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27,462 PhDs

Grind genome and throw students at it.
  (+13, -4)(+13, -4)
(+13, -4)
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We've had the human genome sequence for a long time, and most of the coding regions (genes) have been identified.

This has accelerated research enormously. Previously, researchers interested in a particular biochemical or developmental pathway or disease might spend years homing in on the gene, which they would then sequence. Today, better techniques coupled with the complete genome sequence often make it possible to identify likely candidate genes in days or weeks.

However, most of the proteins encoded by the genes are unknown and unstudied. So, a research may find (by genetic mapping, for instance) a chromosomal region harbouring a likely "disease gene", but the region will contain many dozens of genes, any one of which could be the target. Or they may find a list of a hundred genes which are over- or under- expressed in a given situation, any one of which may be the one they're looking for.

If we knew a bit more about each gene (where it's expressed; what enzymatic activity the protein has; which other proteins it binds to; and so forth), it would be much, much easier to identify candidate genes. For example, if you're looking for the gene involved in a metabolic defect, and you find a dozen candidates of which two have enzymatic roles likely to be involved in that metabolic pathway, you immediately can focus on those two genes instead of the whole dozen.

There are "global" programs to catalogue gene properties (eg, expression patterns; effects of knocking out a homologous gene in yeast, etc), but these are grand surveys which give little insight into each protein.

In contrast, a researcher working on a particular topic will often spend years studying a particular gene and the protein it encodes, and gain a very detailed understanding of it.

I propose a proposal. There must be about 27,462 new molecular biology PhD students each year, worldwide. They all need projects to work on. For one year, and one year only, we assign each new PhD student a gene, which they will work on for the duration of their project. If their host lab is interested in a particular gene or group of genes, then they get to work on one of those, so everyone wins. If not, they can pick one at random from the list of un- analysed genes.

Over the course of three years, studying any one protein is quite likely to turn up something interesting (probably more likely than most PhD projects). More importantly, learning everything you can about one gene and its protein (or proteins - since one gene may encode a number of variants) is an excellent way to develop well-rounded skills, whatever the gene.

In three years' time, then, we'll have 27,462 PhD theses, each with an in- depth analysis of one gene (and its ramifications). These theses would be made available on-line (as I believe all theses should, though few are), linked directly to the many databases cataloguing the human genome. In one swell foop, we'd accelerate research by a significant step.

MaxwellBuchanan, Jun 05 2008

Folding@home http://folding.stanford.edu/
Uses home computers and PS3s to run detailed analysis of protein folding. [mecotterill, Jul 14 2008]

[link]






       Are there many stand-alone genes? I'd have guessed they work, at least in part, with other genes to produce a given outcome. Fault tolerance, if you will.
phoenix, Jun 05 2008
  

       I get my jeans out of the Levis's catalogue... how annoying is that for an annotation?
xenzag, Jun 05 2008
  

       I believe PhDs write 'dissertations'. Anyways, just to clarify, this idea is simply to adopt a gene centric year of research projects for biochemists in order to sustain a library of information relating to each gene? And who is going to pay for it? Who is interested in the gene that encodes for the protein that regulates the gene that encodes for the protein that regulates the gene... I hope you get the point. Nobody is interested in that little gene, however noble it's cause, and nobody is going to pay for the research.
daseva, Jun 05 2008
  

       // nobody is going to pay for the research. //   

       Wrong. Tell "The Government" that it is "a potential weapon". Then everyone pays for it ....
8th of 7, Jun 05 2008
  

       //I propose a proposal// hahah //There must be about 27,462 new molecular biology PhD students each year// haha I like you. + for good phrasing
Flipmastacash, Jun 05 2008
  

       //Are there many stand-alone genes?// No, there are none. However, many researchers focuss on a particular protein, including its interactions with other proteins. Such studies inevitably overlap, which is all to the good.   

       //I believe PhDs write 'dissertations'.// Here, they're usually called theses.   

       //just to clarify, this idea is simply to adopt a gene centric year of research projects...// Yes, except it's three years (all PhDs starting in a given year; a PhD normally takes three years in the UK, or longer in the US where it includes some preliminary work).   

       //who is going to pay for it? Who is interested...Nobody is interested in that little gene, however noble it's cause, and nobody is going to pay for the research.// That would have been the attitude 20 years ago, but not now. First off, almost all genes are interesting if you track them down (this one is a dull copper transporter; but it turns out that a mutant form of it transports chromium and kills people by chromium accumulation in cells; this one is just a foetal globin gene, but it turns out that it's also expressed in adult hypothalamus and helps to maintain yada yada); there are very few dull genes, partly because of the synergies that phoenix mentioned.   

       Second, we already pour huge amounts of money into researching specific genes (or their products), in the course of following a particular biological story. It's very much like the situation in genomics pre 1990's - every researcher went and found and sequenced the gene they were interested in. In the end, it was orders of magnitude more efficient to just sequence the whole damn genome and lay it out on a plate, even though everyone thought most of it would be dull (and much of it is). Likewise, there are proteomics projects already underway and heavily funded to categorize certain aspects of every protein in an industrialized manner. However, this does not give you the depth of knowledge and background that you will get from having one person focussing on one protein for three years.   

       Don't think that this would be drudgery. Almost any research topic is fun and, in the long run, as good a training as any other. You'd have a generation of well- trained PhDs with diverse skills and, into the bargain, detailed personal information on every protein.
MaxwellBuchanan, Jun 05 2008
  

       // detailed personal information on every protein. //   

       "The protein police are watching YOU ....."
8th of 7, Jun 05 2008
  

       But that's how it is. A real understanding of a disease often comes from knowing the habits and behaviours of the relevant proteins - the key players - inside out. If you're looking for a key oncogene, and you have a candidate region containing two dozen genes, it takes an understanding of those proteins to be able to say "well, that one's only a cytoskeletal component; but we know that, oddly, it binds cyclic AMP which is one of the factors that can accelerate growth of these cells in culture..."
MaxwellBuchanan, Jun 05 2008
  

       I accept the goodness of the idea, even though it still strikes me as grossly redundant. For starters, can the whole process be further automated (like the genome)? Let's train a robot to track each and every protein with florescent tags and log the data, and then just let a handful of students hack away at this insurmountable task for a few years. Also, you keep going on about how well trained everyone is gonna be, but once it's done, it's done. They'll be masters at a game nobody plays anymore.
daseva, Jun 05 2008
  

       //Let's train a robot to track each and every protein with florescent tags and log the data, and then just let a handful of students hack away at this insurmountable task for a few years.// This is precisely what's done at present (in flavour if not in detail). It's too shallow - the robotic part (and the mass array screens, and the mass everything else) is actually trivial; the latter part is intensely human and requires huge collective effort. What you're saying is equivalent to saying "let's build a robot to collect forensic evidence and then we just need a few detectives to analyse it."   

       // They'll be masters at a game nobody plays anymore.// No, they won't. There isn't a "game" of analysing protein function - not in a deep sense. Depending on the protein, it will require a huge diversity of skills. For instance, you clone the gene (widely useful skill) and express the protein (itself a black art and widely useful), then maybe use it in a "pull-down" reaction to identify what it might bind to (which is itself a whole host of other sub-skills, all of general utility), then try to identify those proteins by peptide fingerprint mass-spec (again, not made redundant by the goals of this project), then maybe you find that it binds proteins X and Y, but that X also binds Z, so maybe your protein shuts down the activation of Z which is involved in....etc etc. You will need the entire spectrum of molecular biology tools to really understand a single protein in detail; almost all of those skills have wider applications. Plus, we're talking about documenting the normal proteins in human cells - that leaves a few other species.
MaxwellBuchanan, Jun 05 2008
  

       Yes. This needs to be done, immediately. I still think funding is your enemy, though. You need a government 'human proteome project' to collect the bills and dole them out to the schools. In fact, you might want to consider this as a new title. Don't worry about rights, I've already lost them all...   

       Oh wait, your title is funny. Nevermind ;)
daseva, Jun 05 2008
  

       I think a government program (and maybe a 'governments' program - let's not forget the USA) would work. But there is an alternative. Just let the government subsidise 25% of the costs of any PhD which is part of this project.   

       Most research groups would leap at the chance to receive some additional support, and in most cases could easily dovetail a protein-targeted project into their overall research strategy. It's largely a matter of co-ordination and a common goal.   

       Another reason for doing it in one big cohort is that, if it drags on, you'll start to get "formula theses" in a standard format, as each student follows the path of his predecessor; we want to keep the novelty of approach.
MaxwellBuchanan, Jun 05 2008
  

       Does it require PhD level research? This might make good research material for the type of HNC/HND students that I teach. Oh wait, actually, no it wouldn't, unless all the research already existed on wikipedia for them to copy and hand in.
Ian Tindale, Jun 05 2008
  

       Good question. You need to get above a threshold of competence, inasmuch as you don't want to add disinformation to the databases. Beyond that, almost any human analysis - even if it's no more than a good trawl of the existing literature and some clever bioinformatics - can help.   

       But, really, I think you want a spectrum of research to give a comprehensive biography of the protein. I suspect a PhD is about the right length for this, though a Masters might cover it.   

       Incidentally, I'm voting [-] on this because I can see some drawbacks and I don't think it merits unanimous support.
MaxwellBuchanan, Jun 05 2008
  

       April 1 (Bloomberg) -- Harvard College rejected 93 percent of its applicants for next fall's class, the highest rate in its 372-year history.   

       Harvard admitted 1,948 of 27,462 applicants, the Cambridge, Massachusetts, school said in a statement today. That's a 5.3 percent drop from a year ago, when the college, the undergraduate arm of Harvard University, admitted 2,058 from a pool of 22,955.   

       Presumably, the ones who didn't make it go to work in a jean factory or something.
Ling, Jun 05 2008
  

       If you Pile them High and Deep enough, they can do anything. The scientific method: have your grad student do it.
Voice, Jun 05 2008
  

       I think the genes shouldn't just be assigned at random, though, since there are more prized targets than others.   

       Perhaps you should do something like a sports league draft, letting the top grad students get the first pick on projects they would like to work on.   

       Perhaps some big-name institution could fund this, for maybe 100 students or so, working on 100 Open-reading frames of unknown function. If students agree to the stipulations of the draft, and they are accepted based on academic merit, then they get the moneys.
Cuit_au_Four, Jun 06 2008
  

       I can haz jene reseach!
daseva, Jun 06 2008
  

       So, not a new Katie Melua song title?
coprocephalous, Jun 06 2008
  

       I'm having trouble trying to be positive about the idea [MB], but I'm having even more trouble trying to articulate my criticisms without answering them myself. I still remain unconvinced though - this could be a two pipe problem.   

       In the meantime, where you going to get 27,462 half-decent PhD students from?   

       Here's why I ask - there are 126 universities in the UK (just choosing UK because I know the number - we can scale this up for an international reckoning). I don't know how many of them have a half-decent biology department (that has genetic research in its books). Let's be generous and say 75. of that 75, 5 might have big departments and be renowned for genetics research. Could they have 10 PhD students?? I don't know... Anyway, the rest could have 5 PhDs in gene-related research. That's 400 PhDs in the UK per year...   

       Does that sound plausible?   

       Plus there is that fact that some (A lot?!) of PhD students' progress in the first year can be unpredictable.   

       {Just noticed - I take it that molecular biology is a superset of genetics, so my "figures" are subject to debate.}
Jinbish, Jun 06 2008
  

       "Oh my God! - this gene causes people to post complex, humourous ideas lacking rigour and practicality on internet fora!"
hippo, Jun 06 2008
  

       //I can haz jene reseach!// marked for tagline.   

       //where you going to get 27,462 half- decent PhD students from?// Yes, I did sort of pluck that idea out of thin air. My lab recruits maybe 50 a year, so I was guessing 1-2000 across the UK in decent departments, then multiply up by the US, Japan, China (who are pretty good), France, Germany, Malaysia.... But it's a soft number.   

       //Get the post-docs to do this// The problem is that most post-docs have formed their ideas about what they want to research on, and are unlikely to be swayed. Students are more flexible, and would do a good job whilst acquiring a good skills set.
MaxwellBuchanan, Jun 06 2008
  

       Shovelling fries in McBurgers is the usual career path .....
8th of 7, Jun 06 2008
  

       //to the point where many will not complete a PhD.// I don't know what the completion rate is elsewhere, but in the UK I'd guess it's well over 90% (I'm speaking only for molecular biology, and only for the labs I know).
MaxwellBuchanan, Jun 06 2008
  

       I think overall in the UK it's about 50% - or it was when I did my PhD. And my grumble about non-completing PhD students: I get really annoyed with people who tell me "Oh yes, I nearly got a PhD - I had about 6 months of writing-up left and then I went and got a job". They have completely missed the point: The last six months of writing-up is the hard bit.
hippo, Jun 06 2008
  

       Plus, if you drop out with "only the writing up" left to do, it's a pretty good indicator that you didn't have anything worth writing up.   

       I'm surprised it's as high as 50%, though presumably that varies across discisplines?
MaxwellBuchanan, Jun 06 2008
  

       // that varies across discisplines//
No, English doctorates have a much lower drop-out rate.
AbsintheWithoutLeave, Jun 06 2008
  

       Yes, fair points. Not sure that the getting scooped issue is a particular concern - the same's true whatever field you pick.
MaxwellBuchanan, Jun 06 2008
  

       sp: gourds
Ian Tindale, Jul 18 2008
  
      
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