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Prions Evolve Despite Having No DNA

Posted by kdawson on from the wipe-that-foam-off-your-mouth dept.

An anonymous reader writes "Scientists from the Scripps Research Institute have shown for the first time that 'lifeless' organic substances with no genetic material — prions similar to those believed responsible for Mad Cow disease and similar, rare conditions in humans — are capable of evolving just like higher forms of life. The discovery could reshape the definition of life and have revolutionary impacts on how certain diseases are treated."

27 of 214 comments (clear)

  1. genetic material by Anonymous Coward · · Score: 3, Insightful

    Genetic material and DNA aren't really synonymous, are they? Alien life that appeared independently of that on Earth would likely have "genetic material" that served a similar purpose to DNA, but wasn't DNA.

    Prions are proteins that, like viruses, replicate via a host cell. All the high-level principles of evolution by natural selection apply; it's just the low-level mechanisms that are quite different.

    1. Re:genetic material by The+End+Of+Days · · Score: 5, Interesting

      Putting the perils of terming new knowledge "obvious" aside, it does seem obvious that evolutionary mechanisms would have to be preexisting for life to have indeed evolved. Since the most generic definitions of life I've seen boil down to providing some form of localized reverse entropy, evolution of the materials of that reverse entropy should be able to happen before the condition itself is actually achieved.

      To draw an utterly meaningless comparison, you can certainly have a power supply without a computer, but good luck doing any computing without the power supply. If that makes sense. I should probably cut my breakfast rum down to under 5 shots.

    2. Re:genetic material by trum4n · · Score: 3, Interesting

      People over think evolution way to much. Sure, there are a lot of things going on, but simply put: If you suck at your job, you die. If your good at your job, you make babies. That is evolution in a nutshell. There is a slight deviation in every copy of this protein, and the ones that are better at their job reproduce. Ones that arn't so great at it, have trouble reproducing, or just die off.

    3. Re:genetic material by jc42 · · Score: 4, Interesting

      You're correct. If they evolve, they HAVE genetic material; it's a bit of a tautology.

      It might be noted that, before the 1950s, biologists generally argued that DNA couldn't be our "genetic material", because it's structurally too simple. The most widely suggested storage for this sort of information was proteins, because they are the most complex chemical structures in our bodies.

      This hypothesis turned out to be wrong. But there's still an old hypothesis that in the early stages 4 billion years ago or so, the early "living" things on our planet were mostly based on proteins. It's hard to come up with good tests of this, though, because RNA and DNA don't fossilize well, and we have no samples of them older than 100 million years or so.

      In any case, this story is really just about finding some evidence supporting the protein-based inheritance conjecture. It's apparently valid to some degree in our modern world. It might be more widepread than just prions, but we don't know.

      Something that we have known, and which was summarized well by Douglas Hofstadter in "Gödel, Escher, Bach", is that our DNA doesn't actually contain a definition of the mapping of DNA to amino acids. That is done by the proteins that "transcribe" RNA strings into the amino-acid strings for the proteins. It would be possible, by doing a bit of swapping around of the active parts of those RNA-reading proteins, to use a different DNA -> amino acid mapping, and a few variants of this mapping are known in nature. The real complexity comes about from the fact that our DNA contains genes that produce the proteins that do this transcription. But without the already-existing transcription proteins in a cell, there would be no way to discover the mapping that we actually use, because the information isn't actually in the DNA. It's "distributed" between the DNA and the already-existing proteins in the cell.

      Of course, such multi-factorial causation chains (with feedback) are far too complex for most of the media, even the scientific media. So we pretend that our DNA contains all the information needed to produce us. The biochemists have known for some time that this isn't really true, but they don't make a point of it, because it "would just confuse" most of the reading public.

      OTOH, Hofstadter has had pretty good sales of his book. Any nerds or geeks here who haven't read it should do so. It'll teach you a lot of fun stuff about the extreme complexity of the universe we evolved in.

      (Religious people who don't believe in evolution shouldn't bother. The book isn't really about evolution per se, but it'll still get you seriously upset or confused about the nature of the universe. ;-)

      --
      Those who do study history are doomed to stand helplessly by while everyone else repeats it.
  2. Evolution for creationists. by X-Power · · Score: 4, Funny

    http://c.myspace.com/Groups/00017/98/88/17938889_l.gif

  3. Evolution is the good news ... wait, bad news? by Gopal.V · · Score: 5, Insightful

    Natural selection doesn't pre-suppose DNA. Anything which multiplies to produce copies of itself, which can degrade/mutate between generations can evolve just in exactly the same way. Selection pressures work exactly the same. So does the chain reaction effect of multiplication of the survivors, resulting in major shifts in characteristics of a population.

    But the actual story is the bad news part of it. That using anti-prion medication probably won't work all the time as it would just breed a drug-resistant breed of prions by preference.

    Definitely bad news. We can forget about having the "saviour" take a bath in the daily oatmeal for our protection :)

    --
    Quidquid latine dictum sit, altum videtur
    1. Re:Evolution is the good news ... wait, bad news? by famebait · · Score: 5, Insightful

      using anti-prion medication probably won't work all the time as it would just breed a drug-resistant breed of prions

      Not necesarily. Unlike the changes available for lifeforms with their own DNA, there is probably a finite number of ways a given human protein can degrade into a replicating prion configuration. Most proteins probaly have no capacity for becoming prions. For others, the body is perfectly capable of dealing with them.

      The capacity to become a prion is already built into the structure of the host protein in question, not aquired through exposure. So while this evolution is probably real and possibly a stumbling block for therapies, it remains confined to the space of potential configurations already inherent in our proteome, of which only a very small subset will cause trouble as prions.

      --
      sudo ergo sum
  4. Not Surprised. by nog_lorp · · Score: 5, Insightful

    It's time we recognized that the interesting things about "life" are all just products of the fact that all kinds of systems can convey self-replicating entities of some sort, and they tend to be interesting and undergo evolutionary processes and etc. Whether they are non-biological DNA bundles, cellular organisms, oddly folded proteins, crystalized clay, etc.

    So where are the nefarious / useful engineered prions at?

    1. Re:Not Surprised. by MichaelSmith · · Score: 3, Informative

      Fire has a symbiotic relationship with some plants in Australia. The plants help start fire. The fire kills the plants competitors, including other plants and humans.

      --
      http://michaelsmith.id.au
    2. Re:Not Surprised. by tragedy · · Score: 3, Interesting

      Interesting thought on that. I remember an old episode of _Sliders_ where they ended up on a world in the midst of a big fire, and accidentally brought some living (and intelligent) fire with them to the next universe. I got into a discussion (funny, I can't remember who it was with anymore) about what things would be necessary to actually have living fire. In other words, what additional things would fire need to have to be considered living and how could it be achieved in nature. We covered a lot of ground, and the conclusion we sort of got to is that, in a sense, we, and all other aerobic life at least are already a form of living fire. That's what cellular respiration is all about. It was an interesting discussion and, in the end, a lot of it depends on points of view. That of course is the problem. You don't think fire is alive because you know that fire isn't alive and if someone comes along and tells you that fire is now included in the scientific definition of things that are alive, you'll disagree, just like lots of people are still pretty upset that Pluto isn't a planet anymore. If you examine what is and isn't alive in enough detail, the boundary gets fuzzy enough that it becomes harder to know where to draw the line rather than easier.

  5. Re:Where by Anonymous Coward · · Score: 3, Funny

    im in ur prions
    redesigning them

    -- God

  6. I don't see a need to get spiritual about it by Trepidity · · Score: 3, Interesting

    Even from a purely materialist perspective, it seems reasonable to ponder a class of materials that replicate themselves. How exactly they do so might be more or less complex but the basic idea that it's possible to configure matter in a way that it replicates itself doesn't seem that absurd. And there's no particular reason it has to be DNA --- there are even purely mechanical possibilities.

    --
    10 PRINT CHR$(205.5+RND(1)); : GOTO 10
  7. Re:Surprising? by ZorbaTHut · · Score: 5, Insightful

    It's a little more complicated than that. There's basically three properties that are both necessary and sufficient for evolution to take place.

    * Some sort of fitness function
    * Reproduction, largely based on the properties of the "parent"
    * Imperfect reproduction, so that variation can be introduced

    Once you've got those three items, you have the potential for evolution.

    That said, it should be pretty obvious that basically any frequently-duplicated structure in the physical world, whether it be made out of DNA, protein, or metal and gears, is going to have all three of those items - the third just thanks to the physical world being imperfect. Note that it's not required that it be capable of duplicating itself - if all machines were built by copying older machines, we'd get to see "machine evolution" as people tended to copy the ones that worked better and throw away the ones that didn't.

    Of course it's also worth pointing out that none of these requires that the item exist in a physical sense - you can meaningfully talk about memetic evolution, societal evolution, language evolution, joke and humor evolution, so forth ad nauseum.

    --
    Breaking Into the Industry - A development log about starting a game studio.
  8. Re:Rocks Too by glwtta · · Score: 4, Insightful

    Rocks evolve too.

    Hasn't this bullshit "claim" been dredged up enough already? It's just a bit of really weak sensationalism from an attention-whoring geologist.

    He himself doesn't even believe this nonsense, and does say, towards the end of that article that obviously "being changed by your environment" has nothing to do with "evolution", but hey, why not get some free publicity?

    --
    sic transit gloria mundi
  9. Where does Death Begin? by dorpus · · Score: 5, Interesting

    Not really related, but it is entirely possible for humans to be "alive" in a physical sense even after they are brain dead. As long as they are hooked up to respirators etc., they can be kept alive indefinitely. To date, no human being is ever known to have regained consciousness after brain death.

    The _big_ catch here is that most physicians are not properly trained to test for brain death. Most physicians will just see a flat line on an EKG and declare the patient brain dead. I used to work at an organ transplant center, where there were technicians that went through a formal checklist to make sure the patient really is brain dead. It was not uncommon to find patients who did not meet the strict criteria. In the most dramatic example, a 3-yo boy was supposedly brain dead, and he was in the operating room, ready to have his organs removed. The technicians discovered that his pupils did respond to light, so they rushed him out of the OR. On the way back to his room, the boy opened his eyes and smiled. But then he went back into a coma and died 5 days later.

    Needless to say, the boy's parents were furious.

    1. Re:Where does Death Begin? by MPAB · · Score: 4, Informative

      Here are the criteria for brain death. An in the case of children, they must be consistent with repeatedly flat EEGs throughout 48 or 72 hours depending on the place. Also, barbiturate and BZD intoxication must be ruled out.

              * Unresponsiveness
                          o The patient is completely unresponsive to external visual, auditory, and tactile stimuli and is incapable of communication in any manner.

              * Absence of cerebral and brain stem function
                          o Pupillary responses are absent, and eye movements cannot be elicited by the vestibulo-ocular reflex or by irrigating the ears with cold water.
                          o The corneal and gag reflex are absent, and there is no facial or tongue movement.
                          o The limbs are flaccid, and there is no movement, although primitive withdrawal movements in response to local painful stimuli, mediated at a spinal cord level, can occur.
                          o Apnea Test: An apnea test should be performed to ascertain that no respirations occur at a PCO2 level of at least 60 mmHg. The patient oxygenation should be maintained with giving 100% oxygen by a cannula inserted into endotracheal tube as the PCO2 rises. The inability to develop respiration is consistent with medullary failure.
              * Nature of coma must be know
                          o Known structural disease or irreversible systemic metabolic cause that can explain the clinical picture.
              * Some causes must be ruled out
                          o Body temperature must be above 32 C to rule out hypothermia
                          o No chance of drug intoxication or neuromuscular blockade
                          o Patient is not in shock
              * Persistence of brain dysfunction
                          o Six hours with a confirmatory isoelectric EEG or electrocerebral silence, performed according to the technical standards of the American Electroencephalographic Society
                          o Twelve hours without a confirmatory EEG
                          o Twenty-four hours for anoxic brain injury without a confirmatory isoeletric EEG

              * Confirmatory tests (are not necessary to diagnose brain death)
                          o EEG with no physiologic brain activity
                          o No cerebral circulation present on angiographic examination( is the principal legal sign in many European countries)
                          o Brain stem-evoked responses with absent function in vital brain stem structures

  10. Re:Surprising? by sevennus · · Score: 4, Insightful

    This is misleading, and upon second reading, it is some overly-philosophical hand-waving.

    Yes, prions do not reproduce through the conventional genetic mechanisms. From my understanding, they encourage, through some direct protein-protein interaction, other polypeptides to fold incorrectly.

    Think of it this way. HIV and other genetic disorders propagate through normal reproductive means. Like, if a person with an extraordinary innate musical ability has a child, that child will probably possess a natural ability for music.

    However, if a talented musician adopts a child and then teaches him how to read music and how to play instruments, he will probably grow up to be equally talented.

    Prions are similar to the latter case. They are encouraging other proteins, who don't in themselves possess any malicious function, the fold in such a way to attack the host.

    This isn't reproduction. The "parent" prions are not in anyway responsible for the actual formation of the "child" prions. They are just responsible for causing them to become malicious, making them more role-model proteins than actual parents.

  11. Re:This might revive the age-old debate... by Anonymous Coward · · Score: 3, Funny

    a failing one, a subspecies teanominus partius has evolved and is slowly choking out the main species. its sad beacuse teanominus partius cannot survive without the host species. We are watching evolution at work here people.

  12. Do Life and Evolution always go together? by giladpn · · Score: 3, Insightful

    As posts above testify, the word "evolution" is used more and more in contexts that have nothing to do with life.

    For example people talk a lot about the evolution of ideas, societies, and so on... Quite possibly, the philosopher Wilson is one of the popularizers of this approach.

    Anyway, this also leads to a different point - Evolution by itself is not a proof of the existence of Life. For example, Ideas or Societies are not living organisms, yet they do evolve.

    So the fact that prions evolve does not mean they are alive! One can fairly say that they are just a chemical (a protein) that can reproduce itself, evolve, and do damage.

    In Science, Mathematics and Philosophy, it is very common to take "edge cases" in order to better understand the limits of an idea. Prions give us a good example of something that can reproduce and evolve, yet its a chemical not a living organism.

    So what is "Life" ? Perhaps we should require the ability to perceive - awareness of ones surroundings - in order to define true life? In that case Bacteria aren't alive either, which is fine by me.

    Jellyfish and Lizards do qualify as alive. More generally, you would need some sort of functioning nervous system (however primitive) to be "alive". Brain-dead people would possibly not be "alive" by this definition.

  13. Re:Surprising? by chico_the_chihuahua · · Score: 3, Interesting

    I agree - it is important to get away from the concept of evolution as being life-based, and recognise that evolution is an emergent property of a system.

    For the prion example, the key is to remember that incorrectly folded proteins accumulate and cause the prion disease - the proteins themselves are not the disease, but the accumulation is. If one folding configuration is more likely to cause other proteins to fold incorrectly, then it is natural to assume that this configuration will become eventually dominant, until a more effective configuration arises. Also, the accumulation of protein causes a feedback loop, increasing the likelihood of further malign folding. Presumably, the folding is sometimes imperfect, so this is the source of the all important mutations causing variety. Without the accumulation, I would presume that the configuration of folding has a benign effect.

    So, folding configurations that increase the rate of malign folds or increase the rate of accumulation would be more successful in this feedback loop. Does this really justify the tag 'evolutionary'? It just seems that the natural progression of the disease causes what appears to be a natural selection process, but it's not clear at what point we should distinguish between a feedback loop and an evolutionary process, if indeed they are actually one and the same thing...

  14. Re:Rocks Too by Hurricane78 · · Score: 5, Insightful

    But you’re no better. You insult the other side, and bring no arguments to the table. You’re obviously right... to us... but to them, you now just made it worse, making them protect themselves from your pointless attacks even more.

    This time, I’ll do it for you:
    The difference is, that Rocks have no fitness function. Which is the difference between undirected change and directed evolution.

    But the next time, if you wanna act superior, bring an argument. Like a common basis, and proper logic on top of it.

    --
    Any sufficiently advanced intelligence is indistinguishable from stupidity.
  15. The creationists are a little more clever than by NotSoHeavyD3 · · Score: 3, Insightful

    that but not by much. Basically they'll say little changes like that (they call it micro-evolution) can happen but nope, no big ones into other species. (But anybody that's taken Bio 102 and seen how impossible it is to come up with a definitive answer to what is one species is and what is another knows that differential is horse-shit.) Guess they needed that so they could have an excuse why it was ok to take newer antibiotics and such. (You know, so they could allow the evolution that's so obvious you have to be pretty much insane to say it doesn't happen.)

    --
    Did you know 80 to 90% of the moderators on slashdot wouldn't recognize a troll even if one dragged them under a bridge.
    1. Re:The creationists are a little more clever than by Anonymous Coward · · Score: 4, Funny

      "I believe in micro-evolution but not macro-evolution"

      "I believe in centimetres, but not metres"

  16. Re:Why would that be likely? by goodmanj · · Score: 4, Interesting

    Why *wouldn't* it be likely?

    Darwin of course knew nothing of DNA, and his theory of evolution says nothing about it. Darwin didn't put it this way, but the key requirements for an entity to evolve are:

    1. The entity contains the information needed to replicate (self-description)
    2. This information is subject to random changes (mutation)
    3. The environment is hostile -- some but *not all* entities will be destroyed (survival)
    4. Variations between individuals make them more or less likely to survive (fitness)

    DNA-based life fits these restrictions, but so do entities which store their self-descriptive information in RNA, protein, or computer memory. It places no restrictions whatever on the existence of life chemistry based around other atoms than carbon.

    You can make lots of chemistry arguments about why carbon is necessary, but you can't argue it on pure Darwinian grounds. As for your specific point in favor of carbon:

    Carbon has lots of free valences, which allow it to act like a universal lego-block

    Silicon has the same valence properties, and also forms a wide variety of complex molecules. Phosphorus and sulfur can have valences of 5 or 6 in certain situations. Now, carbon *is* special, but not in the way you've described.

  17. Re:Surprising? by ZorbaTHut · · Score: 3, Insightful

    No, this isn't what I mean. The vast majority of devices are built by understanding the concepts involved and designing a new machine off those concepts. If we, instead, just measured a machine that already existed, then built another one to those approximate specs, over and over again, you'd see designs that were slightly "better" flourishing while designs that were slightly "worse" dying out. Thus, evolution.

    --
    Breaking Into the Industry - A development log about starting a game studio.
  18. Re:Surprising? by ZorbaTHut · · Score: 3, Insightful

    But that's exactly my point. It doesn't matter how the formation occurs. If the "parent" can reproduce, in any way, from construction to repurposing to just hanging around the "child" until the child starts acting like the parent, then it counts as reproducing. It's not like I have memes sitting in my head getting pregnant - their "reproduction" is that I say something funny to someone, and he remembers it, and says it to someone else.

    Evolution is in no way restricted to lifeforms that can self-reproduce. Prions have a way to duplicate their important properties - their bizarre folding - and that's all that's necessary.

    (And yes, role models can be a form of reproduction.)

    --
    Breaking Into the Industry - A development log about starting a game studio.
  19. Re:Matter. by Warbothong · · Score: 5, Informative

    Any matter has one mission and one mission only: to find greater order. If matter without DNA or any prior form of order couldn't achieve more order, then life would not exist. Things want to be able to interact with their environment more efficiently, and must evolve to do so.

    All things in the Universe try to minimise the amount of energy they have. In some special cases, like crystals for example, this means becoming more ordered: the energy of each atom/molecule depends on its distance from its neighbours, with each "preferring" the lowest energy distance. Getting as many neighbours as possible at this distance is effectively packing spheres with that distance as their radius, which turns out to be the most efficient with ordered arrangements like hexagonal close packing, so that's what's observed. In the general case, however, the amount of order goes down, see http://en.wikipedia.org/wiki/Entropy . In fact, in every situation which becomes more ordered over time, Thermodynamics says that somewhere else there must be a system becoming even more disordered (as an example, if a system is minimising its energy by becoming ordered then it's exothermic: the energy its losing will come out as heat. This heat is itself disordered, and can disrupt the order of whatever it comes into contact with (which is why so many Physics experiments are done as close to zero Kelvin as possible). Also, the total energy such systems manage to lose is restricted by the fact that they are becoming more ordered, there is an "entropic cost" when becoming more ordered, which means that it requires energy to do and therefore the system must keep hold of that much energy to do it.

    For a simple example of how becoming more ordered takes energy, try stretching an elastic band. The polymers it's made of would, in a totally disordered system, take "random walks", which is very degenerate (there are LOADS of ways to randomly walk a certain distance starting at a point A and ending at a point B is the distance AB is much shorter than the distance you walk, ideally A and B are in the same place). That's the band's preferred state, and as such it isn't particularly long. By stretching it, the distance AB goes up, so there are fewer random walks of the same length which satisfy these new positions. In the extreme case the distance AB will be the same length as the walk, and there would only be one valid random walk between them (ie. going in a straight line). It takes energy to stretch the band because you're making it more ordered, which it doesn't want to be.

    If matter's mission is to find greater order then a stretched elastic band would never snap back ;)