LASIK ignore problems including dry eyes, poorer night vision or haloing in some patients. Those patients will still be counted as "successful" if they had improvement by other measurements (20/60 to 20/30 or whatever). For some people this is worth the risk, but I think it's very important to go beyond the advertising hype, get the best information you can find and decide for yourself.
It is absolutely true that opticians only measure certain characteristics of vision. An example of this is a friend of mine, who had his vision dramatically improved from near-legal-blindness to 20/20, but he has noticed a large decrease in his ability to resolve contrast under some conditions. Doesn't sound too bad if you can just adjust your monitor, but try skiing down a snow-covered hill on an overcast day....
Uh, she, actually...
Speaking of ignorance, someone who states "I just can't say enough about it," [Brad Hill said] "I get at least 30 albums a month or so at 10 bucks a month. That's 10 cents each." does not really impress me with his keen judgement. I will be careful not to run out and read any of his books or articles.
I do wonder if any one has checked out the prevelance of antibiotic resistant bacteria in a situation like an isolated, war-torn country that has not had a drug supply available (or outside visitors) for some time. In theory the bacteria would have lost unneccessary resistance genes, but it only takes one cell with the resistance gene to restart the cycle....
Several points here-- 1) I'm not convinced this would be great!
2) that's not how DNA works. For argument, let's assume that it becomes cheap to sequence all your DNA. The information you would have is your genotype. However, this only -suggests- what your physical and personality characteristics (phenotypes) will be, and only gives a probability that you may get some disease if exposed to correct environmental trigger/health conditions, etc.
3) For most diseases, which are complex and involve many genes, there's a long way to go between identifying some disease genes, and knowing what to change to "fix" them. (The cases like SCID or cystic fibrosis where something could theoretically be fixed by changing a single gene are very rare). This may happen, but I'm not sure if it will be in "our time".
Well, actually,if you read the details, the worms do survive the spin. They don't have any bones to break and their structure is simple enough that it adapts to being squished.