Enzymes can’t evolve genuinely new functions by unguided means?

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December 5, 2014

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Ann Gauger of the Biologic Institute writes to say

Monday we published a paper in the journal BIO-Complexity that demonstrates that enzymes can’t evolve genuinely new functions by unguided means. We argue that design by a very sophisticated intelligent agent is the best explanation for their origin. I want to take some time to lay out our argument against evolution and for intelligent design. It’s important, because it reveals the logical fallacy in most evolutionary thinking. More.

Be grateful you live in a place where people are still permitted to lay out an argument against Darwin. Or magic.

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Comments

What's quite telling is the fact that Dr. Gauger applied in vitro mutagenesis and then selected those mutants that fit her purposes. Sounds somehow familiar but I just cannot remember the specific term. IIRC it started with "e" and ended with something like "volution". Didn't I see many statements here that if true would render her approach impossible (like "mutations are not random" etc.).sparc_{December 6, 2014
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Alicia Regard's thinking; "..well if evolution can't do it.. then aliens could... which is ok, if you have an explanation how aliens have come about... well... blind, and specifically guided faith can do it... It is called in my area: The Larry Moran Slip; If you don't have proof that gods did it... evolution must have done... somehow... even it doesn't make sense...Quest_{December 6, 2014
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Alicia Renard:
"So I’m correct in saying that ID makes no alternative proposal to the observed facts ... I mean, nobody is under the false impression that ID proposes an alternative to Darwinian evolution, do they?"
ID is currently a 'hypothesis' within the current ToE, which sits with equal efficacy along side the hypothesis of natural causation. Neither are empirically confirmable at this time. But in answer to the question of proposed ID methodologies, there are many, from supernatural intervention, to 'set-up' intelligent mechanisms, to intervention by genetic modifications. Pre-Cambrian may have involved more, but I have proposed some post-Cambrian methods, which I have summarized on several posts. From a recent post: "We are on the cusp of being able to alter phenotypic outcomes, by PCR, electrophoresis, and subsequent spicing to alter structures and codes. For our progress at this point, search 'genetic engineering'. While not proof of prior gene altering to alter phenotypes, it is at least evidence that it can be done, while at this juncture, no substantiating evidence exists for random mutations and horizontal gene transfer to alter phenotypes." This from my comment #3 of 15 comments on this newspaper blog. http://www.charlestoncitypaper.com/TheBattery/archives/2014/06/19/sally-atwater-clarifies-her-stances-on-sex-ed-evolutionleebowman_{December 6, 2014
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JDH: I will admit it does not depend on “simple” induction, yet it still comes from induction. We were discussing so-called negative predictions. As we pointed out, the Second Law was originally formulated as a response to widespread experimentation that showed limits to efficiency. In other words, scientists had explored the universe of normal mechanical interactions, and in response formulated the law. This was given a stronger basis through statistical mechanics. JDH: We see some behavior, we make laws which describe the behavior and assume by faith that the universe is a rational place and the laws will not all of the sudden vary from day to day. Or just assume, as one might the parallel postulate.Zachriel_{December 6, 2014
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Zachriel, You said,
Since then, it has been reformulated in statistical terms so it no longer depends on simple induction.
I will admit it does not depend on "simple" induction, yet it still comes from induction. All scientific laws depend on induction whether they are derived from macroscopic principles or micro statistics. We see some behavior, we make laws which describe the behavior and assume by faith that the universe is a rational place and the laws will not all of the sudden vary from day to day. Promotion of scientific observation to law is a statement of faith. The materialist who has rejected God as creator has no reasonable expectation that things will continue behaving as they currently do except by induction. All elevation of physical observations to the state of physical law are a statement of faith and involve a metaphysical assumption which can not be proven. At least I have a scientific/societal basis for my assumption of God as creator. By His resurrection, Jesus Christ demonstrated that He was God and gave evidence to eye witnesses of this. Your assumptions of materialism have no such basis and in their consequence necessarily lead to such unwarranted assumptions as a miraculous unexplainable origin of life, and a multitude of undetectable universes. I simply rationally believe that my metaphysical choice makes more sense.JDH_{December 6, 2014
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Alicia, @18 Very curious why you would peg me as YEC. I believe that YEC is a possible interpretation of Genesis 1, but by no means do I think that it is a necessary interpretation of Genesis 1. The major take aways I get from Genesis 1 and the rest of the Bible regarding the creation of the heavens and the earth and life is. 1. God did it. 2. It was a process that took some amount of time and not an instantaneous one. 3. The timing and sequence was directed by God. 4. It would not have happened except for God's intervention on each epoch (Day). 5. Creation of man was a unique and distinct event. 6. God has made it so obvious that His intervention was necessary at each stage that the only rational belief is God did it. I fully believe that those who refuse to believe in the creation by God are closing their eyes to the truth. I apologize for being so blunt, but I just can not understand how any materialistic explanation for the explanation of earth and life is plausible. I know others disagree with this position. I just do not see it at all.JDH_{December 6, 2014
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"Battleships are not Natural". Not Supernatural either. I guess we consider them Unnatural? How about a hydroelectric dam? A condo complex? Unnatural, not part of Nature? Beaver dam, ant colony - are those considered natural? Is it only sapien that can rise above Nature? Or maybe that battleship and it's design are 100% natural? Just arrangements of atoms and molecules emerging from Mother Earth? I'll go with man is special. Can rise above Nature. One Man even did the Supernatural Thing. Son of man.ppolish_{December 6, 2014
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William J Murray: I would assume by using the materials available, employing and accounting for natural forces and tendencies the same way a designer of a car instantiates his design. Your description is too general to have entailments. Here's a partial answer for cars: http://static.guim.co.uk/sys-images/Guardian/Pix/pictures/2013/2/19/1361280361621/Car-factory-008.jpg We can provide additional details; from the original planning to the final paint job; if you like. Box: So I take it then that you don’t fancy the second law of thermodynamics. The Second Law was original devised as a generalization from a vast number of experiments, and as a limit. Since then, it has been reformulated in statistical terms so it no longer depends on simple induction. In addition, there is evidence that argues against the claimed limit for enzyme evolution. We have phylogenetic evidence, and we have direct evidence. See Schultes & Bartel, One Sequence, Two Ribozymes: Implications for the Emergence of New Ribozyme Folds, Science 2000. Enzymes can be promiscuous, and a secondary function can evolve alongside the primary function.Zachriel_{December 6, 2014
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Alicia Renard said:
But the paper cited by Zachriel shows that prediction to be wrong.
What paper cited by Zachriel?
The problem appears to be that you are equivocating with the meaning of common words.
No, the problem lies in your stubborn refusal to educate yourself in even the most basic aspects of ID theory even when you are repeatedly directed to a resource created for that very purpose. ID makes no case about anything "supernatural". It is a theory about distinguishing between naturally occurring and artificially produced patterns.
So “intelligent design” methods can confirm that battleships are constructed by people. Well, I guess that’s progress of a sort.
It would be progress if an anti-ID advocate could possibly admit that "Intelligent Design" is a term used to describe the capacity of humans to generate patterns/instantiations of matter that could not be accomplished if you took away their intelligence and their capacity to teleologically design instantiations of matter that do not exist at the time of design. There are lots of capacities of humans that have zero bearing on whether or not a battleship can be designed and built. Most of the physical features we share with other animals are useless in generating such an artifact; so it is reasonable to identify with terminology the capacity that makes battleship design and instantiation a plausibility. It is also entirely reasonable to consider that such a capacity might exist in other, non-human entities. Scientists have been exploring the possible intelligence of non-human animals for a long time using various pattern-recognizing and producing schemes, largely involving tool-creation and language use.William J Murray_{December 6, 2014
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Box writes:
For one ID predicts that enzymes can’t evolve genuinely new functions by unguided means.
But the paper cited by Zachriel shows that prediction to be wrong.Alicia Renard_{December 6, 2014
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WJM writes:
Again, are you being purposefully dense? All intelligent designers that we know of “work through natural means”, if by that you mean that we instantiate our designs in the world in a way that accounts for and employs natural laws and tendencies. What is “not natural” about the process is the artificial nature of the design process. Artifice vs natural/random.
The problem appears to be that you are equivocating with the meaning of common words. Natural can be an antonym to artificial. Typically it is used to make some false distinction such as sea salt being natural and refined rock salt being artificial. I'll grant you that it has some value when examining the quality of yoghourt. If you are using natural as an antonym to supernatural then there is no distinction to be made between designed and natural, as an artificial or constructed object is still natural in this sense. And any curious person, presented with an unfamiliar object might wonder what it is for and who or what made it.
A battleship is not instantiated into the world via magic; however, natural forces cannot account for it’s existence. One requires artifice as part of the causal explanation.
So "intelligent design" methods can confirm that battleships are constructed by people. Well, I guess that's progress of a sort. :)Alicia Renard_{December 6, 2014
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What a hoot! Upthread, the Darwin-faithful ask for a roll call on who believes in common descent or not, as if it were a philosophical position or an article of faith! LOL.dgw_{December 6, 2014
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Zachriel: A good hypothesis will make specific predictions, not general can never happen predictions.
So I take it then that you don't fancy the second law of thermodynamics.Box_{December 6, 2014
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Zachriel asks
So how did the designer of life instantiate their design?
I would assume by using the materials available, employing and accounting for natural forces and tendencies the same way a designer of a car instantiates his design.William J Murray_{December 6, 2014
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Box: one ID predicts that enzymes can’t evolve genuinely new functions by unguided means. Did you even read the OP? A good hypothesis will make specific predictions, not general can never happen predictions (unless we can explore the entire universe of possibilities). Unfortunately, that's a negative claim that's very difficult to show directly. In any case, phylogeny strongly implies that they do. And we also have experimental evidence that they do. Box: Are you being purposefully dense? ID is about detecting design. Then it's not a theory as suggested by William J Murray above.Zachriel_{December 6, 2014
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A good theory makes predictions.
Unguided evolution doesn't make any predictions
A great theory, such as Darwin’s Theory of Evolution, spawns entire new fields of study.
And yet there aren't any fields studying unguided evolution. Darwin's concept has proven to be useless.
Your proposed theory should entail empirical predictions, especially those that distinguish the theory from competing theories.
And we have told you what they are wrt ID. Your willful ignorance means nothing here.Joe_{December 6, 2014
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Zachriel: Your proposed theory should entail empirical predictions, especially those that distinguish the theory from competing theories.
For one ID predicts that enzymes can’t evolve genuinely new functions by unguided means. Did you even read the OP?
Zachriel: So how did the designer of life instantiate their design?
Are you being purposefully dense? ID is about detecting design.Box_{December 6, 2014
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Alicia- there isn't any evolutionary theoryJoe_{December 6, 2014
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William J Murray: All scientific theories must account for the observed facts. A good theory makes predictions. A great theory, such as Darwin's Theory of Evolution, spawns entire new fields of study. Your proposed theory should entail empirical predictions, especially those that distinguish the theory from competing theories. William J Murray: All intelligent designers that we know of “work through natural means” So how did the designer of life instantiate their design?Zachriel_{December 6, 2014
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Alicia Renard said:
Well that is very clear. So I’m correct in saying that ID makes no alternative proposal to the observed facts.
I'm not sure what this even means. Observed facts are observed facts. All scientific theories must account for the observed facts.
It merely questions the adequacy of evolutionary theory.
Are you doing this deliberately now? I've corrected you several times. It questions the adequacy of unguided evolutionary theory. ID suggests an additional causal agency which unguided evolutionary theory doesn't permit to account for observed facts which, ID argues, require intelligent guidance.
I’ll stop asking whether ID has a theory or hypothesis now, shall I? I mean, nobody is under the false impression that ID proposes an alternative to Darwinian evolution, do they? The BioLogos position is quite clear. Observed facts are not in question and the creator works through natural means. I don’t understand why OEC folk who don’t like the “unguided” element don’t just work with them.
Again, are you being purposefully dense? All intelligent designers that we know of "work through natural means", if by that you mean that we instantiate our designs in the world in a way that accounts for and employs natural laws and tendencies. What is "not natural" about the process is the artificial nature of the design process. Artifice vs natural/random. A battleship is not instantiated into the world via magic; however, natural forces cannot account for it's existence. One requires artifice as part of the causal explanation.William J Murray_{December 6, 2014
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WJM writes:
We are not arguing “evolutionary theory” vs something else, but rather guided vs unguided evolutionary processes.
Well that is very clear. So I'm correct in saying that ID makes no alternative proposal to the observed facts. It merely questions the adequacy of evolutionary theory. I'll stop asking whether ID has a theory or hypothesis now, shall I? I mean, nobody is under the false impression that ID proposes an alternative to Darwinian evolution, do they? The BioLogos position is quite clear. Observed facts are not in question and the creator works through natural means. I don't understand why OEC folk who don't like the "unguided" element don't just work with them.
Whether or not there is common descent is irrelevant to that argument...
It's beside the point if one is either agreeing or disagreeing with Mike Behe because the facts of common descent are not in dispute. ETA correct garbled grammar!Alicia Renard_{December 6, 2014
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Alicia Renard said:
I see WJM, Axel, Joe all make the same broad claim; that ID proposes some kind of alternative scenario to evolutionary theory. And that would be?
You keep saying "evolutionary theory" even though you have been corrected over and over. ID proposes that instead of unguided evolutionary processes, an intelligently designed/guided process is a better fit to to the evidence. We are not arguing "evolutionary theory" vs something else, but rather guided vs unguided evolutionary processes. Whether or not there is common descent is irrelevant to that argument - information which is covered in the faq I've referred you to several times now. https://uncommondescent.com/faq/William J Murray_{December 6, 2014
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OK. I see WJM, Axel, Joe all make the same broad claim; that ID proposes some kind of alternative scenario to evolutionary theory. And that would be?Alicia Renard_{December 6, 2014
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Is there a place where people- scientists included- can actually support unguided evolution with actual evidence and experimentation? Is there a place where people- scientists included- can produce details, entailments and hypotheses for unguided evolution? Such a place doesn't exist on our planet...Joe_{December 6, 2014
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Alicia Renard:
The difference would be that ID proposes no details; no entailments, no alternative hypothesis.
LoL! Please tell us what details, entailments and hypotheses are for unguided/ blind watchmaker evolution. I have already provided YOU with the entailments and hypothesis for ID. That means you are lying.
Are you saying you don’t dispute the observed pattern of common descent
What observed pattern? BTW Axe has rebutted Hunt- to his face even- go figure.Joe_{December 6, 2014
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' The difference would be that ID proposes no details; no entailments, no alternative hypothesis. 'ID proposes such things; this has been pointed out to you repeatedly. Ignoring it and insisting on repeating this talking point as if it hasn’t been addressed doesn’t move the debate forward.' Shame on you, Alicia! Wilful, selective blindness is worse than mental deficiency.Axel_{December 6, 2014
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Alicia Renard, you would be wrong in your suspicion of me being a YEC. I have always been an old earth creationist. I reject the 'pattern' of common descent simply because there is no 'pattern' for it. The Cambrian Explosion by itself turns Darwin's tree of life upside-down. The fossil record after the Cambrian Explosion is also infamous for being a record of 'top down' sudden appearance and stasis. ,,, And besides Neo-Darwinists having a grossly inadequate mechanism in random variation and selection, the genetic evidence is far more problematic than you seem to realize. Cladistics is joke of a 'science' that assumes into its premises the very conclusion of common descent that it is trying to prove. As for an 'alternative hypothesis', The 'hypothesis' given to us from the evidence itself is as such: A. L. Hughes's New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago - Wolf-Ekkehard Lönnig - December 2011 Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species' particular environment....By mutative reduction of the genetic potential, modifications became "heritable". -- As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The "remainder" has been lost by mutations (accumulation of slightly disadvantageous alleles) -- in the formation of secondary species. http://www.evolutionnews.org/2011/12/a_l_hughess_new053881.htmlbornagain77_{December 6, 2014
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Alicia Renard said:
The difference would be that ID proposes no details; no entailments, no alternative hypothesis.
ID proposes such things; this has been pointed out to you repeatedly. Ignoring it and insisting on repeating this talking point as if it hasn't been addressed doesn't move the debate forward.
Behe’s IC and Dembski’s CSI only purportedly demonstrate inadequacies or impossibilities in evolutionary theory. No alternative scientific explanations are offered.
The scientific theory of ID is offered. ID doesn't just point out the weakness of a presumed unguided evolutionary process, but also reaches an inference to best known explanation for the particular kinds of features in question: intelligent design.
That’s not any clearer. Are you saying you don’t dispute the observed pattern of common descent and the time-span over which it has occurred?
Since it is irrelevant to me and any arguments I engage in, I have no reason to either dispute or promote it.
It’s not irrelevant to Behe, Axe or Gauger, apparently, or why would they be arguing that evolutionary mechanism fail to account adequately for common descent.
I'm not Behe, Axe or Gauger.
Common descent is certainly irrelevant if you reject the observation of common descent as evidenced by phylogeny, molecular analyses and fossil evidence. Do you?
I don't reject or accept it. It's an irrelevant consideration for both my personal views and any arguments I engage in. I don't adopt beliefs or opinions about things that are entirely irrelevant to me.William J Murray_{December 6, 2014
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WJM writes:
I guess the same can be said for materialists; what difference do the details make if you reject the idea of ID out of hand?
The difference would be that ID proposes no details; no entailments, no alternative hypothesis. Behe's IC and Dembski's CSI only purportedly demonstrate inadequacies or impossibilities in evolutionary theory. No alternative scientific explanations are offered.
I question whether the theoretical capacity of supposedly unguided evolutionary mechanisms (1) have been shown by Darwinists to be sufficient, and (2) can be shown to be sufficient even in principle.
That's not any clearer. Are you saying you don't dispute the observed pattern of common descent and the time-span over which it has occurred?
Common descent is an entirely irrelevant consideration as far as I’m concerned.
It's not irrelevant to Behe, Axe or Gauger, apparently, or why would they be arguing that evolutionary mechanism fail to account adequately for common descent. Common descent is certainly irrelevant if you reject the observation of common descent as evidenced by phylogeny, molecular analyses and fossil evidence. Do you?Alicia Renard_{December 6, 2014
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AR: Passed by for a moment on a Windows 8.1 behaviour test (let's hope Win X fixes the mess . . . ). Please, recalibrate your estimator; e.g. BA77 is famously not YEC, and in fact YEC does not seem to be a significant view here at UD, apart from SalC in some moods and Paul Nelson. It may help clarify your perspective to appreciate that the cosmological fine tuning side of ID has spent a fair bit of effort looking at fine tuning and a big bang cosmology that tends to point to an age on the observed cosmos of c 14 BY for several decades. (IIRC, ICR's Russell Humphreys some years back had an idea of a time freeze effect that sets a 15 KY earth in a 15 BY cosmos, but I have not followed up on that beyond noticing it as a curiosity and not seeing onward signs.) KF PS: Win 8.1 seems to be a bit better behaved this morning.kairosfocus_{December 6, 2014
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