Sunday, May 5, 2013

Do Genes Switch Between Opposing DNA Strands For Adaptive Purposes?

As Luck Would Have it

In recent decades biologists have discovered that organisms possess a variety of adaptation mechanisms far more sophisticated than ever imagined. Some of these mechanisms are regulatory in that they influence which genes are used at a given time. Other mechanisms change the genes themselves by mutating the DNA sequences. These adaptive mutations respond to the current environmental challenge and such findings contradict contemporary evolution’s view that mutations are blind to need and are preserved only by the action of natural selection. Now, new research suggests yet another adaptive mutation mechanism.

The DNA double helix consists of two long strands wrapped around each other. Protein-coding genes can be on either strand, but one strand is more prone to mutations. This is because on that strand the DNA copying (replication) machine and the gene copying (transcription) machine move in opposing directions, and so head-on confrontations can occur. The new paper makes good arguments that these confrontations result in a higher mutation rate for genes on that strand.

Yet there are many genes on the “head-on” DNA strand. Why would that be? The new paper provides multiple evidences that not only these genes have incurred more mutations than normal, but that those mutations have often been helpful. That is, those mutations often have been adaptive.

So the paper hypothesizes that those genes are in the “head-on” orientation for good reason. They were genes that needed more mutations. The authors hypothesize a “replication–transcription conflict-mediated mutagenesis” strategy where genes that the organism particularly needs to modify are in the “head-on” DNA orientation.

This new hypothesis is not without its questions. For instance, while the “head-on” genes seem to reveal elevated levels of adaptive mutations, they do not show higher levels of mutations that do nothing to the protein’s amino acid sequence (the so-called synonymous mutations). Synonymous mutations are normally taken to reflect the underlying mutation rate. So if the mutation rate is higher due to a “head-on” orientation, then one would expect the synonymous mutation rate to be higher. That is standard evolutionary reasoning.

Another question is how and why do the genes switch from one DNA strand to the other, in the first place? In other words, this new strategy requires that genes switch from one strand to the other at some regular frequency. Whatever the mechanism, it must perform this switching at a rate that is not too low (or else very few genes would ever switch and evolutionary experimentation would be impossible) and not too high (or else the distribution between strands would be more random).

Finally there is, once again, the issue of serendipity. Under this new hypothesis evolution must have created a gene strand switching mechanism with an appropriate frequency. Such a mechanism would not provide any fitness improvement immediately. Instead the mechanism would set about switching, at random, genes from the strand they are on to the opposing strand.

And any such switches would also fail to provide fitness improvement immediately. But over time, some switches would help when certain genes undergo higher mutation rates. All of this means that evolution would have to create a sophisticated mechanism that only much later would provide benefit.

A typical explanation is that the new mechanism was simply a result of the combining of existing parts that were “lying around.” But this does nothing to reduce the serendipity involved. The bottom line here is that the new evidence forces evolutionary theory to take on even more complexity and serendipity. Evolution creates evolution.

37 comments:

  1. These articles demonstrate over and over what Moronton has admitted. Naturalistic UCA research has nothing to do with probability. This is why plausibility has nothing to do with it. And this is why evidence has nothing to do with it. It's ASSUMED to be true. The rest is just explaining it with ad-hoc positing.

    Unfortunately, such explanation IS subject to probabilistic analysis in some minimal way. An ad-hoc explanation for a given instance of biological variation inconsistent with all SA scenarios and non-genealogical scenarios has a humanly-assignable probability of at most 1/2 (to say otherwise is to be completely arbitrary in a partisan fashion). Thus, all millions of such ad-hoc posited causes/effects each have at most a non-arbitrarily-assignable probability of at most 1/2. Thus, the probability of naturalistic UCA on this approach is 1/2 raised to the power of however many millions of such events are posited to have occurred. We're talking a VERY low probability. And that equates to a VERY low plausibility.

    How many assumptions are required to imply other scenarios? More or less than the millions required for naturalistic UCA? Prove it.

    ReplyDelete
  2. This comment has been removed by the author.

    ReplyDelete
    Replies
    1. Wouldn't be a day without the Creationist dimbulbs crying in their beer and telling each other how ToE is going to collapse any day now...any day now...just wait...any day now. :D

      Hey, it's all they've got so let 'em console each other. The real scientific community will continue its work without missing a beat.

      Delete
    2. It's a good thing that the Creationist, fundamentalist Christians dim-bulbed their way into the whole Scientific Revolution thing, then. Too bad they weren't real scientists.

      And seeing as how nobody considered slavery to be kinda mean until those same dim-bulbs very gradually abolished it over centuries...I'm not sure why you think 150 years is a particularly long time for a bad idea to stick around.

      Delete
  3. Hey jeff and bpragmatic, will you please provide your detailed, scientific explanation for the diversity of life, with supporting evidence?

    ReplyDelete
    Replies
    1. Hey TWT, will you please provide your detailed, scientific explanation for the diversity of life, with support evidence?

      The Darwinism and Neo-Darwinism hypothesis failed, so you must use something else.

      Delete
    2. Tedford the Slow

      Hey TWT, will you please provide your detailed, scientific explanation for the diversity of life, with support evidence?


      Start here Tedford

      Evolution: Mark Ridley

      One of the best undergrad introductory texts on the market. Let us know when you're done reading it and I'll recommend a few dozen more good science texts.



      Delete
    3. TWT

      It's easy.

      Long time ago, molecules accidentally assembled themselves into nano machines. Gamma ray smashed into one of the machine's molecular components and holy mama! nano machine worked little better. Gamma ray decided it was good and it won't smash that same component any more, instead it smashed another one and holy mama! nano machine worked even better....

      yadda yadda yadda

      Justin Beiber!

      Delete
    4. Tedford, here's another excellent textbook on evolution for you to ignore

      Evolution (2nd edition, 2009): Douglas J. Futuyma

      "Evolution, Second Edition is a comprehensive treatment of contemporary evolutionary biology that is directed toward an undergraduate audience. It addresses major themes including the history of evolution, evolutionary processes, adaptation, and evolution as an explanatory framework at levels of biological organization ranging from genomes to ecological communities. Throughout, the text emphasizes the interplay between theory and empirical tests of hypotheses, thus acquainting students with the process of science. Teachers and students will find the list of important concepts and terms in each chapter a helpful guide, and will appreciate the dynamic figures and lively photographs. The content of all chapters has been updated. Contributors Scott V. Edwards and John R. True have once again provided authoritative chapters on, respectively, Evolution of Genes and Genomes and Evolution and Development, two of the most rapidly developing subjects in evolutionary biology. A final chapter on Evolutionary Science and Creationism treats such topics as the nature of science and the practical applications of evolutionary biology."

      You won't read it of course.

      Delete
    5. Eugen,
      Long time ago, molecules accidentally assembled themselves into nano machines.


      Sounds unlikely, though full size machines would seem more unlikely

      . An hypothetical question, if tomorrow the Mars rover found scientific proof of life , would the emergence of life from a merely natural mechanism be , more likely, less likely, or no difference? It Cassini detects life on one of the moons of Saturn, more,less or no difference?

      Just curious, I will give you the report on the star viewing off the clock.

      Delete
    6. Good question Vel

      I think solar system should be "polluted" by extremophile life forms from Earth. They could be knocked out by massive bombardment Earth endured in a distant past. Environment of vacuum, absolute zero and high radiation would test limits of their survivability.

      Maybe we should release some of extremophiles onto Mars soil and let them terraform for five hundred million years. By then we will need a new planet, Sun will become big enough to overheat the Earth and the Moon will get far enough so the Earth axis will destabilize.

      How was the viewing weekend?

      Delete
    7. TWT: Hey jeff and bpragmatic, will you please provide your detailed, scientific explanation for the diversity of life, with supporting evidence?

      J: Why should I be able to do that when no one else has been able to? Neither you nor anyone else on this forum has ever provided one iota of evidence for naturalistic UCA.

      Evidence is a relative concept. A set of assumptions and/or data only serves as evidence for a claim as compared to another set of assumptions and relevant data for a competing claim. To say a claim is evidenced in a non-relative way is to say it is SELF-evident, which is to say it is intuitive. Self-evident beliefs, like the law of non-contradiction, are not scientific hypotheses. They ground the very possibility and intelligibility of science.

      In this case, the options for the origins of biological entities/properties are:

      1) myriads of scenarios of purely naturalistic UCA,

      2) myriads of scenarios of UCA that are NOT purely naturalistic,

      3) myriads of scenarios of purely naturalisitc SA,


      4) myriads of scenarios of SA that are NOT purely naturalistic,

      and

      5) kazillions of non-genealogical scenarios.

      To say that any one of them is indicated by the data while the others aren't, or that one is MORE indicated than others, you have to state the relation the data holds to the assumptions of the explanatory theory that renders that "indication" true per your claim.

      Not one person on this forum has any clue how to do that, seemingly. None of you naturalistic UCA'ists has ever demonstrated you know what evidence even is so as to apply it to the question rationally. Because you're sure not using the normal criteria of parsimony, etc, to do the comparison.

      Oh sure, there are those who are so confused they think a handful of assumptions implies specific UCA lineages when really millions of ad-hoc assumptions are required. But that's because you and yours apparently are literally clueless as to how the hypothetico-deductive method works.

      Delete
  4. Hey Eugen, you forgot the first step... Nothing became something.

    ReplyDelete
    Replies
    1. Or how there exists an Uncaused Cause

      Delete
    2. "Or how there exists an Uncaused Cause"

      We don't need to worry about that one because reality is clearly based on what we consider Supernatural. No way around it.

      Delete
    3. Elijah,
      We don't need to worry about that one because reality is clearly based on what we consider Supernatural


      How so? Clear to whom?

      Delete
    4. anyone who uses his noggin for five minutes straight

      Is it natural in our universe for something to not have a cause? No its not. Its beyond (super) what we experience. Anyway you slice it you have no logical choice

      You either invoke infinite regress which in and of itself is a supernatural appeal

      or

      you say the universe has at least one cause that is totally uncaused that has no explanation, reason or precursor - unlike everything else we have ever experienced in the natural world.

      Beyond is the meaning of the word "Super" and natural is what we see of the universe that everywhere has precursors - Supernatural.


      Just in case you are inclined - don't hurt yourself trying to rebut. You won't be able to do so effectively.

      Delete
    5. Elijah,

      anyone who uses his noggin for five minutes straight


      For someone who bemoans the lack of civility ,you seem to feel no need to heed your own advice. Your claim is a variation of the cosmological argument. And philosophers have been considering it for centuries. Alas they didn't consult you and save their time.

      Is it natural in our universe for something to not have a cause?

      That is the basis of science though quantum indeterminacy is possibly in conflict with our experience at the macro level

      No its not.

      Your expertise speaks for itself.

      Its beyond (super) what we experience

      Are you now saying that all supernatural stuff is Uncaused by definition?

      You either invoke infinite regress which in and of itself is a supernatural appeal

      Unless an Uncaused Cause is finite, an infinite regress is a possibilty.

      you say the universe has at least one cause that is totally uncaused that has no explanation, reason or precursor - unlike everything else we have ever experienced in the natural world.

      I agree.

      Beyond is the meaning of the word "Super" and natural is what we see of the universe that everywhere has precursors - Supernatural.

      Can't really cipher this,I assume your argument is nature cannot cause itself therefore something must exist at some point beyond nature which is non contigent

      Just in case you are inclined - don't hurt yourself trying to rebut. You won't be able to do so effectively.

      If the argument is correctly deployed it is convincing. The question is whether you achieved that.


      Delete
    6. "For someone who bemoans the lack of civility ,you seem to feel no need to heed your own advice."

      I might have succumbed to watching the example you have set in previous threads but not entirely I don't think. I am pointed but not uncivil as I have seen here defended. I honestly believe you have not given it five minutes of thought. Its that clear.

      "Your claim is a variation of the cosmological argument. And philosophers have been considering it for centuries. Alas they didn't consult you and save their time."

      ah the old because an argument has been presented before we can pretend it has been rebutted to sidestep it gambit.

      "That is the basis of science though quantum indeterminacy is possibly in conflict with our experience at the macro level"

      Sorry This will not save your logic. Science can only tell us about things occurring within our present spacetime. IF you claim otherwise then you are back appealing to the supernatural. Though it is popular you cannot side step the issue by explaining that the cause of spacetime is a phenomenon that we observe taking place only within Spacetime. You are bucking up against both the absurd and the supernatural again just as I told you you would.

      I know that people such as yourself believe quantum realities save you from the messiness of the first cause but you are deluded (Krauss being the leader of the deluded). You are still both left with an uncaused cause and given infinity you would be left with a universe where everything is not only possible but must already have actuated (poor krauss believes that the everything would somehow preclude God but he hasn't thought about it for five minutes either) . Unfortunately a supreme being would be one of those everythings so we would be left with a certainty of God's existence and given the nature of infinity a God of infinite origins.

      THink about if for five minutes

      "Unless an Uncaused Cause is finite, an infinite regress is a possibilty."

      I'm sorry but you just completely confused yourself. An infinite regress BY DEFINITION demands an uncaused cause so you are still stuck with the supernatural premise of something (and everything that exists) having no ultimate explanation reason or cause in defiance of everything we see in our universe. AN infinite regress would have no beginning whatsoever and therefore no ultimate cause. Infinite moving forward in time has no end moving back in time it has no beginning.

      Furthermore every ability this infinite entity has would have equally no explanation but merely would be for the reason that it is ( incredibly close to The Old testament name for God given to moses merely as "I AM that I am ).

      This as you see gets you nowhere again but looking at the inevitability of the supernatural.

      Delete
    7. "Are you now saying that all supernatural stuff is Uncaused by definition?"

      No I am not. I am saying that anytime you appeal to something outside of the universe we see and observe you are invoking metaphysics and the supernatural. I am breaking down the meaning of Supernatural. Super - meaning beyond Natural meaning what we see and observe in this universe.

      It really is inescapable but its not something that materialists want to look at and in particularly not atheists because it eviscerates one of their treasured props that the very idea of the supernatural is absurd.

      The fact that both sides end up at the same place makes it inevitable that the only difference between them logically is not in believing in the supernatural but as to whether the supernatural possesses logic and intelligence. It can be argued that that is the ONLY real difference.

      We know of nothing in this universe (and that includes quantum fields, virtual particles or whatever you wish) that does not originate from something or somewhere else.

      "If the argument is correctly deployed it is convincing. The question is whether you achieved that."

      IF the conclusion is escapable on a logical ground I am open to hearing it. If not it has been achieved on the merits not whether this or that human being chooses to accept it. I dont know which you will choose but just stating the facts of that.

      Delete
    8. Therefor yhwh-jesus-holy-ghost?

      Delete
    9. Personally, I define naturalism as the study of the nature of things. Anything which has a nature which distinguishes it from all other things is part of the natural order, whether in this universe or some other. This makes the concept of supernatural effectively redundant since ghosts or even gods, if they exist as such, have their natures and are thus part of the natural world.

      Delete
  5. Eugen

    "Maybe we should release some of extremophiles onto Mars soil"

    Are you sure that none of the expedition to mars take extremophiles there?

    ReplyDelete
  6. Not sure Blas. Maybe NASA is secretly getting ready. Space.com is already selling T shirts
    :)

    ReplyDelete
    Replies
    1. Sorry Eugen for my tardy response,been busy being called an idiot by Elijah.Probably should leave the theology alone.

      Unfortunately you were correct about the light pollution,it had been a couple of years since I had been out there and while better than in the city,it still wasn't dark skies.

      The best part was it was the first time that some of my friends had seen Saturn thru a scope, plus the enthusiasm of amateur astronomers showing off their toys.

      So while the viewing was mediocre, the weather and whiskey and BBQ were superb. Spent the day sitting chatting with old friends enjoying the view of the lake

      It does put a burr under my saddle to hit Ft Davis maybe for the Perseides, need to check the phase of the moon.

      Hope all is well, about time for road construction to start? I still can't get the picture of the batting cage out of my mind,

      Delete
    2. Too bad about the light pollution, Velik. It's similar situation here. In the end, those events are fun no matter what. Discussing and showing off gear (i.e. toys) is a good part of the event.

      I do read comments about theology it but I'm not sure which commenter is doing better.

      Ah, the batting cages...that was a gooood lesson.
      :)

      Delete
    3. Eugen,
      I do read comments about theology it but I'm not sure which commenter is doing better.


      Bet on Elijah, he has certainty and a mission. Moi, just a skeptical nature.

      Delete
  7. What do you want in Entertainment..? Picutres, Videos, Loll Pictures, Hot Pictures, Funny Pictures, Funny Videos, Hot Videos, Entertainment Pictures, Entertainment Articles, Entertainment News, Internet Classified Sites, Buying and Selling Classified Sites, Online Jobs, Online Marketing and all Current Affairs News updates.
    All Current Affairs in Only 1 Best Entertainment Website Network
    hotcurrentaffairs.com

    ReplyDelete
  8. Say - isn't Hunter the guy who took a picture of a wolf, reversed it, altered the contrast, then claimed it was a Thylacine, then compared it to a picture of a wolf and declared that they look so much alike that evolution can't explain it?

    And then, after getting caught, said it was all a 'mistake'? And there are people DEFENDING this guy? Amazing...

    ReplyDelete
    Replies
    1. But he is unsurpassed in his tolerance of dissenting views.

      Delete
    2. Which, compared with Uncommon Descent, is the difference between night and day.

      Delete
    3. I don't know (the real?) Sam Harris. Is that what happened? Why is it not plausible that that would be a mistake?

      Here's Hunter's explanation:
      "you *are* pointing out a mistake in my graphics. Both wolf images were straight off the web, and in my hasty collection of marsupial and placental examples I accidentally got a marsupial wolf graphic confused as a placental. Yes it was a dumb mistake, but it was not at all important to my uncontroversial point, which was that in biology there are many convergences."

      Do you have any evidence that your narrative is the right one, or do you uncharitably assume the very worst about people with whom you disagree?

      Delete
  9. Looking for Best and Trusted PTC Site..?
    Here is a Best and Trusted PTC Site where you can earn money online without any invesment, earn with Just Clicking and Earn upto Daily 10$, Earn More with Referrals, Paid to Click System, Best upgrade plans and Best Advertising Plans. Legitimate Earning Website for ever you want
    HotProClicks.com

    ReplyDelete
  10. Lol is the Laugh out of Laugh where you can Fun Unlimited and Laughing Unlimited. Visit the Best Lol Network Ever, where you can every thing is lol and Funny, Troll Images, Funny Vidoes, Prank Peoples, Funny Peoples, Awkward Text, Prank Text, funny comics, Prank Images, Fail Pictures, Epic Pictures, Epic Videos, Prank Videos, Fail Videos and Much More Fun and Entertainment
    lolsgag.com

    ReplyDelete