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Deciphering the DNA Code of Neanderthal Man 188

Posted by Zonk
from the hey-good-buddy dept.
smooth wombat writes "U.S. and German scientists have embarked on a two-year long project to map the genetic code of Neanderthal man. Their hope is to gain a greater understanding of how modern human brains evolved. This study comes after last years completion of mapping the DNA of chimpanzees, our closest living relative." From the article: "Over two years, the scientists aim to reconstruct a draft of the 3 billion building blocks of the Neanderthal genome -- working with fossil samples from several individuals. They face the complication of working with 40,000-year-old samples, and of filtering out microbial DNA that contaminated them after death. Only about 5 percent of the DNA in the samples is actually Neanderthal DNA, Egholm estimated, but he and Rothberg said pilot experiments had convinced them that the decoding was feasible."
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Deciphering the DNA Code of Neanderthal Man

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  • Sheesh.. (Score:5, Funny)

    by vancondo (986849) on Friday July 21, 2006 @01:52PM (#15758464) Homepage
    You people, with your 'facts' and 'figures'.. 40,000 year old samples?!

    ridiculous.

    Everybody knows that the earth is only 27 years old. [diabolicalplan.com]

  • ad-word-tizzy (Score:3, Interesting)

    by wheatking (608436) on Friday July 21, 2006 @01:53PM (#15758481)
    this and yesterday's article in NYT by the same author (Nicholas Wade) look like placed (indirectly paid for to some PR mavens) ads for 454 lifesciences (if named after the famous chevy engine, a helluva name for a company). 454, having built a fair-to-middling sequencer is trying hard to stay alive in a race to the $1000 genome that will not be won by them or solexa, another startup given their slow pace and limited read lengths of the base pairs. nothing new here. move on folks.
    • The Broad institute has 454 as one of their sequencing platforms in house. Of course, george church is working on an 'open source' sequencing platform that will be obscenely cheap by comparison. I think you need a microscope, some (comparably) reagents, and some open source software to do sequencing.

      You might remember the Broad institute when they were the whitehead center for genome research - the people who sequenced a large (the largest?) part of the human genome. A number of people there seem to thin
  • Sweet (Score:3, Funny)

    by CtrlPhreak (226872) on Friday July 21, 2006 @01:54PM (#15758490) Homepage
    We can have those cavemen all cloned and show up like in the geico comemrcials!

    It'll be great they can be all hairy and be pissed off at the world. Kinda reminds me of my neighbor...
  • And No... (Score:2, Funny)

    by Chatmag (646500)
    Neanderthal man did not run on Linux.
  • by kkamrani (882365) on Friday July 21, 2006 @01:58PM (#15758527) Homepage
    This link, "Announcing a two year Neandertal genome decoding project [anthropology.net]" links to several science blogger's take on this anouncement including a definited Neandertal sequencing post by John Hawks.
    • by jd (1658) <imipak @ y a h o o .com> on Friday July 21, 2006 @03:35PM (#15759381) Homepage Journal
      Definitely interesting, highly contradictory though. The blog directly linked to claims that the neandertal DNA is being found in the bacteria - that the bacteria had somehow made it a part of its own DNA. This seems highly improbable. Bacterial DNA can do strange things, but absorbing large chunks of neandertal DNA is almost certainly not one of them.


      The other descriptions imply that it's contamination through questionable extraction techniques - they're grinding up the fossils, so ALL the DNA in the sample will be mixed together, and strands may well end up getting broken, making it much harder to sequence correctly.


      Sequencing fossil DNA is certainly possible, and is extremely desirable, but the approach seems... odd. The BBC article, for example, claims that they're going to look for the genes that differentiate modern humans from neandertals, such as mental capacity. Given that we don't fully understand what "mental capacity" actually means, or indeed what mental capacity neandertals actually had, they would need to be looking for an unknown difference to identify an entirely theoretical and totally unquantifiable distinction. That's not good science.


      Lastly, we know from studies of neandertal mtDNA that there was a large genetic diversity. Far larger than had been suspected, prior to that study. If these scientists are taking neandertal nucleic DNA from significantly different regions and/or times, they cannot be certain that the nucleic DNA had not evolved or otherwise differed to the point where direct comparison or simple in-lining of the genes would make no sense whatsoever.


      This is a good research project, but I am highly uncertain of their methods and am not convinced it will yield meaningful results. Because repeat studies will be difficult to do, this is an area where those involved HAVE to take extra care to put their results beyond question. This care is NOT being taken, based on what I'm seeing.

      • >they're grinding up the fossils, so ALL the DNA in the sample will be mixed together, and strands may well end up getting broken, making it much harder to sequence correctly.

        To the best of my knowledge (and things may have changed in the last two years) all sequencing is done in tiny chunks because we don't have the technology to accurately sequence long strands(by which I mean even thousands of base pairs, much less billions.) To deal with this, they sequence lots and lots of strands more or less rand
        • You are correct, because they sequence directly. This isn't necessary for Neandertal DNA as we have plenty of reference points from chimp DNA and human DNA, which are already mapped. We only need to sequence those segments that are different from either.

          There is an added problem. Most geneticists use chain termination sequencing, which is good for fairly decent lengths of DNA. 454 uses pyrosequencing which is faster but only good for much smaller lengths. When the unknown elements may contain repeats of unk

          • A: that's really cool. Thanks for the overview.
            B: it makes me wonder if we couldn't use recombination with chopped-up human and chimp dna to show a lot of the differentiation. Fragment radiolabelled human DNA, mix with Neandertal, heat and anneal, then start looking at the overlap sequences. It'd work better and be more automated if there were markers on the human DNA as targets for some sort of ELISA or selective column adsorption. Hm. I miss biochem.
            • B is exactly the sort of thing I was thinking of. There's plenty of known markers on human DNA and chimp DNA, as those are completely mapped, and some of those must be usable as targets for the sort of process you're thinking of. It would seem far more logical to do it that way than to map from scratch, knowing nothing.

              Since you know the biochem side, you might want to write up a paper on how you'd go about this. At worst, you might easily get published, and journals pay very decently. At best, a biotech co

  • by iambarry (134796) on Friday July 21, 2006 @01:58PM (#15758537) Homepage
    Didn't I see this in a movie?

    Maybe scientists should get out more. First they sequence the Neanderthals DNA. Next, they'll be cloning one. Then the clone's start multiplying. Finally they take over the earth. Isn't this obvious to anyone else, or is it just me?
    • They've already taken over Washington.
    • How long before the gorillas freeze to death?
    • by MrFlibbs (945469) on Friday July 21, 2006 @02:42PM (#15758931)
      Don't laugh. Richard Dawkins predicts that "the missing link" will be born by the middle of this century. He has an essay on this in a book titled "The Next Fifty Years: Science in the First Half of the Twenty-first Century". This is an interesting book consisting of 25 speculative essays by leading scientists in various fields.

      Dawkins' argument is that Moore's Law will eventually make the sequencing of genomes cheap enough to be routine. He speculates that a large database of hominid genomes plus expected advances in gene manipulation would support the creation of pre-human DNA. Once this is done, an implanted embryo with the new DNA could be inserted into a human womb, and out pops the new (old?) species. If Dawkins is correct, then other non-human species such as Neanderthals are also potentially viable.

      In the essay, Dawkins briefly discusses the moral implications of such a task. He concludes that any objections are easily overcome by the great service to mankind in proving the correctness of the Theory of Evolution.
      • The female neanderthal's pelvis was extremely wide, which has led to speculation that their babies had a longer gestation period than humans (maybe 12 months), and were born bigger and less helpless. Even assuming the human host mother was going to deliver by C-section, I'm not sure you could delay birth that long.

        But it's wild to imagine the problems it would cause for society. If you could produce beings from anywhere along the spectrum from animal to human, at what point do you let it vote? At what poin

        • at what point do you let it vote?

          Depending on the political climate, whether or not it switched on either Fox or PBS.
        • Born three months premature out of 12 gestation would be rough, but not appalling. My girlfriend was born two months premature and her younger sister was born four months early. Both required hospitalization, but it wasn't that difficult. This would be somewhere between the two. Now, there might be a lot of issues we don't expect because the child wouldn't be homo sapiens, but that could show up anywhere in the pregnancy. I was reading about pre-eclampsia last night, about how it's probably a case wher
          • Note that there are some bad genetic traits in that line. Please don't make more people who can't live without modern medicine.
            • I think it was behavioral not genetic, since the other two kids went to full-term. Plus, it's a matter of weighing what's important. Both my girlfriend and her younger sister are skipped-grades-in-school smart and the kind of pretty that make people slow down to stare and whistle when they're driving by. If that comes at the cost of medical care, not maybe such a big deal.
        • Here are some quotes from Dawkin's essay that might shed some more light on his position:

          "A spin-off benefit, which will perhaps have its greatest
          impact in the United States, is that full knowledge of the
          tree of life will make it even harder to doubt the fact of
          evolution."

          Here's another quote on the moral implications:

          "'Pro life,' for example, in debates on abortion or stem
          cell research, always means pro human life, fo
        • "...But it's wild to imagine the problems it would cause for society. If you could produce beings from anywhere along the spectrum from animal to human, at what point do you let it vote?"

          It obviously will be able to register as a US Republican, no problem.
    • by r00t (33219)
      That would be THEIR concern about US. After all, that's exactly what we did.

      Well, you might be right. The environment has changed. The primary test of evolutionary fitness is now your ability to overcome birth control. You can do this via love of kids, religeous passion (Muslim or Catholic), or sheer stupidity. If the Neanderthals are even dumber than today's welfare moms, then they are more fit to survive.

    • UG-UG BAM-BAM

      Well, given that neaderthal man had larger braincase, and either a same-size, to larger brain. And given that, given the shorter vocal box, and a larger nasal cavity, they had a higher, more nasal voice. And given that they were stockier , yet much stronger, then modern man...

      What I see here is the rise of (possibly) highly intelligent, nasal, and strong individuals with thicker hair...

      I for one welcome our new Jock-Nerd overloards...
    • Gah! How the heck do you bypass the lameness filter and get all caps? I tried a hundred way to make an OGG THE OPEN SOURCE CAVEMAN post, and nothing seemed to work.
  • by jpellino (202698) on Friday July 21, 2006 @02:06PM (#15758597)
    .. they lived almost exclusively on a diet of roast duck with mango salsa.
  • chimpanzees, our closest living relative
    I am wondering if the word "pansy" came from "chimpanzee" or vice versa ?
    • Well given that an adult male chimp is three times stronger than an adult male human I would be very careful about calling one a pansy
  • They will superimpose the DNA image on current human DNA, and find the following message:

    "We apologize for all the inconveniences"
  • Where do I download the screensaver?
  • by digitaldc (879047) * on Friday July 21, 2006 @02:14PM (#15758675)
    ...the evolution of DNA in Homo Sapiens gave them a larger and more complex brain, as well as a larger larynx in order for them to speak deeply, clearly and forcefully.
    Neanderthal man, on the contrary, sounded wimpy and nasal.
    Neanderthals were hated by other humanoids, and were killed off due to their annoying, high-pitched voices.

    See: http://en.wikipedia.org/wiki/Neandertal [wikipedia.org]
    A recent study conducted on the Neanderthal hyoid found that due to the physical characteristics of Neanderthals and the fact that their larynx would have been stouter than that of the modern human, the average note emitted by Neanderthals would have been high pitched and sharper than that of modern man, contrary to the media stereotype of Neanderthals having ape-like grunts.
    The base of the Neanderthal tongue was positioned higher in the throat, crowding the mouth somewhat. As a result, Neanderthal speech would most likely have been nasalized.
    • A recent study conducted on the Neanderthal hyoid found that due to the physical characteristics of Neanderthals and the fact that their larynx would have been stouter than that of the modern human, the average note emitted by Neanderthals would have been high pitched and sharper than that of modern man, contrary to the media stereotype of Neanderthals having ape-like grunts.

      So, basically they would have sounded (or will sound) like this [orbitcast.com].

    • Neanderthals were hated by other humanoids, and were killed off due to their annoying, high-pitched voices.

      The thought occurs that you substituted "French" for "Neanderthals" and changed "killed off" to "killed" it would still be true.
    • by bcrowell (177657) on Friday July 21, 2006 @03:02PM (#15759109) Homepage

      ...the evolution of DNA in Homo Sapiens gave them a larger and more complex brain,
      Nope, the average neanderthal had a bigger brain than the average human. However, both neanderthals and our own ancestors don't appear to have achieved any real level of culture until relatively recently in history; their artifacts don't show any specialization or innovation over tens of thousands of years, and they all come from local stone, indicating a lack of trade. The onset of culture didn't have anything to do with an increase in brain size (which didn't change over that short period). It may have had to do with something like the foxp2 [wikipedia.org] gene, which is crucial for developing complex language. It's possible to make up a lot of stories, and nobody knows which is right. It's possible, for example, that humans first crowded out neanderthals because we were skinnier and could survive on less food, and only later developed speech and culture.

      • I guess it is up to scientific speculation...

        From Wikipedia...
        Their brain sizes have been estimated as larger than modern humans, but their brains may in fact have been approximately the same as those of modern humans.

        I stand (upright) corrected.
      • their artifacts don't show any specialization or innovation over tens of thousands of years


        If scientists find evidence of chair-flinging as a sport, this would truly explain a lot.

      • I guess it could also be because the Neanderthals were having muchstouter body compared to us.
        Basic human physiology, with a stouter body causes for quite a bit of internal heat production.

        And also that the ice age was getting over at that precise period.

        We being much thinner, can survive heat much better. These guys couldnt.

        Since getting heat is easy (wear animal skins ?? ), but cooling off is not (no AC at that time)

        Many factors..
    • Can you imagine a race of people who are bigger than you, yet talk like Elmo? I'd want to kill them off too.

    • so they all sounded like Fran Drescher?
  • Gene Pool (Score:2, Funny)

    by frosty_tsm (933163)
    These guys were kicked out of the gene pool thousands of years ago. Don't risk letting them back in!
  • ... Jurassic Dork!

    (Yes, yes, I know, there were no hominids in the jurassic - it's a joke...)
  • Details (Score:4, Informative)

    by Raindance (680694) * <johnsonmx@@@gmail...com> on Friday July 21, 2006 @02:35PM (#15758855) Homepage Journal
    Here's some background that isn't apparent from the article. The CNN piece talks about Neanderthals in the context of understanding brain evolution, but the million dollar question- in most scientists' minds- is whether Neanderthals and early modern humans interbred, after 500,000 years of separation. It seems at least possible: lions and tigers produce fertile offspring and they diverged 2 million years ago. As the New York Times states [nytimes.com],

            "A longstanding dispute among archaeologists is whether the modern humans who first entered Europe 45,000 years ago, ultimately from Africa, interbred with the Neanderthals or forced them into extinction. Interbreeding could have been genetically advantageous to the incoming humans, says Bruce Lahn, a geneticist at the University of Chicago, because the Neanderthals were well adapted to the cold European climate -- the last ice age had another 35,000 years to run -- and to local diseases.

            Evidence from the human genome suggests some interbreeding with an archaic species, Dr. Lahn said, which could have been Neanderthals or other early humans."

    Now, nobody really knows much at this point. But something that I found interesting was that, via John Hawks [johnhawks.net], "Neandertals will be within the human range of variation for most genes." And the "pilot experiments" Rothberg mentioned is a reference to how their team sequenced the DNA of the cave bear as a test-run. As I understand it this was mostly to convince museums that grinding up some of their prize Neanderthal fossils in the name of research was a good idea. :)
    • The cama. (Score:3, Interesting)

      by Savage-Rabbit (308260)
      Here's some background that isn't apparent from the article. The CNN piece talks about Neanderthals in the context of understanding brain evolution, but the million dollar question- in most scientists' minds- is whether Neanderthals and early modern humans interbred, after 500,000 years of separation. It seems at least possible: lions and tigers produce fertile offspring and they diverged 2 million years ago.

      I have always had trouble understanding why some scientists flatly deny that interbreeding between
      • I have always had trouble understanding why some scientists flatly deny that interbreeding between Neanderthals and modern humans would have even been possible... It would seem to me that Neanderthals and modern humans probably could interbreed, in light of what history tells us about human nature it would be strange if they didn't

        That's exactly why many don't buy it, actually. We know they lived basically side by side for tens of thousands of years in many places - in one location in particular for over

    • Now, nobody really knows much at this point. But something that I found interesting was that, via John Hawks, "Neandertals will be within the human range of variation for most genes."

      Something I've never heard explained: How exactly can we determine the specific origin of an allele of a gene?

      Suppose there were a particular allele that arose as a mutation in one particular Neandertal, and it was sufficiently beneficial that it spread to the entire human species. How would we determine this? How would we
      • Something I've never heard explained: How exactly can we determine the specific origin of an allele of a gene?

        Even if an allele is found only in modern Europeans, and is also found in a Neandertal sample, how would we know where it originated? It could have been a mutation that happened 40,000 years ago in Europe, but how do we know which population produced it?

        That's a good question. From breaking it down into 'when did an allele arise' and 'where did an allele arise' here some examples of how we can answe
        • One thing that stands out is that those are all methods that involve studying and comparing populations. What's the likelyhood that we'll ever have a single population of closely-related Neandertals with well-preserved DNA?

          If we were talking about the possibility that modern Europeans are, say, 30% Neandertal and 70% Cro Magnon, we might be able to do some sort of general population study. But that's not the situation. Nobody thinks the Neandertals could have contributed even 1% of modern European genes
          • You're right- those methods do center on comparing populations. It's not clear from my previous post how useful those methods would be if we only had one data point for one of the populations.

            But one of the stumbling blocks the scientists in this initial decode had to deal with was convincing museums that valuable research would come out of giving them Neanderthal bones to grind up and analyze. If things go as planned, I think it'll be easier for them to ask for more samples. And we've a fair number of rand
            • Yeah, or maybe there's be a concensus that "We really don't know." ;-)

              I've long thought it would be fun (if ultimately meaningless) to learn that, as a person with mostly European ancestry, I might be part Neandertal. It'd be even more fun to verify that they were among my personal ancestors. Then when someone called me a Neandert[h]al, I could say "How'd you know?" with an evil grin. But I'm not very hopeful that I'll ever know for sure.

  • by Bryansix (761547) on Friday July 21, 2006 @02:39PM (#15758900) Homepage
    chimpanzees, our closest living relative.

    I don't know about you guys but my closest living relative is probably my mother or maybe my father.
    • I'm not certain I see your point, Cheeta.
  • I have first decipherd it and then re-calculated the output. Put that data through several checks and the outcome was 42.
  • Pigmy chimp (Score:3, Informative)

    by booch (4157) <slashdot2010 AT craigbuchek DOT com> on Friday July 21, 2006 @03:13PM (#15759207) Homepage
    The closest living relative to human beings is not the common chimpanzee. It's the bonobo [wikipedia.org], also known as the pigmy chimpanzee. Interesting creatures, with even more interesting sex lives.
    • Re:Pigmy chimp (Score:3, Informative)

      by bcrowell (177657)
      The closest living relative to human beings is not the common chimpanzee. It's the bonobo,
      Nope. Chimps and bonobos form a clade together, and their common ancestor split off from our branch at the same time.
    • The closest living relative to human beings is not the common chimpanzee

      Sure? [anthropik.com]

      CC.
      • I was not aware that the fact was disputed. I'd heard it several times. Now I can only say that bonobos have the most interesting sex lives besides humans. Or can you refute that one too? ;)

        That's an excellent article you referenced in support of your position. You must be new here. ;)
    • Actually, we are just as closely related to the bonobos as to the common chimpanzee. The two chimpanzees are each other's closest relatives, and humans are the closest relative to the chimps.

      Consider this phylogenetic tree:

      |----------------- Gorilla
      |
      | |----------- Human
      ---------|
      | |--- Common chimpanzee
      |-------|
  • I, for one, welcome our Neandertal DNA overlords.
  • This is the song that made me stop listening to Dr. Demento:
    I'm a neanderthal man.
    You're a neanderthal girl.
    Let's make neanderthal love,
    In this neanderthal world.
    Repeat about 1,000 times, with a chord change or two.
    • I was thinking more along the lines of something by Kinky Friedman:

      Now I'm a homo erectus
      Got to connect this
      Bone that I discovered yesterday.


      A bit older than Neandertal, of course.
  • Neanderthals mispronounced it as "nuke-you-lurr", opposed embryonic stem cell research, and weren't big fans of evolution either.
  • This really is a bad metaphor. Nobody is cracking any code, not even metaphorically speaking. The code [wikipedia.org] was cracked in the 60s. What's actually happening is that people are still trying to recover the ciphertext.

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