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Medicine Science

Prions Evolve Despite Having No DNA 214

Posted by kdawson
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."
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Prions Evolve Despite Having No DNA

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  • 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 [wikipedia.org].

  • Re:Not Surprised. (Score:2, Interesting)

    by chrb (1083577) on Sunday January 10, 2010 @06:33AM (#30713688)

    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.

    It goes further than that - almost everything that is built is a product of evolution. Bicycles, planes, cars, the computer, have all been subject to the process of evolution. The fact that they can't self-replicate does not mean that the evolutionary process isn't present. No life can replicate without the necessary supporting environmental conditions, and if one of those prerequisite environmental conditions happens to be the presence of humans and amounts of refined steel and other materials, how is this any different to a bacteria requiring sugars and oxygen?

  • by dorpus (636554) on Sunday January 10, 2010 @06:38AM (#30713702)

    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.

  • Re:Not Surprised. (Score:3, Interesting)

    by tragedy (27079) on Sunday January 10, 2010 @06:56AM (#30713736)

    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.

  • Re:Surprising? (Score:3, Interesting)

    by chico_the_chihuahua (925601) on Sunday January 10, 2010 @09:32AM (#30714166)

    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...

  • by famebait (450028) on Sunday January 10, 2010 @09:41AM (#30714198)
    And it is not surprising that many seem to require unnatural diets to occur (feeding meat to herbivores, forcing cannibalism where this is not found in nature, etc). For whatever prions might occur under normal circumstances, evolution has probably equipped us to stop the chain reaction, or deal with the products. Ones that can only spread under circumstances not found in nature OTOH, are "new" to the body and some of them may therefore accumulate in dangerous amounts.
  • by Anonymous Coward on Sunday January 10, 2010 @10:28AM (#30714384)

    "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. "

    Wow, that is simply the most pathetic attempt at creating a human-centric definition of life Ive seen... and Im a biologist, so Ive seen plenty of strange ideas.

    There is not a single form of life that that is completely isolated from its environment. Animals, plants, fungi, bacteria, viruses, prions (I tend to include these last two in my working definition of life, but that is my opinion based on my studies and research) ALL depend on specific environmental inputs in some way in order to exist. The line you try to draw between presence and absence of a nervous system might look fine at a first glance, but most of the elements necessary to build a nervous system are already present in many single-celled creatures, so there is no huge qualitative leap in environmental perception.

    And I love the way you think bacteria can be simply dismissed with a wave of the hand just because theyre non-thinking and seemingly primitive. Guess what? MOST of the life on Earth is bacteria... Scratch that, theres one fact thats even better to make you think a bit about life: a human body is composed of TEN non-animal (bacteria, "protozoa", fungi...) cells for every one "truly living" human cell. So, were just made up of 1 part living stuff and the other 10 parts are non-living crap?

  • Re:genetic material (Score:5, Interesting)

    by The End Of Days (1243248) on Sunday January 10, 2010 @10:55AM (#30714484)

    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.

  • Re:genetic material (Score:3, Interesting)

    by trum4n (982031) on Sunday January 10, 2010 @12:42PM (#30715060)
    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.
  • by foobsr (693224) on Sunday January 10, 2010 @12:47PM (#30715092) Homepage Journal
    It's why it's entirely unlikely that you will ever see something that can be classified as life that isn't carbon-based.

    Sure?

    "From plasma crystals and helical structures towards inorganic living matter
    Abstract. Complex plasmas may naturally self-organize themselves into stable interacting helical structures that exhibit features normally attributed to organic living matter. The self-organization is based on non-trivial physical mechanisms of plasma interactions involving over-screening of plasma polarization. As a result, each helical string composed of solid microparticles is topologically and dynamically controlled by plasma fluxes leading to particle charging and over-screening, the latter providing attraction even among helical strings of the same charge sign. These interacting complex structures exhibit thermodynamic and evolutionary features thought to be peculiar only to living matter such as bifurcations that serve as `memory marks', self-duplication, metabolic rates in a thermodynamically open system, and non-Hamiltonian dynamics. We examine the salient features of this new complex `state of soft matter' in light of the autonomy, evolution, progenity and autopoiesis principles used to define life. It is concluded that complex self-organized plasma structures exhibit all the necessary properties to qualify them as candidates for inorganic living matter that may exist in space provided certain conditions allow them to evolve naturally. "
    http://www.iop.org/EJ/article/1367-2630/9/8/263/njp7_8_263.html [iop.org]

    CC.
  • by goodmanj (234846) on Sunday January 10, 2010 @01:42PM (#30715434)

    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 [wikipedia.org]. 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.

  • by Alrescha (50745) on Sunday January 10, 2010 @01:48PM (#30715486)

    I'm sure that enough heat*time will do it, but I suspect that your food isn't food at that point. Autoclaving is insufficient to destroy prions on surgical instruments, for instance.

    A.

  • by goodmanj (234846) on Sunday January 10, 2010 @01:49PM (#30715500)

    Clever, but misleading (whether or not it was intended as a joke).

    Darwin's theory of natural selection requires an entity to store the information needed to make *more* of itself. You can't make more matter -- at least, not without making an equal amount of antimatter -- so no natural selection is possible.

  • Re:genetic material (Score:5, Interesting)

    by jc42 (318812) on Sunday January 10, 2010 @01:53PM (#30715526) Homepage Journal

    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" [amazon.com], 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. ;-)

  • by DMiax (915735) on Sunday January 10, 2010 @02:01PM (#30715578)

    We have evolution (as in new traits being developed) of plants and bugs due to selective processes. We have evolution of bacteria through adaptation to environment and relative advantage. We observe differentiation of species through ring-species. We can recostruct the evolutionary links between speecies through DNA evidence. We have a pretty, consistent tree of evolution extracted from fossyls. How difficult is it to look at the big picture and say that evolution s the most probable explanation?

    If anything it's creationists that must explain what would forbid "macro-evolution" from happening. Why is it qualitatively different from "micro-evolution"?

    We never actually oserved a gravitationally activated fusion reaction, but we believe the sun burns that way too. We never observed the light travelling for more than one light year at the same rate either and we still believe that the speed is constant. Science is filled with such extrapolations where something is proven only for small scales and taken to be universally valid.

  • Redefining Life (Score:3, Interesting)

    by DynaSoar (714234) on Sunday January 10, 2010 @03:05PM (#30716062) Journal

    In "Energy Flow In Biology" Harold Morowitz posits that an open system between an energy source and an energy sink, containing such elements as can form a variety of bonds and forms, will absorb energy, and form compounds that will persist in that state for a time in inverse proportion to how much energy is required to maintain the state. Increasingly complex forms can be created from those simpler forms if they persist long enough. Those more complex forms can have variations in their subunits locations and forms relative to the components from which it is built. This is the first chapter. The rest of the book is a bit of physics and a great deal of physical chemistry showing why the proportions of organics found on Earth as inevitable given the conditions of the Earth's environment and the combination of elements from which is is made.

    The evolution part applies to the first chapter though. Some compounds self-catalyze, producing more. Some catalysts form that produce other products, but only do so when the first of those products form. Variations such as radicals appearing in different places on a benzene ring produce different forms, and catalysis can cause this to happen step by step, forcing the radical to 'march' around the ring.

    Increasing complexity, with variations in forms of those increasingly complex forms, each of which have more or less ability to contribute to furthering these phenomena, that pretty much describes what life does. Maintaining itself at a level of complexity above the environment (read that 'maintaining itself in a state of negentropy) for a time, using the incoming energy, described something much like how life appears in contrast to its environment.

    Again, this is all based on physical and organic chemistry, pre-biology. It's only logical to expect the activities of living things to mirror the activities of their non-living constituents. No, those compounds are not alive, but if they couldn't do those things, neither could life.

    A marker then for life might be detection of compounds that carry out some functions we see in life, and an environment that allows them to increase in amount and in complexity. Where then do we put the dividing line between life and non? If we can objectively define and predict an emergent property that appears at a certain point in the growing complexity of the chemical soup that is characterized by a behavior which is necessary for life but is absent in the pre-living material, we might be able to describe that sufficiently to say it's one definition of life.

    If it hasn't occurred to you before, it should now: a different environment and collection of compounds might also produce organics (or the equivalent based on other elements) will produce different results. If life, that will be different. Taking the definition from one situation is hobbling yourself when it comes to discovering other forms of life. It might also occur to you that there is no time scales associated with any of this. If we then take the broader view and don't limit 'life' to the result, but include it in the components, we can at least start with a statement about a component being 'alive enough to consider that aspect'.

    We need as broad a view as possible so we will be able to recognize it when we see it elsewhere. A part of science is dedicated to looking for it. With our present definitions, which should be stated "Earth-like life" rather than simple "life", we are primed to not detect any forms of it which we could imagine but which differ significantly from Earth forms.

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