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The One Thousand Genes You Could Live Without

Posted by samzenpus on from the stuff-you-don't-need dept.

sciencehabit writes Today researchers unveiled the largest ever set of full genomes from a single population: Iceland. The massive project, carried out by a private company in the country, deCODE genetics, has yielded new disease risk genes, insights into human evolution, and a list of more than 1000 genes that people can apparently live without. The project also serves as a model for other countries' efforts to sequence their people's DNA for research on personalized medical care, says study leader Kári Stefánsson, deCODE's CEO. For example, the United States is planning to sequence the genomes of 1 million Americans over the next few years and use the data to devise individualized treatments.

111 comments

  1. My Jeans are old, faded, and have holes in them... by Anonymous Coward · · Score: 0, Funny

    But they suit me just fine.

  2. 4 Limbs by Anonymous Coward · · Score: 0

    4 limbs you can live without...

  3. Re:I'm keeping my genes! by Anonymous Coward · · Score: 0

    The feminists would go after Y anyway.

  4. Re:I'm keeping my genes! by Anonymous Coward · · Score: 0

    A feminist is proud of her XX.

  5. Absence of evidence... by mikaere · · Score: 5, Insightful

    is not evidence of absence. I'll be keeping mine, thanks.

    --
    It's good luck to be superstitious
    1. Re:Absence of evidence... by Anonymous Coward · · Score: 3, Informative

      Presumably you can live without them because there are people who live without them and are fine for it.

    2. Re:Absence of evidence... by Anonymous Coward · · Score: 0

      is not evidence of absence. I'll be keeping mine, thanks.

      It's 2015. The fact that you actually think you own anything outright anymore is laughable.

      That especially means your DNA, just in case you were still acting stupid or confused.

    3. Re:Absence of evidence... by RoknrolZombie · · Score: 4, Funny

      Yes, but other people are are largely stupid and completely insane.

    4. Re:Absence of evidence... by rogoshen1 · · Score: 3, Insightful

      Yar, something as complex and time-tested as the human genome can surely be understood and manipulated by us with no unforeseen consequences.

    5. Re:Absence of evidence... by Anonymous Coward · · Score: 0

      But it's nice that they listed the variants/genes in Supplementary Table 4 of their paper.

    6. Re:Absence of evidence... by K.+S.+Kyosuke · · Score: 1

      Humanpedia deletionists are fine with that.

      --
      Ezekiel 23:20
    7. Re:Absence of evidence... by Anonymous Coward · · Score: 0

      I'm going to have to reluctantly agree to this.

    8. Re:Absence of evidence... by jedidiah · · Score: 2

      DNA is a complex language that we are barely beginning to understand. Unlike CRISPr, this kind of thing actually is "hacking the genome" in a clueless fashion. I think this is an area where clearly some corrolary of the Hypocratic Oath should be in effect.

      If it's not broken, then don't try to fix it. Leave it alone. The best thing to do (barring any indications to the contrary) is nothing.

      I suspect that we are still at the "don't know how much we don't know" stage of genetics at this point.

      --
      A Pirate and a Puritan look the same on a balance sheet.
    9. Re:Absence of evidence... by stoatwblr · · Score: 1

      The thing about genetic variation is that there's a minimum set you need to live and extras which make it easier to survive if conditions change (as well as others which may well be negative, such as ones which predispose the carrier to nasty cancers after the reproductive period ends)

      Just because you can live without them _now_ is not evidence they may not be useful later.

  6. Keyword "apparently" by XxtraLarGe · · Score: 3, Insightful

    They said the same thing about "junk" DNA. 10-15 years from now, it may no longer be apparent that you can do without them.

    --
    Taking guns away from the 99% gives the 1% 100% of the power.
    1. Re:Keyword "apparently" by Anonymous Coward · · Score: 0

      Well they looked at DNA extracted from the blood, I'm not sure how they know (or why they think they know) those sequences are representative of those in each tissue.

    2. Re: Keyword "apparently" by Anonymous Coward · · Score: 0

      Loss of repetitive DNA is a speciation event.

      Most of it is not transcribed. Some is. The bidirectional nature creates RNAi effects.

      If I had been able to publish before the sequester took my job, you would be able to see pictures of hybrids.

      New string metrics, new ideas on the origin of life, sequences more conserved than rDNA.... Hurray Sequester budgets.

    3. Re:Keyword "apparently" by turbidostato · · Score: 1

      "Well they looked at DNA extracted from the blood, I'm not sure how they know (or why they think they know) those sequences are representative of those in each tissue."

      You are not sure how they know because you didn't pay attention to your high school biology classes.

      They think they know because they did pay attention to their high school biology classes.

      *All* nucleated cells in a body share the same DNA load (barring local mutations -which are really minimal, and with obvious exception of the germinative line).

    4. Re:Keyword "apparently" by pspahn · · Score: 1

      In fairness to the GP, high school biology is pretty much the worst fucking class ever.

      We had to dissect a fucking shark. It was awful. I can still smell it. The poor souls at the bench next to us had a frozen cat in a bag whose face looked like Scratchy got a rear end stuffed full of cocaine.

      I'll take my D+ and be on my merry way, thank you.

      --
      Someone flopped a steamer in the gene pool.
    5. Re:Keyword "apparently" by Anonymous Coward · · Score: 0

      Well they looked at DNA extracted from the blood,...

      To a first approximation, all of a person's cells have the same DNA. After all, a person does develop from a single (fertilized egg) cell.

      In fact, you can do a whole genome sequence from less than a milliliter of saliva. There are even convenient saliva collection kits - spit in the tube, mix with some stabilizing solution, FedEx it to a sequencing facility, and get your genome sequence (e.g. on a little USB hard drive via FedEx) a month or two later.

      But sometimes the differences in DNA sequence between tissues does actually matter.

      One case is heteroplasmy in the mitochondrial DNA. In mitochondrial disorders, it's common for children of the same mother to have major differences in how severely they're affected - and a key difference may be the copy number of the pathogenic variant in different tissues.

      Another case is that in certain tissues, like blood, where the blood stem cells are continuing replicating, it's also possible to see reversion of the pathogenic mutation - because cells with the pathogenic mutation grow more slowly. In that case, the pathogenic mutation would not be seen DNA sequencing from blood but would be seen in DNA sequencing from other tissues.

    6. Re:Keyword "apparently" by Anonymous Coward · · Score: 0

      In fairness to the GP, high school biology is pretty much the worst fucking class ever.

      There's far more people trained up to do biomedical research than available jobs. So I absolutely wouldn't encourage any one to pursue a career in biomedical research. But, having said that, most of modern biomedical research is nothing like what goes on in the old school high school biology classes. In fact, there are a lot of people doing biomedical research that don't even work in labs: they write and run programs on computers (i.e. bioinformatics and computational biology).

    7. Re:Keyword "apparently" by Cyberax · · Score: 4, Informative

      Most of the junk DNA is still... junk. Basically it's:

      1) 60% of the DNA is _definitely_ junk, as they consist of known repeated elements (LINEs, SINEs and others) and defunct genes. This is not an 'absence of evidence', we know exactly how this DNA has happened.

      2) Around 10% of DNA is structural. While this is technically not 'junk', this DNA does not encode anything useful.

      3) Around 5% are coding sections and regulatory elements.

      4) Another 5% of DNA appear to be stable under mutation pressure. So it might have some function.

      4) And finally we have around 20% of DNA whose purpose is not known, but we know that random mutations in it do not visibly affect the phenotype.

    8. Re:Keyword "apparently" by someone1234 · · Score: 1

      "*All* nucleated cells in a body share the same DNA load (barring local mutations -which are really minimal, and with obvious exception of the germinative line)."

      Except, chimeras?

      --
      Patents Drive Free Software as Hurricanes Drive Construction Industry
    9. Re:Keyword "apparently" by Rei · · Score: 1

      Well, not exactly. The answer to the question of how the immune system can defeat a foe that is mutating and evolving so quickly is "it also is mutating and evolving quickly". Immunoglobulin genes in B cells mutate very rapidly. Those whose antigen binds best with an invader are stimulated to reproduce (and evolve more), ultimately differentiating into plasma B cells (whose job it is to mass produce antibodies) and memory B cells (which stay alive for long periods of time, allowing the body to "remember" how to fight off an invader that it fought off in the past).

      That said, this only applies to genes responsible for antibody production, and only in B cells.

      --
      "99 dead duelists of Dios on the wall. 99 dead duelists of Dios! Take one's ring, pass it around..."
    10. Re:Keyword "apparently" by Anonymous Coward · · Score: 0

      Are you a human or a bot? One thing is clear, you have no research experience.

    11. Re:Keyword "apparently" by Anonymous Coward · · Score: 0

      "There are even convenient saliva collection kits - spit in the tube, mix with some stabilizing solution, FedEx it to a sequencing facility, and get your genome sequence"

      And who has verified this matches with that in each tissue? Who said repair of mutation happens equally everywhere?

      Honestly, I didn't bother looking this up because I read TFJA and they make no reference to any of these issues. I have enough experience to know that means they are assuming it. If I had less experience I may think that is "normal" and my lack of knowledge of such important background info is some fault of my own. I would bet 1 btc that those assumptions are not well established at all. In fact, there is probably no published evidence either way.

    12. Re:Keyword "apparently" by eli+pabst · · Score: 1

      They said the same thing about "junk" DNA. 10-15 years from now, it may no longer be apparent that you can do without them.

      I don't think that's likely. There is a subtle nuance here about what they are claiming. The is a very distinct difference between "genes you can live without" versus something like "these gene are junk and have no function". The claim that you can live without a certain gene is easily proven; find people who have lived to adulthood and are carrying two copies of deletions/disruptions in the same gene (so they have no functional copies of that gene). This is actually not that surprising as your body has evolved to be highly adaptable to accommodate a vast array of environments and diets. So it is very possible that some of those people have subtle deficiencies such as not being able to digest certain sugars or see colors slightly differently. They might not appreciate a Monet in the same way you do, but the fact that they are alive is proof that that gene is not essential for life. You could make the argument that the set of essential genes in Iceland might be different than the set of genes required for life in extreme environments like the Sahara desert or on a tropical island where the only thing to eat is bananas and that sugar metabolism gene now becomes essential, but I would think that list of non-overlapping genes would be small.

    13. Re:Keyword "apparently" by TuringTest · · Score: 1

      60% of the DNA is _definitely_ junk, as they consist of known repeated elements (LINEs, SINEs and others) and defunct genes. This is not an 'absence of evidence', we know exactly how this DNA has happened.

      How do we know that those repetitions are not needed to accelerate (by parallel processing) some important process which, with a single expression, would otherwise be too slow to survive?

      We don't fully understand how the phenotype is developed from the genotype, and it very well might depend on statistical properties of gene appearances in the genome, and not just their presence or absence. Is there something in biology science that could discard such possibility?

      --
      Singularity: a belief in the "God" idea with the "demiurge" relation inverted.
    14. Re:Keyword "apparently" by Cyberax · · Score: 1

      How do we know that those repetitions are not needed to accelerate (by parallel processing) some important process which, with a single expression, would otherwise be too slow to survive?

      You absolutely do NOT want them to be expressed. In fact, your genome tries really hard to suppress them - all they do is replicating themselves. That's the reason so much of your genome consists of them.

      Dependency on statistical properties is doubtful - organisms have more than 100x natural variance in genome sizes within fairly closely related species (just look at plants) without much outward difference. Even in animals, some species have a small and compact genomes (pufferfish) without much junk.

    15. Re:Keyword "apparently" by turbidostato · · Score: 1

      Except chimeras, yes.

      Are you going to claim they appear in any significant number in mammals? (and I know about prions) ...on a thread about somebody ignoring the very basic fact that multicellular organisms own just one genotype?

    16. Re:Keyword "apparently" by turbidostato · · Score: 1

      You are right. I forgot about B cells, and I've should mentioned them since I did it about the germinative line exception.

      Now: do you think talking about B cells makes any difference for the base answer to the original question, "I'm not sure how they know (or why they think they know) those sequences are representative of those in each tissue."?

    17. Re:Keyword "apparently" by Anonymous Coward · · Score: 0

      Mutation and Repair rates for each gene are approximately the same across tissues? Cite?

  7. Primary Source by Anonymous Coward · · Score: 0

    http://nature.com/articles/doi:10.1038/ng.3243

  8. The thousand genes we don't know if are needed. by Chikungunya · · Score: 1, Troll

    If they have not yet done deletion experiments they can't say that we could "apparently" live without those genes.

    1. Re:The thousand genes we don't know if are needed. by Anonymous Coward · · Score: 4, Informative

      RTFA... they found people with double deletions.

    2. Re:The thousand genes we don't know if are needed. by complete+loony · · Score: 2

      I believe they mean that they have identified people who are living without those genes.

      --
      09F91102 no, 455FE104 nope, F190A1E8 uh-uh, 7A5F8A09 that's not it, C87294CE no. Ah! 452F6E403CDF10714E41DFAA257D313F.
    3. Re:The thousand genes we don't know if are needed. by Alomex · · Score: 4, Funny

      This explains republicans....

      (ducks)

    4. Re:The thousand genes we don't know if are needed. by Chikungunya · · Score: 4, Insightful

      Any of those genes could encode a protein whose function can be done by another protein that other people may or not express. Obviously the people identified did not need "that" specific protein to do its work but it may be completely possible that a majority of people do not have the compensating gene.

      Until experimentation is done to evaluate the need of those genes you can say that those "may" not be indispensable, but saying that apparently they are not needed is too strong a conclusion for the work done.

    5. Re:The thousand genes we don't know if are needed. by Anonymous Coward · · Score: 0

      ...it may be completely possible that a majority of people do not have the compensating gene.

      Well, evolution isn't fast enough for various human sub-populations to have evolved their own unique genes. In rare cases, one might imagine a duplication event in a particular sub-population that would compensate for loss-of-function mutation in the original gene. One could also imagine a pair of genes with the same function where there was a loss-of-function mutation in one or the other but not both genes in certain sub-populations. But that would also be rare.

      In the bigger picture, though, the point isn't to knock out these non-essential genes in healthy people. The point is to more easily identify causative mutations in rare genetic disorders by eliminating these non-essential genes from consideration.

    6. Re:The thousand genes we don't know if are needed. by Anonymous Coward · · Score: 1

      The point is to more easily identify causative mutations in rare genetic disorders by eliminating these non-essential genes from consideration.

      Or in the case of Iceland, finding out which of your third cousins it is safe to date.
      With a small population that has been relatively isolated for a long time it can be tricky to avoid relatives and this leads to an extra interest in genetics.

    7. Re:The thousand genes we don't know if are needed. by jandersen · · Score: 1

      What is this about marking people down as 'troll' or similar for expressing a slight note of doubt? This is petty, at best - either reply with something intelligent or ignore it.

    8. Re:The thousand genes we don't know if are needed. by Gilgaron · · Score: 1

      So you put your sequences into a database and are a few queries away from determining if everyone with a double deletion in one position always has an active copy of a gene only likewise required in the converse situation. I've not read the original source but I imagine they already did this. Your username implies virology background, why would you think they would be smart enough to do the first step and not smart enough for the second? The second requires a more robust dataset but isn't really any harder otherwise.

    9. Re:The thousand genes we don't know if are needed. by Anonymous Coward · · Score: 1

      What is this about marking people down as 'troll' or similar for expressing a slight note of doubt? This is petty, at best - either reply with something intelligent or ignore it.

      We need a -1 "Didn't RTFA" mod.

    10. Re:The thousand genes we don't know if are needed. by jandersen · · Score: 1

      We need a -1 "Didn't RTFA" mod.

      Or a more tolerant outlook. TFA may not always be all that interessant to read, and anyway, the point is, should we mod people down for being too lazy to RTFA, when we are too lazy to type in a proper comment?

    11. Re:The thousand genes we don't know if are needed. by Anonymous Coward · · Score: 0

      Why not? If the comment is ignorant and they didn't RTFA then they're barely above the threshold of spam.

    12. Re:The thousand genes we don't know if are needed. by Chikungunya · · Score: 1

      Because having a copy of a gene is only one possibility of compensation, in processes like innate immune response it is common to have more than one pathway of activation, and to a certain point the presence of one protein can compensate the lack of another even if they are not structurally similar. A blast search can't be used in that case to rule out the need of that specific gene in other people. I am simply saying that proving that some people can survive without some genes without really having studied them to a certain degree is not enough to say that is apparently unnecessary for survival, it may be so only on certain populations (the sample in the studio is understandably biased).

      That is of course even without going into genes that could not be necessary all the time but increase the possibility of survival to specific events, for all we know the sample of individuals could represent only the 10% that survive a gene deletion because of a specific diet, certain amount of exercise, lack of exposure to a type of pathogen not common on Iceland, etc.

  9. Missing Variable by Anonymous Coward · · Score: 1

    Reminds me of taking out that missing variable in the source code that you figure isn't being used for anything, except there's no search function to find out what it impacts.

    1. Re:Missing Variable by Anonymous Coward · · Score: 0

      How do you take out a missing variable?

    2. Re:Missing Variable by lazy+genes · · Score: 0

      Wondering if this experiment will finally produce our first real super hero. No reason to give up now.

    3. Re: Missing Variable by Anonymous Coward · · Score: 0

      Remove the declaration for which there was no definition?

  10. Boo, you fad killer! by s.petry · · Score: 4, Insightful

    Today's fad is to try and come up with the "perfect" human. Always happy, 200 IQ, and the personality of a turnip as to not be offensive to anyone at any time. Of course they must be orange skinned, no hair, and no gender features (I hope you saw the South Park episode) because if anything visible marked one of them as "different" the project would be a failure. Perfect is quoted, because this perfection is severely subjective and the person who's ideal you are going to meet probably does not match your own.

    As you point out, there is no way to know what these apparently unused genes do until we start making modifications. These are pretty dangerous times we live in for many reasons. People believing they are smarter than billions of years of evolution gives me no assurance that these people have a clue, let alone care about modifying people.

    --

    -The wise argue that there are few absolutes, the fool argues that there are no probabilities.

    1. Re:Boo, you fad killer! by Sarius64 · · Score: 1

      +1 Eloquent. Apologies for the lack of mod points.

    2. Re:Boo, you fad killer! by turbidostato · · Score: 4, Insightful

      "there is no way to know what these apparently unused genes do until we start making modifications."

      No way? sure?

      What if, for instance, you find a person that simply lacks a gene and still is perfectly functional?

      Now, go read the article.

    3. Re:Boo, you fad killer! by Nemyst · · Score: 4, Interesting

      People believing they are smarter than billions of years of evolution gives me no assurance that these people have a clue, let alone care about modifying people.

      Putting evolution on a pedestal isn't much smarter. It's not some godlike entity which designed humans with a goal in mind, it's a very long, very sinuous process which often gives locally optimal but globally suboptimal results. There is no reason to think that humans, for some reason, can't do better.

    4. Re:Boo, you fad killer! by s.petry · · Score: 0

      I'll avoid the troll because you would lose that debate in a fair platform but alas, Slashdot is not such a platform... I will however address your insinuation that we know enough to be superior to nature. Science today is run by profits, not by philosophical standards. Ethics and Morality are not being questioned, only the outcome which yields the best profits receives funding and publication.

      Long time anti-GMO scientist Bill Nye is a great example, who after spending a month with Monsanto suddenly says "Hey, it's all great stuff and no harm can ever be caused by a GMO!". Buffoons believe this shit, but anyone with a half a wit and understanding of currency should be able to see through the ruse. Even though there are plenty of scientific studies that don't yield positive results for anyone except for giant seed companies money somehow changes the "science".

      Oh, I know.. hybrids must be exactly the same thing as splicing fungus genes into corn right? Further, every GMO food is exactly the same so if we question one we question them all, or contrarily if we claim one is safe they must all be safe right? Hopefully I preempted the normal bullshit covering up any scientific dialogue on the subject, but lets see if you grasp the point I was making.

      After reading not less than 30 studies in the last 20 years regarding how vitamins are healthy, then useless, then healthy, then harmful, then healthy again (you get the point) it should become obvious that we don't know nearly as much about genetics as some people wish to believe. And remember, fats are bad and will cause premature death, but you need them too so they are good and you die without them, and they are carcinogens but needed to fight cancer too (another long series of science, just in case you are lost).

      Claiming that "humans can do it better" is simply a delusion which ignores human nature. Yeah, the worst fucks you can imagine end up rich and funding "science" for their own benefit. If do not realize this, you had best start brushing up on history.

      --

      -The wise argue that there are few absolutes, the fool argues that there are no probabilities.

    5. Re:Boo, you fad killer! by Anonymous Coward · · Score: 0

      Today's fad is to try and come up with the "perfect" human.

      Research like this is actually really important for rare genetic disorders. There are all kinds of such disorders - including some icky ones like babies being born without skin. One major class of such genetic disorders is intellectual disability (mental retardation). But, in this context, intellectual disability doesn't mean having trouble understanding general relativity. It means never being able to walk or talk - and often even death in infancy.

      Thanks to advances in DNA sequencing, it's now possible to sequence an entire genome for $1,500 (30X read depth - 50 genome minimum order). But once you have the sequence, there's still the challenge of identifying the particular causative mutation - because a typical individual will differ from the reference genome at thousands and thousands of locations throughout the genomes. The key strategy in these cases is to look at the variants that occur in healthy individuals. And if a person can be missing both copies of a particular genome with no obvious ill effects then it's unlikely that a mutation in that gene is responsible for a genetic disorder that is causing people to die in infancy.

      While medical privacy is important, making your genome available for medical research can also be a huge help for people with rare genetic disorders.

    6. Re:Boo, you fad killer! by pspahn · · Score: 1

      These are pretty dangerous times we live in for many reasons. People believing they are smarter than billions of years of evolution gives me no assurance that these people have a clue ...

      And CERN? Doesn't it make sense that every black hole in the universe at one time was a really tiny black hole? Is it a good idea to just start making a bunch of those?

      --
      Someone flopped a steamer in the gene pool.
    7. Re:Boo, you fad killer! by Anonymous Coward · · Score: 0

      Long time anti-GMO scientist Bill Nye is a great example...

      No, no he's not. That's like saying Penn Jillette, the former Supreme Court justice....

      Bill Nye's field of expertise has nothing to do with genetically modified anything.

    8. Re:Boo, you fad killer! by Thanshin · · Score: 1

      Humans can do it better. It's a fact proven by a few thousand years of doing it better and so much faster.

      I've lost too much faith in average intelligence to spend time in trying futilely to further explain to you why you're an imbecile.

      Ok, that's enough slashdot for today. I'm tired of this shit.

    9. Re: Boo, you fad killer! by KJSwartz · · Score: 1

      A black hole isn't a purse where you stuff things and are lost forever. They are energetic balloons that feast and starve, and eventually disappear in a pop. I wouldn't be surprised if collapsed super massive black holes would look like the Big Bang.

    10. Re:Boo, you fad killer! by Anonymous Coward · · Score: 0

      This a billion times.

      Evolution is not even a remotely perfect process, it is IMPERFECT, which is where most evolution comes from in the first place. (a sizeable chunk of it is also sheer bad luck, but evolution is not entity, just a process, it literally can't care for a single unit of life)

      There are plenty of things in creatures that aren't needed, there are a lot of redundancies and duplications. (some cases, said duplications lead to barely any illness, but another can cause severe and even lethal issues)

      There is also one plant that is known to have no "junk" DNA for some reason, which still hasn't been figured out.
      It seemingly goes against everything we know about evolution: doing things for no gain. Removing junk DNA is more effort for what seems to be no real optimization or advantage. Who knows, maybe the plant was engineered and nobody wants to come forward and claim some sort of prize.

      Evolution seriously sucks. It is slow, imprecise and inefficient. And even the end goals aren't all that efficient either some times.
      A globally shared intelligence working on a problem is far more efficient than evolution will ever be because evolution very specifically has NO intelligence or direction behind it other than "change because change". Evolution is a massive reaction engine, nothing more.
      There is a reason computers and cars and buildings haven't evolved, because it is beyond what evolution is capable of.

    11. Re:Boo, you fad killer! by LWATCDR · · Score: 1

      1. Evolution is not smart.
      2. Evolution just picks for reproduction.

      Basicly you can drop dead after you reproduce a few kids and you are success by the standards of evolution.

      --
      See my blog http://ilovecookes.blogspot.com/ for light hearted technical information.
    12. Re:Boo, you fad killer! by dbarclay10 · · Score: 2

      What if, for instance, you find that that "perfectly functional" person has a rare modification to another gene that allows them to get by without the missing gene?

      What if, for instance, that gene is only required when you've been exposed to some common element or set of circumstances that the "perfectly functional" person just happened to avoid, by chance?

      What if, for instance, that "perfectly functional" individual isn't, in fact, perfectly functional? What if, for instance, any complications simply haven't yet become apparent?

      The headlines and any articles that say we could do without a given gene are almost certainly sensational. I will give the benefit of the doubt and assume the original paper doesn't make any such ridiculous claims.

      --

      Barclay family motto:
      Aut agere aut mori.
      (Either action or death.)
    13. Re:Boo, you fad killer! by dbarclay10 · · Score: 1

      Hah, I just read the article. Not even the article is sensationalistic - just the headline. The article clearly states that these people haven't been brought in for clinical tests yet, so they can't possibly know whether the subjects missing one of the genes in question are healthy or not.

      --

      Barclay family motto:
      Aut agere aut mori.
      (Either action or death.)
    14. Re:Boo, you fad killer! by Anonymous Coward · · Score: 0

      I should coco. I'm just recovering from a bout of flu, can someone explain to me the evolutionary benefit of being laid-low for a week by this annyoing schlog of viral nastiness?

    15. Re:Boo, you fad killer! by jedidiah · · Score: 1

      The funny thing is that humans are "so good at it" that they don't really need the new fangled approaches with the higher risks. We have been doing "conventional" genetic manipulation for thousands of years. Compared to that, our relatively short experience with direct genetic manipulation really doesn't hold up.

      The "conventional" approach just takes longer and confers no monopoly benefits to any herbicide mongers.

      --
      A Pirate and a Puritan look the same on a balance sheet.
    16. Re:Boo, you fad killer! by orgelspieler · · Score: 1

      What if that is the gene to be allergic to poison ivy, and we just didn't think to check for that? There's no way to know that a gene doesn't just serve some rarely-used purpose. What if it increases your intelligence by 1%, or some other feature that is affected by hundreds of other factors, like weight or hairline. Or maybe that gene's function is being suppressed by some epigenomic thing. Even the GP's suggestion of making changes isn't a winner, either. If the gene has a subtle purpose, changing it isn't going to make any obvious changes.

    17. Re: Boo, you fad killer! by Anonymous Coward · · Score: 0

      Large black holes don't disappear, not in any conventional sense. The number of years it would take for a large black hole to dissipate through hawking radiation is staggering. Perhaps longer than the heat death of the universe.

    18. Re:Boo, you fad killer! by s.petry · · Score: 1

      Complete nonsense! If you wish to draw an analogy, convince me that a Prosecuting attorney can not grasp a legal point that a defense attorney addresses. Claiming that you have to know a specialty knowledge to hold an educated stand or opinion on a subject is propositional fallacy at best, outright lie at worst.

      --

      -The wise argue that there are few absolutes, the fool argues that there are no probabilities.

    19. Re:Boo, you fad killer! by ChrisMaple · · Score: 1

      That humans don't always do it better doesn't mean that humans can''t do it better.

      the worst fucks you can imagine end up rich and funding "science" for their own benefit.

      There are three available possibilities. People can fund science the harms them - why would they do that? People can fund science that has no effect on them - why would they do that? People can fund science that benefits them - a rational activity. People claiming that there's something wrong with the third alternative either aren't deep thinkers or they've got a hidden and vicious agenda.

      --
      Contribute to civilization: ari.aynrand.org/donate
    20. Re:Boo, you fad killer! by Nemyst · · Score: 1

      A troll? Get off your high horse mate, you're just sounding petulant that someone dared disagree with you.

    21. Re:Boo, you fad killer! by s.petry · · Score: 1

      Your troll was this comment "It's not some godlike entity which designed humans with a goal in mind", though you probably know it and are just denying. Nuh uh in this post does not address or argue any of my points, which clearly demonstrate that it's not an issue of my ability or desire to debate. The issue is yours.

      --

      -The wise argue that there are few absolutes, the fool argues that there are no probabilities.

  11. "other countries" by Anonymous Coward · · Score: 0

    "...a model for other countries' efforts to sequence their people's DNA for research on personalized medical care..."
    That would not include the USA where social resposiblity for citizens is on the menu, but rather an appetite to squeeze everly last drop of blood out of the citizenry by rapacious corporations.

  12. $1000 for a genome? by Anonymous Coward · · Score: 0

    This is off-topic, but I keep hearing claims that the cost to sequence a genome is down to $1000. However, I can't find any details. Is this really just sequencing the genes (about 5% of the genome)? It seems a little hard to believe that you can sequence 3 billion base pairs with high fidelity for only $1000.

    1. Re: $1000 for a genome? by Fwipp · · Score: 1

      Yes - Illuminas HiSeq X machine (family) is one of the machines marketed as this. Please note that this is the projected internal per-genome cost of a dedicated sequencing facility - before any customer markup is applied, and only if you have the high quantity of data required to get your money's worth.

    2. Re:$1000 for a genome? by Anonymous Coward · · Score: 2, Interesting

      Last time I checked (about 6 months ago), MacroGen up in Korea will do a whole genome (30X coverage) for $1,500 - but the minimum order is 50 genomes. If you only want one genome sequenced then the cost is $4,500.

      It's worth noting also that you don't need blood, per se. DNAGenotek sells saliva collection kits ($20/kit but 25 kit minimum order). Basically you just spit in a tube, FedEx it to Korea and a few months later they're send you a USB external hard drive with a few hundred GB of your genome sequence data.

      And this is all for Illumina short reads (e.g. 200 base pairs) - so you won't get good mapping to much of the reference genome - e.g. if you're looking for a microdeletion in a repetitive region you may be out of luck. PacBio technology offers longer reads (e.g. 10,000 base pairs) but then even just 1X coverage whole genome sequencing will cost you about $8,000.

    3. Re: $1000 for a genome? by Anonymous Coward · · Score: 0

      ... and only if you supply them with 5 liters of your blood..

  13. viral rootkit by goombah99 · · Score: 4, Funny

    careful my dear replicant, those are kernel extensions injected into your DNA by the Sony reverse transciptase root kit. Evidently you are a replicant. Look for the Sony Copyright and your model number to see if you have a null pre-programmed life expectancy.

    --
    Some drink at the fountain of knowledge. Others just gargle.
  14. Re:My Jeans are old, faded, and have holes in them by Anonymous Coward · · Score: 0

    "Apparently" is the keyword here. "Apparently" you can take them off and feel just as warm and comfortable. Now, if you could do this without disturbing anyone else... It is the same with these proposed GMO organisms that were people, but had 1000 genes taken out.

  15. One^WTwo I could not do without by Anonymous Coward · · Score: 0

    Gene Gene the Dancing Machine

  16. What they're really for. by Anonymous Coward · · Score: 0

    For example, the United States is planning to sequence the genomes of 1 million Americans over the next few years and use the data to raise insurance health premiums

    Fixed that for you.

    1. Re:What they're really for. by Anonymous Coward · · Score: 0

      Actually, proposing to sequence 1 million American is one of the few things Obama has done right - not that it makes up for one of the worst things he did: stomping all over 23andMe. The ability to sequence human genomes at clinical scales is one of the biggest revolutions in the history of medicine. It's on the level of the discovery of antibiotics, vaccines, and aseptic surgery.

    2. Re: What they're really for. by Anonymous Coward · · Score: 0

      I don't think Obama had a hand in that anymore than I think George Bush had a hand in the FDA refusing to permit sale of the morning-after contraception pill.

      Rather, I think both stayed out of the fray lest they set a poor precedent for future presidents. If Obama is culpable its either refusing to step in (which is defensible) or in not more carefully filling FDA leadership roles.

  17. And we start with your food! by Anonymous Coward · · Score: 0

    They started tinkering with your food long ago!

  18. floppy disk by goombah99 · · Score: 2

    What I find staggering to comprehend is that your genome will easily fit on a CD. Even if you allow for all the midochondrial DNA, and epigenetic information it still would fit on a CD. If not all of it's needed maybe there's a Damn Small Linux version of your DNA that would fit on a floppy.

    --
    Some drink at the fountain of knowledge. Others just gargle.
    1. Re:floppy disk by Anonymous Coward · · Score: 0

      And don't copy that floppy!

    2. Re:floppy disk by Anonymous Coward · · Score: 0

      Does that include everything needed to build the DNA-to-meat compiler, or is there some bootstrapping that must happen too?

    3. Re:floppy disk by Rei · · Score: 2

      Where do you get that? Wikipedia says that the human genome is 3,23473 billion base pairs. I mean, you could compress that to fit on a CD, but it won't fit at one byte per BP. Won't even fit at 2 bits per BP.

      And if we want to think of a BP like a letter in a piece of code, with an average programming code line length of say 15 non-whitespace characters, that corresponds to a program 216 million lines long. That'd be no little program...

      Of course, only a tiny fraction of our DNA codes for what we would consider to be the "interesting stuff".

      --
      "99 dead duelists of Dios on the wall. 99 dead duelists of Dios! Take one's ring, pass it around..."
    4. Re:floppy disk by Anonymous Coward · · Score: 1

      I mean, you could compress that to fit on a CD, but it won't fit at one byte per BP.

      Speaking of compression, in a certain sense, a person only needs to know their differences from one of the standard reference sequences. But there's a subtle point: there are still parts of the human genome where we don't know the sequence (e.g. highly repetitive regions near the centromeres). For the well behaved (unique/non-repetitive) parts of the human genome, a person might have somewhere around one difference from the reference every hundred base pairs. So we're talking about very roughly tens of millions of differences - which could fit on a CD. But these days a USB thumb drive can hold 128GB - enough to hold even the raw reads from a genome sequencing run.

    5. Re:floppy disk by Anonymous Coward · · Score: 0

      There is a CD version too.

    6. Re:floppy disk by hodet · · Score: 1

      And when I put it in a CD player, it plays Mozart. True story....

    7. Re:floppy disk by jedidiah · · Score: 1

      3.3 Billion base pairs (nibbles) is not quite that small in terms of raw data. It will fit onto a DVD though.

      --
      A Pirate and a Puritan look the same on a balance sheet.
    8. Re:floppy disk by stoatwblr · · Score: 1

      > Of course, only a tiny fraction of our DNA codes for what we would consider to be the "interesting stuff".

      The hard part is tellling what's "junk" and what's useful data embedded in it. It's a bit like having a ROM dump and trying to work backwards from it without actually knowing what the CPU is. We know what some genes do, but not all of them, nor do we entirely know if they refer to offsets within the code as this changes when DNA is folded up as it is under normal operating conditions.

  19. Curb your enthusiasm by pesho · · Score: 1

    First of all, this is an amazing study. How surprising is that we can live without certain genes? Not that surprising. We have done numerous experiments where we have knocked out genes in mice and other organisms and they do just fine. There is no reason why it should be any different in humans. Keep in mind that these variations in the sequence are predicted to disable the gene, but not verified to do so. For example variants that introduce stop codons in the middle of a gene are typically predicted to disable the gene. However this is not always the case. Sometimes the piece of the gene that has the stop codon gets spliced out and the gene can still produce a functional albeit shorter protein. What is needed now is some experimental evidence showing what fraction of these genes are fully disabled.

  20. It's the comments by Hognoxious · · Score: 3, Funny

    Don't delete anything, comment it out! You never know, you might need to put it back.

    https://www.gnu.org/fun/jokes/...

    --
    Confucius say, "Find worm in apple - bad. Find half a worm - worse."
    1. Re:It's the comments by Rei · · Score: 1

      Nature is one step ahead of you. :)

      --
      "99 dead duelists of Dios on the wall. 99 dead duelists of Dios! Take one's ring, pass it around..."
  21. Up next by wonkey_monkey · · Score: 1

    Up next, the four limbs you can live without.

    --
    systemd is Roko's Basilisk.
  22. Not so sure by Lost+Penguin · · Score: 1

    "Unused gene" may be the "CRC" code.

    --
    I am the unwilling control for my Origin.
  23. Re:I'm keeping my genes! by Bengie · · Score: 2

    There are fully healthy XX males. Not too common, but there are cases where nearly all of the genes from the Y have been transcribed to the X. We have yet to have found a fertile XX male, but it's only because they lack the gene to allow sperm to swim. Move that gene over and we're good to go. Then everyone could be XX.

  24. Math by goombah99 · · Score: 3, Interesting

    3 billion base pairs.

    Each base pair is 2 bits (AGC or T). A byte is 8 bits or 4 base pairs. so

    3E9 / 4 = 750 MegaBytes.

    A CD holds up to 900MB of data. No need to even compress the data, and it would be highly(!) compressible

    Q.E.D.

    --
    Some drink at the fountain of knowledge. Others just gargle.
    1. Re:Math by Anonymous Coward · · Score: 0

      Each base pair is 2 bits (AGC or T). A byte is 8 bits or 4 base pairs. so

      The human reference genome sequence also contains lots of Ns (unknown base pair). And once you're working with more general DNA sequences, you'll find a number of other characters - either for modified base pairs or for subsets of the possible base pairs (e.g. a purine nucleotide - A or G).

  25. Your math is off by factor of 1000 by goombah99 · · Score: 1

    there are 3 billion (US definition of Billion not british) base pairs not 3 trillion.

    base pair = 2 bits (AGC or T).

    3billion bases = 6 billion bits = 750 megaBytes.

    A CD holds up to 900MB.

    So plenty of room even uncompressed.

    --
    Some drink at the fountain of knowledge. Others just gargle.
  26. #PRAGMA by goombah99 · · Score: 1

    Does that include everything needed to build the DNA-to-meat compiler, or is there some bootstrapping that must happen too?

    You are quite correct that you have to bootstrap the compiler.

    I tried to account for that partially by noting that there's plenty of room on the CD to store the epigenetic information. You can think of this epigenetic information as the #PRAGMA compiler directives and differences between non-ANSI compilers. So once we take those into account one could map the source code to the needs of any possible compiler. Thus in principle at least one could build a human using a compiler adapted from another somewhat similar organism. That is to say one could in principle compile a neaderthal on a homosapien compiler or a mammoth on an elephant compiler as long as you have the means to take the epigenetic aspects into account.

    --
    Some drink at the fountain of knowledge. Others just gargle.
    1. Re:#PRAGMA by eric_harris_76 · · Score: 1

      There's more to people than their genes. We're also a bunch of ecosystems: skin and gut, especially.

      Is there room on that CD for the genomes of our bacteria and fungi and such, and the bootstrapping process for each?

      Oh, and where to put them? You probably don't want the colon bacteria on your eyelashes, etc.

      --
      There's no time like the present. Well, the past used to be.
  27. let's see...... by OutOnARock · · Score: 1

    Gene Roddenberry....no
    Gene Simmons..........no
    Gene Wilder...............no
    Gene Siskel................yes
    Gene Hackman..........no


    this could take a while......

  28. probably. by Anonymous Coward · · Score: 0

    Lets wait and see.

  29. Prove it by Anonymous Coward · · Score: 0

    We need living proof

  30. Weight Loss by coinreturn · · Score: 1

    I'm dumping mine immediately. That'll tip the scale in my favor!

  31. What if genes didn't evolve and were created? by rhyous · · Score: 1

    No, I am not saying "believe in God over evolution." I am just saying that looking at DNA without considering the possibility of intelligent design is myopic.

    At least some DNA studies should assume intelligent design.

    Start looking at DNA and everything that interacts with it as a programming language created by something intelligent.

    In a programming language, there is code and data. Code contains all the method and functions to do small amounts of work. Data is used or acted upon by the code. Data can be read only, read/write/delete, etc...

    Think of our bodies as a biological artificial intelligence created using this biological programming language.

    What if it DNA is code or a database.

    Who knows what is used and what isn't?

  32. Just like new programmers by cwsumner · · Score: 1

    That sounds just like a new programmer faced with working on legacy code. The first thing they want to do is delete everything that they don't understand!

    If we didn't need it, it would not be there. There is no room in nature for wasted effort.

    They said the same thing about the appendix, for decades, but now we know it's not true. The appendix is necessary for propper digestion, look it up...