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Science

Darwinian Evolution Considered As a Phase 313

Posted by kdawson
from the everything-you-know-is-wrong dept.
LucidBeast tips a mind-bending report at New Scientist on the latest paradigm-breaking work of Carl Woese, one of whose earlier discoveries was the third branch of life on Earth, the Archaea. Woese and physicist Nigel Goldenfeld argue that, even in its sophisticated modern form, Darwin's theory of evolution by natural selection applies only to a recent phase of life on Earth. Woese and Goldenfeld believe that horizontal evolution led to the rise of the genetic code itself. "At the root of this idea is overwhelming recent evidence for horizontal gene transfer — in which organisms acquire genetic material 'horizontally' from other organisms around them, rather than vertically from their parents or ancestors. The donor organisms may not even be the same species. This mechanism is already known to play a huge role in the evolution of microbial genomes, but its consequences have hardly been explored. According to Woese and Goldenfeld, they are profound, and horizontal gene transfer alters the evolutionary process itself."
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Darwinian Evolution Considered As a Phase

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  • by Blappo (976408) on Tuesday January 26, 2010 @07:30PM (#30911600) Journal

    I strongly suspect it isn't, nor was it ever, one type of evolution over the other, but a complex interaction between many environmental pressures where both types of evolution played a role.

    • by biryokumaru (822262) * <biryokumaru@gmail.com> on Tuesday January 26, 2010 @07:37PM (#30911680)

      Similar to the silly "nature versus nurture" debate, I think the key here is that for different critters, different types of evolution are significantly more dominant.

    • Here's A Tip, Folks (Score:5, Informative)

      by MightyMartian (840721) on Tuesday January 26, 2010 @08:11PM (#30911972) Journal

      Here's a tip, folks. The minute you see some science journalist use the word "paradigm", as in "paradigm shift" or "paradigm breaking" you can be quite certain that what follows will be neither.

      Horizontal gene transfer has been known about for decades, and the notion that the root of the tree of life is more a tangle of interconnecting branches has pretty much been accepted for some time now. We know that particularly with prokaryotes, horizontal transfer happens, and that while more difficult with eukaryotes, can still happen (ie. endo-retroviral insertions). It is yet another facet of evolution, not some independent force.

      • by Dalambertian (963810) on Tuesday January 26, 2010 @08:28PM (#30912116)
        Here's a protip I've learned from watching the internets and reading your first comment: The moment anyone brings to light something most people have been ignoring, there's always someone who comes along claiming that there's nothing new to see here and that anyone who doesn't know that is clearly misinformed. I'm sorry, but I've never heard of this theory before, and I daresay I'm not the only one. So, please, stop trying to take away my sense of wonder.

        Sincerely, the misinformed

        • by MightyMartian (840721) on Tuesday January 26, 2010 @08:37PM (#30912168) Journal

          I'm not trying to take away anyone's "sense of wonder". I'm saying that horizontal gene transfer is one known way in which variation can occur. Remember, evolution requires only that there be variation in populations. For the most part, that variation will either be in allele frequency, but sometimes is also mutational, sometimes due to neutral drift, and probably with considerably less frequency due to horizontal transfer. It ain't new, and neither is trying to make a well known phenomena sound exciting and "paradigm shifting" by announcing it to the world.

          Man, but I hate science journalism.

          • by Artifakt (700173)

            Evolution requires that there be variation in individuals, and that there be selection.
            If the selection rate is such that species organize as fuzzy sets where most individuals are typical and only a few are seriously atypical, then there can be variations within (definable) populations. If the selection rate changes enough, just how fuzzy species membership is becomes an open topic - no one is really sure just how much individuals in a species could vary without the species becoming extinct.
            Mutation without

          • by Jay L (74152) *

            Man, but I hate science journalism.

            It. brought. us. here.

          • Re: (Score:3, Interesting)

            by Fred_A (10934)

            Man, but I hate science journalism.

            While I simply try to keep myself up to date and absolutely don't work in the field, I remember having read about this (namely eukaryotes grabbing strands from viruses) years ago. As I recall the title at the time was more along the line of "viruses sharing dna with organisms may open new research avenues" or something along those lines. Anyway it didn't strike me as being especially sensationalist. Since then I keep an eye open for further news upon those lines.

            OTOH, it seems that labs feel that they are i

        • by Cassius Corodes (1084513) on Tuesday January 26, 2010 @10:00PM (#30912786)
          Depends who you mean - the article says most biologists didn't pay much attention to this and I think that is wrong. However to say most laymen did not know about this is probably correct. Also like GP I hate the phrase "paradigm shift" as I find its often brought up by purveyors of woo.
        • by BrokenHalo (565198) on Tuesday January 26, 2010 @11:12PM (#30913174)
          I'm sorry, but I've never heard of this theory before, and I daresay I'm not the only one.

          OK, here you go, then: Prokaryotes (i.e. bacteria, archea and so forth), by virtue of the comparatively "exposed" genetic material (not condensed or "bunched up" like ours typically is) and because of the structure of their cellular membranes, are very capable of "scraping up" any loose genetic material that may be lying around (e.g. as a result of cellular lysis). If these nucleic acids confer an evolutionary advantage, they are propagated in successive generations. This is why, and how "superbugs" like MRSA are thought to have evolved.

          Microbiologists have used this feature for decades in the genetic engineering of bacteria to induce desired characteristics. The process is much harder and more complicated in eukaryotic (e.g. animal or plant) cells, but it can and does happen.
      • by icebike (68054) on Tuesday January 26, 2010 @08:30PM (#30912132)

        Horizontal gene transfer has been known about for decades, and the notion that the root of the tree of life is more a tangle of interconnecting branches has pretty much been accepted for some time now.

        Further it has nothing at all to do with Darwinism.

        A mechanism of gene transfer plays no role in the "Survival of the Fittest" (a phrase coined not by Darwin, but rather by Spencer), or natural selection. Its not germane.

        Natural Selection is a winnowing process, and a mutation amplifying force, but says nothing about the acquisition or dispersion of said mutations. It was never meant to.

        • Re: (Score:3, Interesting)

          by MightyMartian (840721)

          I think your confusing things here. Of course horizontal gene transfer can potential influence fitness. Evolution requires variability in traits. How exactly that variability gets there (mutation, mitosis, neutral drift, horizontal gene transfer) is the dirty details of evolution. However a trait makes it into a population, once its there, it can be fixed, and thus alter fitness.

          • by icebike (68054) on Tuesday January 26, 2010 @08:53PM (#30912300)

            I fail to see the point of confusion.

            Acquisition of a trait (by whatever means) would never amount to a significant percentage of the gene pool of an organism unless it proffered some usefulness. Mutation or horizontal genetic transfer are but mere mechanisms. Darwinism discusses the overall process, not the details.

            How that transfer took place is mere details. When that transfer takes place is not fixed in time. Horizontal transfer still exists in larger and more complex organisms and their symbiotic partners.

            • Re: (Score:3, Interesting)

              by svyyn (530783)

              Acquisition of a trait (by whatever means) would never amount to a significant percentage of the gene pool of an organism unless it proffered some usefulness.

              Though a popular view, that's not true. Assuming 'trait' means an independent mutation, then that trait can go to fixation in a population by simple chance (the expectation is that this happens to 1/2N mutations). Also, genes that are physically near each other on the genome tend to be passed as a set. Therefore, it is likely that a completely neu

          • Re: (Score:3, Informative)

            by Alphathon (1634555)
            First, if you wish to be taken seriously in an intellectual discussion, please learn the difference between your and you're. I am a grammar nazi (not that I'm proud of it - I can't help it and I blame my mum because she's even worse than I am :S) but things like that show a lack of thought behind posts.

            Anyway, back on topic. Icebike did not say that horizontal gene transfer cannot influence fitness, but that the mechnaism itself has no effect. What has the effect is the genes, not how they got there.

            Her
      • Outstanding concept - and correct, of course!

        Of course, it is great research, but also quite obvious to the rest of us as viral transfer of DNA material has been known for quite some time, and numerous research grants were submitted in the late '70s and early '80s --- unfortunately that was the time of the anti-science of Reagan and the first wave of neocons.

      • by camperdave (969942) on Tuesday January 26, 2010 @09:33PM (#30912644) Journal
        In other words, the tree of life is a banyan [wikimedia.org] tree.
      • by syousef (465911) on Tuesday January 26, 2010 @10:11PM (#30912826) Journal

        Here's a tip, folks. The minute you see some science journalist use the word "paradigm", as in "paradigm shift" or "paradigm breaking" you can be quite certain that what follows will be neither.

        Thank goodness! Relativity and Quantum Mechanics make my head hurt. With this wonderful insight you've provided I can crawl back into my Newtonian clockwork universe shell and ignore them! ;-)

        More seriously. Pardigms do "shift" and get "broken". It's just that almost every journalist wants to sensationalise their news piece to sell it. That doesn't mean there aren't genuine breakthroughs. Just that you can't trust a journalist to tell you about them.

    • Re: (Score:2, Insightful)

      by Anachragnome (1008495)

      I agree.

      It always seemed a little odd that evolutionists minimized such interactions as the bacteria that lives on, and IN, us as little more then a symbiotic relationship.

      The idea that some genetic material might actually be passed from ourselves to these bacteria, or the other way around, seemed to make sense. I'm not talking about large chunks of DNA, but rather a codon or two every dozen generations, or something to that effect. Given that mutations/variations are more likely to occur in two species, as

      • Re: (Score:3, Interesting)

        by Thiez (1281866)

        > The idea that some genetic material might actually be passed from ourselves to these bacteria, or the other way around, seemed to make sense. I'm not talking about large chunks of DNA, but rather a codon or two every dozen generations, or something to that effect. Given that mutations/variations are more likely to occur in two species, as opposed to one, that symbiotic relationship might have accelerated genetic changes in either, or both, species. Who knows, maybe our ability to digest some specific f

        • Well, ass-to-pussy maybe not, but ass to something else has been tried time and again. And research, studies and actual experiments are going on, probably as we speak.

          It's just news to me that it has anything to do with the procreation process.

  • by Monkeedude1212 (1560403) on Tuesday January 26, 2010 @07:31PM (#30911614) Journal

    The first 2 parts of Spore are like Horizontal Evolution, and the later parts are all vertical.

    It makes perfect sense. Clearly Will Wright is a genius.

  • Well duh? (Score:3, Informative)

    by tzenes (904307) on Tuesday January 26, 2010 @07:33PM (#30911636)

    For anyone familiar with the Red Queen Hypothesis ( http://en.wikipedia.org/wiki/Red_Queen [wikipedia.org] ) this should be obvious.

    While direct DNA transfer is not the component usually referred to by this "arms race," it is merely an extension of a known theory.

    No one makes a big hype about this theory, because it doesn't say your grandfather was a monkey and piss off the religious nuts

    • by mrmeval (662166) <mrmeval@NOSPam.gmail.com> on Tuesday January 26, 2010 @07:46PM (#30911776) Journal

      I am going to come over there and take all your stuff and I'm going to kill you and take your weapons and use them for myself!!!

      If you're really nice and sweet I'll beat the crap out of you and then stick you in my kitchen to make food for me.

      The second is referring to mitochondria not kitchen bitches.

    • Also to note, this doesn't supplant Darwinian evolution but adds to it. I can see that this might be plausible in the early stages of life on this planet where microbes would acquire genes from other microbes. I'm wondering if the proponents consider the mitochondria as one example of this horizontal evolution?
      • Re:Well duh? (Score:5, Interesting)

        by CrimsonAvenger (580665) on Tuesday January 26, 2010 @08:48PM (#30912262)

        I can see that this might be plausible in the early stages of life on this planet where microbes would acquire genes from other microbes.

        I saw an article recently about a species of snail that has acquired the genes for making chlorophyll from the algae it eats. It hasn't yet acquired the genes to make chloroplasts, so it has to eat algae to get enough chloroplasts from the algae to allow photosynthesis to work, but after that it is capable of living with no food other than light.

        So, obviously this is still ongoing, and on larger scales than microbes.

        • Re:Well duh? (Score:4, Informative)

          by renoX (11677) on Wednesday January 27, 2010 @09:59AM (#30916536)

          I wonder why this is moderated insightful?
          This is a very different kind of 'acquisition' as the genes for making chlorophyll acquired from the algae are not transferred to its offspring..

          • Re: (Score:3, Informative)

            by Danse (1026)

            This is a very different kind of 'acquisition' as the genes for making chlorophyll acquired from the algae are not transferred to its offspring..

            According to this article [foxnews.com], the genes are transferred, but the offspring, like the parents, can't produce their own chloroplasts, so have to eat enough algae to acquire the necessary chloroplasts before they can survive like that.

    • Re: (Score:3, Informative)

      by Arancaytar (966377)

      To be precise, there is no theory that says your grandfather was a monkey. The religious nuts made that straw-man up all on their own. :P

      • To be precise, there is no theory that says your grandfather was a monkey. The religious nuts made that straw-man up all on their own. :P

        I beg to differ [youtube.com]. Although still struggling for broad acceptance, the theory that you are the retarded offspring of 5 monkeys and a fish-squirrel is being taught in our schools.

  • Capitalism? (Score:2, Interesting)

    by Anonymous Coward

    So, would this "horizontal gene transfer" be like capitalism? Does it become a battle to see who can acquire the most and/or the best genes? Do you end up with winners for a while, until the losers get disgusted and start sparking genetic revolutions? Would Darwinian revolution be a happy meritocracy that arose as a kind of "compromise"?

    However, I've always read Darwinian evolution as "survival of the fittest", with no qualifier as to how you go about surviving. It always implied to me that the organisms

    • Re:Capitalism? (Score:5, Informative)

      by Chris Burke (6130) on Tuesday January 26, 2010 @08:05PM (#30911936) Homepage

      However, I've always read Darwinian evolution as "survival of the fittest", with no qualifier as to how you go about surviving.

      "Survival of the fittest" aka Natural Selection was half of Darwinian evolution. This was the half about how traits were selected for in the environment.

      The other half was how an organism's traits came about, and his theory was that traits were passed from parents to offspring in the reproductive cells via some biological mechanism that allowed for combination and mutation. Eventually we discovered DNA, the very biological mechanism in question that had traits like Darwin predicted (though Mendel was the one who really nailed down the probably behavior of this then-unknown mechanism).

      "Horizontal" evolution doesn't fall into that category, though. So it's not "Darwinian". Even though natural selection (obviously) still applies to what gene transfers result in successful organisms.

      As the summary mentions, this is well known in micro-organisms. In fact as far as I can tell they aren't arguing that it applies to anything but microorganisms. The argument seems more like that because these are the most common life forms on earth and also the oldest, Darwinian evolution is not the most common or dominant form of evolution.

      Which is a good point. Though really, as far as what affects us and other sexually reproducing creatures, Darwinian evolution is still 'it' more or less. The real importance of this breakthrough is in studying how the evolutionary mechanisms themselves evolved -- evolution is of course not immune to evolution. ;) This is going to be a powerful way of thinking about how early aspects of DNA came to be.

      But just to be clear -- if someone says that this proves Darwin was wrong, evolution is a sham, and therefore their beliefs are probably right, go ahead and slap them. :) All this means is that evolution is even more complicated and powerful than previously thought.

      • Re:Capitalism? (Score:4, Insightful)

        by ppanon (16583) on Tuesday January 26, 2010 @10:58PM (#30913096) Homepage Journal

        Which is a good point. Though really, as far as what affects us and other sexually reproducing creatures, Darwinian evolution is still 'it' more or less. The real importance of this breakthrough is in studying how the evolutionary mechanisms themselves evolved -- evolution is of course not immune to evolution. ;) This is going to be a powerful way of thinking about how early aspects of DNA came to be.

        I'm not so sure about that. Endo-retro viruses might still be a major factor for more complex organisms and even chordates. I've been wondering about whether super-retro viruses that can cross-infect multiple species while carrying secondary genetic payloads would be a possible agent for punctuated equilibrium.

        It's interesting that there are people with varying degrees of immunity to retro-viruses like AIDS. While AIDS is not very contagious, other retroviruses could be much more easily transmitted, so you would think that retro-viral resistance would be a very beneficial and common mutation, however it appears to be quite rare. Why? Well, it's possible that such mutations have drawbacks that are more frequently a disadvantage than the immunity advantage (as a parallel, sickle-cell and Thalassemia resistance to malaria), it also might be because susceptibility to retro viruses provides a significant evolutionary advantage in the Red Queen's race for complex organisms just as horizontal DNA exchange does for bacteria.

  • I guess you could push horizontal genetic flow with viruses in the higher organisms, like us. In general however, horizontal genetic flow occurs between plants and bacteria because they have the molecular mechanisims for it. If anything it would suggest horizontal genetic flow was the first stage of evolution, with classic evolution taking over more so as time moved forward since higher organisms have a higher need to maintain genetic continuity due to specific and more complicated form. For instance yo
  • Once again (Score:5, Funny)

    by copponex (13876) on Tuesday January 26, 2010 @07:40PM (#30911704) Homepage

    You know, scientists just keep reforming their ideas until it conforms to observable reality. How can they expect anyone to believe what they say when they're just going to keep changing their minds?

    I prefer my religion. It allows me to conform reality to my ideas.

    • One of the issues I've been thinking a lot about lately is the psychological principle of certainty. When you say "...scientists just keep reforming their ideas until it conforms to observable reality. How can they expect anyone to believe what they say when they're just going to keep changing their minds?" you hit upon something important: certainty of belief. How can the average layperson trust scientific opinion when said scientific opinion says "This is FACT... until it's not"? People require certainty

      • Re: (Score:3, Insightful)

        by Joel Brown (1730506)
        It is important to note that the idea the "science is about truth" is a common intellectual error of modern society. Science has nothing to do with finding truth or learning how the universe actually works or anything of the sort. Science is about building models of observable natural phenomena. The point of the models is to conform with what is observable and hopefully predict something that hasn't yet been observed, but which can then be tested and seen to work. Good science is about building models t
      • by Opportunist (166417) on Tuesday January 26, 2010 @10:04PM (#30912806)

        Science is not the search for "truth". It's the search for an explanation. Unfortunately, it has become the new religion, people simply believe what some scientist says as gospel and, as you identified, are then frustrated and irritated if it is found to be incomplete or utterly false.

        That is not how science is to be treated. Science does not have all the answers. Science is the search for those answers, not the answer itself. Science is not about believing, it is about doubting. About offering a theory and offering ways to test that theory. Especially the latter part is often overlooked by people. A good theory offers an angle to falsify it. I may state that at the center of a black hole is cake. Just to make all the Portal players happy. And while we're at it, before the big bang there was a flat world carried by a turtle. You cannot falsify either theory. You cannot test them. So they have to be true. Right? False! Both are non-theories. They have zero scientific value. At least until we somehow find ways to test them.

        So presenting any theory that offers no vector of testing is, scientifically, worthless. Unfortunately, that's not easy to convey to people. They want explanations. And science cannot offer them. Science is not about certain answers. It is about questioning theories.

    • Re:Once again (Score:4, Insightful)

      by BitZtream (692029) on Tuesday January 26, 2010 @08:47PM (#30912246)

      Most people treat what they call science as a religion. They go wild that someone reads a book and believes the far fetched ideas in it, yet they have no problem reading something off wikipedia and assuming its fact.

      The claim is that you CAN test and confirm it, but they don't, they just blindly assume because someone else wrote it down and some others agree with them.

      I really don't see any difference in the way most nutjobs treat science compared/contrasted to the way religions nutjobs treat religion.

      • Re:Once again (Score:5, Insightful)

        by Cassius Corodes (1084513) on Tuesday January 26, 2010 @10:13PM (#30912844)
        The basic problem is that you don't have infinite time, and as such you have to 'outsource' your knowledge gathering to other people. The problem then becomes one of who do you trust? If you use a heuristic of who has got good results in the past and that leads you to 'blindly' believe in the brand of science - well I can't really find any fault with that. As a researcher, while I know lots about my area, I don't know jack about others so I blindly trust what my doctor, mathematician, physicist tell me. If its an issue of importance I get a second opinion from another doctor etc, but at the end of the day I am blindly trusting them. I don't think there is anything wrong with that.
        • Re:Once again (Score:4, Insightful)

          by phliar (87116) on Wednesday January 27, 2010 @12:07AM (#30913454) Homepage

          It's not quite 'blind' trust, though. It is reasonable trust, because we've seen that in the past, the methods and models those guys talked about have actually been verified. They invented electronic things that have had a profound effect on humanity. History tells us modern medicine has improved human health immensely (if you're rich enough, of course). And I (an ex-researcher) do know how the scientific method works and what its limitations are. Therefore my "belief" in science is reasonable.

          The best part is that it works for you even if you don't believe in it -- so creationists can still enjoy the fruits of science. Science is better.

      • You're right - religion and science are the same in one sense. They are guesses at what reality is.

        The largest difference is that science acknowledges that it is a guess. A very educated guess, which yes yielded modern life as we know it. Religion tries to claim that it is the truth, and the only truth, and expects it's adherents to doggedly follow it's rules and values way beyond their useful context. To give you an example, a slashdot poster recently gave a ridiculously long opinion on whether pig meat cu

  • I dunno... (Score:5, Funny)

    by Dupple (1016592) on Tuesday January 26, 2010 @07:40PM (#30911712)
    I pass on my genes horizontally
  • by ddxexex (1664191) on Tuesday January 26, 2010 @07:41PM (#30911716)
    So does this explain why you can stick "random" genes into a completely different organism and gain traits that wouldn't arise normally? This seems like it'll be very useful in GE if the mechanics of it are explored more.
    • by timmarhy (659436)
      actually that's a myth, you can't just stick random genes into any organism and have it survive. it's one of the nonsense arguments the anti GM fanatics spout while they foam at the mouth about so called frankenfood.
    • Re: (Score:3, Insightful)

      by DragonWriter (970822)

      So does this explain why you can stick "random" genes into a completely different organism and gain traits that wouldn't arise normally? This seems like it'll be very useful in GE if the mechanics of it are explored more.

      Well, except that the mechanisms involved in horizontal gene transfer are already key tools in genetic engineering. The notionally big deal here is the idea that because of the dominance of horizontal gene transfer as a primary mechanism of gene transfer, there was a time when organism-cent

  • by BenBoy (615230) on Tuesday January 26, 2010 @07:41PM (#30911724)
    This really isn't entirely new; Dawkins' book The Selfish Gene [amazon.com] is based around the idea that it's individual genes that are selected for, not organisms.
    • by phantomfive (622387) on Tuesday January 26, 2010 @07:54PM (#30911830) Journal
      Which is nothing more than a restatement of what Darwin said, since a gene is nothing more than an encoded trait. It is the trait that actually matters, not the gene, since the trait is what gives the animal the ability to survive. It doesn't really matter if the trait is encoded as DNA or as biologic etchings on advanced carbon fiber, in either case it is just a representation of a trait.
      • by Trepidity (597)

        In a broad sense, yes, but in a more specific sense, Darwinian evolution, which posits inheritance by natural selection of traits, is often contrasted with Lamarckian evolution, which posits inheritance of adult traits. Horizontal gene transfer is not quite Lamarckian evolution (it's not usually from parents to children), but in the sense that traits acquired in adulthood can be passed on, it's closer to Lamarckian than Darwinian evolution.

        • What you say is accurate, but you seem to have missed the context, since in my post I was referring to Dawkin's Selfish Gene idea that the GGP was referring to, not so much the idea of horizontal gene transfer.

          Referring back to the content of your post, you are right, but to be fair to Darwin, I don't think he really addressed the evolution of microscopic organisms.
    • by Locke2005 (849178) on Tuesday January 26, 2010 @07:54PM (#30911836)
      In social animals, it is the survival of the group that is driving evolution, not the survival of individual or their genes. If the survival of each individual's genes were paramount, there would be no homosexuality and no parents killing their own children, 'cause those are pretty much dead-end paths from the standpoint of survival of the individual. Another way of thinking of this is that altruism really does have survival value; just like with army ants, being willing to sacrifice individuals for the good of the group is a good evolutionary strategy.
      • by timmarhy (659436)
        and what causes them to be social animals? their genetics. no amount of environmental factors is going to cause say, a great white shark, to suddenly become a social animal.
      • by feepness (543479)

        In social animals, it is the survival of the group that is driving evolution, not the survival of individual or their genes.

        The question then becomes... which group.

      • Re: (Score:3, Informative)

        by trouser (149900)

        Not the individual's genes, the individual gene. In all plants and animals it is reproduction combined with mutation and recombination that is driving evolution.

        Social animals posses genetic traits which promote social or herd behaviour. In these animals the trait survives because for these animals in the environment in which the trait emerged it increases the chance of survival and reproduction. The gene promotes itself.

        Worker ants are infertile. They share common genetic information with the queen. To pro

      • Re: (Score:3, Informative)

        by Starker_Kull (896770)

        If the survival of each individual's genes were paramount, there would be no homosexuality and no parents killing their own children, 'cause those are pretty much dead-end paths from the standpoint of survival of the individual.

        You just missed the flaw in your reasoning - you confuse an individual's GENES with the INDIVIDUAL. Consider that a parent only has 50% of their genes in a child; if it turns out that killing the child would allow for the opportunity to invest more in other children, and increase t

    • Re: (Score:3, Informative)

      Exactly. Evolution is a fundamental mathematical process that applies to information, not organisms. To get evolution, you only need two elements:

      1. An information storage medium.

      2. A mechanism for reproducing that information such that certain pieces of information are more likely to get reproduced than others.

      Once you have those, everything else follows, and it doesn't matter what the precise storage mechanism or copying mechanism is. Horizontal gene transfer is just another way for genetic in
  • by Toonol (1057698) on Tuesday January 26, 2010 @07:47PM (#30911784)
    We've already known that evolution depends on both inheritance of genetic matter and mutation of genetic matter. This is a third mechanism for generating traits, but it stills falls under the umbrella of natural selection. If the change is beneficial, and leads to more offspring, the change will be selected for. Certainly worth study, and we may not have known the full scope of the phenomena, but it doesn't really contradict Darwinian evolution at all.

    As a side note... I wonder if the fact this occurs in nature will silence some of the people objecting to genetic splicing?
    • Re: (Score:3, Insightful)

      by Trepidity (597)

      Well, it's a mechanism for directly passing on traits (via a direct transfer), which is closer to Lamarckian evolution than Darwinian evolution, in the classic 19th-century dispute. But you're right that it's not a huge challenge to modern evolutionary theory. What it might pose somewhat more of a problem for are certain areas of phylogenetics, especially cladistics [wikipedia.org] that rely fairly heavily on an assumption that evolutionary trees are indeed trees.

    • As a side note... I wonder if the fact this occurs in nature will silence some of the people objecting to genetic splicing?

      Has the fact that miscarriage occurs in nature silenced the people objecting to induced abortion?

      Has the fact that death occurs in nature silenced the people objecting to murder?

      Has the fact that group conflicts over territory occur in nature silenced the people objecting to war?

      Has the fact that climate changes occur in nature silenced the people objecting to human actions which contri

  • I've always felt that viruses might be the driving force in evolution; they are very good at taking genes from one organism and splicing them into another. Also, one of the first traits that would have evolved after the split into two sexes would have been the ability to choose mates with traits complementary to your own, thus for higher species there is actually some intelligence driving evolution forward.
  • by PaulBu (473180) on Tuesday January 26, 2010 @08:04PM (#30911928) Homepage

    For those who do not care to register for that New Scientist, we still have arXiv... :)

    http://arxiv.org/abs/q-bio/0702015 [arxiv.org]

    Paul B.

    • by radtea (464814) on Tuesday January 26, 2010 @08:31PM (#30912138)

      Thanks, as the New Sensationalist article is full of lies and hyperbole, completely idiotic, transparent falsehoods like, "This code is universal, shared by all organisms, and biologists have long known that it has remarkable properties"

      This simply a lie, as is the claim that 64 combinations producing 20 codons is "redundancy". The reason there are only 20 is well-known to anyone with the least little bit of familiarity with the subject: it is the maximum number of unambiguous combinations, so that if you get six bases in a row there is exactly one way to read them, because no two codons together can result in a third codon being read between them.

      The arXiv article may have something interesting to say, although inter-species genetic transfer has been known to occur amongst micro-organisms for a long time. From a Darwinian perspective the genes available in the environment are just that: another perfectly ordinary part of the environment. Since Darwin's Law depends only on the laws of probability and the fact of imperfect replication, it applies to situations where horizontal transfer takes place just as much as when imperfect copies of genes come from ancestors.

      The details of Darwinian evolution will change a little in the context where organisms are taking genetic resources directly from the environment, but it's still a Darwinian process.

      The weird statements about "questioning if organisms even exist as individuals" are just idiotic marketing hype that pretty much ensure the whole argument is vastly less interesting and important than the authors want to make it appear. Otherwise, why the need for such anti-scientific hype? Unless it is the New Sensationalist characteristically ripping an innocent statement out of context.

      • by rgmoore (133276) <glandauer@charter.net> on Tuesday January 26, 2010 @09:56PM (#30912770) Homepage

        This simply a lie, as is the claim that 64 combinations producing 20 codons is "redundancy". The reason there are only 20 is well-known to anyone with the least little bit of familiarity with the subject: it is the maximum number of unambiguous combinations, so that if you get six bases in a row there is exactly one way to read them, because no two codons together can result in a third codon being read between them.

        Except that isn't true. Every one of the 64 possible 3 base sequences is a valid code for either an amino acid or a stop codon. Some viruses take advantage of this by overlapping protein coding regions, with different proteins being coded by reading in different frames. In eukaryotes, there are some genes that can code for proteins with very different sequence regions because an exon skipping splice variant results in a frame shift that codes for a completely different sequence.

        A more significant complaint about the "This code is universal, shared by all organisms" quote is that it isn't universal. There are small differences in the genetic code between genomes. NCBI lists no fewer than 23 [nih.gov] different versions, but given that a tiny fraction of all species have been studied there are undoubtedly many more minor variants. An especially interesting case- and the place that difference in genetic codes were first discovered- is that human nuclear and mitochondrial sequences use slightly different genetic codes. The mitochondria even have their own distinct ribosomes.

    • by radtea (464814) on Tuesday January 26, 2010 @08:44PM (#30912220)

      http://arxiv.org/abs/q-bio/0702015 [arxiv.org]

      Ok, I've read the original paper now, and it is almost as moronic as the New Sensationalist makes it out to be.

      Their argument is analogous to the following claim:

      I can stand on dry land, or I can swim in the water, but there is the broad swath of territory that is neither dry land nor water so deep I can do nothing but swim in it. Therefore, the concept of "land" (or "water") may actually be completely useless! Aren't we clever?

      Scientists have a tendency toward various kinds of conceptual realism, where they think that there is exactly one way to properly understand the universe, and the entities picked out by that way are "real" and no others are. When they find a case that they can't crisply classify under the existing concepts there are two moves: the smart one, that refines existing concepts and introduces new ones to deal with the boundary cases; and the idiotic one, that claims that since the existing concepts don't deal well with the new case, they must not pick out anything "real" after all and should be thrown away.

      That the biological species concept fails in various ways has been known for a long time. They are now pointing out that certain criteria that would normally be used to delineate individuals might also fail under some circumstances. To this I say: big deal. The biological species concept, like the concept of Newtonian mass, is still incredibly useful in understanding reality under a wide range of circumstances, which is all a scientist can hope for. If their new concepts--which they don't really offer--transform smoothly into the biological species concept in the appropriate circumstances I'll be interested. Otherwise, they're just gabbling.

  • by presidenteloco (659168) on Tuesday January 26, 2010 @08:04PM (#30911930)

    The notion that life probably started by weak, stochastic replication of families of similar molecules.

    By weak, is meant that the replication of the molecule/structure is more imperfect from generation to generation
    than in present day life, and so a class of similar molecules (life codes) is being continued through time
    rather than a singular particular molecule (same genome).

    If this origin theory were true, we would expect the replication capability (continued recreation of imperfect but still somewhat replication-capable molecules)
    to be robust to change of DNA/RNA even today.

    By stochastic, is meant that such imperfect replication is likely to only be stochastically successful in a huge population of the
    initially highly approximate (i.e. weak) replicator molecules.

    In other words, we would not expect this proto-life to be as reliable at being able to continue (or to always reliably grow by recruiting
    surrounding matter into high-fidelity copies.)

    So we might expect these proto-life molecule soups to initially just contain in some regions higher than expected probabilities,
    stochastically, from time to time, of weak-replicator molecule classes.

    Perhaps there is a binary threshold of replication probability and fidelity at which the process self-sustains reliably in the
    generality of environment it finds itself in. Life catches fire, and cannot easily be stopped at its matter and energy recruitment
    game from that point on.

  • It's interesting that infectious viruses may form an essential foundation for our own evolution. It may even be that viruses are a developed strategy for "importing tallent" from competitors or neighbors. It has interesting things to say about inerconnection between organisms in a species and between species. Infectability may be a long term strategy for development.

    Then again, it could be exactly the other way. Advanced organisms are just diverse platforms which viruses have evolved as elaborate tools
    • by BitZtream (692029)

      'may' ?

      A bit of common sense, a little science and a history lesson makes it pretty clear that 'may play a part' really should be 'does play a part'

      EVERYTHING IS INTERCONNECTED. Nothing on Earth would have evolved over the same time period in the same pattern if you change any given part of it. The differences could be subtle enough that no one notices or so massive that an outside observer wouldn't ever think they started from the same point. The entire universe, while made of discrete components is all

  • Viruses (Score:5, Insightful)

    by Arancaytar (966377) <arancaytar.ilyaran@gmail.com> on Tuesday January 26, 2010 @08:13PM (#30911980) Homepage

    Horizontal transfer isn't really over, either - we still have retroviruses.

  • As to the vector for horizontal transmission of genetic material how about viruses?

  • There have been some other interesting discoveries regarding horizontal gene transfer recently. For example, this PNAS paper looks at sea slugs that can photosynthesize by themselves -- http://www.pnas.org/content/105/46/17867.full.pdf [pnas.org]). The sea slugs photosynthesize through a combination of harvesting chloroplasts from the algae they eat and via horizontal transfer of genes involved in photosynthesis from these same algae. This is a bizarre and amazing discovery which demonstrates how genes can move from
  • GM Foods anyone? (Score:2, Insightful)

    by Beerdood (1451859)
    "horizontal gene transfer - in which organisms acquire genetic material "horizontally" from other organisms around them, rather than vertically from their parents or ancestors."

    Genetically modified foods are like the "artificial selection" equivalent of nature / natural selection - if the transfer of genes can happen from one set of species to another, then GM crops are kinds of an accelerated / selective version of this. If I were Monsanto or another big GM food company, I'd be looking to twist this in
  • "You are what you eat."

    Cue the toilet humor in 3... 2... 1...
  • Gene Synthesis (Score:4, Interesting)

    by mosb1000 (710161) <mosb1000@mac.com> on Tuesday January 26, 2010 @08:30PM (#30912130)
    One of the big difficulties I have in understanding evolution is the process of gene syntheses. It seems reasonable that over time certain combinations of genes can win out over others, and certainly in bacteria you see this horizontal gene transfer happen all the time. You even see it in plants now thanks to genetic engineering, and before that you saw it in a more limited way thanks to viruses and cross-pollination and things like that. But all these things have to do with the transfer of genetic information between life-forms.

    The question in my mind is where did all the genes come from in the first place. Proteins are complex macro-molecules. It's not like one protein that catalyzes one reaction can simply mutate into a different protein that catalyzes a different reaction. It's more of an all or nothing thing. It doesn't seem like you would ever see transitional "evolutionary" forms of proteins for that reason. Worse still, you can't (as far as we know) start with a working a protein and reverse-transcribe from it into a strand of DNA or RNA that could code for it.

    What do you think?
    • DNA is what evolves - i.e. instructions to make proteins, not proteins themselves. Of course most random changes to the instructions are maladaptive or at best useless, but very occasionally not.

      I think what happens in practice is that it's the "useless" changes (do no harm, but under current conditions do no good) that may play the largest role... these can accumulate in different populations of a species and become a differentiator when the environment changes (which is the real driver of evolution) and p

    • Re:Gene Synthesis (Score:5, Interesting)

      by brit74 (831798) on Tuesday January 26, 2010 @09:52PM (#30912744)

      It's not like one protein that catalyzes one reaction can simply mutate into a different protein that catalyzes a different reaction. It's more of an all or nothing thing. It doesn't seem like you would ever see transitional "evolutionary" forms of proteins for that reason.

      There are instances of proteins evolving into something that does something different.

      "Biologists have shown that independent but similar molecular changes turned a harmless digestive enzyme into a toxin in two unrelated species -- a shrew and a lizard -- giving each a venomous bite."
      http://www.sciencedaily.com/releases/2009/10/091029125532.htm [sciencedaily.com]

      Generally, what happens in these cases (where a protein evolved into a different protein with a different function) is that the original DNA sequence gets duplicated, and then one of the duplicates starts evolving (and the other copy continues to serve the same original function that it had earlier). One of the things that evolutionary biologists do is look at protein sequences and find similar sequences within the same organism. Very often, there's a tree-like structure showing multiple variations on a single protein within an organism. For example, humans have multiple copies/variations on the hemoglobin gene. They're either inactive or active at different phases in a person's life. Example:

      "Fetal hemoglobin, or foetal haemoglobin, (also hemoglobin F or HbF) is the main oxygen transport protein in the fetus during the last seven months of development in the uterus and in the newborn until roughly 6 months old. Functionally, fetal hemoglobin differs most from adult hemoglobin in that it is able to bind oxygen with greater affinity than the adult form, giving the developing fetus better access to oxygen from the mother's bloodstream."
      http://en.wikipedia.org/wiki/Hemoglobin_F [wikipedia.org]
      http://en.wikipedia.org/wiki/Hemoglobin#Types_in_humans [wikipedia.org]

      There's also the case of the fish antifreeze that evolved from non-protein-coding DNA:
      "Scientists at the University of Illinois have discovered an antifreeze-protein gene in cod that has evolved from non-coding or 'junk' DNA."
      http://www.sciencedaily.com/releases/2006/04/060404090831.htm [sciencedaily.com]

  • Horizontal gene passing is what make several organisms have strains that go from harmless to pathogenic.
    Some useful info for the curious masses:
    http://en.wikipedia.org/wiki/Pilus [wikipedia.org]
    http://en.wikipedia.org/wiki/Horizontal_gene_transfer [wikipedia.org]

  • by panthroman (1415081) on Tuesday January 26, 2010 @08:41PM (#30912194) Homepage

    Have Woese and Goldenfeld a brilliant new idea? All they're saying, I think, is that "parent" and "child" are the appropriate units of selection only when genes are passed vertically: from parent to child. They're suggesting that horizontal gene transfer is underrated as a historical evolutionary force.

    Agree or not, it hardly undermines Darwin. Genes weren't known in the 19th century. Darwin didn't have a clue about genes, so we're gonna knock him for being "wrong" about it? I mean, was Jesus wrong about genes, too? It's anachronistic silliness.

    Science is fundamentally dynamic. Any science that hasn't progressed in 150 years ain't doing too well. (Dear creationists: stop calling us "Darwinists." We've moved on.) I mean, The Origin came out in 1859, for crying out loud! Darwin was more brilliant, more insightful, and rightly more famous than I'll ever be. But if we both had to take a biology test right now, I'd kill him.

    • It was refreshing to read the article and comments without the usual trash-talking between creationists and non-creationists. Maybe the moderators are doing a good job and the trash-talking is just below my threshold, but it's really nice. If civility has broken out on Slashdot, thanks everyone!
  • an example of Darwinian Evolution, but just at a different level?

    For example, if you think of the unit of evolution as a gene instead of an organism and a bacteria as a habitat instead of an organism, then the gene evolves vertically, by replication and duplication. The transfer between two bacteria are just the gene migrating from one habitat to another.

  • A key point of the article that seems to have slipped past a fair number here is that the researchers are attempting to explain the robustness of the gene replication:

    "Evidence for this lies in the genetic code, say Woese and Goldenfeld. Though it was discovered in the 1960s, no one had been able to explain how evolution could have made it so exquisitely tuned to resisting errors. Mutations happen in DNA coding all the time, and yet the proteins it produces often remain unaffected by these glitches. Darw
  • by VShael (62735) on Wednesday January 27, 2010 @06:57AM (#30915176) Journal

    It seems to me that one of the reasons journalism science is so bad, is that they believe (rightly or wrongly) that any article which appears to be saying "DARWIN WAS WRONG!" will sell more copies.

    The article doesn't say that, obviously, but it at a cursory glance it could be perceived as that.

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