Douglas Axe Responds to Larry Moran on Enzyme Conversion

_{Denyse O'Leary

October 23, 2012

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Over at the Biologic Institute blog, Douglas Axe responds to Larry Moran’s response to his work on the prohibitive difficulty of enzyme conversion. Dr. Axe notes,

If it can be shown that natural selection actually has (present tense) the creative capacity attributed to it, then I will certainly join those who are calling everyone to accept this. But if the facts go the other way, as it seems they have, then perhaps the reality check should likewise go the other way.

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I’m sick and tired of Larry Moran and his team of ignorant and blind disciples calling creationists IDiots… I usually enjoy just reading posts on both sides, but I have grown weary of his verbal abuse and name calling… Who does he think he is? I’m not a creationist, but hate when people abuse verbally others just because they believe in something they don’t, or they don’t agree with them… I’ve had enough!!! ThanksJohn Witton_{February 9, 2013
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@JoeCoder That's a pretty good point regarding protein sequence intermediates. I guess the easiest route to go would be to establish an "edge" for what Darwinian processes are capable of in terms of crossing non-functional or harmful sequence space. From there we would just have to search for the nearest functional sequence and see how isolated it is from the nearest functional protein. I know those supporting a Darwinian view will try to escape falsification by suggesting there may have been intermediates that don't exist anymore, but looking into how isolated proteins are from each other should be useful enough to draw some conclusions.Jeffrey Helix_{October 26, 2012
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No worries. I'm also guilty of running in guns-ablazin' sometimes and am trying to get better about it. Asking questions like this is actually part of my attempt. I think the KBL/BioF+ study is an excellent example of the difficulties of protein evolution. But I worry some in the ID camp are taking this study to mean these proteins could not have evolved from a common ancestor at all. This very well may be the case, but I don't see how the experiment proves this.JoeCoder_{October 25, 2012
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Sorry Joe. I must have gotten you mixed up with another Joe. I read the site a lot, but get confused with names sometimes. I didn't double check. Thanks for your gracious response.tjguy_{October 25, 2012
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You can’t convert one to the other by changing only one word at a time and still keeping them logically true.
This may be a bad example, since you can if you get creative enough. But I think my point still holds.JoeCoder_{October 24, 2012
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To clarify, I'm very much in the ID camp and have been for about 12 years now; I even reject common descent. But I like to ask these difficult questions to make sure we're fully considering them. Since I agree with everything else you posted, let's talk specifically on KBL to BioF+. Take these two sentences: 1. Wolves eat chickens. 2. Rabbits eat carrots. You can't convert one to the other by changing only one word at a time and still keeping them logically true. But suppose a third ancestral sentence: 3. Humans eat chickens. Now it's possible to convert this sentence to either sentence 1 or 2 by only substituting one word at a time, and keeping it logically true. Could this be the case with KBL and BioF? I understand that protein space is very sparse and mutations often cause proteins to lose their structural integrity before taking on a new form. But does the research by Axe and Gauger rule out the possibility of a third protein that doesn't lie between the structure of KBL and BioF? I don't think it does. In order to do this, wouldn't they have to find the distance to the nearest structurally viable proteins in every direction, not just the path between KBL and BioF?JoeCoder_{October 24, 2012
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@Joe Coder Joe, you asked
“how do we know there’s not some ancestral protein off to the side that could serve as an intermediate?”
Answer: Perhaps we don’t know, but you are not suggesting that all along the way there just happened to be a whole line of just right intermediate ancestral proteins off to the side that enabled the first molecule to change into a man over time are you? Why don’t we start with what we do know and go from there. We do know from every day experience that life always comes from life, that information always originates with a Sender, that design indicates purpose and the existence of a Designer, that software implies a Programmer, that machines point to purposeful engineering by an Inventor, that all things that have a beginning have a sufficient cause, etc. These are things we all observe and experience firsthand in life. That should count for something I would think. Do you know of any exceptions to these rules/principles of life? So now we come to the genome where there is a prohibitive expanse. Why place all your marbles on the possible yet very unlikely (in my opinion) existence of a line of just right ancestral proteins all the way along to enable evolution to occur instead of on what we actually do know and can verify? Why would BioF+ even turn into KBL if there is a closer intermediate from which it could evolve? It seems BioF+ is an unnecessary part of the equation. Even if some such ancestral protein did exist, how do we know that KBL evolved from BioF+ and not simply from that intermediate protein? But instead of taking a position based on what we do know, you choose to go against all these rules of life and hope for the existence of some such ancestral protein that could help with the prohibitive expanse problem. But this just puts the problem back one step doesn’t it? I mean, now you have two proteins to explain. Where did this ancestral protein come from? How is it that it was just the right intermediate for this transition to occur? How often did chance come up with just the right transitional ancestral protein to help cover these innumerable prohibitive expanses? At some point evolution has to account for novel genes, proteins, organs, and information. You can’t keep on appealing to something that may or may not have already existed as evidence to support your theory. Obviously, the more ad hoc explanations like this that you use to prop up your theory, the weaker your theory is. At what point does it finally crumble? In the end, we don’t know that this protein does not exist, but that certainly is not enough evidence to build a theory on. Isn’t it better, even more scientific, to start with what we do know as I referenced above and then modify the theory as evidence arises that necessitates a change?tjguy_{October 24, 2012
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Bump. In case anyone wants to tackle my question from comment 2.JoeCoder_{October 24, 2012
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In support of the contention that the 'non-local', beyond space and time, quantum properties found in biological molecules may translate from the micro-scale of protein folding (and the helical structure of DNA) to the macro-scale of the overall physiology of the entire organism, I offer this following recent meta-analysis:
Predictive physiological anticipation preceding seemingly unpredictable stimuli: a meta-analysis - October 2012 Excerpt: This meta-analysis of 26 reports published between 1978 and 2010 tests an unusual hypothesis: for stimuli of two or mor e types that are presented in an order designed to be unpredictable and that produce different post-stimulus physiological activity, the direction of pre-stimulus physiological activity reflects the direction of post-stimulus physiological activity, resulting in an unexplained anticipatory effect.,,, The results reveal a significant overall effect with a small effect size [fixed effect: overall ES = 0.21, 95% CI = 0.15–0.27, z = 6.9, p < 2.7 × 10?12; random effects: overall (weighted) ES = 0.21, 95% CI = 0.13–0.29, z = 5.3, p < 5.7 × 10?8]. Higher quality experiments produced a quantitatively larger effect size and a greater level of significance than lower quality studies. http://www.frontiersin.org/Perception_Science/10.3389/fpsyg.2012.00390/abstract Can Your Body Sense Future Events Without Any External Clue? - (Oct. 22, 2012) Excerpt: "But our analysis suggests that if you were tuned into your body, you might be able to detect these anticipatory changes between two and 10 seconds befo rehand,,, This phenomenon is sometimes called "presentiment," as in "sensing the future," but Mossbridge said she and other researchers are not sure whether people are really sensing the future. "I like to call the phenomenon 'anomalous anticipatory activity,'" she said. "The phenomenon is anomalous, some scientists argue, because we can't explain it using present-day understanding about how biology works; though explanations related to recent quantum biological findings could potentially make sense. It's anticipatory because it seems to predict future physiological changes in response to an important event without any known clues, and it's an activity because it consists of changes in the cardiopulmonary, skin and nervous systems." http://www.sciencedaily.com/releases/2012/10/121022145342.htm
supplemental note, many times this consistent physiological effect translates to precognitive thoughts:
Study suggests precognition may be possible - November 2010 Excerpt: A Cornell University scientist has demonstrated that psi anomalies, more commonly known as precognition, premonitions or extra-sensory perception (ESP), really do exist at a statistically significant level. http://www.physorg.com/news/2010-11-precognition.html Quantum Consciousness - Time Flies Backwards? - Stuart Hameroff MD Excerpt: Dean Radin and Dick Bierman have performed a number of experiments of emotional response in human subjects. The subjects view a computer screen on which appear (at randomly varying intervals) a series of images, some of which are emotionally neutral, and some of which are highly emotional (violent, sexual....). In Radin and Bierman's early studies, skin conductance of a finger was used to measure physiological response They found that subjects responded strongly to emotional images compared to neutral images, and that the emotional response occurred between a fraction of a second to several seconds BEFORE the image appeared! Recently Professor Bierman (University of Amsterdam) repeated these experiments with subjects in an fMRI brain imager and found emotional responses in brain activity up to 4 seconds before the stimuli. Moreover he looked at raw data from other laboratories and found similar emotional responses before stimuli appeared. http://www.quantumconsciousness.org/views/TimeFlies.html
bornagain77_{October 24, 2012
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Dollo’s law, the symmetry of time, and the edge of evolution - Michael Behe - Oct 2009 Excerpt: Nature has recently published an interesting paper which places severe limits on Darwinian evolution.,,, A time-symmetric Dollo’s law turns the notion of “pre-adaptation” on its head. The law instead predicts something like “pre-sequestration”, where proteins that are currently being used for one complex purpose are very unlikely to be available for either reversion to past functions or future alternative uses. http://www.evolutionnews.org/2009/10/dollos_law_the_symmetry_of_tim.html Severe Limits to Darwinian Evolution: - Michael Behe - Oct. 2009 Excerpt: The immediate, obvious implication is that the 2009 results render problematic even pretty small changes in structure/function for all proteins — not just the ones he worked on.,,,Thanks to Thornton’s impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed. http://www.evolutionnews.org/2009/10/severe_limits_to_darwinian_evo.html
Of note: the reductive materialism of neo-Darwinism is not even the right presupposition to explain what is found in proteins in the first place!
Physicists Discover Quantum Law of Protein Folding – February 22, 2011 Quantum mechanics finally explains why protein folding depends on temperature in such a strange way. Excerpt: First, a little background on protein folding. Proteins are long chains of amino acids that become biologically active only when they fold into specific, highly complex shapes. The puzzle is how proteins do this so quickly when they have so many possible configurations to choose from. To put this in perspective, a relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows.,,, Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins. That's a significant breakthrough. Luo and Lo's equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics. http://www.technologyreview.com/view/423087/physicists-discover-quantum-law-of-protein/ Falsification Of Neo-Darwinism by Quantum Entanglement/Information https://docs.google.com/document/d/1p8AQgqFqiRQwyaF8t1_CKTPQ9duN8FHU9-pV4oBDOVs/edit?hl=en_US
Verse and music:
John 1:1-5 In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. In him was life, and that life was the light of all mankind. The light shines in the darkness, and the darkness has not overcome it. Brooke Fraser – Lord of Lords(Legendado Português) - music http://www.youtube.com/watch?v=rkF3iVjOZ1I
Supplemental note:
New Scientist Asks: Is There Such A Thing As Reality? https://uncommondescent.com/news/new-scientist-asks-is-there-such-a-thing-as-reality/#comment-435928
bornagain77_{October 24, 2012
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I read and enjoyed the Axe/Gauger paper, but Dr. Moran's article still has me wondering. Take this simple ascii art: . . KBL . ./ . / ? . \ . .\ . . BioF The direct path from KBL to BioF+ is a prohibitive expanse. But how do we know there's not some ancestral protein off to the side that could serve as an intermediate? I don't think the experiment of trying to convert KBL to BioF would uncover one if it exists?JoeCoder_{October 23, 2012
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So now we are at a point where our critics are attempting to escape falsification by saying that evolutionary processes have simply slowed down? Well, looks like we're making some progress after all. I listed these on ENV but I think the kind of escape hatch Moran is using fits under the 3rd way of escaping falsification... 1. We didn't use the right microbial strain. 2. Different test conditions would've produced better results. 3. The experiment just needs a little more time. 4. Evolution never had a "goal" of producing new information, but it could. 5. There must be some kind of multiverse to give enough trials. ...and so on.Jeffrey Helix_{October 23, 2012
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