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Science

Human Chromosome 22 Mapped 208

Posted by jamie from the frame-thy-fearful-symmetry dept.
tuck was the first of many to submit this important milestone in arguably the world's most important scientific endeavor. The Human Genome Project has completed mapping its first entire chromosome, number 22. Second-smallest of our 23 chromosomes, some of 22's genes can cause "heart defects, immune system disorders, cancers, schizophrenia and mental retardation." Portion of its DNA which is "junk" (encodes no protein): 42%. Read it at your favorite source: CNN, MSNBC, the Boston Globe, the Christian Science Monitor, the AP, or Reuters.
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Human Chromosome 22 Mapped More

Human Chromosome 22 Mapped

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  • Whos chromosome did they map? (Score:2)

    by Anonymous Coward
    I could be asking a stupid question here (blame it on my genes), but since everyone has different DNA, how do the scientists decide which genes are normal? I mean, if there is a hereditary disease that only a very few people get, you probably decide that the 'healthy' gene is the more normal gene. But what if the gene f.e. encodes eye-color, how do the scientists decide what gene to map? Or do they simply say that that and that gene encodes eye-color and leave it open what DNA sequence it has?
  • Just one more afterthought. There is a basic difference in sequence strategy between the HGP and TIGR.

    HGP does it by "clone by clone" strategy. That means, the chromosome is cut in smaller pieces, then again in even smaller pieces, the pieces get cloned (cloning in molecular biology means not the Dolly sheep: it means, a certain sequence is inserted into a epigenetic element called plasmid, which itself can propagate and thrive in bacteria), and then sequenced. This is cumbersome and requires a lot of manual work, but it provides unmatched quality of the sequencing.

    TIGR adopted another strategy, the so-called shotgun method. In this strategy, you get a sequence, but you have not the slightest idea where from the genome does it come from. Only you when you have a lot of this sequences you can start assembling - using a lot of CPU, trying to match them one to another, like a puzzle, but trickier: a sequence often contains errors, especially at the end (you can only read a couple of hundreds bases, then the signals are to weak and not clear enough). This strategy requires considerably less highly trained man-power: just a lot of technicians and $$ for expensive sequencing machines (which were provided to TIGR by Perkin-Elmer). However, this method has a serious drawback: there are many sequences in the human genome, which are partly, or totally repeated. This repeat elements can be a royal pain in the sequencing project (been there, done that).

    It is really a good thing that there are two sequencing project with two different strategies: the comparison between the two sequences could provide an enormous insight into a) quality of the sequencing b) human variablity. Venter from TIGR is definitely an enfant terrible, but I don't think he is one of those corporate Bad Guys (TM), rather one who was fed up with the slow pace of conventional scientific projects. On the other hand, HGP, representing "the slow pace", shows us also why a slow pace is needed sometimes.

    Regards,

    January

  • And indeed there are a lot of repetitions in the code. But there's also a simpler reason: only 4 characters are used, so the uncompressed data uses only 2 bits for every 8. Naturally, compression will reduce this to 2.25 bits at worse.
  • Scientists have finally deciphered the genetic code in chromosome 22, discovering the following fragment buried in what was heretofore considered "junk" DNA:

    ...ulation. Instantiation of this code without permission from the author will result in prosecution under applicable galactic laws. This organism is not to be released into the wild except under the supervision of duly appointed and authorized zoological wardens. Consequences of uncontrolled release may include defoliation of local environment, mineral resource depletion, climatic disruption, and unpredictable emergent properties possibly including artistic expression, spontaneous organization, and Monday Night Football. Recommended diet includes a variety of choices from among the following species: 84472626819, 84471836247, 84472464755, 84472...

  • I dunno for sure about Sanger, but WashU and Whitehead in the US are working from the same clone library.

    At the Sanger we've historically been using the RPC-1 library from Pieter de Jong's lab. I have been told several times that the individual can and has been identified. I was told a name as well. More recently we've been moving onto other libraries based on anonymous panels, such as the RPCI-11.2, from the same lab.

  • Not quite true. Sometimes the presence of a particular gene can cause a problem in an area where most random pieces of noise would cause no problem. Not common, but...

    Think of a program that has a statement like:
    qwerty = null;
    where qwerty is some random string of characters. Most often this will have no effect, but if by happenstance it matches the name of a variable that's in use, then a program bug can arise. Occasionally this may fix a bug, but that's not the way to bet.
  • All joking aside, I think you're very close to the mark. But it isn't commentary on the code, I believe it is in fact commented-out code. Or fragments of commented-out code. What happens if a random mutation "uncomments" a section of code comprised of leftover bits of old code that aren't in use anymore? Evolution.
  • Actually, natural selection ensures that it is an efficient process. The more DNA in a given cell's genome, the more energy and the longer time it takes that particular cell to replicate all of its DNA and divide/reproduce. Therefore, it is beneficial for the cell to get rid of any DNA that is not absolutely necessary. You can actually see this working at bacteria; engineer a run of random DNA into a bacterial genome, and you'll see that after a few generations, the cells that have managed to (randomly) excise the extra DNA will grow faster and more efficiently than cells still carrying around the extra baggage. This is where "survival of the fittest" kicks in," allowing the more efficient cells to dominate the population
  • In addition to the types you mentioned, you also have DNA that is not only useless to the organism, is also harmful. For example, a virus may insert itself latently inside the DNA of a germ cell, inadvertantly adding itself to the evolutionary pathway of that species. Should the DNA stay latent (or, more likely, undergo a mutation that keeps it from being expressed), it ends up being a "time bomb" waiting for the right time to be expressed.

    Mice happen to have a lot of this viral DNA, which tend to act as oncogenes (cancer causing genes). Mice (just like everything else) accumulate mutations over their lifespans, and as the mouse gets older, the likelihood of a mutation activating an oncogene increases, until one day the mouse ends up with a tumor. This is a common cause of death for mice.

    As you pointed out, Eukaryotes are big and complex. They are also still "works in progress". Some people seem to think that evolutionary pressures have created the lean, sleek, perfectly adapted creatures that humans are today :) But the thing to remember is that there are also evolutionary pressures for other DNA that doesn't necessarily jibe with our own interests.
  • Cheers, Sean, and congratulations once again on this important milestone.

    Personally, though, I think public money should go to a myriad of smaller projects instead of one big Manhattan/Apollo style push that sucks money from everywhere else.

    If the private sector is willing to plunk the $$$ to sequence genomes, I say let 'em do it and give them patent protection as a quid pro quo.

    But that's just my opinion, not like you asked for it or anything. Cheers!

  • Re:Junk DNA (Score:1)

    by Anonymous Coward
    The appendix is part of the intestinal immune system. AFAIK, it modulates it, and also allows a handy springboard for immune cells into the stream of material that original came from the outside. It also gives a home for some "friendly" bacteria. Without it, people are less well equipped to handle opportunistic infection. It's analagous to the tonsils.
  • Of course there are some cases when it is known exactly how a genetic disorder causes a certain type of illness - you all know of the Down syndrome, thalassomy, sickle cell anaemia - but there is *a lot* more.

  • Imagine hiding easter eggs in junk DNA... Bend the frog's arm the right way and it croaks the genetic engineers' names....

  • The HGP is like the Periodic Table (Score:4)

    by wowbagger ( 69688 ) on Thursday December 02, 1999 @03:18AM (#1488242) Homepage Journal
    The analogy I like to use for the Human Genome Project is the development of the Periodic Table of elements.


    Of itself, the periodic table didn't make any new chemicals. What it did was provide a framework to identify patterns that could be used to predict areas of research. For example, the discovery of helium: the table predicted the existance of the element, and allowed calculation of the spectral lines. The element was then identified in the sun, hence the name (helium, from helios, the sun).


    Similiarly, the HGP of itself won't cure any diseases; rather it will allow the mapping of patterns. We'll be able to say, "This gene, which we know does this in wheat, is present in humans. Perhaps it does the same thing?".


    Once we get one copy of the human genome sequenced, we'll still need to sequence many others, from [tall|short|skinny|fat|bald|hairy...] people, and start cross-referencing the results.


    Think of it as a massive reverse engineering project on a program we only have uncommented object code for.


    Unless the "junk" DNA are comments...

  • The pairs are not identical. Each gene on a cronosome refers to another on the second half of the pair. Some genes are dominant and others are recessive. If a gene is dominant than the behaviour to prescribes is used, recessive genes only surface when bothe genes across the pair are the same ie. brown eyes+brown eyes=brown eyes, brown eyes+blue eyes=brown eyes, blue eyes+blue eyes=blue eyes. It is the differance between the chronosomes in a pair that make us what we are. This also explains why males are more prone to some conditions- ie hymaphilia(sp?) A recessive gene on the X gene is not dominated on the Y chronosome as that gene simply is not there- where as females two of these genes to get it.
  • ..introns. These are base pairs which don't get expressed, however they still are important in how exons are expressed.



    There I've explained that in a sentence even a fool can undertand. Junk DNA my adenosine. Either sloppy journalism or else the researcher explaining this to the journalist was sloppy.

  • It'll be interesting to see if male and female lifespans are equal in another 200 years or so, after sexual equality has been fully established.

    According to Desmond Morris' The Human Sexes [discovery.com], recently rerun on TLC, men's life expectancy was several years longer than women's for most of recorded history.

    It has been only in this century that women's lifespans have caught up with, and exceeded, men's -- Morris attributes this to improvements in medical care, specifically the dramatic reduction in the number of women who die while giving birth.

  • Interesting point, who is the John Doe, whose genes are being mapped ?

  • Of course there are some cases when it is known exactly how a genetic disorder causes a certain type of illness - you all know of the Down syndrome, thalassomy, sickle cell anaemia - but there is *a lot* more.

    DAMNED!!! Why can't I send a cancel message? :-) I pressed the "Submit" button again! Grrr....

    Back to the topic. There are cases, when finding one single disorder which causes one specific disease is easy. There are cases, when you can pin down a certain region - by tracing the genetic tree of the family, whose members have the disease. There are cases, where you are able to tell that - well, there *is* a genetic component of a certain disease. In some cases, you can tell two forms of the disease: a genetically inherited and a genetically independent form (e.g. the early-onset Alzheimers and the age-dependent Alzheimers disease).

    There is yet one thing you have to keep in mind: there is no "gene causing disease X". It's rather: "a gene, whose malfunction or absence causes disease X". For example, a single nucleotide substitution can result in a non-active enzyme, or an enzyme with much slower activity. The whole metabolic pathway, to which this enzyme belongs, is hampered. In some cases a heterozygous organism will have another copy of the gene, which will do the job, or do the job at least in a part - and the disease shows fully in homozygous organisms.

    Regards,

    January

  • My friend says that this is not a real disease. She insists that it would have something to do with the neurons in your stomach and muscles and brain muscles. Doesn't exactly make much sense. I for one believe you, but maybe I am a worthless fool. Please clear this up for us.
  • Probably a stupid question this but who's DNA is being mapped here? Is it someone alive? Is it one or many individuals?

  • Hemophilia is an X-linked recessive disorder. The reason why it is much more prevelant among males is that if a male inherits the recessive allele from his mother, he is hemizygous (expressing the trait in both the recessive and dominant condition) This is because a male has only one X chromosome. A female would have to be homozygous (carry both mutated alleles) in order to be affect. A woman's odds of having hemophilia are about 1 in 100 million,but not impossible.
  • I thought human beings had 46 chromosomes?
  • certain genes have already been patented by pharmecutical companies, largely the insulin gene. If you have a working insulin gene, it's been patented. Some genetic researches have patented whole fragments of code, and are now working on deciphering it.
  • we have 23 PAIRS of chromosomes, for a total of 46. I think. someone tell me im not smoking phillipino crack rock here.
  • You're right... Actually, I think there are 23 *pairs*, and each of them consists of two identical chromosomes.
  • IIRC, we have 21 pairs of autosomal chromosomes and 2 pairs of sex chromosomes (X is sex-linked, Y is sex-limited). Remember that meiosis leaves gametes with only one set of chromosomes, so you're guaranteed to inherit half your chromosomes from each of your parents.

    (This is all an oversimplification, I'm sure.)

  • Most genes have a "normal" important function, and when the gene is mutated in some way, and ceases to "do its job" that genetic disorders occur. In cases of genetic metabolic diseases, mutations that cause a loss of function in a single enzyme can have many pronounced effects. In the case of Cystic Fibrosis, the gene that it was mapped to (q31 of chromosome 7) produces a protein that inserts itself into the plasma membrane of exocrine gland cells. This protein regulates the flow of chloride ions accross the cells plasma membrane. With CF patients, this protein is absent or defective. In most cases, mutated genes can not perform their normal functions.

  • Junk DNA (Score:3)

    by Lerc ( 71477 ) on Thursday December 02, 1999 @02:36AM (#1488260)
    Has any experimentation been done on creatures with differences in only their 'junk' DNA.

    It just seems a bit iffy to say it's junk because it doesn't do something that we know other DNA does.

    To reliably say it does nothing you would have to know how the whole system works, wouldn't you.

  • Re:23 Chromosomes (Score:1)

    by Anonymous Coward
    IIRC, we have 21 pairs of autosomal chromosomes and 2 pairs of sex chromosomes (X is sex-linked, Y is sex-limited). Remember that meiosis leaves gametes with only one set of chromosomes, so you're guaranteed to inherit half your chromosomes from each of your parents.

    22 pairs of autosomes, 1 pair of sex chromosomes.
    (XX is a pair, XY is a pair. Not two pairs per.)
  • In Science news and Discover, They've had articles about the so-called "junk" DNA found in our Chromosomes.
    Some of the genes that have been mapped are very similar to ones related to cancer and other genetic deseise (the posting said that I think).
    One of the most interesting sections of "junk" and "leftover" genes are the ones that look almost identicle to Simian Imunno-deficiancy Virus...That would be the version of HIV that Chimps and Gorrillas get in the wild. This would suggest that , earlier in the evolutionary process, that there was an epidemic of SIV in our (humans) predicessors that the species developed an immunity to. SIV and HIV are actually very similar viruses, so if some genetesist could figure out how the SIV gene gave early man an immunity to SIV, an anti-HIV gene/vacceine could be developed from (most likely) a combination of the SIV gene and parts of HIV viruses...
    All the more reason to let EVERYONE have access to any genetic data of any creature.
  • You also have to consider environmental factors that have been shown to cause genetic mutations. I guess these genetic muations could be stuck in the subfile titled "s**t happens"
  • Not quite, the sex chromosomes form one pair. Females have 2 X chromosomes, while males have one X and one Y. So the sex of a child is determined by which one of the father's sex chromosomes is in the half-set of that particular sperm...

    AFAIK, this is also the reason why males live shorter: the X chromosome is big and contains important information, so having 2 of them can be a life-saver, while the Y chromosome containy hardly any information beyond "this is a male".

  • I think we all know why the "junk" section is aprox. 42% of the chromosome... this just proves that Douglas Adams has been on to something far greater than any of the rest of us could possibly imagine.
  • um tonsils guard against infections

  • Introns are certainly one category of 'Junk', but there's much more. In general the term 'Low Information Density' would be preferre.
  • I have never seen this answered to my satisfaction. Are they using a particular individual's DNA, multiple DNA samples from many individuals, or does it matter?

    The Nature article said that individual human DNA differs from person to person by about 1 base pair in 1000.

    If this is true, it seems like having one individual's sequence might be useful, but it is not going to tell you all that much about the variance from person to person. You'll get a general idea of what's going on, but it seems like you would have to sequence quite a few more individuals before you could really say how genetic changes effect a gene's expression.

    -josh
  • The timing is actually entirely coincidental. We've been working on this for several years, and I've been involved in problem-solving in the closing stages. There's no way we'd have been able to time the finishing to match, and there's no way we (or Nature) would have been willing to delay it to that purpose.

    I'd agree that it's happy timing, though.


  • The Sanger Centre's hoping to be able to announce the completion of Chromosome 20 sometime next year, and I understand that the GSC in St. Louis is hoping to do the same for Chromosome 7. Both have stats pages up, if you're interested. The Sanger's is at http://www.sanger.ac.uk/HGP/stats.shtml
  • The HGP is a joint venture funded by biotechnical outfits. These companies that map this information do so because for the first six months they have patent rights on processes they discover from (or in) this information. These companies only care about "the good of mankind" _after_ the patent window has expired.

    -- The constitution may not be perfect, But it's better than what we got.
  • Your friend is right. Rather than the word 'diseases', I should have probably used 'afflictions'.

    Myoneurogastrointestinal encephalomyopathy.. Shall we break it down, perhaps?

    Myo - muscle
    neuro - nerves
    gastro - stomach
    intestinal - speaks for itself
    encephalo - brain
    pathy - feeling/suffering. So far as I can tell, this means that due to something between the muscles and nerves in the gastrointestinal region, the brain is feeling a plot of pain. Fun, neh?

    ------

  • Hmm, if this DNA-patenting thing gets through, the next thing after the Open Source movement might be the Open DNA movement, where a certain RMS II will fight to regain lost rights of the public to access their DNA... and he will start to license DNA sequences under the DPL (DNA public license) to prohibit corporate entities from taking freely-accessible DNA and making it "proprietary".

    (Disclaimer: if your sense of humor doesn't match mine, please don't take this as flamebait... somebody help me, I've been infected by the GPL virus and I can't stop Open Sourcing every topic that comes up on /.!!! :-O )

  • When I was just a wee undergrad taking cell physiology (I think it was my senior year at UMD)... Anyways I think the theory is that introns are indeed a necessary part of the DNA. Since they don't seem to code for anything in particular, mutations can occur in these areas and nothing will happen to the cell/multicellular organism. The greater number/size of introns may result in a lesser chance of damaging exons.


    So the theory goes.

  • There are various libraries of samples being used, some derived from one person and others from panels of several to many individuals, suitably anonymous and from a wide range of decents.

    Actually, it probably won't make much odds as there's little differewnce between people at that level. The point is, though, to do a Human Genome Project rather than a White European Male Genome Project.

  • While you're at it, please come up with organisms and products that clean up toxic waste spills, produce insulin, kill crop-destroying pests, produce more nutritious food, serve as research tools for developing anti-cancer drugs, and grow new organs from scratch.
    We can agree that these are all Good goals. What more incentive do you need? Go to it!
  • Some employers in the U.S. that sponser employee health insurance already conduct pre-employment assesments using genetic testing. There are fears that this will lead to bias and eventually, an "unemployable underclass".
  • They are the four bases in all DNA. A=adenine, C=cytosine, G=guanine, T=thymidine.
  • . . . and I do take your point that software patents may be counterproductive, but it is precisely the situation you describe -- low marginal costs for each additional unit, be it organism or software -- that intellectual property law is designed to protect. In other words, why spend all your money up-front if it's just gonna be instantly knocked off anyway?

    As for your quote: The producer of the bug would have a massive market lead on any competitor who cloned it anyway. You don't know that. I don't know that. The company who develops it has to assess the risk about whether or not they're going to even recoup their development costs (or if it's even going to work, for that matter), and it's far less likely that they're going to bother without the benefit of patent protection.

    Another benefit of patent law: By law, the patent makes the know-how public. Which means that anybody can look at the patent and think of ways to adapt or improve it. Such as developing a bug to eat toxic waste and produce cotton candy. Yum.

    Finally, everyone: Please learn a little about patent law before you start spouting the doomsday scenarioes mentioned above. Thanks.
  • Correct me if I'm wrong but isn't Christian Science the sect that teaches that bacteria is the symptom of disease, not the cause? And that prayer is the only sure cure (unless God had decided it was your time to go of course)?

    I know the Christian Science Monitor is a respected paper, and I was very impressed with the quality of the articles when I just browsed through, but I find it ironic that the voice of that sect published news about biology and medicine. Scary that their was the most in depth article too. What does that say about the other media?

    ************************************************ ***

  • but I strongly doubt there would be gene that's ONLY function is disease... what sense would that make?

    Why should it make sense? Assuming you don't suscribe to Creationism, there's no reason to assume a reason behind any particular genetic coding, any more than you should assume the function of gravity is to make your milk spill. Rather than 'function', which tends to sound like a design with a purpose, think 'effect' or 'result'. So, the effect of foo genes or gene-sequences is bar desease. A mutation has 4 possible results:

    1. It helps a creature and/or its offspring thrive and reproduce.
    2. It hinders a creature and/or its offspring from thriving or reproducing.
    3. It has advantages/disadvantages which don't (yet) affect the reproduction chances.
    4. It has no effect at all (or yet).

    That's it. No point system other than:
    1. You have children.
    2. They inherit some of your genes and some of your partner's genes, and perhaps some of the genes mutate.
    3. Repeat.

    People tend to think that their's some grand design behind everything that is. I'll leave the resolution of this question to the Philosophers and Theologians, but I think we can agree that if there is one, it's not something we're capable of recognising...

    Chris
  • Interesting you should mention it... but that's another case of a previously-thought-to-be-useless tissue turned out to play a part in the immune system.

    'course, they only found this out after mine was gone.

  • I know next to nothing about DNA but the term junk DNA seems... wrong. First of all contrast the articles in the 6 or so URLs listed. Only one referred to them as junk DNA, this sounds more like the reporters lack of understanding or bias than something the scientist said.

    Second, consider a gene as an information exchange mechanism. Most forms of information exchange include some amount of material that isn't essential to the message but can't really be classified as junk either. It may be redundancy, it may be for error detection or correction or it may be for clarification.

    Run an estimate of the actual needed text in the average paragraph written or spoken in English. The percentage that is 100% essential is pretty astonishinly small. It's a bit higher for a text but a bit lower for a novel. Mathematical proofs are pretty concentrated information but consider what happens if a little bit of information is transmitted wrong, say a sign is reversed. It's difficult to recover from it.

    Likewise I think a 100% essential gene would be very difficult. Any random genetic damage would have impact. Gene replication would have to be absolutely exact and so on.

    As I stated, I don't know anything about genes or DNA, but from an information theory standpoint calling 'unused' DNA junk seems wrong.

    I would like to learn more about genes though, can anybody recommend a good progression of texts on the subject? Something to take somebody from absolute layman to at least having a general idea of the subject?

  • Several of the HGP institutions are involved in the SNP project, which uses a similar chromosome-specific-shotgun strategy to that used by Celera, with the data to be placed in the public domain. This is largely funded by pharmaceutical companies, with the aim of finding single-base differences between individuals that might be relevant to disease and its treatment.

    I was actually at a seminar about it at lunchtime. It seems to be going nicely.

  • Someone correct me if I'm wrong... Are the results of the HGP going to be designated as common public property so everyone can profit from it? Just wondering.
  • One theory put forward by Richard Dawkins is that the 'junk' DNA is sort of like a parasite, it got attached to our DNA long, long ago and is just sort of hitching a ride along with the 'non-junk' DNA's reproductive cycle.

    Dana
  • If you can remove the sequences completely and still have a healthy animal develop, chances are it was indeed junk. This is not surprising, mutations can cause anything, including the inclusion of unused DNA.

    Um... I wouldn't be so quick to believe that something is "junk" just because we human beings can find no reason for its existence, or just because according to one of our profound, sublime theories "junk" is to be expected and therefore anything unknown to us can be safely labelled "junk". Take the example of our appendix. Many believed (and perhaps many still believe) that the appendix was useless. Which is why they called it the appendix in the first place. However, this is wrong. The appendix does serve a function in our body. For many years before this was known, however, people even thought of removing their appendix just to avoid the possibility of getting appendicitis (shudder). I hope we don't do this with our DNA... you might be able to survive without your appendix's function, but screwing up your DNA could permanently damage your offspring. No kidding!

  • Let me be more clear. I agree with your points, but my "make sense" was more like "is propable enough to appear and stay": If there's gene that's there just to make me die, isn't it more propable it will disappear than otherwise? Sure, if it's sickness that comes after I've reproduced, it won't be all like that... but, because people DO live after having spent their age of being able to reproduce, it might imply that old persons would be usable to community. Thus, I don't see why there's still gene that kills us in our gene pool.
  • This is not my idea and I have no specific details for supporting it. But from what I have heard speculated at different places, the "junk-regions" of the DNA could house a chemical history of previous generations for each individual. Don't take my word for it though, it's just a thought to the mind-provoking 'junk DNA'.

    - Steeltoe

  • And remember, one of the 2 X chromosomes is silenced and never used fairly early in embryogenesis (i.e. it's wrapped up into a little ball and tucked into the side of the nucleus). So females effectively have as much X chromosomal material as men.

    This is incidently how you get calico cats (and why all calico cats are female). The two X chromosomes have different color genes, they turn off at random in the early embryo (well not really at random, but imprinting is a a whole 'nother field), and you get areas of the skin containing homogenous or heterogenous populations of the X chromosomes being expressed (i.e. light spots, dark spots, and inbetween spots).
  • Of course it's useful. I wasn't saying that it wasn't useful or that it shouldn't be patented. My point is simply that patents are being issued on biological things. Sure, microbes. But can companies really patent variants of human cells? Or patent DNA altogether? Hmm ....
  • If the private sector sequenced the human genome to a high standard of completeness and released their data into the public domain , then by all means, the private sector should do it.

    A fundamental assumption of the human genome project is that the genome sequence is "precompetitive" information that is best put in the public domain, to spur both additional basic research and commercial innovation. This makes it an obvious target for public, not private investment.

    So far, no company has stepped up and said they intend to make the human genome sequence freely available. Celera is even waffling over their promise to release the Drosophila genome sequence. And somewhat understandably so; a company needs a business model.

  • His name is Duncan Idahoe.

    ...and I'm sorry to inform him, but House Attreides is going to make around 10,000 clones of him over the next few years and...

    ... oh yeah, right. nevermind.
  • Additionally, from an evolutionary "fitness" point of view, having a certain amount of "useless" DNA that does, literally, nothing makes a certain amount of sense. Basically, mutations happen for whatever reason, exposure to chemical agents, being out in the sun, whatever-- there are probably plenty of ways that your DNA can become permanently screwed up s.t. your repair machinery can't fix the stuff, and its going to happen with some probability (lets call it p), now in coding regions of DNA you've got some built in redundancy (4^3 == 64 and we only have 20 amino acids + 2 stop codons (UAA,UAG) and a start codon (AUG) (hmmm... 23, but thats a different story :-)) so we've got 41 extra codons), most amino acids have multiple codons that will code for them (if I remember correctly Tryptophan (Trp) only has a single codon-- UGG)), which reduces the chances that some point mutation due to environmental mishap will change the amino acid a given codon codes (this is known as a silent mutation), which is good since if say a Tyrosine (UAC) gets changed to a stop (UAG) then the transcription/translation process stops early and the protein can't be made anymore. Now lets say it was some regularatory region that gets screwed up and causes the cell to go into massive reproduction mode (read: cancer). Wham, you lose-- no gene pool for you.

    But I digress, we are talking about junk DNA. Ok, so lets consider two organisms hanging out on a beach somewhere. Organism 1 (o1) has NO junk DNA in its genome, somebody went through and "optimized" its genome :-), while Organism 2 (o2) has a genome that is about 50% "junk" (not useful in any way). Now, let's say they've got some regulatory region that, if it gets mutated, will cause uncontrolled growth (cancer) and kill the organism. Now just to simplify things lets say that any change in the regulatory region will cause cancer and the region is 10 nucleotides long. Assuming all nucleotides have an equal chance of being mutated in the event that a mutation occurs then P(Regulatory Region Changes|Mutation Occurs) = 10/n, where n is the number of nucleotides in the organisms genome, BUT o2 is 50% junk, so if 10/n is the probability of the mutation in o1, then 10/2n or 5/n is the chance of the mutation occuring in o2. Thus, o2 is 1/2 as likely to get cancer and die-- an evolutionary advantage.

    Of course the amount of "junk" we can have is probably limited by some factors (stability of the DNA molecule or some sort of mechanical constraint-- I don't know) that keeps the amount of DNA from getting out of control (or we just haven't been evolving long enough and having an infinite amount of DNA is selected for). Disclaimer: I'm not really able to back this up with any hard data-- its mostly just my guess as to why we have some much apparently useless DNA, its just a hypothesis so I could be wrong :-)
  • unfortunately this is the case. the researchers want patents on all the genes they discover, so they will have exclusive research rights to them (unless somebody else pays for the right). however, there is a French team out there (can't remember who offhand) which is trying to beat the Americans to the sequence so they can *donate* the entire genome to the UN, and people will be free to research what they want without having to pay. research moves slowly as it is, and is terribly underfunded (if you consider everything we are attempting to learn). in this case, i hope the French team wins.
  • Perhaps the introns are really nature's way of saying, "Hmmm... This isn't useful now, but I might like it in the future." :-) OK, so that probably isn't it.

    Perhaps God is using our Intron DNA sequences as a large distributed storage for his pr0n and mp3 collections?
  • The "junk" DNA also contains strucural (telomeres, etc) and regulatory elements (promoters, response elements, etc). The term of "junk" DNA has been around for a while in the scientific community, not just in journalism, left over from earlier days of this type of research. Mike
  • Don't know about the leangth of life(though it is true for a few specific diseases-show me a woman with hemophilia) but as i recall, the two items recorded on the Y chromosome are the This is Male, and the ears do have hair in them.
  • Yeah, I don't really like the idea of open-sourcing the genome. There is always the risk of a fork of the code base, and before you know it, we are two different species! Wouldn't you hate not being able to mix genes with everyone? Eh, I mean, like, 50% of everyone.

    Lars

    --
  • Actually, introns != junk DNA . Introns are intervening sequences within genes that are spliced out before the RNA is translated into protein. Introns often contain regions important for regulation of gene expression and serve as a way to generate more diversity in gene products (by the production of alternatively spliced RNA transcripts). Junk DNA refers to regions of DNA between genes with function (if any) unknown. Just want to keep the discussions accurate.
  • They are doing the MDMI (multiple data many individuals) approach. What they get is basically an average genome. And certainly a good map of the genome.

    The next step is to hunt for SNP:s, which stands for Single Nuceleotide Polymorphisms. And the race has already started. Both companies and universities are hunting for them. They are expected to be useful for things like identifying inheritedable deseases.

    Lars

    --
  • some research now shows that the "junk dna" actually forms secondary structures that are important in proper protein production
  • Comment removed based on user account deletion
  • Sickle cell anaemia seems to be sustained by natural selection, because people with this disease are immune to malaria.

    Although the malfunctioning genes were quickly eliminated during human evolution (now it changed, because people with even grave diseases can still live or even reproduce), there are some DNA sequences which are more prone to errors during replication than others, due to the DNA chemistry and nature of eukaryotic replication mechanisms. Of course, theoretically such "weak spots" could be eliminated by natural selection - but in most cases probably the enhancements in the repair mechanisms would cost more then a sporadic mutation. Don't forget that natural selection does not act on organisms, but on genes.

    Regards,

    January

  • Imagine this:

    You are a computer programmer, faced with the task of decyphering almost a gigabyte of machine code, which was written by billions of programmers making random changes and seeing if the result was an improvement.

    And you thought Perl was hard to read...

    --
    Patrick Doyle
  • Junk DNA is one of the worst misnomers possible, coined back when researchers honestly believed that non-coding DNA had no purpose. I believe what they mean is junk = introns + intergenic space, i.e., all non-coding sequence on chromosome 22.
    This is a bad misnomer because the junk DNA is required for the proper expression of all of our genes. We have on the order of a trillion cells, so 100,000 proteins (all combinations of 2, representing gene A regulating gene B) can only differentiate, at best, 10 billion. The complexity, and where a lot of the interesting research will be in a few years, is in how these genes are regulated to properly create all of our cells, each of which "knows" what it is, and what it is supposed to do.

    I must also say that I am surprised at their estimate of only 42% non-coding. The usual estimates are of ~3% (at most 10%) coding sequence in the genome as a whole, which gives a greater than 90% non-coding estimate.

    So... the interesting question, maybe I should send this to Ask Slashdot, is ... "How will what we're learning about our genes today affect medicine X years down the road?" where X = 10, 20, 50, 100.

    -Todd
    "I'm almost done with classes! Again!" (me)
  • Remember that DNA formed by trial and error. There could be "commented out" code in the genome that is no longer used. If there is no selective advantage in deleting it, it will hang around.

    --
    Patrick Doyle
  • Discover had a short article on the so-called "junk" DNA. Apparently, these sequences have served legitimate purposes in our evolution, doing things like enhancing or reducing the effect of other genes.
    If anything, these genes with unknown purpose add to the genetic diversity of the species. Who knows, maybe they may confer some immunity for as yet undiscovered virus.
    BTW, today on NPR there was a short news piece on genetically engineered crops and their (possible) deleterious effects on other plant species. We've seen articles on Slashdot (?) about glow-in-the-dark Christmas trees too. By introducing these genes to the world (controlled until some bee cross-pollinates a similar uncontrolled species) we are crap-shooting. I am not yet convinced that genetically engineering crops is ultimately economical.
  • I realize that many people here are hackers, and the push to write great code is very strong. But none of us should discount the possibility that our DNA (which the article claims is 42% "junk") is merely heavily commented. That might be a bit overkill on the comments, but we should all resolve to take a hacker's lesson from our genetic heritage, and add a few comments in our code here and there.

  • For those of you who can't stand not having the source code for everything you use , you can download the results of the human genome sequencing project from http://www.ncbi.nlm.nih.gov/genome/seq/ [nih.gov] .

    (Before you all rush and slashdot the site, please ask yourself whether you really need to download over one gigabyte of what is, to the uninitiated's intents and purposes, a random string of A's, T's, C's and G's.)

  • The last time I studied this stuff was back at University 12 years ago. I think you'd be fairly surprised to know just how well genetics was understood even then.

    In other words, we know with a high degree of certainty that introns aren't involved in regular gene transcription, because we do know exactly how gene transcription works.

    A gene first needs to be switched on and off by a specific signals from other nearby genes, and then they need to have the correct start and stop sequences if they are to be transcribed at all. Introns by definition are stretches of DNA which do not have these operon genes. And without operons, it's like having a program with a subroutine which has no statement to call it. It might just as well not be there at all.

    There are various mechanisms via which non-coding DNA can get into the genome: viral insertion, inversion, other kinds of mutation. Maybe even uptake from free DNA floating in the air. Or in your food. We don't know for sure about those last two. The point is that the introns get there by accident just like the good stuff does. But the introns are DNA mutations that didn't result in transcribable genes.

    Consciousness is not what it thinks it is
    Thought exists only as an abstraction
  • That's just not going to happen. Mutations happen randomly, and therefore most mutations that happen to non-junk DNA will break something important.

    Mutations that happen to intron DNA are as likely to put something extra in as they are to take something out. So the only factor that could cause a shrunken genome would be a strong selection pressure in favour of it. Perhaps if lower food requirements or faster healing after injury resulted from removal of the introns, then we'd see a progressive downsizing of the genome of humans in the wild over a period of several hundred thousand years.

    But I think it's also necessary to take into account to what degree civilisation might mitigate against these selection pressures with its health care programs, free education systems, equal rights legislation, abundant food supply, restrictions against murder, etc. Most of all, remember that successful individuals in today's civilised societies aren't likely to produce that many more offspring than less successful individuals with slightly poorer genes.

    Consciousness is not what it thinks it is
    Thought exists only as an abstraction

  • What exactly does "mapped" mean?

    In general it means that the location has been established relative to known markers. In this case, though, the chromosome has been sequenced : the areas have had their composition established base-by-base.

    Does that mean they know what all the bases are in the average human?

    Roughly, yes. The sequence is a mosaic derived from several people.

    Does this imply any knowledge of the pattern of such variations?

    Not in itself, no, although other work is continuing to establish this.

    Does it imply any knowledge of the function of the encoded proteins?

    Again, not in itself. Many of the identified genes have been studied already. Others have similarities to genes already known, either from humans or other creatures. Some have been inferred from features of the sequence itself and are of totally unknown function.

    A biology class I took said that human DNA was 96% junk (not protein encoding).

    Was this biology class wrong?

    No. The vast majority doesn't code for protein, and most of this has no known function. Closely related species have widely differing amounts of this, so (together with other reasons) the current hypothesis is that it doesn't do much that's useful for the organism. Some of it is composed of "selfish" elements such as transposons : it might be the case that in a looser sense a lot of it is.

  • I Decoded the Junk DNA...OH NO (Score:4)

    by MagusOceanus ( 61084 ) on Thursday December 02, 1999 @04:23AM (#1488340)
    I extracted the Junk DNA and respliced it so that it would stand without the DNA that is neccessary to humans, inserted it in a cell and watched it grow. 5 hours later to my horror it took a flat retangular shape, black lines appeared on a white surface. They connected to form letters in clear English which read...

    "Mr _________ , You have been selected as a final entry for the Publisher's Clearinghouse largest drawing, enclosed is a Check worth $30,000,000 if you have the winning number!!! Please open and send your entry form within the next 24 hours, and get a GUARANTEED prize."

    I tried the Junk DNA of other chromosomes and got ads for term life insurance, timeshares, and then the Junk DNA materialized in front of me into a pushy Amway distributer!!!! The horror!!! Cellular SPAM!!! AGHHHHHHHH

  • Re:Open Source Human (Score:3)

    by jquiroga ( 94119 ) on Thursday December 02, 1999 @04:32AM (#1488347)
    Of course, that would be awful, but what about the installation process? Everyone would want to improve it.

    Currently, parents are forced to accept all the default values, and many are clamoring to get at least an installation menu, to be able to choose hair color, IQ and IP address :-)
  • I don't know about this statement:

    If it were truly junk, any mutation that discarded it should be advantageous since it would take less resources to replicate the mutated version than the "junky" version.

    You are assuming that of course mutation is an efficient process, like a hedge trimmer going in and snipping and improving just what needs to be done.

    What color is the inside of my linen closet painted? It doesn't matter, and it won't make a difference to the resale value of my house.

    We're evolved machinery. Now that we can see the source code, we know that it's not very well written, and has lots of sections that ramble or go nowhere. It's natural to resist facts that challenge our species' well developed sense of being the pinnacle of design. Look at how people dumped on Darwin during and after his lifetime!

    Instead, we should be impressed that we work so well, despite how we're written.




  • Does that make it "holy writ"?
  • The Sanger centre [sanger.ac.uk] has more info on chromosome 22 [sanger.ac.uk].

    Congratulations to all who participated in its sequencing. We look forward to the first draft of the human genome by spring 2000.

  • "unemployable underclass".



    That "underclass" will strive to become as large as possible.

    Remember at the end of 1984, the fake society is falling apart. The proles, being the vast majority, are poised to take over.

    If "most" people are in this underclass, they have
    the opportunity to organize and the sheer size of the class makes them predominate.

    As long as they are the minority, they haven't a chance.

  • What does that mean? (Score:5)

    by jw3 ( 99683 ) on Thursday December 02, 1999 @02:50AM (#1488369) Homepage
    In a recent /. discussion [slashdot.org] we argued about the Human Genome Project v. TIGR [tigr.org]. As you see, the HUGEP is doing quite well. The raw data from the sequencing project should be available next year.

    Will this finish a task? No, it is just a beginning - having the sequence, the real work starts: searching ORFs (Open Reading Frames - sequences which could possibly be genes), running database searches, and slowly passing to the most exciting fields of modern molecular biology - from genomics to transcriptomics and proteomics. Transcriptomics is looking for genes, which actually got expressed, and proteomics - similarly, looking for expressed proteins. Making transcription / translation (translation is the process in which proteins get synthetized) profiles can lead us to 1) function of proteins (e.g. protein X. is expressed under this and this conditions, so it must take part in this and this metabolic response) 2) regulation - DNA is a single strand, but various enzymes are present in various copy numbers under various conditions.

    Those are enormous projects. A lot of work has to be done before the raw sequence will actually be of any use; nethertheless, it is a milestone of molecular biology and will be a fine achievement for the end of our century.

    Another project will be to determine the variability of human genome: screening for different gene allels, mutations etc. This will be one of the most important goals in human genomics in the next few years.

    Whats on the catch... erm, chromosome 22? 22 is 33,400,000 bases long (Mycoplasma pneumoniae, one of the smallest bacteriums, has about 816,394 bases). It contains several already known genes responsible for various genetic disorders, and possibly a gene responsible for certain types of schizophrenia.

    By the way, a much better source of information is the Nature science update [nature.com] page - the original scientific publication has been published today in Nature [nature.com].

    Regards,

    January

  • Thanks for the explanation!

    Regards,

    January

  • Are they using a particular individual's DNA .. ?

    After we finish mapping some DNA we can go munch on some grindage, buuuuuuuuudy! :-)
  • I heard somewhere that the sequence "GATTACA" actually appears at least once in every single human gene (this being why they chose it for the movie title). Furthermore, it's the only sequence that does that.

    I'm no genetic researcher, and neither is the person who told me this, but I suppose it's possible.
  • I'd be careful calling it that. Someone proposed the idea that it's mutation fodder (that is, a safe place for mutations to occur). That's a possibility.

    But there've also been posts talking about a lot of redundancy and such. It's possible that all this "junk" DNA still has uses that we haven't seen yet. I guess we won't know until we've mapped out the whole thing.

    Who knows... maybe someday we'll all have something like a mini-RAID coded into our DNA.
  • You're wrong, I'm afraid.

    The human genome project is funded in the US by the National Institutes of Health and the Department of Energy, and in Britain, by the Wellcome Trust, a charitable organization.

    Every base that we sequence is put in the public domain.

    We strongly oppose the patenting of sequences. Some of our strategies are designed to preempt attempts by companies to patent sequences from the human genome.

  • Confidentiality: the person being sequenced (Score:3)

    by seaneddy ( 121477 ) on Thursday December 02, 1999 @06:22AM (#1488393) Homepage
    Several ./'ers have asked who we're sequencing.

    AFAIK, most of the genome sequence being produced by the HGP is from a single male individual. (Male, because we need to see a Y chromosome too.) I dunno for sure about Sanger, but WashU and Whitehead in the US are working from the same clone library.

    The identity of this person is a closely guarded secret, as well it should be: this person's genome sequence will be available on the Internet. We'd like to avoid a nightmare scenario where a well-meaning "genome hacker" discovers a fatal disease gene in the sequence, and calls this guy up out of the blue to tell him.

    That's just an extreme example. Basically, there's serious privacy and confidentiality issues. We consider the genome sequence to be a "reference sequence" or a "typical example", and we don't need (or want) to know who it came from.

  • Open Source Human (Score:3)

    by jquiroga ( 94119 ) on Thursday December 02, 1999 @02:56AM (#1488400)
    Soon we will be Open Source. I fear that the temptation to develop and try patches will be irresistible to many.

  • causing and associated with (Score:3)

    by xnixnix ( 31045 ) on Thursday December 02, 1999 @02:58AM (#1488402)
    From the CNN article:
    More than 30 human disorders are already associated with changes to
    genes of chromosome 22. These include a form of leukemia, disorders
    of fetal development and the nervous system, and schizophrenia.
    From the introduction:
    some of 22's genes can cause "heart defects, immune system disorders, cancers, schizophrenia
    and mental retardation."
    Is it just me or is there not a big difference between causation and association? Seems to me along the line of correlation vs. causation. Anyway, I believe that scientists have still
    a long way to go before they find the genes that cause certain disorders. And then they will still have to prove that these genes are in no way responsible for any other functions in the human body to safely alter them. Seeing all the good possible uses for medicine it still gives me the creeps how through the use of genetics and monocausal argumentation a new "scientifically backed" racism could emerge again. Now don't scream technophobe but how would you all react once the genes allegedly causing things like alcoholism, homosexuality, autism, criminalism, lazyness or whatever unwanted psychic or physical trait you can think off where identified? Have we got our ethics ready to handle this or will it be "what can be done will be done"? On whom will we test genetic engineering for a better race? The inhabitants of prisons, mental institutions, military institutions or just unwanted embryos? Will we allow babys to live with these disorders? Will we allow people to work without mandatory testing of genetic normality?
    History has shown that scientists have often produced technology that was later misused by the
    willing. Hopefully this time they think more before they hand this Pandoras box to the masses.
  • It is still an open question what role the junk DNA, technically called introns [uq.edu.au] plays in organism development. Unlike the simple unicelluar critters (prokaryotes) such as bateria, all higher level organisms (eukaryotes) have these long non-coding sequences [sciam.com] which have been retained across evolutionary generations despite the extra energy/space required. The whole area is akin to the physists search for all the various subatomic particles after the cracking of the atom. We can see the bits and pieces, we can assemble the various sequences, but there's no unifying standard model of how or why. With Nobel prizes and new killer apps in the air, it is not surprising that universities and institutes are throwing money into the research.

    The 19th centure might have been the dominance of physics and engineering but there's a lot of speculation and anticipation (especially by the empty hands of the biologists and zoologists) that the next century will be their turn at the gravy train :-). Fun times ahead.

    LL

  • To understand "junk" DNA, look at the big picture (Score:4)

    by whuppy ( 33165 ) on Thursday December 02, 1999 @06:53AM (#1488412)
    First of all, "junk" is a loaded term, which is certainly evidenced by all the nonsense it has spawned in this discussion. So let's do this by enumerating the different types of DNA a typical eukaryotic genome contains:
    1. Coding Regions. DNA that gets transcribed to RNA. RNA transcripts in turn have exons, which get translated into proteins, and introns, which get spliced out before translation. Why this added level of complexity? Many reasons. In sexual reproduction, new chromosomes are produced by mixing and matching old chromosomes at random. It's more likely for the new chromosome to be functional if the crossover point is in an intron because crossovers can introduce mutations, especially a nasty sort of mutation called a frameshift which would render everything downstream unintelligible. Exons also allow for a certain modularity of function, evolutionary mutations can involve entire exons being combined instead of having to try changes on a base-by-base level.
    2. Regulatory regions. DNA that turns other bits of DNA up or down. Mainly used to control transcription, but also used to control DNA replication.
    3. Structural regions. Eukaryotic DNA is a huge, long, string requiring a certain amount of overhead to prevent it from becoming an unmanagable tangle. Lots of the chromosome is dedicated to binding to structural proteins, generally known as histones, around which the DNA is wound. Also centromeric and telomeric proteins.
    4. Repeats, cryptic genes, etc: In order to avoid overloading the term "junk," let's call this category "cruft." Cruft arises for lots of reasons. For example, sexual reproduction produces gametes, and it's far from perfect: Regions get repeated, regions get dropped. So called cryptic genes are probably the result of a spliced RNA being reverse-transcribed back into DNA and reinserted into the genome without introns or regulatory elements. What's useful about the cruft is that it provides fodder for further evolution.
    In summary: Eukaryotes are big and complex, which means that you have to allow for a certain amount of overhead and slop.
    I hope this has helped.

  • Support the HGP (Score:3)

    by cyoon ( 99971 ) on Thursday December 02, 1999 @03:10AM (#1488432)
    /.ers should be trying to support the HGP as much as they can. Yeah, we joke about how it's all Open Source and all, but there's a very real possibility that chromosomes can be patented. Many organisms have already been patented (famous example: microbe that eats oil spills). Many human derivative cells have been patented and are under license right now. Companies are right now in a race against the HGP to map chromosomes and then patent them! I wish I had URL's available, but if you go to Google [google.com] and type in "human genome project patent" [google.com] you'll find a lot of sources where patenting DNA sequences is discussed.

    Bottom line: human chromosomes may be patented. Fight it.

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