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Time for serious pursuit of post-Darwinian theory, says new BIO-Complexity paper

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From Ann Gauger at the Biologic Institute new BIO-Complexity paper:

Five family members from the GabT-like protein family. The first three are very similar. These enzymes are considered by current standards to be homologous, that is, evolutionarily derived.

The five enzymes shown above are clearly related in structure, especially the three on the left. Yet none of the others can replace BioF2’s function in the cell, even when mutated and made in large amounts. Why is that? Probably because each enzyme is a structural whole, whose sequence is made to work together as a whole. Substituting or changing little bits doesn’t work.

Here are the concluding paragraphs of our recent paper where we explain the problem and propose a new way of thinking about it:

“Although there is as yet no satisfactory theory of biology to take the place of Darwinism, we believe the time has come for serious pursuit of such a theory. To quote one of our previous papers [45]:

The insights we gain from the critique of neo-Darwinism can and should inform the construction of a new theory to take its place. That is, in pinpointing the key problems with the old theory we are identifying crucial respects in which its replacement must differ from it. We ourselves have become convinced that intelligent causation is essential as a starting point for any successful theory of biological innovation. If this is so, what is needed now is an elaboration of the general principles by which living things have been designed.

To that end, one of our inferred principles of design is this [45]:

The substantial reworking of a homologous structure needed to give it a genuinely new function is more suggestive of reapplication of a concept than adjustment of a physical thing.

And another is this [45]: … More. (Reeves MA, Gauger AK, Axe DD (2014) Enzyme families—Shared evolutionary history or shared design? A study of the GABA-aminotransferase family. BIO-Complexity 2014 (4):1-16. doi:10.5048/BIO-C.2014.4.)

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57 Replies to “Time for serious pursuit of post-Darwinian theory, says new BIO-Complexity paper

  1. 1
    gpuccio says:

    News:

    Very interesting paper. Thank you.

  2. 2
    Silver Asiatic says:

    Sentences that convey different ideas may have similar structures, but when we write a sentence we start with the idea, not the sentence structure. We never take a sentence that conveys some other idea and ask which letters can be changed to make it better suited for our present purpose.

    Good analogy. Evolution supposedly moves from one functional idea to another by changing the letters in each sentence.

  3. 3
    Zachriel says:

    Silver Asiatic: Evolution supposedly moves from one functional idea to another by changing the letters in each sentence.

    And through recombination of existing motifs.

  4. 4
    Silver Asiatic says:

    A motif is an idea.

    “And through recombination of existing motifs.”

    Therefore:

    “Through a recombination of existing functional ideas.”

    Therefore:

    Silver Asiatic: Evolution supposedly moves from one functional idea to another by changing the letters in each sentence.

    No – evolution moves directly from one functional idea to another, supposedly, as it has been said.

  5. 5
    Zachriel says:

    Silver Asiatic: Through a recombination of existing functional ideas.

    Well, functional structures at least.

    Silver Asiatic: No – evolution moves directly from one functional idea to another, supposedly, as it has been said.

    What we were pointing out is that evolution doesn’t work merely through simple letter changes, but through recombination as well.

  6. 6
    Joe says:

    What we were pointing out is that evolution doesn’t work merely through simple letter changes, but through recombination as well.

    The debate is about whether or not evolution is blind, mindless and without goals. How was it determined that recombination is a blind watchmaker mechanism?

  7. 7
    Silver Asiatic says:

    Silver Asiatic: No – evolution moves directly from one functional idea to another, supposedly, as it has been said.

    Z: What we were pointing out is that evolution doesn’t work merely through simple letter changes, but through recombination as well.

    Yes, I understood what you already said. Motifs. You were pointing out (claiming) that evolution moves directly from one functional structure to another. So, in response to Ann Gauger’s paper, there should be no concern about “alteration” because evolution can just recombine functions.

  8. 8
    gpuccio says:

    Zachriel:

    “Motifs”, especially if simple, are usually not functional in themselves. A function must be there to be selected. It must be implemented at biochemical, molecular level.

    It is certainly possible that similar motifs, or domains, or exons, can be shuffled or re-utilized in different proteins. That is often seen in all forms of modular design, and especially in Object Oriented Programming.

    However, neo darwinists always overstate that point, especially when they have difficulties in even trying to explain how those motifs, domains or exons got there in the beginning.

    Re-mixing existing information is just that: re-mixing what already exists. What already exists had to come into existence by random variation, according to your theory, and that means usually by single bit variation, or by multibit variation which has nothing to do with existing structures. Even re-mixing existing exons or whatever requires much more than random combinatorics: object oriented programming is not done by simply re-mixing objects, and requires careful engineering.

    Gauger’s paper is a new important step in trying a top down analysis of protein functional space: a much needed understanding, which is strangely overlooked by official academic researchers. Strange that those people who are so sure that the functional protein space is so filled with functional states of all kinds are not trying to demonstrate that that is the case.

  9. 9
    Zachriel says:

    Silver Asiatic: So, in response to Ann Gauger’s paper, there should be no concern about “alteration” because evolution can just recombine functions.

    Not even sure your point. As for Gauger, she has a conclusion, but no evidence other than a failed experiment.

  10. 10
    Silver Asiatic says:

    Z:

    Not even sure your point.

    I just clarified your point. Just observing the process of restatements and linguistic engineering was interesting enough. Eventually, what you were actually saying became clear.

  11. 11
    Zachriel says:

    gpuccio: Re-mixing existing information is just that: re-mixing what already exists.

    Both are required in evolution. There has to be a source of novelty as well as shuffling of existing motifs. Larger structures can evolve from simpler structures.

  12. 12
    Silver Asiatic says:

    gpuccio:

    However, neo darwinists always overstate that point, especially when they have difficulties in even trying to explain how those motifs, domains or exons got there in the beginning.

    Yes, it’s interesting. They often know it is overstating, so they try to disguise that with understated language. That’s NDE in itself – an enormous claim, understated in terms of minor, tiny, easily accepted changes.

    Re-mixing existing information is just that: re-mixing what already exists. What already exists had to come into existence by random variation, according to your theory, and that means usually by single bit variation, or by multibit variation which has nothing to do with existing structures.

    Exactly again. The problem in building the first “sentences” letter by letter remains. But I noticed how that was avoided by moving to the idea that evolution merely swaps functions.

    Even re-mixing existing exons or whatever requires much more than random combinatorics: object oriented programming is not done by simply re-mixing objects, and requires careful engineering.

    Very well said. I would hope that point would be strikingly obvious to anyone who read the responses thus far. The notion that evolution moves from one function to another, as a means of avoiding the problem of how to build the components of modular design (so to speak) was left standing as an explanation.

  13. 13
    humbled says:

    “Larger structures can evolve from simpler structures.”

    Could you please provide an example where a larger structure has evolved from a simpler structure? Thanks.

  14. 14
    Zachriel says:

    Silver Asiatic: The problem in building the first “sentences” letter by letter remains.

    The analogous case in English is easy if the sequences are selected for length and meaningfulness.

    humbled: Could you please provide an example where a larger structure has evolved from a simpler structure?

    The mammalian middle ear is a canonical example.

  15. 15
    Mapou says:

    Zacky:

    Silver Asiatic: The problem in building the first “sentences” letter by letter remains.

    The analogous case in English is easy if the sequences are selected for length and meaningfulness.

    This is a lie. Unless there is a system in place that prevents existing good sequences from being destroyed by random mutations, all that is left is gobbledygook. Such a sequence repair mechanism would have to be highly complex and would have to know in advance which sequence is good and which is bad. Evolution is a gigantic lie. It is a relentless fraud perpetrated on the public by a-holes with an agenda of imposing their one true state religion on the world. Like all lies, it will not succeed.

  16. 16
    Joe says:

    The mammalian middle ear is a canonical example.

    Imagination is neither an example nor evidence.

    BTW, remixing existing information is not required for evolution

  17. 17
    Zachriel says:

    Mapou: Unless there is a system in place that prevents existing good sequences from being destroyed by random mutations, all that is left is gobbledygook.

    That is incorrect. Consider replication with occasional mutation, say one mutation per hundred letter copies. Start with the string “gobbledygook”. Let’s say it has the following two offspring:

    gobbledygoop
    gobbledygook

    The first child is, unfortunately, stillborn. The second child, however, is a clone and survives just fine. Unless the mutation rate is very high, at least some of the offspring will be clones.

  18. 18
    bornagain77 says:

    As to:

    “The five enzymes shown above are clearly related in structure, especially the three on the left. Yet none of the others can replace BioF2’s function in the cell, even when mutated and made in large amounts. Why is that? Probably because each enzyme is a structural whole, whose sequence is made to work together as a whole. Substituting or changing little bits doesn’t work.”

    As to the problem that ‘working together as a whole’, i.e. context dependency, presents for neo-Darwinism, I highly recommend Wiker & Witt’s book “A Meaningful World” in which they show, using the “Methinks it is like a weasel” phrase that Dawkins used from Shakespeare’s play Hamlet to try to illustrate the feasibility of Evolutionary Algorithms, that the problem is much worse for Darwinists than just finding the “Methinks it is like a weasel” phrase by a unguided search.
    This is because the “Methinks it is like a weasel” phrase doesn’t makes any sense at all unless the entire context of the play of Hamlet is taken into consideration so as to give the “Weasel” phrase its proper ‘meaning’. Moreover the context in which the weasel phrase finds its meaning is derived from several different levels of the play. i.e. The ENTIRE play, and even nuances of the Elizabethan culture, who said it, why was it said, where was it said, etc,,, provides the contextual meaning for providing the meaning for the individual “Weasel” phrase.

    A Meaningful World: How the Arts and Sciences Reveal the Genius of Nature – Book Review
    Excerpt: They focus instead on what “Methinks it is like a weasel” really means. In isolation, in fact, it means almost nothing. Who said it? Why? What does the “it” refer to? What does it reveal about the characters? How does it advance the plot? In the context of the entire play, and of Elizabethan culture, this brief line takes on significance of surprising depth. The whole is required to give meaning to the part.
    http://www.thinkingchristian.n.....821202417/

    Dr. Gauger has also shown that the problem of context dependency, i.e. ‘working together as a whole’, extends past the primary sequence of a protein and is also present for the secondary structure and for protein domains as well:

    “Why Proteins Aren’t Easily Recombined, Part 2? – Ann Gauger – May 2012
    Excerpt: “So we have context-dependent effects on protein function at the level of primary sequence, secondary structure, and tertiary (domain-level) structure. This does not bode well for successful, random recombination of bits of sequence into functional, stable protein folds, or even for domain-level recombinations where significant interaction is required.”
    http://www.biologicinstitute.o.....ned-part-2

    Moreover, even the entire protein structure themselves are found to be ‘context dependent, in that many proteins are now found to be multifunctional depending on the overall context (i.e. position in cell, cell type, tissue type, etc..) that the protein happens to be involved in. Thus, the sheer astronomical brick wall that Darwinian processes face in finding ANY novel functional sequence for any protein to perform any specific single task in a cell in the first place, (Axe; Sauer), is only exponentially exasperated by the fact that many proteins are multifunctional and, serendipitously, perform several different ‘context dependent’ functions within the cell:

    Human Genes: Alternative Splicing (For Proteins) Far More Common Than Thought:
    Excerpt: two different forms of the same protein, known as isoforms, can have different, even completely opposite functions. For example, one protein may activate cell death pathways while its close relative promotes cell survival.
    http://www.sciencedaily.com/re.....134623.htm

    The Gene Myth, Part II – August 2010
    Excerpt: “It was long believed that a protein molecule’s three-dimensional shape, on which its function depends, is uniquely determined by its amino acid sequence. But we now know that this is not always true – the rate at which a protein is synthesized, which depends on factors internal and external to the cell, affects the order in which its different portions fold. So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape (Intrinsically Disordered Proteins), taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous (very weak or slight) influence over their functions.
    ,,,,So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used. Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent.
    Stuart A. Newman, Ph.D. – Professor of Cell Biology and Anatomy
    http://darwins-god.blogspot.co.....rt-ii.html

    podcast – Dr. Jonathan Wells: Biology’s Quiet Revolution – September 17, 2014
    “We are talking about 1/3 of the proteins in our body, (may be Intrinsically Disordered Proteins)” – Jonathan Wells
    http://www.discovery.org/multi.....evolution/

    Context dependency, and the problem it presents for ‘bottom up’ Darwinian evolution is perhaps most dramatically illustrated by the following examples in which ‘form’ dictates how the parts are used:

    What Do Organisms Mean? Stephen L. Talbott – Winter 2011
    Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: “Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements … take unique meaning from their context.[3]“,,,
    http://www.thenewatlantis.com/.....nisms-mean

    Timelapse Video Reveals Electric Face in Embryonic Tadpole – July 2011
    Excerpt: “When a frog embryo is just developing, before it gets a face, a pattern for that face lights up on the surface of the embryo. We believe this is the first time such patterning has been reported for an entire structure, not just for a single organ. I would never have predicted anything like it. It’s a jaw dropper.”
    http://www.sciencespacerobots......ole-718111

    In the following podcast and article, Dr. Jonathan Wells reveals that the ‘bioelectric code’, which is what is apparently dictating the ‘form’ of the organism in the preceding video, is not reducible to sequences of DNA as is presupposed in neo-Darwinism:

    podcast – Jonathan Wells: Is There Biological Information Outside of the DNA?, pt. 3 – Bioelectric code
    http://intelligentdesign.podom.....5_52-07_00

    Not in the Genes: Embryonic Electric Fields – Jonathan Wells – December 2011
    Excerpt: although the molecular components of individual sodium-potassium channels may be encoded in DNA sequences, the three-dimensional arrangement of those channels — which determines the form of the endogenous electric field — constitutes an independent source of information in the developing embryo.
    http://www.evolutionnews.org/2.....54071.html

  19. 19
    Mapou says:

    zacky the magician:

    gobbledygoop
    gobbledygook

    The first child is, unfortunately, stillborn. The second child, however, is a clone and survives just fine. Unless the mutation rate is very high, at least some of the offspring will be clones.

    Not true. Nothing survives because it never gets to that point. Why? Because, as every programmer knows, the number of deleterious mutations is far greater than the number of viable mutations by many orders of magnitude. Even if one sequence survived (and I’m being infinitely generous), the next mutation will kill it dead.

    There is an even bigger problem than the above. Before the organism can even get to the point of selection, it must evolve a reproductive capability.

    I repeat: unless there is mechanism in place that protects sequences from deleterious mutations, all you got is crass pseudoscience and superstition. It does not matter if you jump up and down, foam at the mouth and recite 1000 Hail Marys.

    In conclusion, it is obvious that Darwinian evolution and naturalism are stupid, stupid, stupid, STUPID, STUPID…

  20. 20
    Zachriel says:

    Mapou: Not true.

    It’s self-evidently true. We provided an example.

    Mapou: Because, as every programmer knows, the number of deleterious mutations is far greater than the number of viable mutations by many orders of magnitude.

    In the example we provided, 100% of the mutations were deleterious.

    Mapou: Even if one sequence survived (and I’m being infinitely generous), the next mutation will kill it dead.

    Unlikely in the example we provided. Given a reasonable population of variants, it won’t ever happen.

    Mapou: Before the organism can even get to the point of selection, it must evolve a reproductive capability.

    We didn’t introduce word evolution. That was Gauger.

  21. 21
    Mapou says:

    Zacky, what’s with the “we” shit, huh?

    And how do you get to a population when anybody with 2 neurons between their ears knows you have to start with a single individual? Did an entire population suddenly poof itself into existence?

    PS. I’m gonna call you the poof meister from now on.

  22. 22
    Zachriel says:

    Mapou: And how do you get to a population when … you have to start with a single individual?

    Reproduction with variation. Let’s say you start with a single letter word, o. Given moderate rates of mutation, most of its offspring will be identical to the original, but some will mutate. Offspring such as q, xo, fo die, but some mutants will form new words, so we end up with o, or, a, of, ox, to and so on. After that, we might have box, ore, at, off. Then add recombination for the real fun.
    http://www.zachriel.com/mutagenation/Sea.htm

  23. 23
    Mapou says:

    So, Poof Meister, how did your single individual evolve the ability to reproduce? And how does it know about “box, off, etc?” It poofed its knowledge into existence?

    And again, what’s with the “we” shit? Did you poof it into existence too?

  24. 24
    Zachriel says:

    Mapou: how did your single individual evolve the ability to reproduce?

    That’s not part of word evolution, which presupposes reproduction. Keep in mind, we didn’t introduce word evolution. That was Gauger.

  25. 25
    Mapou says:

    Poof Meister:

    That’s not part of word evolution, which presupposes reproduction.

    And that, ladies and gentlemen, is the biggest unsolvable problem of evolution: it never started in the first place. Unless, of course, you believe in poofery.

  26. 26
    Moose Dr says:

    Zachriel, please help me to understand your view about “motifs”. I would presume that you are saying that within a particular “gene” (codes for a protein) there are, well, subroutines. When I look at pictures of proteins, I often see patterns, twisty coiley things that look like hair that has been curled, for instance. A twisty coily would be a “motif”, correct?

  27. 27
    Mung says:

    Evolution assumes the existence of a system capable of evolution. Is this the most news-worthy item we’ve seen yet today or what?

    Any robust theory of evolution should be able to describe the requirements that such a system must meet. Yet another in the long list of reasons why there is no coherent theory of evolution.

    kairosfocus has his challenge that remains unmet, and so does Upright Biped. Mine is similar. What are the minimal requirements for a system capable of Darwinian evolution? Where’s the theory that ought to be fundamental to the entire evolutionary edifice?

  28. 28
    Zachriel says:

    Moose Dr: I would presume that you are saying that within a particular “gene” (codes for a protein) there are, well, subroutines.

    Protein motifs, whether structural motif or sequence motif, represent common functional elements of proteins. For instance, a zinc-finger is a fold that holds a zinc ion.
    http://www.rcsb.org/pdb/101/motm.do?momID=87

    With the analogous situation for word evolution, it’s far more likely for the recombination of syllables from existing words to form a new word than for random letters to form a new word.

  29. 29
    computerist says:

    Zachriel,

    If I play at the slot machine, anything I win will likely be put back into the machine as long as I continue playing it (overtime) as the odds are stacked against me given the nature of the algorithm. That’s how casinos take everyone’s money. Next thing you know I will be taking out money at the ATM using a “magical credit card”.
    Are the odds not constantly against beneficial mutations from occurring? If not, why not? Is there a “magical credit card” you forgot to mention?

  30. 30
    Mung says:

    Slot machines can produce wins in spite of the odds.

    http://faculty.rwu.edu/aespino.....lation.pdf

  31. 31
    rvb8 says:

    OOL and Evolution are separate topics. The requirements of evolution are random mutations, followed by the the sifting process known as natural selection, and aided by sexual selection and perhaps gene transfer. The requirements of OOL, are chemicals and energy. What in the world is so difficult to grasp?

  32. 32
    Moose Dr says:

    Zachriel (28): “With the analogous situation for word evolution, it’s far more likely for the recombination of syllables from existing words to form a new word than for random letters to form a new word.”

    Help me to understand. I understand that there are a variety of mutational types beyond the “point mutation”. There’s insertions, deletions, inversions, etc. You are saying that there is a mutational type called a recombination?

  33. 33
    Mapou says:

    I realize that I am in the minority but, IMO, OOL and evolution are not separate topics for the same reason that ID and designer are not separate topics. They are intrinsically and inseparably linked.

    Furthermore, RM + NS are not sufficient for survival. You must also have a viable reproductive capability and a gene repair mechanism to conserve the vast majority of the genome. In addition, complex organisms must also have an adaptive mechanism based on epigenetics. Epigenetics does not need RM + NS. It modifies certain genes in response to environmental cues. It is a front loaded mechanism that anticipates future requirements.

    As I have mentioned elsewhere, some trees can change their genetic signatures during their lifetime in such a way that the top of the tree has a different genetic signature than the bottom. Neither natural selection nor random mutations are necessary or useful.

  34. 34
    Moose Dr says:

    RVB, “The requirements of OOL, are chemicals and energy. What in the world is so difficult to grasp?”

    You certainly are well informed, aren’t you. ‘Tell you what, I’ll light a big bon fire. That should provide the energy. You provide the chemicals. Please produce a new life-form for me.

  35. 35
    rvb8 says:

    “I’ll light a big bonfire. That should provide the energy. You provide the chemicals. Please produce a new life-form for me.”

    Wow, the level of being ignorant in this statement is truly astounding. Steer clear of real science site Moose, you won’t like what you read.

    I believe there was an icon of Design, a Christian engineer whos name escapes who disproved evolution because life failed to appear in a jar of peanut butter he left standing for a period of time. Kirk Cameron and Ray comfort disproved evolution because they asked the truly egregious question, “where are all the Crocaducks?”

    Aquinas or one of the Church fathers gave advice to Christians not to argue (unless well prepared) with learned men, lest they bring Christianity into disrepute by showing its followers to be yokels.

  36. 36
    computerist says:

    Thanks Mung, I have skimmed over that paper and it seems that their understanding of slot machines in general must be flawed if they’re using it to support their position.

    The fact is that the model they present in the paper doesn’t work for the simple reason we already know that mutations override mutations.

    Last I recall slot machines have a theoretical “overtime” payback percentage on average around 90%, but if that was the case then casinos wouldn’t make as much money as they do, this is because partial wins are quickly overridden by subsequent losses, ensuring that input > output throughout the process. Natural selection (in this case the individual playing the slot machine and making the decision if they want to continue playing or not) cannot preserve what it doesn’t have (in this case money) and what it can quickly lose if it does have it.

    And obviously we cannot really use the literal jackpot analogy as that would be analogous to obtaining a complex protein in a single random shot or winning the lottery (of course many combinations do not map evenly since virtual reels increase the odds “behind the scenes” of a certain “higher” combination from appearing)

    Natural selection cannot preserve what it doesn’t have and can quickly lose if it does have it.

  37. 37
    Moose Dr says:

    RVB, “I believe there was an icon of Design, a Christian engineer whos (sic) name escapes who disproved evolution because life failed to appear in a jar of peanut butter he left standing for a period of time.”

    Um, his name is Louis Pasteur. ‘Might of heard of that religious whack-a-doodle. His experiment is still running.

    Please site me the science experiment in the annals of “Science Fair” projects, or any other source for that matter, where you mix chemicals together, add energy and get life.

  38. 38
    rvb8 says:

    What’s a ‘whack-a-doodle’? Mildly insane?

    Well the peanut-butter produced nothing, except a tasty spread and so proved nothing, Pasteur grew germs, and proved ‘Germ Theory’, but don’t worry it’s just a theory. Yes, religion was important throughout Pasteur’s life, and….?

  39. 39
    keith s says:

    rvb8:

    I believe there was an icon of Design, a Christian engineer whos name escapes who disproved evolution because life failed to appear in a jar of peanut butter he left standing for a period of time.

    His name is Chuck Missler, and he is indeed a “religious whack-a-doodle”, as Moose Dr puts it.

    Peanut Butter, the Atheist’s Nightmare

  40. 40
    Moose Dr says:

    Sorry for the spelling error, see: http://www.urbandictionary.com.....ackadoodle

  41. 41
    Moose Dr says:

    Keith S, please help me and rvb8 out. Please show us an experimental setup that produces life from non-life.

  42. 42
    keith s says:

    Moose Dr:

    Keith S, please help me and rvb8 out. Please show us an experimental setup that produces life from non-life.

    Moose Dr,

    Please wash and wax my car. And while you’re out, could you pick up some of that Australian-style yogurt? Lemon and blueberry.

  43. 43
    humbled says:

    “The requirements of OOL, are chemicals and energy.” Just like that huh Rvb8? So simple. Pity we can’t demonstrate it. Miller/Urey tried and failed.

    So we have a field of research, called ool, based on assumptions that we have never witnessed nor have we been able to duplicate/verify. This passes as science these days does it?

    I’m curious as well to hear how energy and chemicals, along with the laws of physics etc originated and organised itself into a fine tuned system allowing the conditions for life to exist in the first place?

    Sounds like materialistic nonsense and secular fairy tales. You folks are still pushing spontaneous generation.

  44. 44
    Silver Asiatic says:

    “The requirements of OOL, are chemicals and energy.” Just like that huh Rvb8? So simple.

    LOL. Chemicals and energy, then you have life. What is so difficult to understand?

    So we have a field of research, called ool, based on assumptions that we have never witnessed nor have we been able to duplicate/verify. This passes as science these days does it?

    Exactly. And if you doubt the speculations based on imaginary evidence, then you supposedly know nothing about “real science”.

  45. 45
    Zachriel says:

    computerist: If I play at the slot machine, anything I win will likely be put back into the machine as long as I continue playing it (overtime) as the odds are stacked against me given the nature of the algorithm.

    On the other hand, if you play draw poker with multiple draws, you’ll probably end up with a better hand than you started with.

    computerist: Are the odds not constantly against beneficial mutations from occurring?

    Beneficial mutations are relatively rare, but evolution means you get to keep you current hand and wait for the beneficial mutation.

    Moose Dr: There’s insertions, deletions, inversions, etc. You are saying that there is a mutational type called a recombination?

    Yes, and it occurs in both diploid and haploid organisms.
    http://en.wikipedia.org/wiki/Genetic_recombination

    Mapou: I realize that I am in the minority but, IMO, OOL and evolution are not separate topics for the same reason that ID and designer are not separate topics.

    It’s certainly something biologists are very interested in, however, evolutionary theory is self-supporting just as a theory of planetary motion doesn’t require explaining the origin of planets. There may be a period between the biotic and abiotic realms, a parabiotic period, but this is just conjecture.

    Mapou: You must also have a viable reproductive capability and a gene repair mechanism to conserve the vast majority of the genome.

    RNA replication doesn’t seem to need a repair mechanism, and it is posited to have preceded the DNA world.

    Mapou: In addition, complex organisms must also have an adaptive mechanism based on epigenetics.

    Epigenetics is just an expression of phenotype.

  46. 46
    Joe says:

    It’s certainly something biologists are very interested in, however, evolutionary theory is self-supporting …

    BWAAAAAAAAHAHAHAHAHAHAHAHAHAHAHAHAHAHA. Please link to this alleged evolutionary theory so we can see how self-supporting it is.

    AGAIN how life originated directly impacts how it evolved. It is only if blind watchmaker-type processes produced living organisms would we infer they are solely responsible for its diversity. On the other hand if living organisms were intelligently designed then we would infer that the bulk of the evolution is also via intelligent design- as in organisms were intelligently designewd to evolve and evolved by intelligent design (for example via Spetner’s “built-in responses to environmental cues). That evos continue to ignore that fact exposes their desperation.

    RNA replication doesn’t seem to need a repair mechanism,

    RNA replication appears to need an intelligent designer

  47. 47
    Joe says:

    rvb8:

    OOL and Evolution are separate topics. The requirements of evolution are random mutations, followed by the the sifting process known as natural selection, and aided by sexual selection and perhaps gene transfer. The requirements of OOL, are chemicals and energy. What in the world is so difficult to grasp?

    It is only if blind watchmaker-type processes produced living organisms would we say that they also produced its diversity. On the other hand if living organisms were intelligently designed then we would infer that the bulk of the evolution is also via intelligent design- as in organisms were intelligently designed to evolve and evolved by intelligent design (for example via Spetner’s “built-in responses to environmental cues).

    Why is that so difficult to understand?

    That said, both genetic and evolutionary algorithms are perfect examples of intelligent design evolution/ evolution by intelligent design. No one knows how to model unguided evolution.

    And yes, Intelligent Design implies there was an Intelligent Designer but we get to the Intelligent Design by first detecting and then studying the intelligent design and all relevant evidence.

  48. 48
    Dionisio says:

    Interesting comments on related subject:
    http://www.reasons.org/article.....-believing

  49. 49
    Moose Dr says:

    Zachriel, “Yes, and it occurs in both diploid and haploid organisms.”

    Interesting. Now, you draw the analogy to syllables in English. If I were to write a program that recombined syllables in English to search for new words, I would start with a sense of what a syllable was, and would recombine on the syllable boundary. If, on the other hand I just recombined English words with random length/offset, I would likely not recombine on the syllable boundary. How does recombination work. Does recombination have a sense of motif boundaries, or is it just recombining random chunks here and there?

  50. 50
    Moose Dr says:

    RVB8, Please take note of Keith S’s snide comment (42). Remember, Keith S is on your team. He’s well more knowledgeable than you. He can’t point to an experimental setup that produces life. Whether such an experiment will ever be found is a question, but such has not been found yet. In any case, your “energy + chemicals = life” formula is a bit faulty.

  51. 51
    Zachriel says:

    Moose Dr: If, on the other hand I just recombined English words with random length/offset, I would likely not recombine on the syllable boundary. How does recombination work.

    Compared to randomization, word evolution is much, much faster when recombining bits and pieces of existing words whether or not you splice on syllable boundaries. That’s because the same basic structures are used over and over again. English language words are not distributed evenly through sequence space, and it appears that they are largely connected by single steps of mutation or recombination.

    Moose Dr: Does recombination have a sense of motif boundaries, or is it just recombining random chunks here and there?

    There are many different ways to recombine. Most recombination is homologous, such as sexual recombination. Exons, which usually code for specific protein structures, can be shuffled over the course of evolution. Breaks can occur anywhere, and when combined with various types of mutation, can recombine at any point.

  52. 52
    Moose Dr says:

    Zachriel, thanks for the response. I always viewed recombination in the context of sexual reproduction. I think that there is a certain algorithmic recombination that goes on during sexual reproduction. Am I correct in that? (No, I don’t consider this an evolution killer. Organisms have all sorts of what I would call algorithmic activity.)

    It seems to me that random recombination, while periodically potentially doing something useful, would mostly be really good at producing unsightly DNA. After all, it sounds like what happens when I shuffle a deck of cards.

    Oh, Zachriel, I recall looking at a program you wrote that uses the basic mutation types to produce English words. I thought it quite intriguing. However, I do see a major flaw in your algorithm. You seem to have a dictionary lookup technology that offers a “selection”, rejecting unacceptable mutations. It would seem fair, however, for there to also be a grammatical lookup. It would seem fair to me that if the new word sequence was devoid of grammatical logic, it should be rejected. Am I not correct?

    In truth, it would seem that mutations should only be selected if the resulting sentence provide, well, meaning. The latter, however, is something I don’t know how to automate, making it a difficult requirement for your program.

    Do you believe that your program will get very far if every new word had to pass the “grammatically correct” test?

  53. 53
    Zachriel says:

    Moose Dr: However, I do see a major flaw in your algorithm. You seem to have a dictionary lookup technology that offers a “selection”, rejecting unacceptable mutations.

    Not unacceptable mutations, but mutants that don’t form words. That’s rather the whole point. They die. Most mutants die.

    Moose Dr: It would seem fair to me that if the new word sequence was devoid of grammatical logic, it should be rejected.

    Grammar is a property of the relationship between words.

    Moose Dr: It would seem fair, however, for there to also be a grammatical lookup.

    Been there, done that. Added iambic rhythm and alliteration, the result was the same. Evolution can easily traverse the landscape.

    Moose Dr: it would seem that mutations should only be selected if the resulting sentence provide, well, meaning.

    If you mean mutants, then sure. For starters, words found in the dictionary always have meanings.

    Moose Dr: The latter, however, is something I don’t know how to automate, making it a difficult requirement for your program.

    Imagine a dictionary of every valid phrase in English. If we use a subset of that dictionary, we are actually making the problem even more difficult because we would be rejecting many valid phrases and sentences. So to make the problem reasonable, we use a subset. Again, an evolutionary algorithm easily traverses the landscape.

  54. 54
    Moose Dr says:

    Interesting. Where can I observe your program at work, making coherent sentences at each mutational step?

  55. 55
    Zachriel says:

    Moose Dr: Where can I observe your program at work, making coherent sentences at each mutational step?

    Phrases, not necessarily sentences. The software is rather decrepit so we won’t vouch for it. You might start with Word Mutagenation to see how it works.
    http://www.zachriel.com/mutagenation/

  56. 56
    Moose Dr says:

    Thanks, Zachriel, I’ve downloaded all three zips, but am unable to look at them right now as the business of Christmas, and an extended vacation is upon me.

  57. 57
    rvb8 says:

    Moose, ” take note of keiths’ snide comment.. he’s well more knowledgeable than you.” (Is this a snide comment?) I’m sure he is, you may even be, on certain topics, however a working theory is something you don’t have.

    OOL and the corollary RM+NS=Ev is a working theory. Certainly life hasn’t been artificially produced but betting against it is, as the fields progress, foolish (despite anger that we as a species should be so presumptive). And this anger also shows a deep misunderstanding of evolved human nature; curiosity, which you by the way possess very little of.

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