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OOL is a Sticky Situation

Experimenters have recently found that genes–whereby they mean particular sequences of DNA–can “find” one another without the intervention of proteins or other factors. It appears to be strictly an effect caused by electrical charges along the DNA strand; the longer the ‘gene’ (that is, sequence length), the greater theapparent ease in ‘finding’ one another. The experimenters feel that this finding is a help for figuring out what happens during homologous recombination.

Here’s part of what they say: The researchers observed the behaviour of fluorescently tagged DNA molecules in a pure solution. They found that DNA molecules with identical patterns of chemical bases were approximately twice as likely to gather together than DNA molecules with different sequences.

Professor Alexei Kornyshev from Imperial College London, one of the study’s authors, explains the significance of the team’s results: ‘Seeing these identical DNA molecules seeking each other out in a crowd, without any external help, is very exciting indeed. This could provide a driving force for similar genes to begin the complex process of recombination without the help of proteins or other biological factors. . . .’

The article from ScienceDaily is here.

I have an OOL question: This study strongly suggests that similar DNA sequences have a preferential attraction for one another. And the longer the similar sequence, the greater the attraction. If that is the case, then, if a particular ‘gene’ began to ‘replicate’, wouldn’t the replicated ‘genes’ congeal together?

If this is true, then it would seem that the DNA would, per force, need to be isolated from other similarly sequenced DNA. And this, in turn, implies some kind of membran surface. The dilemna that I see, is that in order to replicate the DNA sequence needs a membrane-like environment; but doesn’t his mean that the membrane must also replicate along with the DNA so as to keep the two ‘genes’ apart. Yet, unless directed by a whole host of ‘genes’, why, and how, would the membrane know to divide? So, in a free solution, how do you keep replicated DNA from congealing? Seems like this is just one more headache to resolve for those who think the first cell/first DNA just happened.

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31 Responses to OOL is a Sticky Situation

  1. Very interesting.

    I have a serious question.

    If life is too complex for us to be able to explain, how can we possibly explain whatever created life?

  2. “Seeing these identical DNA molecules seeking each other out in a crowd, without any external help, is very exciting indeed. This could provide a driving force for similar genes to begin the complex process of recombination without the help of proteins or other biological factors. . . .”

    A similar effect has been observed when autumn leaves of a given biological variety “seek each other out in a crowd” and spontaneously collect under bushes, along street curbs, and by the inside corners of nearby buildings. This phenomenon is very exciting and could explain – without recourse to intentional beings – the driving force behind the curious recombinations of leaves that we often find inside large, plastic, twisty-tied bags.

  3. See: DNA Double Helices Recognize Mutual Sequence Homology in a Protein Free Environment,
    Geoff S. Baldwin,* Nicholas J. Brooks, Rebecca E. Robson, Aaron Wynveen, Arach Goldar, Sergey Leikin,* John M. Seddon, and Alexei A. Kornyshev, J. Phys. Chem. B, 112 (4), 1060 -1064, 2008. 10.1021/jp7112297

  4. Sorry, messed up the formatting of the link. Hope it’ll work like this.

    http://pubs.acs.org/cgi-bin/sa.....12297.html

    Otherwise you can find it at:

    http://pubs.acs.org/journals/jpcbfk/index.html

    and searching for the title of the paper: “DNA Double Helices Recognize Mutual Sequence Homology in a Protein Free Environment “

  5. I have an OOL question: This study strongly suggests that similar DNA sequences have a preferential attraction for one another. And the longer the similar sequence, the greater the attraction. If that is the case, then, if a particular ‘gene’ began to ‘replicate’, wouldn’t the replicated ‘genes’ congeal together?

    Obviously the attractive forces are not sufficiently strong to ‘congeal’ genes. Otherwise, every PCR (polymerase chain reaction) run in labs hundreds of thousands of times in labs all over the world would result in ‘congealed DNA’. They do not. Even at very high concentration identical copies of genes remain in homogeneous solution.

  6. Hi, ptet. You wrote:

    I have a serious question.

    If life is too complex for us to be able to explain, how can we possibly explain whatever created life?

    How uncomfortable would you feel about the notion that we, ourselves, are creatures…and therefore unable to completely understand and explain whatever created us?

    Martin Buber, in his book “I and Thou” raises the interesting possibility that we may not be exclusively the subject, studying objects. Instead, it may be the case that we, ourselves, are the objects of creation…able to enter into a relationship with our creator as with another subject.

    (“For as the heavens are higher than the earth, so are my ways higher than your ways, and my thoughts than your thoughts. (Is 55:9)

    Thou hast beset me behind and before, and laid thine hand upon me.
    Such knowledge is too wonderful for me; it is high, I cannot attain unto it. (Psalm 139:5,6))”

  7. Hi Lutepisc

    Thanks for your post.

    Is it the God of Abraham who helps identical DNA molecules seek each other out in crowds to begin the complex process of recombination?

    Is He personally involved each time this happens?

    Thanks!

  8. Hi ptet,

    If life is too complex for us to be able to explain, how can we possibly explain whatever created life?

    We will never obtain perfect knowledge so we have to use reason to make intelligent deductions. We know the universe started with the big bang were time and matter was created. Therefore we can conclude God is very powerful and intelligent (but not necessarily all powerful as aome Greek and modern philosophers conclude – otherwise, why didn’t he create a perfect world?). It is also reasonable to conclude that God is able to communicate with us. And since we were created, and almost everyone has an innate understanding of God it is reasonable to conclude that God loves us. We are learning more everyday about God’s creation and therefore learning more about His awesome intelligence. To learn more about God, Himself, we have to rely on the knowledge He revealed to us in the Bible.

  9. ptet:

    Our task is not to explain the Designer, but to detect, and acknowledge, design. If the Creator made gravity, then we have proven the capacity to understand it’s subtlety, as with quantum mechanics and such. Though our minds cannot wrap itself completely around the Creator, that doesn’t mean we can’t understand elements of what the Creator created. IOW, I don’t need to understand quantum mechanics to use a microwave; but a microwave oven uses quantum mechanics, and I know that it does; but I don’t know quantum mechanics.

    An analogy presents itsself. In QM, the hydrogen atom is known with exquisite precision; and science likes to pat itself on the back about this. But the hydrogen atom consists of one electron and one proton. But after that, to describe all the other elements, approximations of the hydrogen atom (!) are used. So, no one understand atoms other than hydrogen with precision, but using hydrogen as a model we can get good approximations of the other elements. We will never know God with precision; but we can still understand Him in some way, some ‘approximate’ way.

    But, again, the job of ID is to identify ‘design’, not to draw pictures of what the ‘designer’ looks like.

  10. 10
    Unlettered and Ordinary

    Greeting!

    Sorry to be off topic…

    But Does anyone know where in DNA fingerprints are stored?

    It just occurred to me that fingerprints are not necessary for survival, and everyone has different fingerprints, relatively everyone. They totally unique to the individual except with identical siblings.

    Do the coded areas code my fingerprints or is it in the non-coded area?

  11. 11
    Unlettered and Ordinary

    Greetings again!

    In the OOL inquiry is ATP used as energy for RNA transcription and Protein synthesis?

    I just trying to understand the relationship between DNA, RNA, Proteins and “ATP.” What role does ATP play? Is it an essential part of the DNA, RNA, Protein relationship? If it plays a part can it be replaced by other energy mediums?

  12. Actually, the fingerprints of identical twins are not identical – remarkably similar, but nevertheless distinguishable.

  13. 13
    Unlettered and Ordinary

    Greetings!

    Gerry Rzeppa, Cool I did not know that.

    Thanks!

  14. Hi Peter and PaV

    Thanks for your responses.

    As I see it, if I accept the idea that the Universe appears to be designed, then there is no reason to accept that there was just one designer. There could be any number of agents and events happening, in this dimension/universe, which might have a bearing on our Universe which we have no way of measuring or distinguishing? Is this correct?

    And separately… Is it not reasonable to say “I don’t know” rather than “there might be a creator or creators but I don’t know what they might be”?

    This all seems so obvious to you, but it does not appear obvious to me.

  15. ptet, you wrote:

    Is it the God of Abraham who helps identical DNA molecules seek each other out in crowds to begin the complex process of recombination?

    Is He personally involved each time this happens?

    Why not seek an answer to your question at a church, synagogue, or mosque? Why ask it on an ID blog?

    (Unless, of course, you’re basically here trolling…)

  16. 16
    Unlettered and Ordinary

    Greetings!

    ptet, No, accepting the design in the universe does not mean it was one designer. Science cannot comment on the designer or designers, only on the design itself.

    I take it you buy into the multiverse hypothesis. Something that has no bases in science at all, but may or may not exist. We cannot measure beyond our universe, only what is in our universe. At least for now.

    Mount Rushmore appears to be designed but I know nothing of the designer or designers. I know nothing of the time it took or how many steps it took. One thing I do know, the four faces were put there artificially because no blind random natural cause has the accuracy or precision to carve out the faces in such detail.

    So I can conclude that there was a creator or creators of the Mount Rushmore Faces. Could I be wrong? Yes, but when you compare the probability of the design coming about by narural causes, one could say I am not likely wrong.

    OOL has a set of probabilities for each part of its inquiries. DNA for now stands at 0 probability, RNA also 0 probability, Functional Proteins 0 probability. So 0 x 0 x 0 = 0 probability of life coming into existance by natural causes. So one can conclude that there was an unnatural cause, no matter if the cause is super natural or artificial. That is just the stuff coming into existance not even about there design inplications.

    This is kinda like find’n plastic on another planet. Plastic as I understand it does not exist naturally, so I can conclude that some life may have existed or still exists on said planet. But still if I found that that plastic had a very specific sequence and pattern that was also not likely to occur naturally I would have more evidence of intelligent life on said planet.

    The same techniques and principles used to identify designs and technologies of dead cultures and civilizations, can be used to identify designs and technologies in living things, and even to the universe itself.

    Why do you think very skeptical atheists after studying the universes physics become theists? The same goes for some who study the OOL inquiry. No one twists their arm, they come to the conclution after studying the evidence that these things were designed.

    So further inferences can be made; since these things are designed, naturally something or someone designed them. Further extrapolation is not possible.

    So the Mount Rushmore Faces, It is reasonable to say “I don’t know” rather than “there might be a creator or creators but I don’t know what or who they might be?”

    But it is just as reasonable to say “there might be a creator or creators but I don’t know what or who they might be?” for the Mount Rushmore Faces.

  17. ptet,

    “if I accept the idea that the Universe appears to be designed, then there is no reason to accept that there was just one designer.”

    There is a remarkable similarity between the creation of life and the first chapter of Genesis in the Bible if a “day” is interpreted as an “age.” The probability of the story of Genesis getting its facts correct is about zero. It had to be revealed by God. This is further confirmed when comparing the creation myths of other cultures. For more information on this see Hugh Ross’ web site Reasons to Believe. The story of Genesis is a strong indication that the God of the Bible is the only creator. This goes way beyond what most scientist are comfortable including in science, nevertheless, Ross’ interpretations are reasonable, and a lot more rigorous then those of his critics.

  18. Sorry Peter, but the day-age theory can’t possibly be the correct interpretation of Genesis 1. To cite but one well-known difficulty: birds are created on the fifth day, and land creatures on the sixth. In the fossil record, the order is the other way round. We’re on good philosophical and scientific ground when we aregue that life was designed. A strong philosophical case can be made for a Designer of the cosmos. Arguing that this Designer created the world in precisely the order narrated in Genesis 1 is unhelpful to ID – and in any case, it’s poor theology, as it assumes that the author of Genesis 1 intended to write a scientific account. To me, the framework interpretation of Genesis 1 (which is discussed in detail on Craig Rusbult’s web site at http://www.asa3.org/ASA/educat.....usbult.htm ) makes a lot more sense.

  19. Unlettered and Ordinary –

    You make a lot of good points. I think you’d agree that we are so made that we are able, in most cases, to recognize design when we see it. That’s why a three-year-old can not only locate a grasshopper in a parking lot, but he can also tell you that the bug is alive and the cars are not – without recourse to a clear definition of life or an in-depth understanding of automotive engineering!

    I have to take exception, however, when you say that “Further extrapolation [about a designer] is not possible”. If you study a handful of houses designed by architect Frank Lloyd Wright, for example, you will find that you can later recognize other houses built from his designs. Likewise, I think we see the same kind of “signature” in many of the creations on our planet. So it seems reasonable (to me) to conjecture that the same designer produced multiple works in our universe. And when we consider the remarkable integration of the whole thing, we can, with the aid of Occam’s Razor, extrapolate to a single Designer. Or, at the very least, a tightly knit group of Designers with exceptionally precise communication and coordination abilities!

  20. hrun0815 (#5):

    I looked at the citation. It appears they artifically brought the double-stranded DNA close to one another. So, really, the potential problem might be the reverse. If you have DNA inside a small-diameter membrane, then, without the proper machinery to separate them, any replicated sequences would have a tendency to attach to one another. The whole point here is that this discovery seems to make OOL look just that more like an irreducibly complex system.

  21. ptet: (#14)

    And separately… Is it not reasonable to say “I don’t know” rather than “there might be a creator or creators but I don’t know what they might be”?

    Thomas Aquinas has 5 ‘proofs’ of God’s existence. I think logic itself leads one to a Creator—the Prime Mover of the Greeks, if nothing else. If one attempts to get around the Big Bang with the multiverse approach, this makes things, literally, infinitely more complex. Doing that doesn’t seem to be the right way of reasoning.

  22. I looked at the citation. It appears they artifically brought the double-stranded DNA close to one another. So, really, the potential problem might be the reverse. If you have DNA inside a small-diameter membrane, then, without the proper machinery to separate them, any replicated sequences would have a tendency to attach to one another. The whole point here is that this discovery seems to make OOL look just that more like an irreducibly complex system.

    So first the problem appeared to be that without a membrane system you would get DNA sticking/congealing together. Now the problem is that with a membrane system you would get DNA sticking/congealing together.

    All I can say is this: If you take a small volume of water with a very high concentration of identical strands of DNA (be they produced by PCR reactions or by isolation from bacteria), even in the complete absence of proteins and salts, the DNA does not congeal.

    So I just don’t see how this discovery should make OOL ‘more like an irreducibly complex system’

  23. PaV (20)

    “I think logic itself leads one to a Creator—the Prime Mover of the Greeks, if nothing else. If one attempts to get around the Big Bang with the multiverse approach, this makes things, literally, infinitely more complex. Doing that doesn’t seem to be the right way of reasoning.”

    Essentially, neither of them are satisfactory. I agree with you about the multiverse, but the Prime Mover does require explanation of where it came from – especially if it’s intelligent, which complicates matters way beyond even the multiverse approach. My own feeling is that when it comes to the origin of the universe the most likely answer is a kind of quantum burp – the kind of borrowing of energy that we see experimentally (such as in the Casimir effect) and which is described by the Uncertainty Principle.

  24. Clarence:

    You say that the Prime Mover must be explained, but you seem not to be bothered about the origin of the energy that is being “borrowed”. Interestingly, we have all kinds of conservation laws for energy, such as: energy can neither be created or destroyed. Now, if this makes energy eternal, then this means that we are all comfortable with the idea of some things always existing and not needing an explanation for its beginning. The Prime Mover falls into that category. But if we want to object that with quantum fluctuations as the cause of all else happening, we can now explain the generation of all things, this doesn’t explain however how things go from being non-descript to being descript. Our only experience is that of agency bringing about such a transformation. So, we can now posit an eternal agent who brings all things out of nothing—using quantum fluctuations. Wouldn’t we want to call that agent God?

  25. hrun0815:

    So I just don’t see how this discovery should make OOL ‘more like an irreducibly complex system’

    It’s one more hurdle—and there’s already gobs of them to begin with.

  26. It’s one more hurdle—and there’s already gobs of them to begin with.

    PaV, the point is, that there is no justification to assert that this is ‘one more hurdle’. As I explained, even at high concentration of identical DNA molecules, there is not propensity for DNA molecules to ‘congeal’. PCR reactions and plasmid preparations make this very clear.

    As I stated before (in a now deleted post), there is also an attractive force between any object with a non-zero mass. This does not mean that everything with a non-zero mass congeals- even without active intervention.

    For example, Brownian motion alone might be sufficient to keep DNA strands from ‘congealing’.

  27. Clarence:

    I sympathize with your difficulty regarding the Prime Mover. For you, the central fact about the Prime Mover which needs to be explained is not its existence per se but its complexity. PaV’s argument that “we are all comfortable with the idea of some things always existing and not needing an explanation for [their] beginning”, is well-taken, but does not address your concern that an “intelligent” Prime Mover “complicates matters” owing to its complexity. May I suggest the following points:

    (1) Beware of assuming that “intelligent” implies “complex.” Even if this is true for every intelligent agent that we are familiar with, that does not make it necessarily true.

    (2) Even if the Prime Mover is complex, this does not entail that it requires an explanation – unless you assume that complexity per se requires an explanation. It may not. Certain kinds of complexity may just be brute facts.

    (3) What kind of complexity could (or should) just be taken as a given, you ask? Let’s turn the question on its head. What is it about complex things that bothers us in the first place? Surely it is the fact that they don’t hang together very well. They strike us as fragile entities, whose components could fall apart at any instant. And I agree with you that a complex entity of this sort would require an explanation, even if it existed from all eternity.

    (4) Now I would like to ask you: what if there were a complex being whose parts hung together perfectly, in such a way that they were inseparable – none of the parts could be isolated from any of the others? Would it require an explanation? I put it to you that it would not. Such a being would be indestructible.

    (5) The situation is different with an entity whose parts are such that none of them can function without all of the others (irreducible complexity). For one can still imagine that such a being could have its parts broken up by outside interference. Irreducibly complex entities may still be destructible.

    (6) If, however, there were an irreducibly complex entity whose parts were inseparable because (a) they were perfectly integrated with each other, and (b) they required nothing outside themselves, then we would indeed have an entity that required no explanation.

    (7) A complex Prime Mover obviously meets condition (b) – it is independent, because it is uncaused. Moreover, I see no reason why it could not also meet condition (a) – for why should such a being not have inseparable parts? Indeed, one would expect that.

    (8) A final question: could an unintelligent entity meet both requirements? It may seem so: for instance, one might imagine a geometric structure that explains all of reality, like the dazzlingly complex and beautiful mathematical structure (E8) envisaged by physicist Garrett Lisi in his exceptionally simple theory of everything.

    (9) However, the central difficulty is that even here, the parts are still not logically inseparable: they hang together beautifully, but not perfectly, in such a way that one cannot imagine any part existing without the others. I put it to you that the same applies for any physicalistic explanation of the cosmos that we are likely to dream up.

    (10) So, we are left with something we cannot conceive, which is either (a) simple or (b) complex and seamlessly integrated, and which cannot be cashed out in terms of its spatio-temporal characteristics or its physical strcuture. Why would we want to call such a being intelligent? For two reasons: one positive and one negative. The positive reason is that only an Intelligence behind the cosmos can guarantee that the universe is, and always will be, intelligible to us (i.e. that its laws continue to hold up and make sense, in a way that intelligent beings, especially scientists, can recognize and understand). The negative reason is that knowledge and love are the only attributes we know of that have no built-in physical limitations. A being with any other attributes has a certain specificity, a this-ness about it, that strikes us as metaphysically arbitrary. A being whose nature consisted entirely of knowing and loving would be a totally open-ended entity, and would not require such an explanation.

    I hope that helps.

  28. I’ve got a watch here, that displays the time in either 24-hour mode or a.m./p.m. mode — my choice — and also, the day of the week. Push a button, and it displays the date. Push another button, and it wristwatch becomes a stopwatch, complete with a lap function. Push another button, and the dial lights up enough to be read in the dark. Push various combinations of buttons and you can set all the various functions.

    Maybe it’s me, but I feel pretty safe in making a design inference about this thing.

    Nevertheless, try as I might, I have no way of knowing whether my presumed designer is a she or a he, smokes Marlboros or Kools, drives a Ford or a Chevy, drinks champagne or beer, has a dog or a cat for a pet, or likes Classic Rock, Cool Jazz or both.

    That said however, I’m pretty sure that she/he is Chinese, because of the letters engraved on the back that say “Made in China.”

  29. hrun0815 @ 22
    See world expert Robert Shaphiro’s comments on water & DNA:

    “water does nasty things to DNA. For example, there’s a process I heard you mention called DNA animation, where it kicks off part of the coding part of DNA from the units—that was discovered in my laboratory.

    Another thing water does is help the information units fall off of DNA, which is called depurination and ought to apply only one of the subunits—but works under physiological conditions for the pyrimidines as well, and I helped elaborate the mechanism by which water helped destroy that part of DNA structure. I realized what a fragile and vulnerable molecule it was, even if was the center of Earth life. After water, or competing with water, the other thing that really does damage to DNA, that is very much the center of hot research now—again I can’t tell you to stop using it—is oxygen. . . .
    The half-life of pure ribose in solution, a different experiment and a very good one, by Stanley Miller is of the order of one or two hours, and all of the other sugars prominent in Earth biology have similar instability.

    Without the self reproducing cell, there appears to way to assemble the components let alone that cell.

  30. Without the self reproducing cell, there appears to way to assemble the components let alone that cell.

    If that is the case and this matter is completely settled, then I don’t know why PaV would try to add to it with an example that just does not hold up to scrutiny.

    Clearly, the research cited in the original post does not lead to the conclusion that DNA in water will congeal once there are multiple copies present. I enumerated practical examples that demonstrate that it is not the case and I demonstrated with a thought example, that attractive forces do not necessarily lead to ‘congealing’.

    Nowhere did I make an argument about how self-reproducing cells came about. I merely pointed out that this research does not have any direct bearing on the issue (at least not in the way suggested by PaV).

  31. 31
    Unlettered and Ordinary

    Greetings!

    Gerry Rzeppa, I totally agree.

    I just have one semi-objection. If I found 1000 paintings and the artist was unknown. I could after careful examination conclude all the painting were painted by one painter or at least a close group of painters, like you said. But other than the information from the painting, we would have a limited capability in describing the painter or painters. We could only glean information from the paintings and make inferences from that information. This is the limitation of investigation.

    But I still totally agree with you.
    I just see the limitation of what science can actually tell us. Science yields much discovery and wonder. But it does have its limitation.

    What we cannot observe we cannot study. What we cannot study we cannot know. That is in strictly scientific terms of course.

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