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Science

First Sequencing Of Plant Genome 62

Posted by Hemos from the more-information-still-coming dept.
cthugha writes: "The genome of Arabidopsis thaliana has just been completely sequenced, making it the first plant species to have its genome fully sequenced. The fact that we have animal and plant genomes now should give us greater insight into the common aspects of eukaryotic life. Nature has good coverage here. The ABC has a shorter and easier-to-digest report, but the emphasis is on the fact that Australian scientists could not participate due to lack of funding rather than on the technical details."
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First Sequencing Of Plant Genome More

First Sequencing Of Plant Genome

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  • Re:Genetic Sequencing (Score:1)

    by Anonymous Coward
    Mapping and sequencing are different. Mapping is basically identifying major landmarks in the genome and their relationship to one another. Mapping is an essential first step to sequencing, but sequencing goes into greater detail. It identifies every "letter" of the genome. However, while it is a major acheivement, merely having the full DNA sequence of an organism is only part of the puzzel. We still have to figure out what it all means and how it all works. What part of the genome codes for genes? What part of the genome regulates expression of which genes? How do those gene products fold into functional proteins... So, by mapping & sequencing the genome, we are neither figureing out what every gene does in a plant, nor are we figuring out in a vague way what groups of genes do. Instead, we are documenting significant amounts of information which will assist in both those pursuits.
  • WARNING: according to some mail I subsequently received from the investigators at the Max Planck Genome Intitute, the above sequence is incomplete and was intended only as a private communication within their research group. Please don't download it.

  • source code available online (Score:3)

    by jbuhler ( 489 ) on Saturday December 16, 2000 @07:27AM (#554617) Homepage
    If you want to, um, compile your own version of A. thaliana, see

    ftp://warthog.mips.biochem.mpg.de/pub/cress/MAR/
  • Haploid Genome Sizes (collected from various sources):

    Homo sapiens (human): 3.3 x 10^9 bp, # of genes unknown

    Drosophila melanogaster (fruit fly): 1.8 x 10^8 bp, 13,601 genes (if you believe Celera has sequenced it all)

    Caenorhabditis elegans (worm): 95.5 x 10^6 bp, 19,820 genes.

    Saccharomyces cerevisiae (yeast): 12 x 10^6 bp, 5,885 genes.

    E. coli (bacterium): 4,639,221 bp, 4,377 genes.

    Hemophilus influenzae (simpler bacterium): 1,830,138 bp, 1,738 genes.

    Arabidopsis thaliana: 1.17 x 10^8 bp, ~25,000 genes.

    Wheat: 16 x 10^9 bp, ~30,000 genes.
  • While I certainly agree that analyzing genomes will be something that will take decades, it is somewhat misleading to say that a whole organism is thousands of times more complicated than a virus. Yes, viruses only have a few genes, but this is only because most of their functions are handled by the host organism.
  • By mapping the genome, are we actually figuring out the underlying structure of what every gene serves to do in a given plant? (more like a decision tree) or are we just figuring out in a vague way what groups of genes do what (more like a bayesian belief net)?

    Neither, unfortunately. Basically a genome is analogous to the binary code of an executable -- you can't just look at it and follow the logic of the program (or organism, as the case may be). However, there is a field of study called bioinformatics which attempts to extract useful information from the raw genomic data, and in order to do this, many techniques from AI and machine learning are used, such as Hidden Markov Models.
  • Simply put, with finding out what whole genomes do, you get a pretty precise roadmap of what's going on. Not only that, if you can't zoom in too much on one part of the map, you can go find another map that has a similar part and zoom in on that. Got it?


    Well, that's a bit of a stretch. For example, to really understamd what's going on you have to have gene expression information, and you can't get that from the genome -- you have to use microarray data ("gene chips"). And even then you can argue that what you really want to look at is the complete set of proteins and their abdudances (the "proteome") and not the genome at all.
  • The human genome has yet to be fully sequenced. What you are thinking of is the announcements of several draft sequences, with many missing and erroneous areas. The complete sequence won't be available until next year at the earliest.

    Secondly, although I'm all for enthusiasm for genomics, the human genome actually will be (at least for the forseeable future) one of the *least* useful genomes. Why? Because we can't do experiments on humans. When we have sequenced many plants and animals and gotten a good idea of how they work from experiments, then (and only then) will the human genome be of any practical use.

  • Re:Maybe I missed it... (Score:4)

    by Jonathan ( 5011 ) on Saturday December 16, 2000 @05:42AM (#554623) Homepage
    It was picked because
    1) it has a small genome -- many plants actually have genomes longer than the human genome.

    2) Arabidopsis is is a small, fast growing plant, well suited for experimentation.

    It is important that people realize that sequencing a genome is a beginning and not an end. Having a genome means that more sophisticated studies can be done -- it doesn't mean that we now know everything about the plant.
  • Wheat is a hexaploid plant, meaning 6 duplicated sets of each chromosome. It is thought that all wheat is descended from three individuals about 10 years ago. By multiplying chromosome sets new species can arise extremely quickly in plants.

    So, that's why wheat has a lot of genes.
  • Well, I meant 10 THOUSAND years ago, not 10 years. I remember eating bread sometime before 1990 on more than one occasion.

  • The current paradygm in genetics is that life is
    the genetic code and essentially information.
    And it is very complicated to unravel, using one
    of the largest supercomputing configurations on
    the planet.
  • Its been fully sequenced for a decade, yet
    people don't fully understand how it works.
    Image understanding plants or animals with tens of thousands of genes.

  • wheat == five humans (Score:3)

    by peter303 ( 12292 ) on Saturday December 16, 2000 @05:26AM (#554628)
    Quantity is confusing in the genetic world.
    Wheat has 16 billion base pairs or five times human.
    Plant genes tend to duplicate alot according to the first plant genome.
    With regards to animals, the fly genome has only 2/3rds the gene of the worm genome.
    The low end of human of human estimates- 35,000
    genes- is not much more than these plants or animals.
  • Lemme know when they map that sucker, and figure out how to make regular lawn grass produce 60% THC....hehehe
  • Last I heard we had the human genome completed. Why all of a sudden move on to the plant. We were all hyped with what the discovery could do to medicine and how it would change our lives. It seems as if they just filed it away and moved on. I for one would like to see some real life applications to what these scientists are doing. It would be as if I wrote a program that could recover ANY windows crash and just saved it on cd and threw it in my filing cabinet.
  • ...grow your own Drosophilia!"

    I've done that, and you can too. Just leave a banana sitting on a countertop for a couple weeks.

    Yeah, I know, spontaneous generation was debunked over a century ago, and baby Drosophila (Drosophilae?)come from mommy and daddy Drosophila(e). So please no "what are you, stupid?" rants.
  • Thank you for providing a concrete example of the high costs of research. However I don't see that it supports your argument. Oil exploration is expensive too, but you don't see oil companies patenting the use of oil as fuel. (Maybe they just wish they'd thought of it sooner)

    Research is damned expensive and without assurance of return, it's not entirely feasible to invest the resources.

    Assurance? What assurance? There aren't any assurances of a return on investments (for projects like the sequencing of Arabidopsis). There's the off-chance of a return, and big payoffs get more probable when patents are awarded, but it's still not much of an assurance.

    Patents are a means of holding information hostage. I understand the need for them but I don't have to like them. I particularly don't like them when what is being patented is a process that a living organism has been doing for free since time immemorial.

    If I invent a new widget, I have the right to hold the schematics hostage, releasing them only to those who pay. But who invented the gene that codes for usefulase? I don't claim to know, but I'd bet money it's not the one applying for the patent!

    IANAL.

  • Re:Genetic Sequencing (Score:3)

    by SEWilco ( 27983 ) on Saturday December 16, 2000 @07:17AM (#554633) Journal
    This level of analysis has been compared to a map. You can see where the streets are and perhaps the buildings, but you can't see the colors of the houses and the windows and doors.

    Further analysis is needed to figure out what molecules are created by each gene and under what circumstances. For example, neurons have on part of their surface a receptor for serotonin. This "receptor" is a molecule of a certain shape which the serotonin molecule fits into, and when this happens the receptor causes a change in behavior in the cell. There's a gene sequence someplace which builds the receptor molecule and adds it to the surface of the cell -- but this level of genetic maps don't tell us exactly where this gene sequence is and what the shape of the receptor is. Further research is needed to find the location of this genetic sequence, to analyze the exact genetic code, and what molecules that code can build.

    Even that won't tell us everything about a cell -- some drugs work by fitting into a receptor near a receptor whose action they are targeted to block, and the drug works because the rest of its physical shape crowds the target receptor so what usually activates that target receptor cannot reach the receptor. It takes a lot of study to figure out the 3-D shape of the surface of a cell to understand what can be going on in the molecular soup of life.

  • Research is damned expensive and without assurance of return, it's not entirely feasible to invest the resources. Nobody has ever work solely for the public good, you know. Either they are seeking fame or they are being funded by someone higher up who has a vested interest in their results.
    I am an active researcher in the field of plant biology, so
    I can speak with some authority on the costs involved in doing basic research. I have an assay that I do routinely to directly measure the rate of transcription of a single gene, called a nuclear run-on-assay. Each one of these assays costs around 300 dollars to run and takes bout two weeks from start to finish. To get statistically valid numbers, I need to repeat each experiment twice, effectively tripling the cost (900.00) and the time to over a month (And this does not count the cost of paying me). If I want to ask any meaningful set of questions, I am going to need to run a lot more of these under different conditions. Can you see how the cost adds up? It would cost even more if I didn't make a lot of my own materials from scratch.
    Other assays and techniques are equally expensive. A friend of mine is getting ready to clone a "promoter", which is the part of a gene that actually controls how it's expressed. The minimum cost for cloning and sequencing this promoter will be around 2000 dollars. Actually doing experiments on it later will cost even more.
  • Hi,

    > I particularly don't like them when what is being patented is a process that a living organism has
    > been doing for free since time immemorial.

    I couldn't agree more. There is however one class of patents I can "kind of tolerate". I think research done for tax-payers money (ie. at the (state?) universities and gov. organizations) should be protected from the greed of corporations (pharmaceutical and bio|agro-tech in particular).
    Regards,
    kovi
  • Like other have said, other organisms can (and many do) have more base pairs than we do - just like they have more chromosomes. For instant, a fern plant has something in the ballpark of 1200 chromosomes! Compared to us, you would think the fern is a super-being. However, there is much less information per chromosome in the fern, whereas in a human chromosome, the information is much more dense. It is nature's way of making things more efficient perhaps. Just because there is more "Stuff" there, that doesn't mean there is more information in the stuff. Remember, quality, not quanity. :)
  • I was working there for little while during the summer. The way they explained it Arbidopsis is a very genetic plant and can be thought of as the mother plant or something like that. Cornell's department was trying to see links between arabidopsis and the tomato plant.

    And as someone else pointed out earlier, sequencing the half the job. The actual research goes in when the sequences are clustered and compared against other sequences. Anyway, good day for plant science.

  • This is an honest question.. If there are thousands, millions, or billions of genes in an organsim, and I decide to make a subtle change to one of those genes how can we predict the effects of that change on the organism as a whole??

    Let's simplify the problem a bit.. Let's say there are 10 genes in the organism of interest. We have no equation, or set of equations, to govern the response of the system to a change.. So the best option we have requires some sort of empirical approach. So I gather up a large subset of the population, examine each, and note their differences. Then I'd compute something like a two-point correlation tensor.. So if I have 10 genes and, coincidently I find 10 differences, that's a 10x10 matrix of relations between the "causes" and "effects". So that's not bad, right?

    Wrong.. This is a non-linear system, and a subtle change in one gene may have an enormous impact on a handful of genes. Then another subtle change in a second gene, may negate the effects of the first change.. I'm curious what sort of training the geneticists working on these sequencing problems have with non-linear systems?

    This is not an attack: I'm curious.. I've spent a lot of time over the last few years trying to get a handle on the inner workings of simple turbulent flows, and even with a set of governing equations to guide my efforts, the problem of predicting how subtle changes will affect my flow is non-trivial!.

  • you are assuming that all gene are created equal. The likely metaphor might be a little like blue-print of a house. what happen if we change something randomly? will the house collapse? hot water pipe explode? or just the door handle kinda get crooked. plus, the gene map is pretty robust, mother-nature is no full in creating live. She device way to handle copying error.

    Well.. I certainly agree that Mother Natue is pretty bright, and anyone who doesn't see that is pretty crazy.. But my point is that you're thinking about things in a VERY linear way.. A change in one gene has one specific quantifable effect. That maybe the way the genome works, but I'd be pretty surprised.. I prefer to think of it like I do with turbulent flows.. The genome is a set of initial conditions (input parameters) and the equations that govern the flow, or life in this case, are nonlinear and extremely sensitive to initial conditions. Small changes in the initial conditions can often be used to make enormous changes in the mean flow.. Don't believe me? Go take a look at some of the literature on "Turbulent Flow Control", where an excitation consisting of 0.001% of the mean momentum of the flow can occasionally be used to persuade a normally separating flows to reattach..

    Let's think about this as a large software project.. You change a couple subroutines very subtly. Those changes may have little or no affect on the parameters you're monitoring, BUT what about the parameters that fall outside your view.. This may not be a huge problem when we're writing and compiling code for chips we have the specs to, but what happens when you're trying to code a "processor" that has an unknown set of parameters?.. Right now there are effictively an infinite number of possible solutions to the human genome. So, we have no equations and a whole bunch of unknowns!!!

    I'm not entirely opposed to the idea of trying to reverse engineer the human genome (basically we're looking at the assembly for a processor we know nothing about, right?).. My concern is that we can't keep track of all the variables as we tweek the gene sequence.. Attempting to classify the internals of this black box is not as easy as passing white noise to it, and watching a few output ports.. How far can gene 2.2.18 be tweeked before the system becomes unstable?

    Mother Nature has a great mechanism for eliminating copying errors.. Typically they're referred to as diseases, or mutations, and those errors usually weed out copies that are "weaker" in one form or another. That's sort of the premise of evolution as I understand it..

  • (Disclaimer: my day job is as a sysadmin at one of the Human Genome Project centers, but I'm not a biologist or bioinformatics specialist.)

    First off, as others have noted, the human genome isn't "completed"--the draft version is "substantially complete," which in genomics terms means about 85% complete with lower than expected quality and lots of gaps. (Actual finished-to-the-full-spec sequence is about 33%, and an additional third is "deep shotgun" which is good quality with some gaps.) That doesn't make it "not useful", it just means that the whole thing isn't finished yet. This will obviously delay the availability of specific applications developed based on the data.

    Second, as another poster has mentioned, it's not exactly practical to do genetics experiments on humans. Even if you ignored the ethical and legal problems involved, generations are too long. Fruit flies, plants, and mice are much easier to experiment with, especially when you're trying to figure out what a specific gene does when it's mutated or disabled. Those experiments can then be used to guide research into homologous genes in humans.

    Third, there's the whole area of comparative genomics. As I mentioned above, it's much easier to figure out what a gene does when you can experiment with it and compare it to similar genes in other organisms. The more organisms you have, the more useful comparisons you can make.

    Finally, it's still early days for genomics. The completion of the human draft sequence was not the beginning of the end, but the end of the beginning. To use your example of "a progran that could recover ANY windows crash" it's closer to the situation where we now have a hex dump of all of Windows 2000; quick! Debug it! Make it work better! Now imagine that instead of having code that's been consciously (arguably even "intelligently" at times :-) designed by multiple people since 1980 or so, it's code that's been hacked on by nature for millions of years...written for an architecture you have no instruction set list for...and uses all those self-modifying code tricks that old copy protection schemes had. Have fun!

  • Aside from what's already been mentioned, scientists have traditionally had certain 'model organisms' which are intensivly studied and then used as models for other organisms. White mice, E.coli, arabadopsis etc.

    There are a disproportionate number of papers detailing the workings of E.coli.

    I'm not sure how long arabadopsis has been a model plant organism- whether before the start of the human genome project or not.

  • Didn't you see all those pictures of tobacco plants that had the gene that allowed metabolism of luciferase from fireflies? Water the plants with water containing luciferase and they glow. Now why they couldn't also put a gene in so that you didn't have to water them with luciferase, I'll never know. I would have bought one.

  • To state it in a form that may be relevant to a programming mentality; how else would you go about testing a program which was essentially self modifying?

    i.e. some genes can regulate the expression of other genes.

    You can figure out that some variables may affect a particular portion of the program.

    Of course, just because one gene produces one protein, this dosen't mean that one protein only has one use. Just as variables can affect several parts of a program, enzymes can take part in a number of very different metabolic processes.



  • A lot of biological systems tend to 'normalize' themselves. Inject yourself with a 1 cc of sugar water and your body will return itself to normal in less than an hour, most likely. I'm assuming, that would make initial conditions in the physics sense a little less important, especially since biological output tends to be much more fuzzy to begin with. Anyone want to contradict me here? I'm not a biologist, though I ended up taking an ungodly number of life science courses in school. They've come in quite useful on Slashdot :)

  • related story.. (Score:3)

    by gargle ( 97883 ) on Saturday December 16, 2000 @04:42AM (#554645) Homepage
    Cornell researchers have used the genome sequence of the Arabidopsis to obtain information on its origins as a species. See here. [cornell.edu]
  • Haploid Genome Sizes (collected from various sources):
    A more comprehensive list of genome sizes is here:
    http://www.cbs.dtu.dk/databases/DOGS/abbr_table.by size.txt [cbs.dtu.dk].
    These pages show how much of each organism is finished and publically available:
    http://www.ebi.ac.uk/~sterk/genome-MOT/MOTgraph.ht ml [ebi.ac.uk]
    http://www3.ebi.ac.uk/Services/DBStats/ [ebi.ac.uk]
    Arabidopsis thaliana: 1.17 x 10^8 bp, ~25,000 genes.
    25000 genes is near the low end of the range for the estimates of the number of genes in the human genome:
    http://www.ensembl.org/Genesweep/ [ensembl.org]
  • Together with Celera maps Fruit Fly genome [slashdot.org], what is the best guesstimate before biotech companies will create the fruit fly-fruit plant chimera?

    5 years? Can we expect banana plantations buzzing away towards the local refuse depot? And who'll be eating those bananas anyway?

    Or maybe we will have "fruit fly seed pots -- grow your own Drosophilia!" or so...

  • After careful consideration for quite a few long moments, I can't decide if this is a good thing or not!

    On one hand, we have the potential for greater understanding.

    On another, we have the potential for some crazy shit.

    On still another hand (for you freaks that have three hands, heh), neither of the two cases could be the case, in which case it is neither good or bad, but just another tidbit of information to be archived on /. and eventually float off into cyberspace...

  • The plant can't have more genetic information than us.

    Why not? :) (but in this case, it doesn't...)

    The Nature article talks about giving away 5000 CDs containing the data, and mentiones somewhere that the dataset is 120 Megabytes.

    No, it said 120Mb, which is 120 mega base pairs... geneticists don't talk about DNA in megabytes :) The ABC article seems to be off by 3 orders of magnitude. I think the human genome is around 3 billion base pairs, so it's probably right about that.

  • (And just how much information is there per base pair? Is my translation of four nucleotides to 4 possible states (2 bits) correct?)

    If you want to think of one base as being the same as two bits with four possible states, that's fine. In class, they told us to think of it more as an alphabet with four letters, but that's just another way to visualize the unvisualizable.

    What makes it tricky is that it's a group of three bases together that actually expresses for anything. Therefore, out of your three-bit word you can express up to 64 different items. Each "word" codes for one amino acid, and there are only twenty-odd of them known. Whatever makes a protein more unique than the steak I'm grilling now is the number of amino acids present and the order they're in.

    And if I got anything wrong, it's because I'm an ecologist and not a geneticist, but /. never does anything on centrarchid feeding behavior.

  • Last I heard we had the human genome completed. Why all of a sudden move on to the plant.

    It ain't finished. The Human Genome Project still has an awful lot of the human genome that isn't sequenced and that they don't understand. The reason for researchers to work on this plant is that it a: may be a little simpler than humans; and b: has a very fast generation time: months at the outside in the lab, vs. 20-30 year generations for humans. Shorter generations mean that whatever crops up can be recognized and assessed sooner.

    We were all hyped with what the discovery could do to medicine and how it would change our lives.

    Changes don't happen overnight. We've known what virii were for decades, but still don't have a cure for any viral diseases. We have some understanding of how fusion works, but we still burn coal. And we know how to make a stable OS but 90%-plus of the desktops in the US still use Windows.

    It seems as if they just filed it away and moved on. I for one would like to see some real life applications to what these scientists are doing.

    There's more than one team working in genetics right now. In the US there are easily a few hundred research universities with genetics labs, not counting CDC, NIH, and some very fine labs overseas. They're not all going to be working on the exact same things.

  • Alrighty then....

    First off (and I'm not being deliberately snotty here), we're not talking about physics here. Current biology has nowhere near the decimal point accuracy, etc. that modern physics does.

    Let's talk about bacteria (since it's a simpler problem - but most applies with minimal changes to studies of other organisms). Let's, furthermore, say I am interested in something like nutrient uptake. There are proteins on the cell surface which are involved in either passing (or not passing) external molecules to the cell interior. It is possible (let's not get into details) to get a good idea as to which surface proteins are involved with passing different classes of external molecules into the cell.

    ok then. I have a protein of interest, I have a 'behavior' of interest, what next? believe it or not, the next step is usually trial and error. I induce mutations in the bacterium (by x-raying it or adding some chemical to a culture, etc.) and look for colonies that do weird things vis-a-vis my system of interest (in this case uptake of some particular nutrient - since this is /., let's say caffeine).

    As bacteria reproduce like crazy and I have induced mutations in a population of, literally, millions of individual bacteria - there are bound to be some which do funky things as regarding caffeine uptake. I cannot attribute this necessarily to some change in my protein, but I can check the interesting mutants to see if my protein is different from the 'normal' sequence. If it is not - well then, no change in this protein is directly involved in the funky behavior. If it is changed, there is still much more to be done.... because, of course, it may be that some other mutation elsewhere produced the new, funky behaviour, and not my new, improved protein of interest.

    One then zeros in on the effect of the changed protein by inserting or otherwise point mutating 'wild-type' bacteria to attempt to determine what effect the changes in sequence have... etc..

    of course, having written all this, I realize that I haven't answered the question you asked. And the answer is that biologists, especially molecular types like me, don't predict!

    We create mutants and see what happens. You would be astounded at the number of different mouse lineages out there with specific mutations and disease susceptibilities. If something is eventually to be used in humans, you start by seeing what it does to mice, move on to monkeys, then move on to human cells in vitro (cells in a tube, basically), and finally if animals/cells are not dying, etc. move on to trials in humans.

    Prediction would be nifty, but even with whole genomes, its just not in the cards for the near future.

  • You misunderstand some of the key concepts of genomics, and the history of genomes and patents. First off, though, I'd like to point out that "enormous effort" should not justify patents- they are only supposed to be granted for "unique and non-obvious inventions" or something like that. Genes do not meet any of these qualifications, as I'll explain later.

    A common and utterly incorrect assumption is that Celera beat the crap out of the HGP. This misses the mark completely. Celera's sequencing technology is fundamentally more risky and would never have been considered when the HGP started. It mostly relies on massive computing power to assemble overlapping sequence fragments, and on the high-throughput sequencers Dr. Venter helped create. This approach is increasingly considered to be scientifically sound and much more efficient- but only thanks to a decade of advances in computing power. Imagine trying to assemble DNA on a SPARCStation 1 instead of on a brand-new P4 or AlphaServer.

    Certainly Celera's progress spurred the HGP on, and I think the best result of this may be the refining of the "shotgun" technique. However, it is absurd to say that Celera should get patents for its "enormous effort" when the HGP's approach was in fact much more difficult.

    The genome itself cannot be patented; Celera is charging a hefty subscription fee for access to the mouse genome, but a public project will release their own results in the spring (though unfortunately mouse genes will have by then been snapped up by biotechs). The standard for patents on genomic data is ridiculously unclear; single-nucleotide polymorphisms appear to be patentable now. This has led a large public-private consortium mapping these polymorphisms to withold scientific data from everyone out of fear that rival biotechs will steal the results and patent them.

    It isn't that hard to find a gene. Do you think companies will perform gene knockout experiments on humans? No, they'll use a gene-finding program, many of which exist. Hell, my lab is doing this now. On the simplest level, all one needs to do is identify suitably long open reading frames (ORFs) and check for homology to known proteins. The only real limitation is how many and how fast your computers are. It's not rocket science; a basic understanding of genetics and some good Perl code will do it. This doesn't prove anything is a gene, but the USPTO probably won't give a shit if it sounds interesting.

    A researcher from a local biotech recently boasted of their "patent wizard"- fill in the blanks and you've got a 10-page patent application. This is why patents scare the shit out of so many people. I'm afraid that by the time I'm out of grad school there'll be so many patents that any research I do will have to dodge licensing provisions just to be completed, or that any results of mine will have to be suppressed for fear of lawsuits from biotechs.

    This sort of bullshit could destroy public scientific research and destroy America's leadership in this fields, and I'm upset to see people promoting the free-market/privatization view with little or no understanding of the field.
  • I thought the public could get copys of this stuff. Where is it?
  • I am curious, for those Biology buffs out there (I suck at it), how revealing is genetic code to understanding how things are made? What do I mean? Well, for example, if you looked at artificial intelligence, some methods (decision trees, bayesian belief networks) show you as a person information about how decisions are being come to, but others (neural networks, genetic algorithms) tend to be more of a black box.

    By mapping the genome, are we actually figuring out the underlying structure of what every gene serves to do in a given plant? (more like a decision tree) or are we just figuring out in a vague way what groups of genes do what (more like a bayesian belief net)?

    (Obviously, a having the understanding at the "neural net" level implies no mapping at all, so it can't be like that.)

  • I thought the public could get copys of this stuff. Where is it?

    It's in your cells. RTFM!

  • what they patented is the enormous effort that those companies expended in discovering a secret that I could never have discovered on my own.

    I think patents have more to do with non-obviousness than with hard work or dollars of investment. The investment is just a side-effect of state-sanctioned monopolies. The effort required in not considered. I could have a flash of intuition in which I come up with a brilliant new patentable device. My research investment was zero (or quite small, at least) and yet my invention still qualifies as patentable. Non-obviousness is becoming more difficult for inexpert (or even well-trained) bureacrats to correctly determine. That's why it seems to me that intellectual property protection is nearing the end of its useful life. It was useful and effective when mail travelled by horse, but today it does more to benefit lawyers than the public.

    If there hadn't been a chance for serious financial gain, the sequencing would have taken years longer.

    I'm no expert, but wasn't the issue more one of logistics and methodology rather than just brute financing? Celera, if I remember correctly, claimed that they could sequence genes more inexpensively than the NIH. The money was already there. The method that Celera used could have been implemented without the help of venture capital.

    Would you have set the whole process back that far just so you didn't have to worry about some licensing fee?

    I think the original post was raising ethical concerns rather than financial ones. I imagine that even with gene therapy, one can only charge what the market will bear. So the cost of "renting" genes to patients would have to be within reason. It's not the money that worries people, I think. We all assume that we have to spend money to live. Most people would be more upset that a corporation or a government could own parts of their bodies.

    Can you see where that same rejection of capitalism would have utterly crippled the advancements of the computer industry over the past 30 years?

    I don't see

    • How this person's post is a criticism of capitalism
    • How you arrive at the conclusion that an ideological rejection of capitalism could affect the computer industry. Business is business. Capitalism is just an idea
    Computer innovation could (and did) take place in communist countries as well as in capitalist ones. People's minds are filled with wonder and imaginative ideas no matter what political philosophy they espouse.

    Without those computer advancements, we wouldn't have been ready to undertake the sequencing of genomes for decades. Can you see how these advances build upon each other, and if a system like capitalism can help us to build faster, it's probably a good thing?

    Advances can only build upon each other if people are reasonably free of constraints preventing them from utilising existing technology. Some may argue (I'm one who will) that patents have as much negative as positive impact in terms of stimulating new development based on existing material.

    Secondly, you assume that building more and faster, regardless of the direction, is something desirable. Many people would disagree with you, including me. I'm not against technological progress, but it is irresponsible of us as human beings to offer wildly advantageous conditions to producers (aka patents) at a time when caution is demanded. Sure, if you offer a free gold bar to everyone who does some research lots of people will do research, but is that the wisest way to marshal the resources of a civilized society? Not everyone would agree that it is.

  • The plant can't have more genetic information than us
    well it can, a lot off species have more base pairs then a human(If I remember my biology class correctly) it's all about redundancy and also a lot of info isn't used at all(well you could say there's a whole lot of cruft in in us)

  • From the ABC article: (Score:3)

    by Moderator ( 189749 ) on Saturday December 16, 2000 @04:39AM (#554659)
    "These genome projects are the way to gather intellectual property positions, for example if we identify the function of a useful gene we could patent it. Without participation in this type of pure research, we will be left behind."

    This is a shame. All that scientists are worried about these days is patenting the genome of something so they can get rich. Whatever happened to research for the benefit of mankind? Whatever happened to putting politics aside when it came to science? A damn shame.

    --

  • Au contraire, I read both the Nature pdf file end to end and the ABC article. I did not come across anything that would answer my questions. I was a physicist, not a biologist, nor do I remember my grade school biology teaching us the difference in the number of bases between species (doesn't mean they didn't tell us, just means I don't remember every sentence 12 years later).

    But I will agree, my post didn't deserve a 4. When I wrote it, I distinctly thought to myself "this isn't worth any points, but some of the answers might...", so I of course didn't use my +2.

  • Contradictions... (Score:5)

    by ckedge ( 192996 ) on Saturday December 16, 2000 @04:53AM (#554661) Journal

    There are some strange contradictions in the ABC article.

    It first claims that "The sequencing of 118.7 billion base pairs of the nuclear genetic complement of a model plant is enormously significant". Then it says something near the bottom regarding "the 3.2 billion base pairs of the human genome". So what's going on here? The plant can't have more genetic information than us.

    The Nature article talks about giving away 5000 CDs containing the data, and mentiones somewhere that the dataset is 120 Megabytes. So I presume that is compressed, down from the 3.2(*2) billion bits that ABC quotes. Are these numbers accurate? (And just how much information is there per base pair? Is my translation of four nucleotides to 4 possible states (2 bits) correct?)

  • Is this interesting? This implies we already can understant human genome? No.

    Doing a comparison with computers: If you had the binary executable of a program of an architecture you don't know... how would you suppose what means every bit of this file? And, the most important, how would you discover the instructions this processor can understand?

    The "solution" is to search for species with small sequences of DNA and compare to others. Finally you could try to modify some of this to see what changes in the final individual. But we won't get anything in a near future, perhaps we won't see any real use for this in our lifes.

    --
    To visit or not to visit: findusclub.com [findusclub.com]

  • I just finished with a class that touched on the genome mentioned here. Most of the gene functions are, as has been mentioned earlier, deduced by comparison to other genes of known function in other species. This is usually done using algorithms like BLAST/PSI-BLAST/Gapped BLAST (Basic Local Alignment Search Tool) that compare sequences in question to data stored in a large database like GenBank. More information on these topics can be found at the National Center for Biotechnology Information [nih.gov], run by the National Library of Medicine at the National Institutes of Health.
  • I'm not sure if they're finished or not, but why isn't it helping us? THESE BASTARDS [uspto.gov] let them have a patent on the DNA that is in every single one of your cells (well, half in gametes, none in red blood cells..), so if I wanted to make a genetic therapy to say, fix colorblindedness, I would have to pay one of the Human Genome project's sponsors.
  • Very good opinion on what i see as the "other side", however, I still see the patents as a hinderance. Joe Startup can't, say, make a genetic cure for cancer and then get a license for it without some serious serious venture capital. If these companies weren't so greedy, they could (im no open source zealot) patent it, but "open patent" it, as in, say, Joe Startup can make and patent their cure for cancer, but Joe Patentholder gets rights on the cure for cancer, too. Perhaps that could work?
  • ...but was there a reason why this plant was picked? Some obscure scientific reason? Because it is a 'simple' plant? Because some scientist was on a walk decided to pick the first interesting looking weed he found?

    Kierthos

  • When you say similar what exactly are you comparing? Physical appearance? Certain characteristics? (if so which ones?) or is it sequential data (i.e. DNA or something along those lines) within these genes.

    I am not a biologist and the realities of this concept eludes me.

  • hahaha, you are sooooo wrong. read up on it. This genome sh1t is cool. Already researchers are talking about the 'post-genomic era' and the differnce it'll have on research. Comparing the human genome to a computer program is just plain dumb. OK so they may have analogies, but it is veerrryyy different
  • Cos there isn't a species that _isn't_ being sequenced at the moment!

  • To be truthful, it's a little bit of both. There are some genes which are common across life, including humans, so we have a general idea of what they do already. Even if we don't know the exact function of the gene, if we know it's similar enough to another gene, it's a decent start.

    For example, I just did a project for a class where I had to analyze all of these different gene sequences. Though the exact product of one of the genes was not known, it was easy to deduce from other data. Therefore, in a weird way, if you have a vague idea of what a gene does, you can design experiments to find exact what it does. Also, this capability extends across organisms. If I know a gene in humans is similar to a gene of a known function in A. thaliana, I could design an experiment to find out more specifically what it might do in humans. I hope this clarifies stuff.

    Simply put, with finding out what whole genomes do, you get a pretty precise roadmap of what's going on. Not only that, if you can't zoom in too much on one part of the map, you can go find another map that has a similar part and zoom in on that. Got it?

    Oh, and please feel free to trash my gene analysis program code. http://www.eden.rutgers.edu/~tbghtown/code [rutgers.edu] :)

  • I agree that the notion of giving a patent to someone for something I have inside of me seems intuitively unfair. But looked at another way, what they patented is the enormous effort that those companies expended in discovering a secret that I could never have discovered on my own.

    If there hadn't been a chance for serious financial gain, the sequencing would have taken years longer. Maybe even a full decade.

    Would you have set the whole process back that far just so you didn't have to worry about some licensing fee?

    Can you see where that same rejection of capitalism would have utterly crippled the advancements of the computer industry over the past 30 years?

    Without those computer advancements, we wouldn't have been ready to undertake the sequencing of genomes for decades. Can you see how these advances build upon each other, and if a system like capitalism can help us to build faster, it's probably a good thing?

    With that said, I don't think that issuing patents for things should be undertaken lightly. We have to weigh the benefits of encouraging capitalistic interests to make tough discoveries vs the detriment of letting greedy companies squat on obvious discoveries. It's not as black and white an issue as your original post depicted.
  • Okay, now we can really start working. Up until now the genomics community has had to do very labor intensive sequencing of any genes it wanted to investigate. Now, however, we can do the really interesting work of finding out what all of these genes actually do, and even what it means to be a gene! Considering we already have worm, fly, and several bacteria genomes, and that mouse, rat, puffer fish, and zebra fish are coming soon, we should see a huge explosion in the comparative genomics field.

    We now have the book of life, let's learn to read.

  • I believe the A. thaliania Genome Initiative website lists the total sequence length being around 118 million bases. 2 bits per base pair, you are correct. But you are wrong that plants can't have more genetic information than humans. Many organisms can and do have a lot more genetic information that us. What will be really significant is when all of the alleles of all of the genes are known.
  • The number is indeed wrong... It is about 118Mb...

  • HOW? I can't! Please use tt as well.

  • Thanks for modding me as a troll. I'm so happy I'll forget all the markup now.

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