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Have you seen this or this? Those are actually fairly well-defined at least, but they read like something that was supposed to be punched into cards.

I may very well be missing the point you're trying to make here, but there seems to be a disconnect between the example you use, and what the post is about.

Money today, seems to me like an abstraction layer between people and the economy at large.

There are no abstraction layers in nature. Form *IS* function, if you want to be pithy about it.

This is the reason there are >88'000 macromolecular structures deposited in data banks; it's been shown over and over again to be very useful information. http://www.rcsb.org/pdb/statistics/contentGrowthChart.do?content=total&seqid=100

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

MRi is technically just a euphemism for Nuclear Magnetic Resonance (NMR) imaging. The N was dropped because it of the obvious stigma that word possesses outside of scientific circles. We already have structures of these proteins solved by NMR. The next challenge is indeed to view these molecular systems in-vivo. I doubt that these techniques will actually make it out of the research setting. MRi's with fields higher than 3T are having trouble being approved by the FDA for clinical use. This is complicated by the fact that high field instruments are really expensive to begin with. Other scientists are working hard to advance the image quality in other ways.

While most of the professional molecular modeling software (InsightII, Sybyl, MOE, etc) will likely be out of the price range of a high school course, ArgusLab is free and pretty decent for some basic small molecule type stuff. The Accelrys Discovery Studio Visualizer is a freely-available version of Discovery Studio, which is also pretty decent. There's a Windows and Linux version of this.

Depending on how advanced your students are, you may want to introduce them to some molecular dynamics. NAMD is freely-available for Windows/Linux/Mac, and there are some good tutorials available. However, this might be getting a bit too advanced for a basic high school course, and might be a bit better to introduce at the undergraduate/graduate level. For most high school students, I'd probably teach them the basics would ArgusLab first.

David Goodsell does excellent illustrations and explanations of various biological molecules. Check out the molecule of the month at the RCSB. Among those is the ribosome

David Goodsell does excellent illustrations and explanations of various biological molecules. Check out the molecule of the month at the RCSB. Among those is the ribosome

"If any (non-trivial) treatment consisting of specifically folding proteins is found, then there will be exactly one way to produce said drug : genetic manipulation. Only a genetically modified cell will be able to produce those custom proteins."

This is not necessarily the case. We can predict with reasonable accuracy (about 80%) what sort of secondary structure (alpha helix, beta sheet, or coil, basically) a protein will have based solely on the protein sequence. For example, if you were to put the protein sequence lkgtlgqdvidirtlgskgvftfdpgftst, into Jpred you get this prediction:
LKGTLGQDV IDIRT LGSKGV FTF DPGFTST
------------------EEEEE-------------EEE
Where E is the code for beta sheet, and the dash is coil. Jpred is smart enough to also search through the Protein Data Bank and see if that sequence belongs to a protein that has already had it's structure solved, which is the case here. I told Jpred to go on with the prediction anyway, and by comparison to the known protein structure iIt doesn't do horribly bad, correctly predicting that most of this sequence is coil, getting close with the first bit of sheet secondary structure, and misinterpreting the second sheet bit when it should be another type of structure (a turn--several different ones are defined but make up only small amounts of structure, being largely transitions between the other secondary structure types). However as the example sort of hints at, protein structure can be squishy. If your protein is an enzyme, then it must bind substrate, catalyze a reaction, and release product. There will be some structural change that accompanies this, meaning that small molecules can have an impact on protein structure. Sometimes but not often this can involve radical change. I knew a guy a few years ago who designed a protein, such that he could control the secondary structure of a short stretch by the addition of a small molecule. If present, part A was helix, part B was coil. If absent, part A was coil, part B was helix. I'm running out of time, but there are also examples in nature of a protein in the course of it's biological function that has parts swap between sheet and helix structure. Lastly, we come to diseases caused by misfolding proteins. The mutations are often small ones, that disrupt proper folding of structural proteins. It may be possible to treat disorders at least to some extent by introducing a small molecule that will favor the properly folded state as opposed to the disease-causing improperly folded protein state (I'm thinking of Lou Gehrig's disease aka amyotrophic lateral sclerosis, ALS). Such a small molecule probably can't do anything about existing misfolded protein stuck in a plaque in the cell, but the small molecule might interact with protein as it is being made or before it joins the plaque and prevent an increase in the plaque size. It is at least conceivable that a conventional drug treatment could affect this part of ALS and halt or slow the progression of the disease.

I tend to think the authors of the article are refering to the problems of a "useable form" for the structures and easy access of many of these databases. The first problem is mearly a problem of converting between the various structural file formats out there, something a good programmer (or grad student) can solve is a few weeks or less. The second is a bureaucrat issue and not a scientific one.

The problem will be in jump-starting the supply of 3D data about molecules and everything else.

"No Risk"
By no means do I suggest that these researchers necessarily acted dangerously or that their research and research like it should be stopped, but I have to say that complex efforts with potentially "devastating" [your term] results should not be reassured against with phrases like "there was no risk". Your explanation of "The resultant virus was disabled so that, after replicating once in a cell, the daughter viruses could not replicate" only inspires a dubious curiosity for how this was done.

Indeed, also hearing the allegation that "the researchers couldn't be absolutely sure about Phoenix's infectivity" and that only biosafety level 3 was used while a level 4 was recommended, a layperson is left to wonder. (What the hell is a biosafety level in the first place, ?)

These researchers are Dr. Frankensteins in their pursuit of knowledge. And let them be! The pursuit of knowledge is unquestionably good! Just let them be careful while doing it, or they may also be Dr. Frankensteins in their poor safeguarding, Unleashing The Ritz on us.

Biodiversity & Nanomachines
In support of the investigation, let me say that I recently wondered, on the tail of some ethics reading regarding ecology, what other utility values nature could provide us beyond simple resources and recreation. Thinking of how proteins are basically nanomachines; and how much of the unused portions of our genome may be disused codes for once-useful, now-retired proteins; and how hard it must be to design a working nanomachine (just look at how hemoglobin contorts so bizarrely with the simple addition of an oxygen molecule); I came to wonder whether there might be a goldmine of blueprints for tested nanomachines in us. In us and every species we destroy.

Yes, please figure out how to mine genomes for molecular machines. In the meantime we'll see about preserving all these genomes.

Ob. Plural Of 'Virus'
Don't say 'virii'. That isn't even just wrong yet. You probably mean 'viri', which is just wrong. It wasn't used in the plural (being a mass noun, not a count noun) and there may not have been a proper plural form of it in Latin. My guess is that it is actually a 4th declension neuter with a plural of 'virus' (long 'u' sound), but what the hell do I know? Well, more than someone saying 'virii', by a long shot. Be safe, inflect it in English rather than classically: viruses.

Knowing the details of the debate makes you a pedant. I mean, how important is it really? But using the certainly wrong classical form makes you ignorant.

http://en.wikipedia.org/wiki/Plural_of_virus

If, however, the pathway of genes responsible for creating the sap can be isolated and cloned into a plant more suitable for crop farming, that would be mind-bogglingly cool. So in that sense some serious biotech tinkering is certainly in order.

But in terms of reverse engineering how a plant actually does photosynthesis, plant physiologists and biophysicists have been doing this for years and basically it appears to be so complex and highly tuned it's unlikely we can outdesign billions of years of selection for efficiency.

That said it's so tempting to think about optimizing it (at least for me). The enzyme that actually does the carbon fixation is called RuBisCo, arguably the most important enzyme on the entire planet, and its a really, really lousy enzyme. Its a protein of molecular weight ~5,000,000 which can process a lousy 3 CO2 molecules per second. The only reason plants can grow at all is by brute force, something like 60% of the dry weight of a plant is rubisco. If we could make it just a bit more efficient . . .

It is interesting to note the biochemistry of carbon fixation was discovered by the nobel laureate Melvin Calvin (which is why it's called the calvin cycle). He was also one of the pioneer researchers of Copaifera trees as a source of biodiesel, and dreamed of splicing the genes into weeds to solve our dependence on foreign oil. Sadly I've seen very little work published about this since his death in 1997.

Your sig: actually it's the collagen.

The following coordinates are from people at a university who used a small molecule from a company (Scios) to get their protein to crystallize. The structure of the small molecule doesn't appear anywhere in the paper (of course, a clever person could use the now-released electron density to calculate its structure).

http://www.rcsb.org/pdb/cgi/explore.cgi?pid=400211 11511253&page=0&pdbId=1IAS

You can use the status search link at PDB

http://www.rcsb.org/pdb/status.html

to find lots of things on hold (I found 211 when searching for Status "release on a certain date" AND "Release date" > 1 April 2005.

Also, I work at a pharma company, do publish and have seen lots of competitors do the sort of thing above.

The following coordinates are from people at a university who used a small molecule from a company (Scios) to get their protein to crystallize. The structure of the small molecule doesn't appear anywhere in the paper (of course, a clever person could use the now-released electron density to calculate its structure).

http://www.rcsb.org/pdb/cgi/explore.cgi?pid=400211 11511253&page=0&pdbId=1IAS

You can use the status search link at PDB

http://www.rcsb.org/pdb/status.html

to find lots of things on hold (I found 211 when searching for Status "release on a certain date" AND "Release date" > 1 April 2005.

Also, I work at a pharma company, do publish and have seen lots of competitors do the sort of thing above.

Does it have a function, it surely does, check out this site if you're really interested

It appears that open source is making its way into the data side of things... See the The RCSB Protein Data Bank , the human genome sequencing, etc.

But the bottom line is the following:

It costs (currently) about US$800 million to $1 billion to develop a drug. That is all of the initial trials, screening, 3 phase clinical trials, etc. This is typically a 10 year process-(there are some exceptions, but this is generally true).

The _reason_ why any company would invest this sort of money is so that they could have a monopoly on making it for 20 years. If everything were open sourced, and anyone could make anyone else's drug, why would companies put this much money into developing it? They would have no incentive to do so.

As someone else mentioned- this is not the sort of thing that you can just do in your basement. The company I work for makes a fancy robotic incubator to help you crystallize proteins. People want to do this so they can put them in an xray machine to get their structure, which can lead to possibly designing drugs that might interact with that protein. This machine costs about US$250,000. People need it because protein crystallography is hard- there's no way to predict under which conditions it will crystallize. You typically need to try 10,000-100,000 different conditions to get a reasonably sized crystal, that you can diffract and get the structure from. Some proteins _never_ crystallize.

This is way before you are even trying _anything_ in a biological screen, let alone animal trials, let alone phase 1, 2, and 3 (human) clinical trials.

If you do successfully crystallize the protein (and determine the structure, which is very straightforward once you have a good crystal), you can (and everyone does) submit it to the protein databank, and you can publish these conditions in a paper. So in this sense, lower level biotech is/becoming open source. But the higher level stuff requires a lot more thought and resources.

I'm not saying that there's no waste or greed in big pharma- Of course there is, like any other industry. Perhaps its higher than average, due to the large potential amount of money to be made.

My point is that the places that open source is successful- coding, which requires a $300 computer with an internet connection; wikipedia, which requires the same; there is a very low cost of entry to contribute. Even if companies and universities start open sourcing the lower level stuff more than it is now, Animal and human trials costs very large sums of money. Why would a company invest $10's of millions on one part of a trial if someone else could end up making (and selling) the drug?

I agree that cheap drugs would be great. But if its open source, and people start dying because of a side effect of the drug, who is liable? Not to mention who will fill out the FDA paperwork (there has to be $10's of millions invested just in complying with the paperwork. I've heard estimates that it is basically a medium sized room full of paper. And that's for 1 (one) drug.) -E

Well, like everything, this is a complex issue. A lot of data is already "open". You can go to NCBI and download the entire genome of SARS or Bacillius anthracis (Anthrax) if you so wish.

Also, if you are creating bioinformatics tools on Federal funding (NFS, NIH), a lot of times the stipulation is that the source code must be made available. This makes sense because your peers has to make sure that the way you did your calculations are actually correct. If people are to use your data or program in their publications, your program had better be correct. Many times there are no way to tell except to look at your source code.

But before we talk about open source, the real issue is standarization of formats. Bioinformatics is like a jungle right now, and every one has different formats for describing the same thing. NCBI has their formats, the europeans have theirs, and it's a terrible mess. I just spent the past week writing code to parse PDB files. This format has been around for ages, and is so inadequate. File formats designed by biologists do not lend themselves well to compuation. What we need right now is an open standard, based on XML and open APIs for parsing these standard files. This will go a long way towards information sharing, and can save a lot of duplicated effort.

Just some examples of how bio very much is open already..

In biotech software, there's lots of open source. BioJava, BLAST.. etc.

As for what they're talking about, e.g. databases.. Most data already IS open. The human genome, protein structures and sequences.

To argue that using crops to produce pharmaceuticals (so-called 'pharming') is inefficient and impractical is definitely open to discussion. Say what you will about the ethical nature (or lack thereof) of the major biotech and pharmaceutical companies--one thing they do know is money. Presumably they aren't investigating these techniques just so that they can piss off environmentalists.

Some protein products don't fold correctly in e. coli or other bacterial systems. Maintaining bacterial cultures requires pristine vats and utterly aseptic conditions. Temperature, humidity, nutrients...all have to be monitored and controlled.

Rice requires some care, but certainly not the level that culturing demands. It grows outdoors, in dirt. To determine which choice is more economical would require quite a bit of study and probably depends a great deal on the product you're interested in. I'm sure that the bean counters are watching this closely.

What really irks me is that they are producing drugs which will possibly be leaked into the ground after degradation or harvesting. If there happen to be bacteria in the ground with some sort of drug resistance that can be transmitted to other bacteria by plasmids/recombination through contamination of the crops, there will be big problems.

It's inappropriate to make blanket statements about the dangers of these crop products being released into the environment. Some products will degrade rapidly once the plant dies. Others may persist. An environmental assessment can and should take this into account.

In this case, the compounds in question are lactoferrin and lysozyme. They are naturally and widely-occuring compounds that already exist in many organisms and perform as natural antimicrobial agents. Exposure of organisms in the soil and around the field to these compounds will not generate mutant superbugs; microbes are exposed to these compounds every day inside our bodies. Since these are naturally occuring compounds, any resistance genes that could come about already exist.

Incidentally, these are compounds that you probably couldn't generate using e. coli, since they're toxic to bacteria. There are definitely some compounds that for safety reasons I wouldn't want to see pharmed, but these...well, they ain't them.

The specific virus that Venter et al synthesized is called Bacteriophage phiX174. They probably chose it because it has such a short genome.

In fact, it's genome is so short that at first it confused researchers. It's genome is shorter than it should be. That is, there are fewer codons in the genome than there are amino acids in the virus's proteins. Normally, there would need to be a 1:1 codon:amino-acid ratio.

This lead researchers to the amazing discovery that phiX174 contains "genes within genes" and "overlapping genes". (Link to Genetic Map of phiX174) In several instances, one gene is entirely contained within another gene. In another, there are two genes (A and A*) that overlap with "reading frames" that are off by one.

This discovery challenges notions of what a gene is. With this knowledge, you can't say that a gene is simply a particular region of DNA.

These overlapping genes also call attention to the improbability of the evolution of phiX174. Commonly when a genetic mutation occurs, one base changes. This could affect one amino-acid in the protein for which the gene codes. In phiX174's case, a single base mutation could change 2 amino-acids in 2 proteins. This means that the evolution of these proteins is interdependent. That two functional proteins evolved in this manner is absolutely extraordinary.

Of course, now that it has evolved that way, it gives phiX174 an advantage of genetic economy. It takes less energy to maintain and reproduce a shorter genome. So phiX174 gets more bang for it's genetic buck by overlapping genes in this way.

-c

-c

Proteins are biological polymers that are produced in living cells; they are composed of amino acids whose sequence is translated from DNA. The reason why the genome is of such great interest is that proteins provide the "molecular machinery" of the cell, to put things crudely; the genome provides a blueprint on how to assemble proteins, and the diversity of proteins gives rise to much of the cellular functionality essential for life.

Determining the 3D structure of proteins is a very hard but essential part of learning how they work. Unfortunately, knowing the sequence of a protein (which you can derive from DNA) only gives hints about the 3D structure. There are a number of large computational projects such as Folding@Home and Blue Gene that are devoted to predicting protein folding from a 1D sequence of amino acids to a 3D structure.

X-ray crystallography is the traditional way of determining the structure of proteins; you basically analyze the diffraction pattern of X-rays from a crystal of the protein of interest.

Now to your question: a multispan transmembrane protein is a protein that typically sits in the cell membrane that encloses the cell (alternatively, there are other internal membranes as well). Most of these proteins pass through the membrane several times, back and forth. These proteins are very important because they are involved in cell signalling and transport of substances into and out of the cell; ion channels are a prime example of transmembrane proteins. But transmembrane proteins are also notoriously difficult to study and crystallize because they do not solubilize without detergents, and are challenging to reconstitute in their native form.

If you look in the Protein Data Bank, there are lots of proteins that have been crystallized; but only a very small portion of them are transmembrane. This year's Nobel prize in part recognizes advances in studying the structure and function of these important proteins.

He did it through straight x-ray crystallography. See abstracts from the papers here and here. Find the structure here.

When I read the blurb for this story, I had a feeling of deja vu, as just two days ago I hopped over to the Protein Data Bank, mostly just so I could verify that I had correctly set up my Chime plug-in to work in Opera. There I found that they had chosen the aptly-named "Green Fluorescent Protein" as their Molecule of the Month, and had an informative article about its mechanism and uses. This is the protein from the jellyfish (Aequorea sp.) inserted into the zebrafish- what's really interesting is that the jellyfish actually also makes a bioluminescent protein called aequorin that emits blue light. which it uses to charge the chromophore in GFP and causes it to emit lower-energy green light. UV light from the sun has been shown to have a similar effect on purified GFP.

When I read the blurb for this story, I had a feeling of deja vu, as just two days ago I hopped over to the Protein Data Bank, mostly just so I could verify that I had correctly set up my Chime plug-in to work in Opera. There I found that they had chosen the aptly-named "Green Fluorescent Protein" as their Molecule of the Month, and had an informative article about its mechanism and uses. This is the protein from the jellyfish (Aequorea sp.) inserted into the zebrafish- what's really interesting is that the jellyfish actually also makes a bioluminescent protein called aequorin that emits blue light. which it uses to charge the chromophore in GFP and causes it to emit lower-energy green light. UV light from the sun has been shown to have a similar effect on purified GFP.

To answer the third question first: organism have a truly massive number of proteins encoded in their genome, (almost) all of which have a specific and well-defined 3-dimensional structure. Currently the structures for several thousand proteins have been determined, and the structures are deposited at the Protein Data Bank (PDB). Most of these are solved using xray crystallography, which is part of what I'm studying. We've learned that if you are carefull, you can coax purified protein to crystallize rather than just fall out of solution in an uniteresting and useless glop. Hampton Research is one company specializing in supplies relating to the crystallization of proteins, and has some pictures of protein crystals on their site. It had been known for a long time that if you put a nice ordered object (like a crystal) into an xray beam, you would get a diffraction pattern from it. The diffraction pattern can tell you some information about the internal makeup of the crystal, such as how big the repeating unit of the crystal is (crystals are made up of a large number of small units that are stacked next to each other in a lattice). Eventually it was found that you could rotate the crystal in the beam and collect many diffraction patterns from different angles and with a large amount of effort calculate the structure of the molecules in the crystal. In the bad old days in the 60's this meant that you hired a couple of math majors to be human calculators and after five years you would have your protein structure. With computers you can go from data collection to solved structure in only a few months.

I don't quite get the "20 years" thing either. The Advanced Light Source (ALS) at Berkeley was built in 1942, or at least the original building was. It has naturally gone through a number of upgrades, the last being a totally new synchrotron built in 1987-93?. I don't know about wear and tear on the facility but we've found that as far as macromolecular crystallography (usually meaning proteins) goes, xray intensity is no longer an issue. A complete data set collected at the Advanced Photon Source at Argonne Nat'l Labs took me less than an hour. That's just 1 second exposures to xrays as opposed to up to an hour or more on our lab's xray source. The big change occuring at synchrotrons for macromolecular crystallography is automation--it takes more time for a newbie to get trained and get set up for their first collection than to actually collect their data, but robotics for this kind of thing are relatively new--also data processing and structure determination is still very time consuming. Structural genomics (basically have structures of all the proteins in an organism determined) is also taking off and automation is a Very Big Thing for them as they screen 100,000's of protein crystals--Syrrx is probably the most advanced at this so far. Of course the problem with structural genomics is that you generate 100's of structures that lay around uniterpreted--a process that still requires a human touch. Anyway, hope that's some help.

Synchrotrons are used for x ray crystalography. they can produce X-ray photons at a wide range of frequencies and you can carefully select the photons you want using an x-ray monochromator.

The X-rays will not tell you anything about the nuclei of the molecules you are looking at, as the photons go through the electrons in the crystalised protein they will make an interference pattern, and from that you can calculate the shape of the electron cloud around the molecule.

Note that this gives you no infomation on the quantum state of the nuclei, which is what this quantum computer needs to know.

Nuclear Magnetic Resonance molecular analyisis works in a similar way to Magnetic Resonance Imaging, just on a smaller scale.

for more information click here

Do you work for a big pharm company?

No, and I have never had any sort of connection with any of them. I'm a programmer affiliated with the med school of a very large private university, doing computational biology (I was a molecular bio major). I do not work on anything remotely AIDS-related, nor does the group I'm in receive any AIDS-related funding, but quite a few other scientists here do.

(Actually, my university does make some money off AIDS therapies developed here too, but this pisses off a lot us anyway. It doesn't indicate ulterior motives, because like most universities they try to commercialize anything they can, and AIDS research is only a small part of that.)

even though you don't provide any evidence that Duesberg believes such a thing, so you could be making it up

It says so on that page you quoted, fairly close to the top- Duesberg tried to claim the award. This is one of the things that bugs me; the HIV-is-bogus lobby can't even agree on this. And you didn't read the page before posting it, either. Shame.

As for the genome, protein structures, etc., you could always do a Google search, but that would require an open mind. HIV-RT is (indirectly) of interest in my line of work, so I do actually know a little bit about it (and the people down the hall know quite a bit more). A few of the many, many structures are this, this,
or this, and you can find many more by simply going here and doing a search for "HIV" or "reverse transcriptase". The genomes of HIV1 and HIV2 can be found, like almost every other genome, at the NCBI here and here.

Yes, the nasty side-effects are obvious, but trying to cloud them with language such as "brute force attack on reverse transcription" only makes your argument more suspicious, particularly in light of the questions that you've failed to answer. What, exactly, are the side effects of AZT?

I don't see how that's clouding the language; you're making a big deal about the side effects but you don't appear to know much about pharmaceuticals or molecular biology. AZT is a nucleoside analogue chain terminator, meaning it replaces thymidine in nascent DNA chains but prevents further addition to the chain. I believe the problem is that it fucks with normal transcription too, and it was originally intended as an anticancer drug. I don't know anything about the actual external side effects, only the molecular ones, but I seem to recall it involves some sort of anemia. (Okay, other pages say it basically just makes you feel horribly ill.)

I'll agree AZT is a nasty drug. But you didn't answer my question: what about other therapies that do appear to be successful? Some of these can't be taken in combination with AZT, so you have to leave that out of your argument.

How do you explain it under your belief system, you know, the one that dictates that HIV==AIDS?

"Belief system"? Um, well, the evidence doesn't necessarily dictate anything- medical science isn't advanced enough. I would argue that "AIDS is (usually) cause by HIV", which is a good bit different, and I don't have an answer for what happened to those children. There are plenty of weird examples like that involving AIDS, but they don't mean existing hypotheses about the role of HIV are wrong, only that disease resistance and molecular biology are very complicated. And we knew that already. You can't use anecdotal evidence as proof of a broad generalization; it's just not statistically valid.

As a counter-example, how do you explain the 2.2 million Africans who died from AIDS last year, where they can't afford AZT and certainly aren't doing many poppers? And, for that matter, I'm not clear on how you can cite the children as an example when you believe they were misdiagnosed in the first place. Did they have HIV and not get AIDS- either because of weird biology (my argument) or HIV's harmlessness (Duesberg's argument)- or did they not have HIV in the first place? If the latter, does this mean everyone who's tested positive for HIV does not have any such virus in them?

So, the first problem here is that all you're able to do is nitpick. The second problem is that your hypotheses, to be correct, require that there be a vast conspiracy on the part of the news media, the medical establishment, and the pharmaceutical companies to fabricate AIDS so that GlaxoSmithKline can boost its revenues. It's one thing to claim that Gallo acted inappropriately, but to extend this to accuse a vast number of AIDS researchers of falsifying data is sort of absurd. You clearly haven't even bothered to do the most cursory sort of investigation, and you seem to have virtually no knowledge of biology beyond what you've read on the Virus Myth web page. And I'm a bit peeved that you keep accusing everyone of working for pharmaceutical companies- heck, the assholes didn't even read my resume when I sent it to them last spring.

Here's a challenge: read this from beginning to end and see if you understand it.

Do you work for a big pharm company?

No, and I have never had any sort of connection with any of them. I'm a programmer affiliated with the med school of a very large private university, doing computational biology (I was a molecular bio major). I do not work on anything remotely AIDS-related, nor does the group I'm in receive any AIDS-related funding, but quite a few other scientists here do.

(Actually, my university does make some money off AIDS therapies developed here too, but this pisses off a lot us anyway. It doesn't indicate ulterior motives, because like most universities they try to commercialize anything they can, and AIDS research is only a small part of that.)

even though you don't provide any evidence that Duesberg believes such a thing, so you could be making it up

It says so on that page you quoted, fairly close to the top- Duesberg tried to claim the award. This is one of the things that bugs me; the HIV-is-bogus lobby can't even agree on this. And you didn't read the page before posting it, either. Shame.

As for the genome, protein structures, etc., you could always do a Google search, but that would require an open mind. HIV-RT is (indirectly) of interest in my line of work, so I do actually know a little bit about it (and the people down the hall know quite a bit more). A few of the many, many structures are this, this,
or this, and you can find many more by simply going here and doing a search for "HIV" or "reverse transcriptase". The genomes of HIV1 and HIV2 can be found, like almost every other genome, at the NCBI here and here.

Yes, the nasty side-effects are obvious, but trying to cloud them with language such as "brute force attack on reverse transcription" only makes your argument more suspicious, particularly in light of the questions that you've failed to answer. What, exactly, are the side effects of AZT?

I don't see how that's clouding the language; you're making a big deal about the side effects but you don't appear to know much about pharmaceuticals or molecular biology. AZT is a nucleoside analogue chain terminator, meaning it replaces thymidine in nascent DNA chains but prevents further addition to the chain. I believe the problem is that it fucks with normal transcription too, and it was originally intended as an anticancer drug. I don't know anything about the actual external side effects, only the molecular ones, but I seem to recall it involves some sort of anemia. (Okay, other pages say it basically just makes you feel horribly ill.)

I'll agree AZT is a nasty drug. But you didn't answer my question: what about other therapies that do appear to be successful? Some of these can't be taken in combination with AZT, so you have to leave that out of your argument.

How do you explain it under your belief system, you know, the one that dictates that HIV==AIDS?

"Belief system"? Um, well, the evidence doesn't necessarily dictate anything- medical science isn't advanced enough. I would argue that "AIDS is (usually) cause by HIV", which is a good bit different, and I don't have an answer for what happened to those children. There are plenty of weird examples like that involving AIDS, but they don't mean existing hypotheses about the role of HIV are wrong, only that disease resistance and molecular biology are very complicated. And we knew that already. You can't use anecdotal evidence as proof of a broad generalization; it's just not statistically valid.

As a counter-example, how do you explain the 2.2 million Africans who died from AIDS last year, where they can't afford AZT and certainly aren't doing many poppers? And, for that matter, I'm not clear on how you can cite the children as an example when you believe they were misdiagnosed in the first place. Did they have HIV and not get AIDS- either because of weird biology (my argument) or HIV's harmlessness (Duesberg's argument)- or did they not have HIV in the first place? If the latter, does this mean everyone who's tested positive for HIV does not have any such virus in them?

So, the first problem here is that all you're able to do is nitpick. The second problem is that your hypotheses, to be correct, require that there be a vast conspiracy on the part of the news media, the medical establishment, and the pharmaceutical companies to fabricate AIDS so that GlaxoSmithKline can boost its revenues. It's one thing to claim that Gallo acted inappropriately, but to extend this to accuse a vast number of AIDS researchers of falsifying data is sort of absurd. You clearly haven't even bothered to do the most cursory sort of investigation, and you seem to have virtually no knowledge of biology beyond what you've read on the Virus Myth web page. And I'm a bit peeved that you keep accusing everyone of working for pharmaceutical companies- heck, the assholes didn't even read my resume when I sent it to them last spring.

Here's a challenge: read this from beginning to end and see if you understand it.

Do you work for a big pharm company?

No, and I have never had any sort of connection with any of them. I'm a programmer affiliated with the med school of a very large private university, doing computational biology (I was a molecular bio major). I do not work on anything remotely AIDS-related, nor does the group I'm in receive any AIDS-related funding, but quite a few other scientists here do.

(Actually, my university does make some money off AIDS therapies developed here too, but this pisses off a lot us anyway. It doesn't indicate ulterior motives, because like most universities they try to commercialize anything they can, and AIDS research is only a small part of that.)

even though you don't provide any evidence that Duesberg believes such a thing, so you could be making it up

It says so on that page you quoted, fairly close to the top- Duesberg tried to claim the award. This is one of the things that bugs me; the HIV-is-bogus lobby can't even agree on this. And you didn't read the page before posting it, either. Shame.

As for the genome, protein structures, etc., you could always do a Google search, but that would require an open mind. HIV-RT is (indirectly) of interest in my line of work, so I do actually know a little bit about it (and the people down the hall know quite a bit more). A few of the many, many structures are this, this,
or this, and you can find many more by simply going here and doing a search for "HIV" or "reverse transcriptase". The genomes of HIV1 and HIV2 can be found, like almost every other genome, at the NCBI here and here.

Yes, the nasty side-effects are obvious, but trying to cloud them with language such as "brute force attack on reverse transcription" only makes your argument more suspicious, particularly in light of the questions that you've failed to answer. What, exactly, are the side effects of AZT?

I don't see how that's clouding the language; you're making a big deal about the side effects but you don't appear to know much about pharmaceuticals or molecular biology. AZT is a nucleoside analogue chain terminator, meaning it replaces thymidine in nascent DNA chains but prevents further addition to the chain. I believe the problem is that it fucks with normal transcription too, and it was originally intended as an anticancer drug. I don't know anything about the actual external side effects, only the molecular ones, but I seem to recall it involves some sort of anemia. (Okay, other pages say it basically just makes you feel horribly ill.)

I'll agree AZT is a nasty drug. But you didn't answer my question: what about other therapies that do appear to be successful? Some of these can't be taken in combination with AZT, so you have to leave that out of your argument.

How do you explain it under your belief system, you know, the one that dictates that HIV==AIDS?

"Belief system"? Um, well, the evidence doesn't necessarily dictate anything- medical science isn't advanced enough. I would argue that "AIDS is (usually) cause by HIV", which is a good bit different, and I don't have an answer for what happened to those children. There are plenty of weird examples like that involving AIDS, but they don't mean existing hypotheses about the role of HIV are wrong, only that disease resistance and molecular biology are very complicated. And we knew that already. You can't use anecdotal evidence as proof of a broad generalization; it's just not statistically valid.

As a counter-example, how do you explain the 2.2 million Africans who died from AIDS last year, where they can't afford AZT and certainly aren't doing many poppers? And, for that matter, I'm not clear on how you can cite the children as an example when you believe they were misdiagnosed in the first place. Did they have HIV and not get AIDS- either because of weird biology (my argument) or HIV's harmlessness (Duesberg's argument)- or did they not have HIV in the first place? If the latter, does this mean everyone who's tested positive for HIV does not have any such virus in them?

So, the first problem here is that all you're able to do is nitpick. The second problem is that your hypotheses, to be correct, require that there be a vast conspiracy on the part of the news media, the medical establishment, and the pharmaceutical companies to fabricate AIDS so that GlaxoSmithKline can boost its revenues. It's one thing to claim that Gallo acted inappropriately, but to extend this to accuse a vast number of AIDS researchers of falsifying data is sort of absurd. You clearly haven't even bothered to do the most cursory sort of investigation, and you seem to have virtually no knowledge of biology beyond what you've read on the Virus Myth web page. And I'm a bit peeved that you keep accusing everyone of working for pharmaceutical companies- heck, the assholes didn't even read my resume when I sent it to them last spring.

Here's a challenge: read this from beginning to end and see if you understand it.

Do you work for a big pharm company?

No, and I have never had any sort of connection with any of them. I'm a programmer affiliated with the med school of a very large private university, doing computational biology (I was a molecular bio major). I do not work on anything remotely AIDS-related, nor does the group I'm in receive any AIDS-related funding, but quite a few other scientists here do.

(Actually, my university does make some money off AIDS therapies developed here too, but this pisses off a lot us anyway. It doesn't indicate ulterior motives, because like most universities they try to commercialize anything they can, and AIDS research is only a small part of that.)

even though you don't provide any evidence that Duesberg believes such a thing, so you could be making it up

It says so on that page you quoted, fairly close to the top- Duesberg tried to claim the award. This is one of the things that bugs me; the HIV-is-bogus lobby can't even agree on this. And you didn't read the page before posting it, either. Shame.

As for the genome, protein structures, etc., you could always do a Google search, but that would require an open mind. HIV-RT is (indirectly) of interest in my line of work, so I do actually know a little bit about it (and the people down the hall know quite a bit more). A few of the many, many structures are this, this,
or this, and you can find many more by simply going here and doing a search for "HIV" or "reverse transcriptase". The genomes of HIV1 and HIV2 can be found, like almost every other genome, at the NCBI here and here.

Yes, the nasty side-effects are obvious, but trying to cloud them with language such as "brute force attack on reverse transcription" only makes your argument more suspicious, particularly in light of the questions that you've failed to answer. What, exactly, are the side effects of AZT?

I don't see how that's clouding the language; you're making a big deal about the side effects but you don't appear to know much about pharmaceuticals or molecular biology. AZT is a nucleoside analogue chain terminator, meaning it replaces thymidine in nascent DNA chains but prevents further addition to the chain. I believe the problem is that it fucks with normal transcription too, and it was originally intended as an anticancer drug. I don't know anything about the actual external side effects, only the molecular ones, but I seem to recall it involves some sort of anemia. (Okay, other pages say it basically just makes you feel horribly ill.)

I'll agree AZT is a nasty drug. But you didn't answer my question: what about other therapies that do appear to be successful? Some of these can't be taken in combination with AZT, so you have to leave that out of your argument.

How do you explain it under your belief system, you know, the one that dictates that HIV==AIDS?

"Belief system"? Um, well, the evidence doesn't necessarily dictate anything- medical science isn't advanced enough. I would argue that "AIDS is (usually) cause by HIV", which is a good bit different, and I don't have an answer for what happened to those children. There are plenty of weird examples like that involving AIDS, but they don't mean existing hypotheses about the role of HIV are wrong, only that disease resistance and molecular biology are very complicated. And we knew that already. You can't use anecdotal evidence as proof of a broad generalization; it's just not statistically valid.

As a counter-example, how do you explain the 2.2 million Africans who died from AIDS last year, where they can't afford AZT and certainly aren't doing many poppers? And, for that matter, I'm not clear on how you can cite the children as an example when you believe they were misdiagnosed in the first place. Did they have HIV and not get AIDS- either because of weird biology (my argument) or HIV's harmlessness (Duesberg's argument)- or did they not have HIV in the first place? If the latter, does this mean everyone who's tested positive for HIV does not have any such virus in them?

So, the first problem here is that all you're able to do is nitpick. The second problem is that your hypotheses, to be correct, require that there be a vast conspiracy on the part of the news media, the medical establishment, and the pharmaceutical companies to fabricate AIDS so that GlaxoSmithKline can boost its revenues. It's one thing to claim that Gallo acted inappropriately, but to extend this to accuse a vast number of AIDS researchers of falsifying data is sort of absurd. You clearly haven't even bothered to do the most cursory sort of investigation, and you seem to have virtually no knowledge of biology beyond what you've read on the Virus Myth web page. And I'm a bit peeved that you keep accusing everyone of working for pharmaceutical companies- heck, the assholes didn't even read my resume when I sent it to them last spring.

Here's a challenge: read this from beginning to end and see if you understand it.

mhack

Well, I kinda agree and I kinda disagree.

First, you can't expect to go from no success to complete success overnight. People have been trying to fold proteins for some time now and have basically failed because it is freakin' hard. The theory is in principle in place, a least to a first approximation, but the calculations are so intensive that they have basically beaten every comer. As an undergraduate I remember how everyone in the field thought getting bigger and better grants and buying bigger and bigger computers was the answer. Oh to be SGI in those days. They sum up the problem pretty well in the Nature paper, essentially a modern (desktop) computer would require a few decades to crunch through a single useful length simulation. Then you need to do it many times to get a useful answer (say 100-1000). Even supercomputers are going to balk at that kind of calculation. Moore's law what it is, we should then be able to get through an in silico simulation in a week on a single computer (when its this fast crystallography really will be dead) by, oh say 2040 at best. (somebody want to calculate that exactly, 10000yrs -> 0.02yrs is how many doubles). So yes, this hasn't gotten rid of x-ray crystallography just yet.

But this is still really cool. Complaints about interface and maintenance aside, this was a great system. It relied on four pretty bright insights.

First, that distributed computing is essentially the poor man's (cough, the academic's) super computer. Also, it automatically adapts itself to technological improvements. People will buy new computers from time to time and, hopefully, reload your software.

Second, that there was no reason other than no one had sufficiently brute forced the process that the existing methods shouldn't work. They use a bunch of 'cheating' techniques to make this managable during the screen saver timescale, such as a united atom model (I think that means they ignore aliphatic hydrogens) and implicit solvent (don't treat it as individual solvent molecules, just a uniform field). It was an open question as to whether this approach would work at all or if you had to go over to much more explicit methods to get it to work at all. It appears that this has kinda worked with the cheater methods in place.

Third, choice of a test case. Yes they chose something that was small. This isn't surprising. They wanted to be done sometime this decade, remember there is a graduate student as the primary author here. Small was necessary. However they also chose a FAST-FOLDING protein. That was clever. Basically, even with distributed computing, it is still hard to simulate a full microsecond of time. Thus they chose something that had some chance of completing its folding one the time scale that they could look at.

Fourth, they remembered their P-Chem. It is really hard to run these things to completion... so they didn't. You don't have to run the simulation until 99% of the molecules have completely folded, just until an appreciable number have folded and you can extrapolate the behavior from that. They ran a 20ns simulation (at the longest). The thing takes 7us for ~60% to fold. As a result only once in a great ong while did one of the simulations actually produce a folded protein. But by doing it ~10000 times they could figure out how that translated into the rate constant. That's clever.

That said, yes there is a long way to go on this, but its still a really clever paper. No we haven't cured cure cancer yet, but its still progress. And forget an in silico structure of the ATPase, that's largely understood already (check the RSCB/PDB there's a bunch). The real challenge will be getting a structure that size that hasn't been solved by other methods and convincing anyone else that you're right! Disclosure- I don't have PhD in this area yet, but I'm close.

Looked a bit further.. There are two structures deposited in the protein data bank: 1L2Q and 1L2R. But alas, they're not available yet, 'release on publication'.

Chimera (unix, linux, windows) is a molecular modeling program developed by UC San Francisco, but it was funded by a government grant from the NIH, so guess what, you can download it for free provided you don't want to make money using it.

The NIH (government orginization) has actually REQUIRED that people that use their money to come up with a protein sequence should deposit it in a freely accessable database

Also, just a side note. If anyone wants to download the program, just grab some protiens from the protien database and load them up. Some stuff you might find interesting in the way of proteins.

tryptophan

hemoglobin

Alcohol Dehydrogenase

DNA (not a protein, but oh well)

Insulin

more...

Enjoy,
Steve

Chimera (unix, linux, windows) is a molecular modeling program developed by UC San Francisco, but it was funded by a government grant from the NIH, so guess what, you can download it for free provided you don't want to make money using it.

The NIH (government orginization) has actually REQUIRED that people that use their money to come up with a protein sequence should deposit it in a freely accessable database

Also, just a side note. If anyone wants to download the program, just grab some protiens from the protien database and load them up. Some stuff you might find interesting in the way of proteins.

tryptophan

hemoglobin

Alcohol Dehydrogenase

DNA (not a protein, but oh well)

Insulin

more...

Enjoy,
Steve

Chimera (unix, linux, windows) is a molecular modeling program developed by UC San Francisco, but it was funded by a government grant from the NIH, so guess what, you can download it for free provided you don't want to make money using it.

The NIH (government orginization) has actually REQUIRED that people that use their money to come up with a protein sequence should deposit it in a freely accessable database

Also, just a side note. If anyone wants to download the program, just grab some protiens from the protien database and load them up. Some stuff you might find interesting in the way of proteins.

tryptophan

hemoglobin

Alcohol Dehydrogenase

DNA (not a protein, but oh well)

Insulin

more...

Enjoy,
Steve

Chimera (unix, linux, windows) is a molecular modeling program developed by UC San Francisco, but it was funded by a government grant from the NIH, so guess what, you can download it for free provided you don't want to make money using it.

The NIH (government orginization) has actually REQUIRED that people that use their money to come up with a protein sequence should deposit it in a freely accessable database

Also, just a side note. If anyone wants to download the program, just grab some protiens from the protien database and load them up. Some stuff you might find interesting in the way of proteins.

tryptophan

hemoglobin

Alcohol Dehydrogenase

DNA (not a protein, but oh well)

Insulin

more...

Enjoy,
Steve

Chimera (unix, linux, windows) is a molecular modeling program developed by UC San Francisco, but it was funded by a government grant from the NIH, so guess what, you can download it for free provided you don't want to make money using it.

The NIH (government orginization) has actually REQUIRED that people that use their money to come up with a protein sequence should deposit it in a freely accessable database

Also, just a side note. If anyone wants to download the program, just grab some protiens from the protien database and load them up. Some stuff you might find interesting in the way of proteins.

tryptophan

hemoglobin

Alcohol Dehydrogenase

DNA (not a protein, but oh well)

Insulin

more...

Enjoy,
Steve

Chimera (unix, linux, windows) is a molecular modeling program developed by UC San Francisco, but it was funded by a government grant from the NIH, so guess what, you can download it for free provided you don't want to make money using it.

The NIH (government orginization) has actually REQUIRED that people that use their money to come up with a protein sequence should deposit it in a freely accessable database

Also, just a side note. If anyone wants to download the program, just grab some protiens from the protien database and load them up. Some stuff you might find interesting in the way of proteins.

tryptophan

hemoglobin

Alcohol Dehydrogenase

DNA (not a protein, but oh well)

Insulin

more...

Enjoy,
Steve

I've seen added value. The lab I work in does some modelling of protein movements. We can use multigifs or MPEGs, but this limits the viewer to the angles we incorporate. With VRML, you can view the protein from any angle. This is something that is of interest to people in the field- I don't think standard molecular graphics packages support this type of application.

Unfortunately changing VRML standards have broken all our files, and we do not intend to replace it. All of our content is created automatically on a Linux server, ruling out pretty much any alternative (and many of our viewers will use non-Windows platforms). For a good idea what VRML can be used for, though, look at the Protein Data Bank website. Try '1tim' as the search key- click on the 'view structure' link. They've done a fabulous job with this.

How big is this single molecule anyway? It could be conceivably any size! A quick search of the Protein Data Bank (yes I was bored, but there's a fairly interesting mail about it) and it turns out that some molecules are 132,000 atoms big (or even bigger). You could probably build a whole cpu out of something that big...

Note that the structure they have is only about half of what is already a small (96 amino acids) protein, so the 3D models are not too impressive. Pretty amazing how something so simple can be so deadly, though.

The site has JPEG graphics that anyone can visualize, plus, if your browser supports Java, there is a simple interactive viewer applet, too.