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New mechanism of evolution — POOF

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Each species has large numbers of unique genes that seem to have magically arisen without any ancestor. Evolutionists are saying they essentially POOFed into existence. These genes are referred to as ORFans or orphan genes. From the Max Plank Institute:

However, with the advent of sequencing of full genomes, it became clear that approximately 20–40% of the identified genes could not be associated with a gene family that was known before. Such genes were originally called ‘orphan’ genes
Evolutionary Origin of Orphan Genes

20-40% of the genes discovered cannot be explained by common ancestry or common descent. So what mechanism is left to explain it? Special creation? But evolutionists can’t accept special creation, so they just pretend they’ve made a discovery of a new mechanism of evolution that can work just as well. They haven’t given it a name yet, so let us call it POOF. What is POOF? POOF is the mechanism by which proteins can easily arise out random nucleotide sequences like a poem can emerge out of randomly tossed scrabble letters. I bold one of their euphemisms for the POOF mechanism in the following paragraph:

Orphan genes may have played key roles in generating lineage specific adaptations and could be a continuous source of evolutionary novelties. Their existence suggests that functional ribonucleic acids (RNAs) and proteins can relatively easily arise out of random nucleotide sequences, although these processes still need to be experimentally explored.

😯

The reasoning they use goes like this, “we have all these genes that can’t be explained by slight successive modifications, so they must have arisen spontaneously out of nowhere. Because evolution is fact, this implies evolution can just take random material and create functional systems in a flash. We’ve made a fabulous discovery about the miracles of evolution even though we can’t demonstrate it experimentally.”

Experiments actually refute such assertions, but that won’t stop evolutionists from promoting demonstrably false ideas as some new discovery! And it’s not only the genes but the regulatory mechanisms that poof into existence:

On the other hand, there is now little doubt that new genes have arisen throughout the phylogenetic history and the general model of de novo evolution of genes appears to be well supported by now. However, this also raises several new questions. The foremost one is the question of how new promotors with a defined regulation can arise.

“de novo evolution of genes” is also another euphemism for the POOF mechanism.

But it’s not just the genes and regulatory regions, but also developmental mechanisms that deploy these novelties to create radical new species (like multicellular ones from single cellular ones).

gene lists can be associated with major evolutionary steps, such as the origin of germ layers, or the origin of multicellularity . Interestingly, this approach showed also that younger genes tend to be increasingly more developmentally regulated compared with evolutionary older genes

Not only do the orphan genes emerge, they emerge with the most infrastructure to integrate them into the POOFED species. So genes, proteins, and developmental mechanisms, and new species also POOFED into existence. They sound almost like closet creationists!

The evolutionists conclude, evolution can do far more than we ever supposed because evolution can POOF thousands of genes and regulatory mechanisms into sudden existence rather than through slight successive modifications of an ancestor. What a wonderful discovery. 🙄

NOTES

1. Behe, who accepts common descent, is said to have jokingly used the phrase, “puff of smoke” to describe the mechanism that can create irreducible complexity. In internet debates, the phrase got converted to “POOF” to emphasize the magical character of the mechanism. It seems now, evolutionary biologists are seriously resorting to Behe’s POOF mechanism whether they want to admit it or not.

How did Behe arrived at the POOF mechanism which evolutionary biologists are now only discovering?

I lectured at Hillsdale College as part of a week-long lecture series on the intelligent design debate. After Michael Behe’s lecture, some of us pressed him to explain exactly how the intelligent designer created the various “irreducibly complex” mechanisms that cannot–according to Behe–be explained as products of evolution by natural selection. He repeatedly refused to answer. But after a long night of drinking, he finally answered: “A puff of smoke!”

Larry Arnhart
http://darwinianconservatism.blogspot.com/2006/09/has-anyone-seen-evolution.html

2. Orphan genes have made the Irreducible Complexity argument that much stronger.

Comments
Dr. Axe challenges a Darwinist to create a single new gene by Darwinian processes: Show Me: A Challenge for Martin Poenie - Douglas Axe August 16, 2013 Excerpt: Poenie want to be free to appeal to evolutionary processes for explaining past events without shouldering any responsibility for demonstrating that these processes actually work in the present. That clearly isn't valid. Unless we want to rewrite the rules of science, we have to assume that what doesn't work didn't work. It isn't valid to think that evolution did create new enzymes if it hasn't been demonstrated that it can create new enzymes. And if Poenie really thinks this has been done, then I'd like to present him with an opportunity to prove it. He says, "Recombination can do all the things that Axe thinks are impossible." Can it really? Please show me, Martin! I'll send you a strain of E. coli that lacks the bioF gene, and you show me how recombination, or any other natural process operating in that strain, can create a new gene that does the job of bioF within a few billion years. http://www.evolutionnews.org/2013/08/a_challenge_for075611.htmlbornagain77
August 17, 2013
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Mr. Fox you state:
I especially like “exposed to evolutionary testing”!
And exactly what would this 'evolutionary testing' look like Mr. Fox? Would it be some type of environmental shift?
Here is a Completely Different Way of Doing Science - Cornelius Hunter PhD. - April 2012 Excerpt: But how then could evolution proceed if mutations were just neutral? The idea was that neutral mutations would accrue until finally an earthquake, comet, volcano or some such would cause a major environmental shift which suddenly could make use of all those neutral mutations. Suddenly, those old mutations went from goat-to-hero, providing just the designs that were needed to cope with the new environmental challenge. It was another example of the incredible serendipity that evolutionists call upon. Too good to be true? Not for evolutionists. The neutral theory became quite popular in the literature. The idea that mutations were not brimming with cool innovations but were mostly bad or at best neutral, for some, went from an anathema to orthodoxy. And the idea that those neutral mutations would later magically provide the needed innovations became another evolutionary just-so story, told with conviction as though it was a scientific finding. Another problem with the theory of neutral molecular evolution is that it made even more obvious the awkward question of where these genes came from in the first place. http://darwins-god.blogspot.com/2012/04/here-is-completely-different-way-of.html
Mr. Fox, if this is the type of imagined scenario you are envisioning, let me be the first to inform you that such imagined scenarios for 'evolutionary testing fall far short of scientific proof. Mr. Fox, but what would real, not imagined, 'evolutionary testing' really look like if random neo-Darwinian processes truly were looking for new proteins in sequence space???
Dr. Durston elaborates on how futile an evolutionary search is to find a single functional protein: Excerpt: From this, we can come up with a very rough estimate for the total number of stable, folding 3D sequences in 300 residue sequence space … roughly 10^74 sequences that will give stable 3D folds (this is very rough, but it will illustrate my point and help one see why scientists don’t search for novel stable 3D folds from a library of random sequences). One might think that 10^75 sequences is an enormous number, however, it is miniscule in comparison with 20^300, which is the total number of sequences in 300 –residue sequence space. This is why the theory that an evolutionary search, even if it involved all the planets in all the galaxies of the known universe, is utterly implausible. https://uncommondescent.com/biophysics/kirk-durston-a-common-either-or-mistake-both-darwinists-and-id-theorists-make/#comment-466489
Even using the atheists own overly optimistic number (one in a trillion) for finding functional proteins in sequence space revels the ludicrous nature of this imagined 'evolutionary testing' you are so smitten with Mr. Fox:
How Proteins Evolved - Cornelius Hunter - December 2010 Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function. http://darwins-god.blogspot.com/2010/12/how-proteins-evolved.html
Moreover, as if all of that was not bad enough for the notion of 'evolutionary testing', it is found that ribosomes are a stickler for protein fidelity that precludes any such 'evolutionary testing' scenario from being realistic:
The Ribosome: Perfectionist Protein-maker Trashes Errors Excerpt: The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist...the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products... To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is "shocking" and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis. http://www.sciencedaily.com/releases/2009/01/090107134529.htm
And exactly how is the evolution new life forms suppose to 'randomly' occur if it is prevented from 'randomly' occurring to the proteins in the first place? Moreover Mr. Fox, as if all that wasn't bad enough for your preferred Darwinian worldview, it is now found that many ORFans are deeply embedded in the genome and are not recent evolutionary add ons:
Age doesn’t matter: New genes are as essential as ancient ones – December 2010 Excerpt: “A new gene is as essential as any other gene; the importance of a gene is independent of its age,” said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. “New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked.” http://www.sciencedaily.com/releases/2010/12/101216142523.htm
This finding is particularly troublesome for your imagined 'evolutionary testing' scenario since ORFans deeply embedded in genomes presents its own unique set of insurmountable difficulties for Darwinists:
Darwin or Design? - Paul Nelson at Saddleback Church - Nov. 2012 - ontogenetic depth (excellent update) - video Text from one of the Saddleback slides: 1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determine what follows. 2. Thus, to change -- that is, to evolve -- any body plan, mutations expressed early in development must occur, be viable, and be stably transmitted to offspring. 3. But such early-acting mutations of global effect are those least likely to be tolerated by the embryo. Losses of structures are the only exception to this otherwise universal generalization about animal development and evolution. Many species will tolerate phenotypic losses if their local (environmental) circumstances are favorable. Hence island or cave fauna often lose (for instance) wings or eyes. http://www.saddleback.com/mc/m/7ece8/
Needless to say, none of this is good for your imagined 'evolutionary testing' conjecture that you have placed your ill-founded hope in Mr. Fox!bornagain77
August 17, 2013
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I especially like "exposed to evolutionary testing"! :)Alan Fox
August 17, 2013
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Oops
It appears that genomes harbour many transcripts in a transition stage from nonfunctional to functional genes, also known as protogenes, which are exposed to evolutionary testing and can become fixed when they turn out to be useful.
Alan Fox
August 17, 2013
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From the abstract:
It appears that genomes harbour many transcripts in a transition stage from non-functional to functional genes, also known as protogenes, which are exposed to evolutionary testing and can become ?xed when they turn out to be useful.
Just so!Alan Fox
August 17, 2013
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The simple point, however, is that functional proteins can never derive from non coding DNA by the neo darwinian mechanism of RV + NS. Design is the only reasonable explanation for such a transition.
Disagree with this assertion. When I am talking about a functional protein, I mean useful in some organism's biochemistry in some circumstances. Orphan genes as a source of variation that can be selected for seems a most elegant demonstration of the power and breadth of evolutionary processes.Alan Fox
August 17, 2013
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Ah mung, my little dissembler! *chuckles* Of course AVS is correct. He is making a specific point about paper "the Evolutionary Origin of Orphan Genes" linked in the OP. I was making a general point about how organisms stumble upon useful new proteins. In fact the paper supports this point most elegantly!Alan Fox
August 17, 2013
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Mung, no one is saying sequences randomly assemble out of thin air except your friend Alan here.
If "Alan" refers to this commenter, then you are mistaken on two counts. 1. I certainly don't think "sequences randomly assemble out of thin air" and I can't imagine that anything I have ever written would give that impression. 2. I leave that to the reader as an exercise in comprehension. ;)Alan Fox
August 17, 2013
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gpuccio asks:
I have been away for some time. What thread are you referring to?
This one!Alan Fox
August 17, 2013
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AVS: I am saying that when the paper refers to “de novo” generation of genes, it means they arise from noncoding stretches of DNA that are already there, but are not currently expressed as protein. Just to be simple, I believe that you are right and Alan is wrong. The only reasonable explanation for the emergence of new proteins, at present, is that they derive from non coding DNA. The simple point, however, is that functional proteins can never derive from non coding DNA by the neo darwinian mechanism of RV + NS. Design is the only reasonable explanation for such a transition.gpuccio
August 17, 2013
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Mark: There is an order in things. The first, fundamental problem is to identify when and where an irrefutable design implementation took place. That is exactly what ID is trying to do at present. Durston's work on protein families has identified many structures for which a reliable design inference can and should be made. Axe and Behe have done much to fix the level at which a design inference is necessary to explain the emergence of new protein structures. Meyer has recently debated in detail the Cambrian explosion as a very well localized example of design implementation. Identifying protein families or superfamilies as the basci unit of new design implementation will naturally give us a map of the inferable design activity in the course of natural history. Many aspects of the "how" depend critically on the growing understanding of the emergence of new proteins. At present, we still don't know if new proteins really emerge from non coding DNA, which would be a very reasonable assumption, or in other ways. If the non coding DNA hypothesis acquires support, a whole new scenario opens for detailed studies. ID is a much better framework for that than neo darwinism, which certainly cannot explain the transitions from random non functional sequences to ordered functional ones in cosmic times. If we don't discard the irrational dogma that those transitions had to happen by RV + NS, we will never understand what really happened and how. The deeper "how", IOWs, how some conscious being could manipulate matter and input information in it, is certainly open to future scientific approach and discussion, but I think that at present that would be mere philosophy, until we have greater details about the previous points. The same is true for the deeper "why", but obviously a lot of simpler "whys" are open to inquiry in an ID framework. For example, we can wonder why some protein family appears at some time in natural history, and try to explain or understand that in terms of its functional potentialities, instead of the old dogma of fitness advantage. Whatever you can say, it is obvious that the acceptance, even if only as operative hypothesis, of the ID framework can give science a whole new way of looking at facts and interpreting them, helping us to get rid of an old and wrong paradigm which leads nowhere.gpuccio
August 17, 2013
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AVS:
I am saying that when the paper refers to “de novo” generation of genes, it means they arise from noncoding stretches of DNA that are already there, but are not currently expressed as protein.
Yes, I understand that is what you were saying. Alan, otoh, assures us that's not the way evolution works. He claims that "Evolution takes functional proteins and tries minor variations.." He is contradicting you. He probably didn't bother to read your post or did not understand it. I was just trying to bring it to his attention. His statement that "It [evolution] does not randonmly assemble sequences from thin air" is a straw-man. You statement that "no one is saying sequences randomly assemble out of thin air except your friend Alan here" demonstrates that your reading comprehension is right up there with Alan's. Are we having fun yet? ...but they were there the whole time as noncoding sequences. No, they weren't. They arose from non-coding sequences, according to your source. They weren't just "always there" as noncoding sequences. Your claim is contradicted by your own source. Did you even bother to read it?
The de novo evolution of genes out of random sequences has become a realistic possibility and this develops into the major model for orphan gene evolution (Siepel, 2009; Bornberg-Bauer et al., 2010; Tautz and Domazet-Loso, 2011).
This model posits that a new gene starts from an initially spuriously transcribed genome region that acquires some additional mutations to convert the resulting ribonucleic acid (RNA) into a stable heritable transcript...
Sheesh. Note that the sequence is transcribed. So much for the objection raised by wd400 (or was it franklin), who also seems to have not bothered to read the paper.Mung
August 16, 2013
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Mung, no one is saying sequences randomly assemble out of thin air except your friend Alan here. I am saying that when the paper refers to “de novo” generation of genes, it means they arise from noncoding stretches of DNA that are already there, but are not currently expressed as protein. Scordova and Alan would obviously like you to think that scientists say these sequences are just “poofing” out of nowhere, but they were there the whole time as noncoding sequences. I suggest you start getting your science info from a reputable source (not here).AVS
August 16, 2013
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you haven’t learned a thing in four years.
Thank you.jerry
August 16, 2013
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jerry said,
I was more sarcastic back then. But some other things have not changed.
Ah, a blast from the past. You're right; you haven't learned a thing in four years.Daniel King
August 16, 2013
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AVS:
No, its not. They clearly state in the abstract that genes arising “de novo” means arising from non-coding DNA
Alan Fox:
Evolution takes functional proteins and tries minor variations. It does not randonmly assemble sequences from thin air.
Oh good grief. Can't you even read?Mung
August 16, 2013
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A comment directed at Mark Frank over 4 years ago on the nature and whereabouts of the designer: https://uncommondescent.com/intelligent-design/complex-specified-information-you-be-the-judge/#comment-305339 I was more sarcastic back then. But some other things have not changed.jerry
August 16, 2013
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'Can you point me to any place where they consider how, why or when the design was implemented?' You would probably have to be baptised and lead a devout life to learn that, Mark, and even then there would be no guarantee, since it would be at God's discretion. God would probably, however, say: 'How? Don't be presumptuous,' 'Why? ditto.' "When? I always reside in eternity, so can't help you there.' Your continuing incorrigibility will doom you to continue your Sisyphean task.Axel
August 16, 2013
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'.... but it is undeniably an area of continuing research with hypotheses and data subject to refutation and confirmation i.e. science. On the contrary it is only a slight variant of the much cited definition of madness: in this case, pursuing a blinkered approach to research on the basis of the groundless assumption of materialism, and expecting it to bear fruit. Arguably, even, in the circumstances, to 'poof fruit', if that's not overloading the ambiguous imagery. Admit it, Mark: You're into scientism in a big way, making an idol of a paradigm based on a spurious hypothesis, a priori considering it more scientific than ID. I just hope you are not employed in an area which owes nothing to quantum mechanics or biomimetics. Though the former is perhaps impossible today, biomimetics, with the reverse engineering it undertakes, has screamed intelligent design from the dawn of history to the unswerving conviction of the final, great scientific paradigm-changers', namely, the giants of maths and physics of the early-to-middle part of the last century. And that, without an inkling if what is currently known about the sublime engineering, scale and beauty of the simplest cell, for example. 'Self-organisation' needs an explanation for why chaos should produce order, the absolute converse of the Christian axiom, that it falls to us to create order out of chaos, in imitation of the creator. I believe I read earlier today some minuscule, half-baked example of order emerging from chaos, immediately 'shot down in flames' as to trivial to count.Axel
August 16, 2013
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Gpuccio #38
What do you think Behe, Axe, Durston and others are doing?
Pondering on the improbability of certain biological events happening according to evolutionary theory. Can point me to any place where they consider how, why or when the design was implemented?Mark Frank
August 16, 2013
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Alan Fox: I have been away for some time. What thread are you referring to?gpuccio
August 16, 2013
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Mark #38: What do you think Behe, Axe, Durston and others are doing? And believe me, they are scientists, whatever you may think. However, many possible developments of ID theory do depend on the general research in biology, whoever is doing it. Facts are facts. IMO, all good biological research is ID research. It is the duty of ID theorists to interpret facts from general research in the light of ID theory. That's what they do.gpuccio
August 16, 2013
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I started a philosophical discussion about the question of POOF mechanisms: https://uncommondescent.com/philosophy/if-poof-was-the-way-it-happened-how-could-you-infer-it-repeatability-vs-non-repeatability-naturalism-vs-supernaturalism/scordova
August 16, 2013
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An excellent example of one of the beliefs in the evolutionist's Statement of Faith.tjguy
August 16, 2013
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Naturalist use the poof concept all the time. They don't say the actual word "poof," they say "emerge." It means the same thing. Something just came into existence which we cannot explain. It poofs or it emerges. Same-same.jerry
August 16, 2013
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Did someome say POOF? Poof, the magic Mutant (to the tune "Puff the Magic Dragon") Poof the Magic Mutant, a-t-g-c And changed them just by randomness just to see what he could be. Little Richard Dawkins, loved that rascal Poof. And wrote him books to appease the kooks, oh what a silly goof! Oh Poof the Magic Mutant, a-t-g-c And changed them just by randomness just to see what he could be Poof the Magic Mutant, a-t-g-c And changed them just by randomness just to see what he could be Together they would mutate Poof into a beluga whale Richard kept a spectroscope trained on Poof’s mutating tail. Nobel things and atheists bowed whene’er they came Scientists would lower their flasks when Poof mutated a mane Oh Poof the Magic Mutant, a-t-g-c And changed them just by randomness just to see what he could be Poof the Magic Mutant, a-t-g-c And changed them just by randomness just to see what he could be Mutations can’t go on forever, just like little boys Antennaed wings and giant things doom nature’s mutant ploys One gray night it happened, natural selection said no more And Poof that Magic Mutant, mutated one last roar His head was bent in sorrow, his tears fell like rain Richard no longer went to write it gave him so much pain Without his life-long friend Dick could not be brave So Dick that evo-poofer sadly slipped in to his cave Oh Poof the Magic Mutant, a-t-g-c And changed them just by randomness just to see what he could be Poof the Magic Mutant, a-t-g-c And changed them just by randomness just to see what he could be (repeat chorus and fade...)Joe
August 16, 2013
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Mark Frank:
You think new genes are poofery. What about those that deny common descent?
What about those who accept it? They still have nothing but "poof"- well that is what developmental biology is saying anyway.Joe
August 16, 2013
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Mark Frank:
One way of characterising the difference between ID and evolutionary science ...
What evolutionary science? Not one evolutionary biologists knows what makes an organism what it is. Not one kbnows how many mutations it takes to get a functional multi-protein configuration. So what evolutionary science is Mark refering to?Joe
August 16, 2013
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Is this the first use of “poof” on UD? https://uncommondescent.com.....mment-3427
Whoa, how'd you find that! The phrase poof was used at ARN prior to UD. There was a discussion (at ARN I think) that the term got used as a term of derision against ID proponents and the term started being used more frequently against IDists because of Behe's "puff of smoke" comment.scordova
August 16, 2013
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One way of characterising the difference between ID and evolutionary science is that ID is happy to say the designer took care of the poofery end of story while scientists try to find explanations.
I totally respect that, but what if poof really was the way it happened? Seriously, this raises an interesting question, if an unrepeatable, unobservable poof was the way it happened, how could we scientifically lend credence to such a hypothesis. I'd argue, exactly the way ID proponents and especially creationists are going about the question, criticizing existing OOL and evolutionary mechanisms accepted today and any evolutionary mechanisms that might proposed in the future even in principle. The criticism follows these lines: 1. the problem of information via chemistry and physics alone 2. irreducible complexity 3. probability 4. population genetics 5. genetics, phenetics, cladistics, phylogenetic anomalies like orphans genes, novel body plans, etc. 6. criticism of the geological time scales I respect that reasonable people would like a observable repeatable mechanism, but what if an unrepeatable unobservable poof really was the way life came to be, how could we infer it? 1. the designer would have to make biology such that all evolutionary mechanism will fail as explanations (the biotic message) forcing only one conclusion 2. the mechanisms present and yet-to-be-proposed are demonstrated to actually fail based on data and theory I totally respect your position as I've shared the same concern myself. I listed lack of repeatability and observability as the #1 good reason for rejecting ID: https://uncommondescent.com/intelligent-design/good-and-bad-reasons-for-rejecting-id/ Evolutionary biologists really don't like what ID proponents and creationists are doing in trying to falsify evolutionary ideas, but that is exactly the correct scientific approach if one is defending a poof-type hypothesis. We saw a smaller scale of this in cosmology, and the POOF mechanism got a derogatory name that stuck, namely, "The Big Bang".scordova
August 16, 2013
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