This is the first time Level 3 pathogens have been imaged in this way.
The Slashdot story isn't "we've determined the structure of a virus" - it's "we've got a new way of taking its picture."
If you'd like to interpret "we've got a new way of taking its picture" to mean "we're taking its picture in a new lab with slightly different equipment from all the other facilities around the world where X-ray diffraction studies of virus are done" then I would agree with you.
They have an automated BSL3-level end-station on a beam at Diamond, so that viral crystals of pathogens can be studied. Apart from it being new at Diamond, there is nothing "first time" about this arrangement.
The rules are changing - for the early structures I'm sure care was taken, but the current strict containment rules didn't exist. I can't imagine rocking up to the beamline with poliovirus in your cryostat would be regarded as appropriate behaviour any more... I know that in the past I have been prevented taking crystals of human rhinovirus to some facilities even though as a pathogen it's hardly BSL 3!
The only thing that the OP noted that was of interest was the Diamond now has an on-site BSL3 facility so that you can handle such pathogens within the current regulations.
What they're doing that is genuinely novel, AFAIK, is crystallizing actual infectious virus in a biosafety level 3 facility. Usually crystallographers work with just the capsid or some other subset of viral proteins, which requires fewer (if any) special precautions.
No, we don't. Intact viral particles are the norm.
The native virus particles are typically studied by EM, which typically doesn't yield as high resolution as crystallography, but has the advantage of requiring much more portable and less expensive equipment than crystallography.
While there are lots of EM studies of viral particles, X-ray studies are much more common - 33 full EM models versus 317 diffraction structures. The page I linked in the first response to this article shows just a few of the picornavirus structures that have been determined by X-ray diffraction studies over the past several decades. There are other virus structures out there as well, with an excellent website for anyone interested being Viper.
The page is the summary, at the public repository for all biomolecular structures, of the viral capsid structures (determined by X-ray diffraction, just as in the OP linked story) for picornaviruses including polio and foot-and-mouth as well as less pathogenic virus such as rhinovrius. EV71 is just another picornavirus. If you'd taken the time to actually read anything on the page I linked you'd have noticed hyperlinks to the detailed structures for each virus, such as the PDB entry 2PLV for poliovirus whose structure was determined in 1989... http://www.rcsb.org/pdb/explore/explore.do?structureId=2plv
There are *lots* of HIV vaccines in development, many reaching phase I and others going further. There's even one recent phase III showing some evidence of a preventative effect.
Reuters is your reference source for scientific news? Hmmmm...
Anyway, there is an undoubted recent increase in pertussis cases amongst immunized children due to:
1) Shorter protection time than expected indicating boosters are required
In spite of such evidence, evolution believing geologists build models based on today's observed rates of change and expect these to produce reliable results reaching back millions or billions of years.
Allow me to interrupt you there...
The geological observations that lead to the model of a multi-billion year old earth were made by creationist geologists. Many before the theory of evolution had been proposed.
This is one of the minor errors in your contribution. The accuracy and 'linearity' of radiometric dating has been demonstrated (both theoretically and experimentally) and confirmed beyond any shadow of reasonable doubt - your beliefs notwithstanding. Please learn something about the history of geology, evolution and the philosophy of science before commenting on them again.
Of course, it's hard to be anything but a creationist when that's what you're taught and before someone comes up with a rational alternative.
And in any case, none of whom were scientists. Natural philosophers perhaps, but it's not the same thing; the 'scientific method' came about, in part, due to their work. Note that the word 'scientist' wasn't even coined until the 19th Century and wasn't in common use until the 20th Century.
You're confusing 14C radiometric dating with 13C/12C isotopic ratio dating. There is no decay rate issue for 13C/12C dating - well, except maybe for theoretical proton decay!
I think you might be thinking of nylon, not citrate.
Citrate has been around in biological systems for a long, long, long, long time.
See: http://en.wikipedia.org/wiki/Citric_Acid_Cycle
What is particularly unfortunate is that many drugs (including tamiflu and the superior inhaled drug relenza) were invented by relatively small biotechs. (OK, Gilead isn't small any more, but Biota is *tiny*). Small biotechs are absolutely reliant on the fees and royalties they generate through licensing their inventions to Big Pharma, who have the money to get them through the FDA approval process and marketed.
Break a patent for Roche or GSK, they'll be annoyed but hardly notice the change in cash-flow. The biotech, however, will lose its sole cash-flow life-line. Biota are collaborating with Japanese pharma Sankyo to produce a second-generation antiviral for influenza that looks like being needed once-weekly for both prophylaxis and treatment. Be a real pity to destroy promising biotech-level research like that by cutting profits at the Big Pharma end of town.
Disclaimer: Yes I work for a biotech - own shares in them too.
If that was all they'd done I find it difficult to see how this differs from doing a multiple sequence alignment for a family of proteins, then making a gene for the consensus sequence.
Checking the paper (and related News and Views article) in Nature itself (http://www.nature.com/nature/journal/v437/n7058/i ndex.html ) (subscription required) indicates they've done more than that. By including the effects of coevolution - where one position in the protein mutates in concert with another to maintain optimal contacts - they generate a substantially better algorithm for manufacturing particular folds. (ie: 25% success in achieving folding versus 0% for conservation alone. 60% presence of wild-type function in the 'designed' proteins.)
Interesting, but I'm suprised it made it into Nature. (OK then, jealous...)
There was an important series of debates about the scientific basis for evolution versus religious arguments to the contrary. They happened back in the 1800s. Science won.
I'm a biochemist - I guess you would call me an 'evolutionist' though that's like calling a programmer an 'electricalist' because computers are based on the observed fact of electricity.
I also regard myself as 'informed'.
And I'm fully aware that there are multiple observed speciation events. Not one or two, lots. Dozens. Go and read the scientific literature on the subject before you comment next time.
You're welcome to state your opinion, but only if it's informed. Until that point, please label yourself as one of those uninformed individuals and shut up.
It's a bit different for the doctors - particularly the interns. The interns have set amounts of time they *have* to spend doing various different streams in the hospital. There are also a certain number of graveyard/weekend shifts each, certain holiday allowances, required separations between weekend shifts etc. But I agree, quantifying *all* the variables is going to be a bitch.
Still, if the system can spit out a base schedule that would save a lot of time. They already have a system where 'personal requests' (religious issues, personal likes/dislikes) are up to the individuals to sort out through swaps and if you can't arrange a swap with someone, tough.
Slashdot Mirror
This is the first time Level 3 pathogens have been imaged in this way.
The Slashdot story isn't "we've determined the structure of a virus" - it's "we've got a new way of taking its picture."
If you'd like to interpret "we've got a new way of taking its picture" to mean "we're taking its picture in a new lab with slightly different equipment from all the other facilities around the world where X-ray diffraction studies of virus are done" then I would agree with you.
They have an automated BSL3-level end-station on a beam at Diamond, so that viral crystals of pathogens can be studied. Apart from it being new at Diamond, there is nothing "first time" about this arrangement.
The rules are changing - for the early structures I'm sure care was taken, but the current strict containment rules didn't exist. I can't imagine rocking up to the beamline with poliovirus in your cryostat would be regarded as appropriate behaviour any more... I know that in the past I have been prevented taking crystals of human rhinovirus to some facilities even though as a pathogen it's hardly BSL 3!
The only thing that the OP noted that was of interest was the Diamond now has an on-site BSL3 facility so that you can handle such pathogens within the current regulations.
The press release is horribly written.
On this we agree...
What they're doing that is genuinely novel, AFAIK, is crystallizing actual infectious virus in a biosafety level 3 facility. Usually crystallographers work with just the capsid or some other subset of viral proteins, which requires fewer (if any) special precautions.
No, we don't. Intact viral particles are the norm.
The native virus particles are typically studied by EM, which typically doesn't yield as high resolution as crystallography, but has the advantage of requiring much more portable and less expensive equipment than crystallography.
While there are lots of EM studies of viral particles, X-ray studies are much more common - 33 full EM models versus 317 diffraction structures. The page I linked in the first response to this article shows just a few of the picornavirus structures that have been determined by X-ray diffraction studies over the past several decades. There are other virus structures out there as well, with an excellent website for anyone interested being Viper.
The page is the summary, at the public repository for all biomolecular structures, of the viral capsid structures (determined by X-ray diffraction, just as in the OP linked story) for picornaviruses including polio and foot-and-mouth as well as less pathogenic virus such as rhinovrius. EV71 is just another picornavirus. If you'd taken the time to actually read anything on the page I linked you'd have noticed hyperlinks to the detailed structures for each virus, such as the PDB entry 2PLV for poliovirus whose structure was determined in 1989... http://www.rcsb.org/pdb/explore/explore.do?structureId=2plv
http://www.rcsb.org/pdb/101/motm.do?momID=20
There are *lots* of HIV vaccines in development, many reaching phase I and others going further. There's even one recent phase III showing some evidence of a preventative effect.
For a review check: http://www.ncbi.nlm.nih.gov/pubmed/22710904
http://alexbellos.com/wp-content/uploads/2010/04/maths.pdf
Log scale = intuitive (ratios - there's twice as many of those as these)
Numberline != intuitive (counting, ordering etc.)
1) Shorter protection time than expected indicating boosters are required
(See: http://www.ncbi.nlm.nih.gov/pubmed/22423127 for example)
and
2) Emergent bacterial strains with modified surface antigens being selected due to evolutionary pressure (gasp!) from the acellular vaccine
(See: http://www.ncbi.nlm.nih.gov/pubmed/22416243 for example)
If you want to understand the science, go to the scientific literature. Not 'naturalnews.com'...
Oops - just realise I wasn't logged in when I posted this. It was Me! It was Me! Does that stop me being an anonymous coward?
Reading the article it seems they're actually trying to patent a preferred method of pig-fucking... Not sure if that's better or worse.
In spite of such evidence, evolution believing geologists build models based on today's observed rates of change and expect these to produce reliable results reaching back millions or billions of years.
Allow me to interrupt you there...
The geological observations that lead to the model of a multi-billion year old earth were made by creationist geologists. Many before the theory of evolution had been proposed.
This is one of the minor errors in your contribution. The accuracy and 'linearity' of radiometric dating has been demonstrated (both theoretically and experimentally) and confirmed beyond any shadow of reasonable doubt - your beliefs notwithstanding. Please learn something about the history of geology, evolution and the philosophy of science before commenting on them again.
And in any case, none of whom were scientists. Natural philosophers perhaps, but it's not the same thing; the 'scientific method' came about, in part, due to their work. Note that the word 'scientist' wasn't even coined until the 19th Century and wasn't in common use until the 20th Century.
You're confusing 14C radiometric dating with 13C/12C isotopic ratio dating. There is no decay rate issue for 13C/12C dating - well, except maybe for theoretical proton decay!
OK, may I do want to be a pedant. :)
I think you might be thinking of nylon, not citrate. Citrate has been around in biological systems for a long, long, long, long time. See: http://en.wikipedia.org/wiki/Citric_Acid_Cycle
What is particularly unfortunate is that many drugs (including tamiflu and the superior inhaled drug relenza) were invented by relatively small biotechs. (OK, Gilead isn't small any more, but Biota is *tiny*). Small biotechs are absolutely reliant on the fees and royalties they generate through licensing their inventions to Big Pharma, who have the money to get them through the FDA approval process and marketed.
Break a patent for Roche or GSK, they'll be annoyed but hardly notice the change in cash-flow. The biotech, however, will lose its sole cash-flow life-line. Biota are collaborating with Japanese pharma Sankyo to produce a second-generation antiviral for influenza that looks like being needed once-weekly for both prophylaxis and treatment. Be a real pity to destroy promising biotech-level research like that by cutting profits at the Big Pharma end of town.
Disclaimer: Yes I work for a biotech - own shares in them too.
...made of wood and full of horseshit?
If that was all they'd done I find it difficult to see how this differs from doing a multiple sequence alignment for a family of proteins, then making a gene for the consensus sequence.
Checking the paper (and related News and Views article) in Nature itself (http://www.nature.com/nature/journal/v437/n7058/i ndex.html ) (subscription required) indicates they've done more than that. By including the effects of coevolution - where one position in the protein mutates in concert with another to maintain optimal contacts - they generate a substantially better algorithm for manufacturing particular folds. (ie: 25% success in achieving folding versus 0% for conservation alone. 60% presence of wild-type function in the 'designed' proteins.)
Interesting, but I'm suprised it made it into Nature. (OK then, jealous...)There was an important series of debates about the scientific basis for evolution versus religious arguments to the contrary. They happened back in the 1800s. Science won.
Get over it.
I'm a biochemist - I guess you would call me an 'evolutionist' though that's like calling a programmer an 'electricalist' because computers are based on the observed fact of electricity.
I also regard myself as 'informed'.
And I'm fully aware that there are multiple observed speciation events. Not one or two, lots. Dozens. Go and read the scientific literature on the subject before you comment next time.
You're welcome to state your opinion, but only if it's informed. Until that point, please label yourself as one of those uninformed individuals and shut up.
It's a bit different for the doctors - particularly the interns. The interns have set amounts of time they *have* to spend doing various different streams in the hospital. There are also a certain number of graveyard/weekend shifts each, certain holiday allowances, required separations between weekend shifts etc. But I agree, quantifying *all* the variables is going to be a bitch.
Still, if the system can spit out a base schedule that would save a lot of time. They already have a system where 'personal requests' (religious issues, personal likes/dislikes) are up to the individuals to sort out through swaps and if you can't arrange a swap with someone, tough.
Exactly!
Still, the Outlook/Exchange method of enforcement has it's pluses.
Except, of course, that she can DO this job and the hospital won't spend any money looking for another option.
She's asked.
Lots.