VIDEO: Doug Axe presents the thesis of his new (and fast-selling) book, Undeniable

How about : in comparison to CERNE, BA77 ? A fraction closer, maybe. But it's really akin to trying to assess the degree of honour Jesus bestows on his mother, as his mother. No matter how vast it is, it will be in a different ball-park to infinity. A strange thought to try to get you mind round. Put another way, what would be the maximum honour God could bestow on her, short of the infinite honour due to Himself. Anything less than that maximum would surely be outright lese-majeste. But I digress - no doubt to the jeering horror of scientism's 'fundies'. Considering the simplicity of the case for intelligent design, referred to, I think Arthur is shameless. At least Lewontin evinced some self-awareness, however crazily accepted by him. Axel

Dion, the take home message for me, as they continue unravel more and more levels of overlapping, integrated, complexity in DNA, is that DNA gives every appearance of being exquisitely designed. Evidently, exquisitely designed by an intelligence far, far, superior to man's intelligence since man has nothing close in comparison to DNA in terms of information processing and in terms of the overlapping, integrated, complexity found in DNA. Comparing computers to DNA is like comparing primitive stone tools to the tools found in a NASCAR garage (if even that :) ). bornagain77

BA77 @40 Time to update the [biology] textbooks? Oh, no! Again? Is that serious? Ok, but hold on, don't rush to the press yet... the next discovery that could render biology textbooks [partially] obsolete (again) is probably about to be published. Is this the "unending revelation of the ultimate reality"? :) PS. Thank you for posting this. Here's the original paper abstract: http://www.nature.com/nsmb/journal/vaop/ncurrent/full/nsmb.3270.html Here's another reference to the same paper: http://phys.org/pdf389267839.pdf Maybe Arthur Hunt knows something we don't know about this too? :) Dionisio

Hi Art Thank you very much for your response.

I think this range reflects, not so much some characteristics of any given protein (although this would be a factor) but rather the nature of the assays being used to generate these numbers (that, I must emphasize, are not probabilities). As I explain in the PT essay, the larger exponents (as you write them – 10^64 in this case) is obtained because the approach used deliberately excludes almost all of the sequences that may have enzyme activity. The smaller numbers (e.g., 10^10) are more representative because the assays used sample a more realistic range of functional sequences.

It would be helpful to get a definition of enzyme activity as it pertains to evolution. It seams as the enzyme has a more specific task to do, its AA sequence needs to be more specific. If the requirement is to catalyze the reaction of any molecule then many AA sequences can do the job. What if its requirement is to catalyze a reaction of a specific molecule or bind to a specific molecule? bill cole

UB @41 Arthur Hunt honored me first in this thread. :) Apparently he has not responded or commented on my questions/comments addressed to him @21, 30, 31, all before your post @32. :) Actually, I've posted more questions/comments for AH @34, 35, 38, which have not been responded/commented on yet. I like your very accurate statement about AH passing on responding to your comments:

That’s fine. You can ignore me and perhaps I will go away, but the facts on the ground are not going to go away.

Keeping in mind that what you wrote here is available to the anonymous visitors, onlookers, lurkers, who could read it and draw their own conclusions, maybe it's nice to have folks like AH who motivate you and others to write for all the readers who are genuinely looking for information. Dionisio

Hi Art, I see you passed on responding to my comments at #32. That's fine. You can ignore me and perhaps I will go away, but the facts on the ground are not going to go away. I see your comments, and it is clear that you concentrate exclusively on the mere physicality of the system. The problem is that you have no mechanism to establish RNA as an informational medium, nor organize it to be *about* something in memory. It's misguided. You should grasp this from the simple fact that you have to have two complementary descriptions of the translation of RNA in order to explain it. At some point you must set aside mere physicality and deal with the subject-object/genotype-phenotype paradox. You can't legitimately avoid it forever.

No, the real difficulty is not in the physics of the phenomenon; it lies elsewhere, and deeper, involving our own understanding, our intuition of it. There is really no paradox or miracle; but a flagrant epistemological contradiction ... In fact the central problem of biology lies with this very contradiction, which, if only apparent, must be resolved; or else prove to be utterly insolvable, if that should turn out indeed to be the case. -Monod

...cheers Upright BiPed

Of semi-related note:

Scientists have just uncovered a major difference between DNA and RNA Time to update the textbooks. FIONA MACDONALD - 3 AUG 2016 Excerpt: Back in 1953, Watson and Crick first published their model of the DNA double helix, and predicted how the base pairs - A & T and G & C - fit together.,,, researchers struggled to find evidence that the base pairs were bonding in the way that Watson and Crick had predicted - something they called Watson-Crick base pairs. Then in 1959, biochemist Karst Hoogsteen managed to take a picture of an A–T base pair, showing a slightly more skewed geometry, with one base rotated 180 degrees relative to the other. Since then, researchers have observed both Watson-Crick and Hoogsteen base pairs in images of DNA. But five years ago, Al-Hashimi and the Duke team found something that had never seen before: DNA base pairs constantly morphing back and forth between Watson-Crick and the Hoogsteen bonding configurations. This adds a whole other dimension and level of flexibility to DNA's structure. It turns out that DNA appears to be using Hoogsteen bonding when there's a protein bond to a DNA site - or if there's chemical damage to any of its bases - and once the damage is fixed or the protein is released, the DNA goes back to Watson-Crick bonds. That discovery was a big deal in itself, but now the team has shown for the first time that RNA doesn't have this ability, which could explain something that scientists have puzzled over for years: why DNA forms the blueprint for life, not RNA.,,, "The finding will likely rewrite textbook coverage of the difference between the two purveyors of genetic information, DNA and RNA," said a Duke Universitypress release.,,, "There is an amazing complexity built into these simple beautiful structures, whole new layers or dimensions that we have been blinded to because we didn't have the tools to see them, until now," said Al-Hashimi. http://www.sciencealert.com/scientists-think-they-finally-know-why-our-genes-are-made-of-dna-not-rna

bornagain77

AH, Pardon, but there is no insistence for abiogenesis or other areas that:

. . . abiogenesis necessarily and always must be defined by sequences of L-amino acids

. . . or the equivalent for cosmological fine tuning. First, John Leslie has long since highlighted the issue of local isolation of operation points (speaking of cosmology but applicable to this and other contexts):

. . . the need for such explanations does not depend on any estimate of how many universes would be observer-permitting, out of the entire field of possible universes. Claiming that our universe is ‘fine tuned for observers’, we base our claim on how life’s evolution would apparently have been rendered utterly impossible by comparatively minor alterations in physical force strengths, elementary particle masses and so forth. There is no need for us to ask whether very great alterations in these affairs would have rendered it fully possible once more, let alone whether physical worlds conforming to very different laws could have been observer-permitting without being in any way fine tuned. Here it can be useful to think of a fly on a wall, surrounded by an empty region. A bullet hits the fly Two explanations suggest themselves. Perhaps many bullets are hitting the wall or perhaps a marksman fired the bullet. There is no need to ask whether distant areas of the wall, or other quite different walls, are covered with flies so that more or less any bullet striking there would have hit one. The important point is that the local area contains just the one fly.

Adjust to co-adapted chemical and/or biological components requiring correct arrangement and coupling to achieve function and the point remains. Fine tuning is deeply informational and finding that locally isolated zones in large configuration spaces are observed, raises profound search challenges. Not just for individual molecules [proteins etc], but for the relevant functional cluster. Similarly, what is to be explained is the existence of the kind of life we actually observe. Per Newton's common sense rules, it is appropriate to ask whether blind chance and mechanical necessity in the early earth or wherever have been empirically warranted as accounting credibly for the functionally specific, complex organisation and/or associated information. (And yes, complex functionally specific configuration is inherently highly informational, as Orgel long ago pointed out.) We know that design routinely generates such FSCO/I. Indeed, in any other context not dominated by the imposed agendas at work on origins, the mere fact of observing such FSCO/I would rightly be taken as a convincing signature of design. KF kairosfocus

Arthur Hunt @25:

Which is why all the babbling about information that we see here, and in the more proper ID literature, is quite irrelevant.

You may want to take a look at this reference to a recent research paper posted @1783 in the thread pointed to by this link: https://uncommondesc.wpengine.com/intelligent-design/mystery-at-the-heart-of-life/#comment-614489 :) PS. FYI, I'm a wannabe student. I'm currently biology-illiterate, chemistry-illiterate, etc. The only thing I know very well is that I don't know much about practically anything. I'm trying to learn how to use effectively Xamarin+Unity3D for a multi-platform project I'm working on in MSFT Windows 10 (also using MSFT Windows 8.1 on a Surface tablet). Also for the same project, I've been trying to selectively gather and store references to research papers on certain topics of biology, using Zotero + Mind Meister + MS Visio. Now you can see why my questions are rather simple and easy to answer. Dionisio

"What happens is this classical information (of DNA) is embedded, sandwiched, into the quantum information (of DNA). And most likely this classical information is never accessed because it is inside all the quantum information. You can only access the quantum information or the electron clouds and the protons. So mathematically you can describe that as a quantum/classical state." Elisabeth Rieper – Classical and Quantum Information in DNA – video (Longitudinal Quantum Information resides along the entire length of DNA discussed at the 19:30 minute mark; at 24:00 minute mark Dr Rieper remarks that practically the whole DNA molecule can be viewed as quantum information with classical information embedded within it) https://youtu.be/2nqHOnVTxJE?t=1176 Quantum entanglement holds together life’s blueprint – 2010 Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours. “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford. http://neshealthblog.wordpress.com/2010/09/15/quantum-entanglement-holds-together-lifes-blueprint/

Moreover, this quantum entanglement/information, which is found in DNA and protein molecules, requires a 'non-local', beyond space and time, cause in order to explain its effect,,,

Looking beyond space and time to cope with quantum theory – 29 October 2012 Excerpt: “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,” http://www.quantumlah.org/highlight/121029_hidden_influences.php Physicists find extreme violation of local realism in quantum hypergraph states - Lisa Zyga - March 4, 2016 Excerpt: Many quantum technologies rely on quantum states that violate local realism, which means that they either violate locality (such as when entangled particles influence each other from far away) or realism (the assumption that quantum states have well-defined properties, independent of measurement), or possibly both. Violation of local realism is one of the many counterintuitive, yet experimentally supported, characteristics of the quantum world. Determining whether or not multiparticle quantum states violate local realism can be challenging. Now in a new paper, physicists have shown that a large family of multiparticle quantum states called hypergraph states violates local realism in many ways. The results suggest that these states may serve as useful resources for quantum technologies, such as quantum computers and detecting gravitational waves.,,, The physicists also showed that the greater the number of particles in a quantum hypergraph state, the more strongly it violates local realism, with the strength increasing exponentially with the number of particles. In addition, even if a quantum hypergraph state loses one of its particles, it continues to violate local realism. This robustness to particle loss is in stark contrast to other types of quantum states, which no longer violate local realism if they lose a particle. This property is particularly appealing for applications, since it might allow for more noise in experiments. http://phys.org/news/2016-03-physicists-extreme-violation-local-realism.html

Dr. Hunt, exactly where does this non-local, beyond space and time, quantum information come from? Verse:

John 1:1-4 In the beginning was the Word, and the Word was with God, and the Word was God. The same was in the beginning with God. All things were made by him; and without him was not any thing made that was made. In him was life; and the life was the light of men.

The implications of beyond space and time quantum information in biology are not very friendly to the nihilistic beliefs of atheists.

Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff - video https://www.youtube.com/watch?v=iIyEjh6ef_8

bornagain77

Hunt claims

"all the babbling about information that we see here, and in the more proper ID literature, is quite irrelevant."

Actually, contrary to the materialistic presuppositions of Darwinists, and due to advances in quantum mechanics, information is now found to be its own independent entity that is separate from matter and energy. In other words, information is not 'emergent' from a material basis as is held in Darwinian thinking.

Quantum Entanglement and Information Quantum entanglement is a physical resource, like energy, associated with the peculiar nonclassical correlations that are possible between separated quantum systems. Entanglement can be measured, transformed, and purified. A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. The general study of the information-processing capabilities of quantum systems is the subject of quantum information theory. http://plato.stanford.edu/entries/qt-entangle/

In fact, in quantum mechanics it is information that is primarily conserved not matter-energy,,,

Quantum no-hiding theorem experimentally confirmed for first time Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment. http://www.physorg.com/news/2011-03-quantum-no-hiding-theorem-experimentally.html etc.. etc..

Moreover, classical information is shown to be a subset of quantum information by the following:

Quantum knowledge cools computers: New understanding of entropy – June 2011 Excerpt: No heat, even a cooling effect; In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy. Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.” http://www.sciencedaily.com/releases/2011/06/110601134300.htm Scientists show how to erase information without using energy - January 2011 Excerpt: "Landauer said that information is physical because it takes energy to erase it. We are saying that the reason it (information) is physical has a broader context than that.", Vaccaro explained. http://www.physorg.com/news/2011-01-scientists-erase-energy.html New Scientist astounds: Information is physical - May 13, 2016 Excerpt: Recently came the most startling demonstration yet: a tiny machine powered purely by information, which chilled metal through the power of its knowledge. This seemingly magical device could put us on the road to new, more efficient nanoscale machines, a better understanding of the workings of life, and a more complete picture of perhaps our most fundamental theory of the physical world. https://uncommondesc.wpengine.com/news/new-scientist-astounds-information-is-physical/

Moreover, quantum entanglement/information, though at first thought to be impossible to be in life, is now found in proteins and DNA: Whereas the slightest environmental noise presents extreme difficulties for man in his quest to build quantum computers of any significant size, on the other hand, life is apparently designed in such an ingenuous way that “Environmental noise drives a persistent and cyclic generation of new entanglement”

Quantum entanglement in hot systems – 2011 Excerpt: The authors remark that this reverses the previous orthodoxy, which held that quantum effects could not exist in biological systems because of the amount of noise in these systems.,,, Environmental noise here drives a persistent and cyclic generation of new entanglement.,,, In summary, the authors say that they have demonstrated that entanglement can recur even in a hot noisy environment. In biological systems this can be related to changes in the conformation of macromolecules. http://quantum-mind.co.uk/quantum-entanglement-hot-systems/ 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.,,, Today, Luo and Lo say these curves can be easily explained if the process of folding is a quantum affair. By conventional thinking, a chain of amino acids can only change from one shape to another by mechanically passing though various shapes in between. But Luo and Lo say that if this process were a quantum one, the shape could change by quantum transition, meaning that the protein could ‘jump’ from one shape to another without necessarily forming the shapes in between.,,, 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/ Classical and Quantum Information Channels in Protein Chain - Dj. Koruga, A. Tomi?, Z. Ratkaj, L. Matija - 2006 Abstract: Investigation of the properties of peptide plane in protein chain from both classical and quantum approach is presented. We calculated interatomic force constants for peptide plane and hydrogen bonds between peptide planes in protein chain. On the basis of force constants, displacements of each atom in peptide plane, and time of action we found that the value of the peptide plane action is close to the Planck constant. This indicates that peptide plane from the energy viewpoint possesses synergetic classical/quantum properties. Consideration of peptide planes in protein chain from information viewpoint also shows that protein chain possesses classical and quantum properties. So, it appears that protein chain behaves as a triple dual system: (1) structural - amino acids and peptide planes, (2) energy - classical and quantum state, and (3) information - classical and quantum coding. Based on experimental facts of protein chain, we proposed from the structure-energy-information viewpoint its synergetic code system. http://www.scientific.net/MSF.518.491 Quantum criticality in a wide range of important biomolecules Excerpt: “Most of the molecules taking part actively in biochemical processes are tuned exactly to the transition point and are critical conductors,” they say. That’s a discovery that is as important as it is unexpected. “These findings suggest an entirely new and universal mechanism of conductance in biology very different from the one used in electrical circuits.” The permutations of possible energy levels of biomolecules is huge so the possibility of finding even one that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,, “what exactly is the advantage that criticality confers?” per Medium dot com

bornagain77

Arthur Hunt @25:

Which is why all the babbling about information that we see here, and in the more proper ID literature, is quite irrelevant.

Did you comment on this recent thread about functional information associated with protein domains? "The highly engineered transition to vertebrates: an example of functional information analysis" Here's the link to that thread: https://uncommondesc.wpengine.com/intelligent-design/the-highly-engineered-transition-to-vertebrates-an-example-of-functional-information-analysis/ :) Dionisio

Arthur Hunt I've noticed -by reading your comments- that you seem to know about biology a lot more than most folks in this forum. Were my two assumptions @31 incorrect? :) Dionisio

vjtorley, I hope you are not taking my use of the term "fabrication" as a perjorative. If so, I apologize. It is simply terminology to illustrate a common flaw in the arguments bandied about here. That having been said, I think your demand for a code is pretty analogous to my quip about L- amino acids. And frankly, your quote about the activities of Fox's protocells is just plain wrong. There is actually a pretty rich literature that shows this. Finally, the supposed reply by Axe to my criticism of his work is no reply at all. The article you link to focuses almost exclusively on statements made by others. You can tell that he is ducking my criticism by searching the article for the term "temperature sensitive". This term lies at the heart of my chief criticism, and he avoided the issue then, as he does to this day. Arthur Hunt

enzymatically active polypeptides actually carry no information. Zero. Zip. Nada.

Enzymatic activity is a rate-dependent process, and is generally non-controversial. The issue at hand is the establishment of a medium, and the organization of rate-independent constraints – enough of them to have the informational capacity to record themselves into memory.

Which is why all the babbling about information that we see here, and in the more proper ID literature, is quite irrelevant.

I'm sure you are aware, there is no class of enzymatic activity that organizes rate-independent constraints. Upright BiPed

Arthur Hunt, At this point I will assume you missed seeing the questions @21. You may respond them at your convenience or ignore them completely. But they are very easy. Some folks may not like to answer that kind of easy questions, because apparently by doing so they could expose -at least partially- their attitude and real motives. But I'm assuming this isn't that case. :) Dionisio

Arthur Hunt, Did you respond the questions @21? Dionisio

In Response to Meyer-Dawkins Dispute, Misconceptions About My Research Resurface – Douglas Axe - March 25, 2016 - (Doug Axe responds to Art Hunt, Steve Matheson and Dennis Venema) http://www.evolutionnews.org/2016/03/in_response_to102723.html Hunt claims

if one is assaying, say, one liter of a very dilute solution of polypeptides of random sequence (say, 10^-11 moles/L), the probability of finding activity would be about 1. The probability of finding all of the activities in the excerpt given by BA77 above (5, or ten, doesn’t matter) in the very same one liter, at the same time, would be 1. Not 10^-110, as calculated by Tyler Hampton.

In regards to this generous estimate for achieving 'simple' self replication

If all the operations needed for a small autonomous biology were ten functions—this is before evolution can even start to help—the probability is 1 in (10^11)10, or 1 in 10^110. This is more than the number of seconds since the Big Bang, more protons than there are in the universe. In considering a similar figure derived in a different context, Tawfik concedes that if true, this would make “the emergence of sequences with function a highly improbable event, despite considerable redundancy (many sequences giving the same structure and function).”44 In other words, these odds are impossible.,,, Tawfik soberly recognizes the problem. The appearance of early protein families, he has remarked, is “something like close to a miracle.”45,,, “In fact, to our knowledge,” Tawfik and Tóth-Petróczy write, “no macromutations … that gave birth to novel proteins have yet been identified.”69

Perhaps Hunt would care to demonstrate for all the world to see exactly how "one liter of a very dilute solution of polypeptides of random sequences" can produce simple self replication so as to win a Noble prize? The 1 in 10^110 math stands because all the polypeptides have to happen in exactly the same place at exactly the same time. And if Hunt continues to disagree, please see the above request for a Noble prize worthy demonstration. Shoot, instead of just one liter, you can have as much dilute solution as you want.

Origin of Life: An Inside Story - Professor James Tour – May 1, 2016 Excerpt: “All right, now let’s assemble the Dream Team. We’ve got good professors here, so let’s assemble the Dream Team. Let’s further assume that the world’s top 100 synthetic chemists, top 100 biochemists and top 100 evolutionary biologists combined forces into a limitlessly funded Dream Team. The Dream Team has all the carbohydrates, lipids, amino acids and nucleic acids stored in freezers in their laboratories… All of them are in 100% enantiomer purity. [Let’s] even give the team all the reagents they wish, the most advanced laboratories, and the analytical facilities, and complete scientific literature, and synthetic and natural non-living coupling agents. Mobilize the Dream Team to assemble the building blocks into a living system – nothing complex, just a single cell. The members scratch their heads and walk away, frustrated… So let’s help the Dream Team out by providing the polymerized forms: polypeptides, all the enzymes they desire, the polysaccharides, DNA and RNA in any sequence they desire, cleanly assembled. The level of sophistication in even the simplest of possible living cells is so chemically complex that we are even more clueless now than with anything discussed regarding prebiotic chemistry or macroevolution. The Dream Team will not know where to start. Moving all this off Earth does not solve the problem, because our physical laws are universal. You see the problem for the chemists? Welcome to my world. This is what I’m confronted with, every day.“ James Tour – leading Chemist https://uncommondesc.wpengine.com/intelligent-design/origin-of-life-professor-james-tour-points-the-way-forward-for-intelligent-design/

bornagain77

Arthur Hunt, Thank you for you reply. You accuse me of creating a biased definition of life, which specifies that it must be defined by sequences of L-amino acids. I do no such thing. My definition specifies that life should have a code, and that its constituents should not bond together randomly. Those are non-arbitrary features. I quoted several scientists as writing that "there is no evidence that proteinoids differ significantly from a random sequence of amino acids, with little or no catalytic activity." Frankly, I wouldn't care if they had all R-amino acids, instead of L. Your objection to Douglas Axe's experimental approach has been answered fully by Axe himself. See http://www.biologicinstitute.org/post/19310918874/correcting-four-misconceptions-about-my-2004 and especially see the response to Objection 3. That's all for now. Got to go. vjtorley

I'll ask again. Go back and read all of Axe’s research on the subject and answer this: were any of the allegedly non-functional variants in the mutational “determination” of functional sequence space actually assayed (directly) for enzyme activity? Arthur Hunt

vjtorley, thanks for the comment. Hopefully, if you read my reply to bill cole, you can see why the criticisms you raise to my example of abiogenesis are completely irrelevant. You, and those who proffered the original criticism, are doing something that Dembski warned against in one of his books. Which is - you have found an arrow sticking out of the side of a barn (that would be life as we know it), painted a target around it (this would be a universal, allegedly unbiased definition of life, regardless of where in the universe we are), and proclaimed that someone aimed an arrow at the barn and hit the target. (In the vernacular, your definitions of life are what Dembski would call a fabrication.) Your logic is fundamentally flawed, specifically the insistence that abiogenesis necessarily and always must be defined by sequences of L-amino acids. Arthur Hunt

bill cole, thanks for the comments and questions. I have read you paper challenging Axe’s probability numbers. The ranges you come up with are less but similar. Do you still stand by the article you wrote in Panda’s Thumb in 2004? Yes. What do you think are the elements (protein characteristics) creating a range of probabilities that you mentioned in your paper? I think the range you mentioned was 10^10 to 10^64 for 100AA proteins. I think this range reflects, not so much some characteristics of any given protein (although this would be a factor) but rather the nature of the assays being used to generate these numbers (that, I must emphasize, are not probabilities). As I explain in the PT essay, the larger exponents (as you write them - 10^64 in this case) is obtained because the approach used deliberately excludes almost all of the sequences that may have enzyme activity. The smaller numbers (e.g., 10^10) are more representative because the assays used sample a more realistic range of functional sequences. As far as my comment about probabilities - the numbers you cite, bill cole, and those BA77 copied and pasted above, are ratios, not probabilities. They may be used to estimate probabilities, but one needs to factor in the population of sequences being sampled. In other words, if the ratio of active to all sequences is 10^-10, and if one assays a single individual, then the probability of obtaining activity would be along the lines of 10^-10. OTOH, if one is assaying, say, one liter of a very dilute solution of polypeptides of random sequence (say, 10^-11 moles/L), the probability of finding activity would be about 1. The probability of finding all of the activities in the excerpt given by BA77 above (5, or ten, doesn't matter) in the very same one liter, at the same time, would be 1. Not 10^-110, as calculated by Tyler Hampton. Curious thing - using the silly math that the ID proponents here use, one would calculate that these polypeptides would have lots of information. By applying the proper values for information (real probabilities, and not ratios), one finds that enzymatically active polypeptides actually carry no information. Zero. Zip. Nada. Which is why all the babbling about information that we see here, and in the more proper ID literature, is quite irrelevant. Arthur Hunt

VJTorley Good explanation. thank you. However, here's a question: Is AH willing to understand it? We don't know, but i doubt it. Those who are not seriously willing to at least try to understand what is being discussed, maybe should consider going back to their natural habitat in the beautiful Norwegian fjords? :) Dionisio

Hi Arthur Hunt, I had a look at the page you directed readers to in #14 above. It briefly comments on a 2008 paper by Nowak and Ohtsuki, before going on to defend a version of the proteinoid hypothesis proposed by Sidney W. Fox, that proteinoids were a precursor to the first living cells (protocells), citing a 1987 paper by T. Nakashima which reviews the hypothesis. Short reply: if you want to know what's wrong with Nowak and Ohtsuki's paper, see this article by Jonathan McClatchie and scroll down to "The Origin of Replication." To find out what's wrong what the proteinoid hypothesis, have a look at this outstanding comment by Barb (who used to comment pretty regularly on Uncommon Descent). Longer reply: (Highlighting below is mine - VJT.) Here's the relevant excerpt from McClatchie's article on Nowak and Ohtsuki's paper:

It's not entirely clear in what sense the authors are using the term "information," nor that they understand it. They tell us that "prelife is a generative system that can produce information." We are also told that "Evolution needs a generative system that can produce unlimited information. Evolution needs populations of information carriers." They also tell us on the first page that they "can define a prebiotic chemistry that can produce any binary string and thereby generate, in principle, unlimited information and diversity." Since when was a set of random strings of characters a sound definition of "information" -- at least in any meaningful sense as applied to biology? The authors here seem to indiscriminately consider any polymer that out-competes the others, by virtue of being more abundant, as a forerunner to the origin of life. Note the assumption here that all sequences are equally conducive to life. How can this be justified? There comes a point when the abundant polymer must contain functional information. Indeed, the simplest micro-organisms that we know require a minimum of two or three hundred genes (or a few hundred thousand base pairs of DNA). The model proposed in this paper is highly theoretical and speculative -- with no substantive practical experimental research to back it up.

In your article, you defend the notion that proteinoids are alive:

They display: electrotactism (the ability to sense an electrical field) aggregation (the ability to collect into colonies) mobility (the ability to move more or less at will) osmosis (the ability to absorb material from the environment) permselectivity (the ability to selectively pass materials across a semi-permiable barrier) fission (the ability to break about into smaller functional units) reproduction (the ability to create functional copies) conjugation (the ability to join directly to another) communication (the ability to pass information directly to another) excitability (the ability to generate and utilize energy, especially electrical fields) In addition, “(p)roteinoids or proteinoid microspheres have many activities. Esterolyis, decarboxylation, amination, deamination, and oxidoreduction are catabolic enzyme activities. The formation of ATP, peptides or oligonucleotides is synthetic enzyme activities.” (From the review by Nakashima.) Ask a high school bio student (e.g., perform a sort of “toddler test”) if these characteristics would qualify something as being alive, and the answer very likely would be yes.

I notice that neither a genetic code nor the ability to evolve are included in the above list. In her comment, Barb points out some other relevant differences between proteinoids and living things:

1. Proteinoids do not have anything coding their sequences, and the amino acids bond together randomly. 2. Proteinoids do not fold into a predictable three-dimensional conformation (since their sequences are not deterministic, for example). 3. Proteinoids contain both left- and right-handed amino acids in equal amounts, and even if the experiment begins with all left-handed amino acids, some are converted to the other form. 4. The amino acids in proteinoids are not all bonded together by alpha bonds: the amino acid chain in proteinoids is branched and “kinked” instead of being linear (due to incorrect bonding, for example, involving side groups). 5. Proteinoids have bonds other than peptide bonds joining their amino acids. Some of the starting amino acids are converted into pigments, which are incorporated into the proteinoid. These scientists also noted a distinct difference between proteinoids and proteins: “To this product Fox gave the name proteinoid, a cautious choice since proteinoids are far from having the regular chainlike structure of peptides.” (Christian de Duve, Vital Dust:Life as a Cosmic Imperative, Basic Books, 1995, p. 29)

Barb went on to quote the testimonies of other esteemed scientists working in the field of the origin of life, on the inadequacies of proteinoids:

“The products obtained were not natural proteins, however, even though they were made from amino acids. The special amino acids mentioned above contained either an extra amino or an extra acid group. In normal proteins, these extra groups do not take part in chain formation, but this had occurred in the heating process. Unnatural chains, even branched chains, had been produced. Further, some of the amino acids had been converted into their mirror-image forms, so both types were present. Others had been converted to colored substances, pigments, which were also built into the chains. The term proteinoid rather than protein was applied to the product, because of these features which distinguished it from anything present in earthly biology.” (Origins: A Skeptic’s Guide to the Creation of Life on Earth, Robert Shapiro, Bantam Books, 1987, pp. 193-194) “Studies using nuclear magnetic resonance (NMR) have shown that thermal proteinoids “have scarce resemblance to natural peptidic material because [beta], [gamma], and [epsilon] bonds largely predominate over [alpha]-peptide bonds.” (Charles B. Thaxton [Ph.D. in Chemistry], Walter L. Bradley [Ph.D. in Materials Science], Roger L. Olsen [BS in Chemistry, Ph.D. in Geochemistry], The Mystery of Life’s Origin: Reassessing Current Theories, Lewis and Stanley, 1984, pp. 155-156) “A third kind of question [concerning proteinoids] was that of crosslinks such as have not been reported for protein. Reactions might be postulated, for example, between side chains of such amino acids as lysine and aspartic acid. Moreover, linkage through the amino groups of some lysine residues has been shown in a number of studies (Harada, 1959; Harada and Fox, 1965a; Suzuki, 1966; Heinrich et al., 1969). (Molecular Evolution and the Origin of Life, Sidney W. Fox and Klaus Dose, W. H. Freeman and Co., 1972, pp. 148-149) “Fox has produced some quite long peptides, which he terms proteinoids, using this method. Unfortunately, the resemblance between Fox’s proteinoids and real proteins is rather superficial. For example, real proteins are made exclusively of left-handed amino acids (see page 71), whereas proteinoids are an equal mixture of left and right.” (The Fifth Miracle: The Search for the Origin and Meaning of Life, Paul Davies, Simon & Schuster, NY, 1999, pp. 90-91) “...there is no evidence that proteinoids differ significantly from a random sequence of amino acids, with little or no catalytic activity.” (Charles B. Thaxton [Ph.D. in Chemistry], Walter L. Bradley [Ph.D. in Materials Science], Roger L. Olsen [BS in Chemistry, Ph.D. in Geochemistry], The Mystery of Life’s Origin: Reassessing Current Theories, Lewis and Stanley, 1984, pp. 155-156).

Proteinoids? Replication without information? I am underwhelmed. Seriously, though, you really should buy Douglas Axe's latest book, because it's the best book you're ever likely to see on the subject of Intelligent Design. It is extraordinarily well-written and carefully argued, in a style which displays the author's learning, but which is immediately accessible to laypeople who know little or nothing about biology. The approach deliberately taken by Axe is a naive one, which is at the same time scientifically informed: his aim is to present laypeople with an argument for design which doesn't require mastery of technical details (although he does go into those, for readers who are curious). vjtorley

Cheers for the book and its success. These are the books that matter these days in origin/operation issues of the universe. They are a challenge that also has a defence. The opposition should try to defend themselves but in the end error has trouble defending itself. Robert Byers

Arthur Hunt @14 Is this the link you provided @14:? https://aghunt.wordpress.com/2008/11/09/protocells-the-origins-of-life-and-the-rna-world/ Is this sentence in the first paragraph:?

I’m moved to this by a recent a recent article in PNAS.

[Yes, the expression "a recent" appears twice, where the second instance contains the link to the allegedly "recent" paper. Did you repeat "a recent" intentionally or by mistake? :)] Anyway, is this the paper you referred to:?

Prevolutionary dynamics and the origin of evolution Martin A. Nowak† and Hisashi Ohtsuki PNAS vol. 105 no. 39 14924–14927 doi: 10.1073/pnas.0806714105

When did you post that reference in your blog? Isn't it a 2008 paper? In light of the accelerated pace of biology research and the resulting discoveries, I think a 2008 paper is kind of old. There could be rare exceptions, but I would be careful to base your flaky speculations on a paper that is 8 years old. Besides, that paper says almost nothing relevant to prove anything. It definitely belongs in the prestigious "Where's the beef?" category. But better I let Mina tell you exactly what that paper says: https://www.youtube.com/embed/1hejSyjn760 If you don't understand Italian language, you may ask gpuccio to translate it for you. :) Almost 8 years after the paper you referenced we see this:

Unfortunately, biologists do not recognize that describing a mechanism is not the same as knowing how it actually works. Nowhere is that more apparent than in evolution theory, which is composed of metaphoric Just So Stories instead of testable, refutable, hypothesis testable science.

The Cell as the First Niche Construction John S. Torday Biology (Basel). 5(2): 19. doi: 10.3390/biology5020019

And even the latter paper is far from having a clue. :) Dionisio

Arthur Hunt, I seriously don't think Darwinists should EVER be talking about mathematics since,,, #1 they do not pay attention to what their own mathematics from population genetics is telling them about their theory #2 Darwinists have no rigid mathematical basis to test against, as other overarching theories of science have, so as to qualify their theory as a science instead of a pseudo-science #3 The applicability of mathematics is itself a 'miracle' that is inexplicable to the materialistic presuppositions of Darwinists Notes: #1

the mathematics of population genetics is not kind to Darwinian claims in the least. Three devastating problems are revealed by population genetics. The Waiting Time problem, Natural selection is ineffective, and perception of reality itself is shown to become illusory. (July 2016) https://uncommondesc.wpengine.com/intelligent-design/81705/#comment-613650

#2

“On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?” – Berlinski, D., “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003 The main reason that Darwinian theory can offer nothing in comparison to quantum electrodynamics or general relativity is because it has no demarcation criteria based in mathematics to make it a testable theory like quantum electrodynamics and general relativity have a demarcation criteria based in math so as to make them testable and potentially falsifiable. Deeper into the Royal Society Evolution Paradigm Shift Meeting – 02/08/2016 Suzan Mazur: Peter Saunders in his interview comments to me said that neo-Darwinism is not a theory, it’s a paradigm and the reason it’s not a theory is that it’s not falsifiable. http://www.huffingtonpost.com/suzan-mazur/john-dupre-interview-deep_b_9184812.html Peter Saunders is Co-Director, Institute of Science in Society, London; Emeritus professor of Applied Mathematics, King’s College London. Peter Saunders has been applying mathematics in biology for over 40 years, in microbiology and physiology as well as in development and evolution. He has been a critic of neo-Darwinism for almost as long. read more here https://uncommondesc.wpengine.com/peer-review/high-rate-of-false-discoveries-mars-science/#comment-614313

#3

The Unreasonable Effectiveness of Mathematics in the Natural Sciences - Eugene Wigner - 1960 Excerpt: ,,certainly it is hard to believe that our reasoning power was brought, by Darwin's process of natural selection, to the perfection which it seems to possess.,,, It is difficult to avoid the impression that a miracle confronts us here, quite comparable in its striking nature to the miracle that the human mind can string a thousand arguments together without getting itself into contradictions, or to the two miracles of the existence of laws of nature and of the human mind's capacity to divine them.,,, The miracle of the appropriateness of the language of mathematics for the formulation of the laws of physics is a wonderful gift which we neither understand nor deserve. We should be grateful for it and hope that it will remain valid in future research and that it will extend, for better or for worse, to our pleasure, even though perhaps also to our bafflement, to wide branches of learning. http://www.dartmouth.edu/~matc/MathDrama/reading/Wigner.html "You find it strange that I consider the comprehensibility of the world (to the extent that we are authorized to speak of such a comprehensibility) as a miracle or as an eternal mystery. Well, a priori, one should expect a chaotic world, which cannot be grasped by the mind in any way .. the kind of order created by Newton's theory of gravitation, for example, is wholly different. Even if a man proposes the axioms of the theory, the success of such a project presupposes a high degree of ordering of the objective world, and this could not be expected a priori. That is the 'miracle' which is constantly reinforced as our knowledge expands." Albert Einstein - Letters to Solovine - New York, Philosophical Library, 1987 "Either mathematics is too big for the human mind, or the human mind is more than a machine." Kurt Gödel As quoted in Topoi : The Categorial Analysis of Logic (1979) by Robert Goldblatt, p. 13 Mathematics and Physics – A Happy Coincidence? – William Lane Craig – video https://www.youtube.com/watch?v=BF25AA4dgGg 1. If God did not exist the applicability of mathematics would be a happy coincidence. 2. The applicability of mathematics is not a happy coincidence. 3. Therefore, God exists.

bornagain77

Arthur I have read you paper challenging Axe's probability numbers. The ranges you come up with are less but similar. Do you still stand by the article you wrote in Panda's Thumb in 2004? What do you think are the elements (protein characteristics) creating a range of probabilities that you mentioned in your paper? I think the range you mentioned was 10^10 to 10^64 for 100AA proteins. bill cole

BA77, in the excerpt you posted, there is a fundamental, basic, almost comical error made in the calculation of probability. If you don't see or understand it, you probably should not be participating in discussions such as this. (Rather than trying to bluff your way thru this, ala DT, you might try thinking about what I have posted and asking some questions to try and fill in the gaping holes in your understanding.) Sorry to be blunt, but it's clear that you haven't a clue, about the subject or about the (mostly, pretty decent) article you are misrepresenting. Arthur Hunt

Hunt, I certainly don't think Darwinists should be lecturing anybody on probabilities:

Laurence Moran's Sandwalk Evolves Chloroquine Resistance - Michael Behe August 13, 2014 Excerpt: That's the reason I issued the challenge in the first place. In my experience almost all Darwinists and fellow travelers (Professor Moran doesn't consider himself a Darwinist) simply don't think quantitatively about what their theory asks of nature in the way of probability. When prodded to do so, they quickly encounter numbers that are, to say the least, bleak. They then seem to lose all interest in the problem and wander away. The conclusion that an unbiased observer should draw is that Darwinian claims simply don't stand up to even the most cursory calculations. http://www.evolutionnews.org/2014/08/laurence_morans088811.html Bernard d'Abrera on Butterfly Mimicry and the Faith of the Evolutionist - October 5, 2011 Excerpt: For it to happen in a single species once through chance, is mathematically highly improbable. But when it occurs so often, in so many species, and we are expected to apply mathematical probability yet again, then either mathematics is a useless tool, or we are being criminally blind.,,, Evolutionism (with its two eldest daughters, phylogenetics and cladistics) is the only systematic synthesis in the history of the universe that proposes an Effect without a Final Cause. It is a great fraud, and cannot be taken seriously because it outrageously attempts to defend the philosophically indefensible. http://www.evolutionnews.org/2011/10/in_this_excerpt_from_the051571.html Here’s That Monumental Evolution Blunder About Probability Again - March 2012 Excerpt: Laplace didn’t rebuke this argument two centuries ago for no good reason—the fallacy has been around forever and evolutionists continue to employ it.,,, It is truly incredible to see evolutionists work their chicanery so they can uphold complete nonsense as the truth. So the evolutionists would credulously accept all manner of bizarre events. If all their roulette wheel bets turned out winners, if their poker hands always gave a royal flush, if random Scrabble letters spelled out CONSTANTINOPLE, it all would be just another small probability event from which nothing can be concluded. This monumental blunder leads them into all kinds of ridiculous conclusions: http://darwins-god.blogspot.com/2012/03/heres-that-monumental-evolution-blunder.html

Of related interest:

"In light of Doug Axe's number, and other similar results,, (1 in 10^77), it is overwhelmingly more likely than not that the mutation, random selection, mechanism will fail to produce even one gene or protein given the whole multi-billion year history of life on earth. There is not enough opportunities in the whole history of life on earth to search but a tiny fraction of the space of 10^77 possible combinations that correspond to every functional combination. Why? Well just one little number will help you put this in perspective. There have been only 10^40 organisms living in the entire history of life on earth. So if every organism, when it replicated, produced a new sequence of DNA to search that (1 in 10^77) space of possibilities, you would have only searched 10^40th of them. 10^40 over 10^77 is 1 in 10^37. Which is 10 trillion, trillion, trillion. In other words, If every organism in the history of life would have been searching for one those (functional) gene sequences we need, you would have searched 1 in 10 trillion, trillion, trillionth of the haystack. Which makes it overwhelmingly more likely than not that the (Darwinian) mechanism will fail. And if it is overwhelmingly more likely than not that the (Darwinian) mechanism will fail should we believe that is the way that life arose?" Stephen Meyer - 46:19 minute mark - Darwin's Doubt - video https://www.youtube.com/watch?v=Vg8bqXGrRa0&feature=player_detailpage#t=2778

bornagain77

Hunt, You really should read the articles that are referenced before you embarrass yourself again like you just did

Dan S. Tawfik Group - The New View of Proteins - Tyler Hampton - 2016 Excerpt: NASA’s Andrew Pohorille and Michael New supply three reasons to doubt an RNA world:51 1. Protein building blocks are more easily formed than RNA building blocks, which are notoriously difficult to form. 2. RNA cannot easily achieve the crucial aspects of metabolism, such as energy capture and transport. This may have been necessary from the beginning.52 No ribozymes have ever been observed to do something as crucial as establishing a proton gradient to produce ATP energy or synthesizing nucleotides for new RNA strands.53 3. An RNA world would seem to offer a great deal of confusion to natural selection. “[S]ince there is no relationship,” Pohorille and New write, “between the function of a catalytic RNA and the function, if any, of the protein for which it can code, there is no clear path from the ‘RNA world’ to today’s world of protein catalysis and nucleic acid information storage.”54 Further serious problems remain. RNA enzymes emerge at about the frequency suggested by Szostak for proteins, so no relief of probabilities is offered. Additionally, RNA enzymes that break bonds or perform irrelevant tasks may more frequently emerge than the few that would do a cell much good. Any good gained could be lost in this mix. Finally, the backbone structure of RNA suggests that it was impossibly fragile in early watery conditions.55 http://inference-review.com/article/the-new-view-of-proteins

Oldie but goodie:

The RNA world hypothesis: the worst theory for the early evolution of life (except for all the others) - July 2012 Excerpt: "The RNA World scenario is bad as a scientific hypothesis" - Eugene Koonin “The RNA world hypothesis has been reduced by ritual abuse to something like a creationist mantra” - Charles Kurland "I view it as little more than a popular fantasy." - Charles Carter http://www.biology-direct.com/content/pdf/1745-6150-7-23.pdf

bornagain77

A tennis instructor makes a fundamental, basic error in calculating probabilities, and BA77 laps it up. It's almost as if Donald Trump has joined the conversation here.... Arthur Hunt

Extend to a stew of chemicals, moving about in a pond. On what empirical observation sustained grounds do you have that this can plausibly end in a cell based life form? Enjoy! AH, and the actual, currently observed evidence of an RNA world as actually existing is? ZERO. Please, come again, in accord with Newton's common sense rules. KF Arthur Hunt

Dan S. Tawfik Group - The New View of Proteins - Tyler Hampton - 2016 Excerpt: one of the most favorable and liberal estimates is by Jack Szostak: 1 in 10^11. 42 He ascertained this figure by looking to see how random sequences—about eighty amino acids in length, long enough to fold—could cling to the biologically crucial molecule adenosine triphosphate, or ATP. At first glance, this is an improvement over Salisbury’s calculations by 489 powers of ten. But while an issue has been addressed, the problem has only been deferred. ,,, ,,, nucleotide synthesis, requires several steps. If five enzyme functions were needed (ten are needed in modern adenine synthesis), 43 then the probability would be 1 in (10^11)5, or 1 in 10^55. If all the operations needed for a small autonomous biology were ten functions—this is before evolution can even start to help—the probability is 1 in (10^11)10, or 1 in 10^110. This is more than the number of seconds since the Big Bang, more protons than there are in the universe. In considering a similar figure derived in a different context, Tawfik concedes that if true, this would make “the emergence of sequences with function a highly improbable event, despite considerable redundancy (many sequences giving the same structure and function).”44 In other words, these odds are impossible.,,, Tawfik soberly recognizes the problem. The appearance of early protein families, he has remarked, is “something like close to a miracle.”45,,, “In fact, to our knowledge,” Tawfik and Tóth-Petróczy write, “no macromutations ... that gave birth to novel proteins have yet been identified.”69 The emerging picture, once luminous, has settled to gray. It is not clear how natural selection can operate in the origin of folds or active site architecture (of proteins). It is equally unclear how either micromutations or macromutations could repeatedly and reliably lead to large evolutionary transitions. What remains is a deep, tantalizing, perhaps immovable mystery. http://inference-review.com/article/the-new-view-of-proteins

bornagain77

AH, kindly take a bucket, maybe a bait bucket. Fill with parts for an ABU 6500 C3 reel. Shake. How long before a functional reel will result? Extend to a stew of chemicals, moving about in a pond. On what empirical observation sustained grounds do you have that this can plausibly end in a cell based life form? And so forth, on through origin of body plans including the well-known gaps of AA chaining space. Remember, per Newton's common-sense rules, only mechanisms shown to be capable of the like results can be appealed to. It seems rather that it is you, sir who lack credible evidence but are relying on an ideological imposition; methodological naturalism. For, it is manifest that functionally specific complex organisation and associated information, on trillions of cases in point, does have just one readily observed effective cause: intelligently directed configuration. Indeed, your own comment is a case in point. When you can show such FSCO/I beyond 500 - 1000 bits created by blind chance and mechanical necessity, then you have something to say. Until then, you do not. KF kairosfocus

I added a 4th screen shot, which surfaces the isolated islands of function search challenge issue. 'Tis really not an issue at all. Go back and read all of Axe's research on the subject and answer this: were any of the allegedly non-functional variants in the mutational "determination" of functional sequence space actually assayed (directly) for enzyme activity? In case anyone is wondering, growth of E. coli is a very, very poor proxy for the enzyme activity that Axe is claiming to be studying. If that is all Axe (and Gauger) have, then they actually have no data to support their claims. None whatsoever. Arthur Hunt

It may be of interest to some to learn that the 'context dependency' of protein chains makes the probability of finding a specific functional protein by random search, as difficult as it currently is, far more difficult than Axe's current 1 in 10^77 number. Dr. Durston puts the situation with 'context dependency' like this:

(A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics – 2012 Excerpt (Page 4): The Probabilities Get Worse This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search. http://powertochange.com/wp-content/uploads/2012/11/Devious-Distortions-Durston-or-Myers_.pdf

The following paper demonstrated that protein chains are indeed 'context dependent'?

Proteins with cruise control provide new perspective: "A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order." http://www.princeton.edu/main/news/archive/S22/60/95O56/

A 'Cruise Control' mechanism permeating the entire protein structure? That is an absolutely fascinating discovery. Moreover this ‘oneness’ of context residing along the entire protein chain can only be achieved through quantum entanglement principles, and is inexplicable to the reductive materialistic framework of neo-Darwinism! And as Dr. Durston mentioned, "These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well." And just how many orders of magnitude is the probability reduced when the 'context dependency' of 'quantum' proteins is taken into consideration? I believe the following paper gives us a conservative ballpark estimate:

Quantum criticality in a wide range of important biomolecules Excerpt: “Most of the molecules taking part actively in biochemical processes are tuned exactly to the transition point and are critical conductors,” they say. That’s a discovery that is as important as it is unexpected. “These findings suggest an entirely new and universal mechanism of conductance in biology very different from the one used in electrical circuits.” The permutations of possible energy levels of biomolecules is huge so the possibility of finding even one that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,, “what exactly is the advantage that criticality confers?” https://medium.com/the-physics-arxiv-blog/the-origin-of-life-and-the-hidden-role-of-quantum-criticality-ca4707924552

As to the question in the last paper, “what exactly is the advantage that (quantum) criticality confers?”, I think the following paper gives us a big clue as to exactly what one advantage might be:

Symphony of Life, Revealed: New Imaging Technique Captures Vibrations of Proteins, Tiny Motions Critical to Human Life - Jan. 16, 2014 Excerpt: To observe the protein vibrations, Markelz' team relied on an interesting characteristic of proteins: The fact that they vibrate at the same frequency as the light they absorb. This is analogous to the way wine glasses tremble and shatter when a singer hits exactly the right note. Markelz explained: Wine glasses vibrate because they are absorbing the energy of sound waves, and the shape of a glass determines what pitches of sound it can absorb. Similarly, proteins with different structures will absorb and vibrate in response to light of different frequencies. So, to study vibrations in lysozyme, Markelz and her colleagues exposed a sample to light of different frequencies and polarizations, and measured the types of light the protein absorbed.,,, The researchers were also able to see that the vibrations endured over time, challenging existing assumptions. "If you tap on a bell, it rings for some time, and with a sound that is specific to the bell. This is how the proteins behave," Markelz said. "Many scientists have previously thought a protein is more like a wet sponge than a bell: If you tap on a wet sponge, you don't get any sustained sound." http://www.sciencedaily.com/releases/2014/01/140116084838.htm

Put simply, quantum criticality of proteins gives evidence of photon/phonon communication between proteins:

The Real Bioinformatics Revolution - Proteins and Nucleic Acids 'Singing' to One Another? Excerpt: the molecules send out specific frequencies of electromagnetic waves which not only enable them to ‘see' and ‘hear' each other, as both photon and phonon modes exist for electromagnetic waves, but also to influence each other at a distance and become ineluctably drawn to each other if vibrating out of phase (in a complementary way).,,, More than 1 000 proteins from over 30 functional groups have been analysed. Remarkably, the results showed that proteins with the same biological function share a single frequency peak while there is no significant peak in common for proteins with different functions; furthermore the characteristic peak frequency differs for different biological functions.,,, The same results were obtained when regulatory DNA sequences were analysed. http://www.i-sis.org.uk/TheRealBioinformaticsRevolution.php

Of related note: Photons emitted from the human body 'are well described by the signal in a quantum squeezed state of photons':

Photocount distribution of photons emitted from three sites of a human body - 2006 Excerpt: Signals from three representative sites of low, intermediate and high intensities are selected for further analysis. Fluctuations in these signals are measured by the probabilities of detecting different numbers of photons in a bin. The probabilities have non-classical features and are well described by the signal in a quantum squeezed state of photons. Measurements with bins of three sizes yield same values of three parameters of the squeezed state. http://www.ncbi.nlm.nih.gov/pubmed/16520060

It should also be noted that photon/phonon communication between proteins in a cell, (and even between cells), that is apparently achieved by some means of 'quantum criticality' along the entire protein structure, is a far more advanced means of communication than man has ever achieved in any of his machines. And is also as different from the 'randomly colliding' means of communication between proteins, that Darwinists had originally envisioned, as night is different from day:

"We have always underestimated cells. Undoubtedly we still do today. But at least we are no longer as naïve as we were when I was a graduate student in the 1960s. Then, most of us viewed cells as containing a giant set of second-order reactions: molecules A and B were thought to diffuse freely, randomly colliding with each other to produce molecule AB -- and likewise for the many other molecules that interact with each other inside a cell.,,,, But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered. Proteins make up most of the dry mass of a cell. But instead of a cell dominated by randomly colliding individual protein molecules, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines." - Bruce Alberts, "The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists," Cell, 92 (February 6, 1998): 291-294) Editor-in-Chief of Science (2009-2013). Dr Alberts served two six-year terms as the president of the National Academy of Sciences

Verse and Music:

Isaiah 40:28 Have you not known? Have you not heard? The LORD is the everlasting God, the Creator of the ends of the earth. He does not faint or grow weary; his understanding is unsearchable. How Great Thou Art as performed by Carrie Underwood and Vince Gill https://www.youtube.com/watch?v=q2T1csHUgF4

bornagain77

@1:14:20 question: What is undeniable? The design intuition that is universally inherent in the human being, but gets pushed down and suppressed as we grow older and get deeper into this world. I believe Dr. Axe's book won't bring anyone to Christ, but it might stir up strong curiosity to seriously approach God's general revelation (i.e. His creation) and eventually encounter the truth in God's special revelation (i.e. His word). Dionisio

Dr. Axe's presentation is very interesting. The Q/A session that follows is very insightful too. Early in his presentation Dr. Axe said he was not committed to trying to convince the inconvincible. That's an excellent concept, which is biblical. None of us can write or say anything that would convince an inconvincible person. Only God can ultimately do that, if it's according to His will and for His glory. Christ Himself converted the most zealous anti-Christian Saul of Tarsus into the apostle Paul -the most prolific Christian writer in history, author of a substantial part of the New Testament. Through Paul's letters God has convinced the most inconvincible people. The same may apply -to some extent- to the debates that take place here in this site. The way a person answers simple questions may reveal whether that person has genuine desires to know the truth. The Bible tells us not to squander precious time on senseless arguments with anyone who does not desire to join others in finding the truth. Dionisio

Very interesting subject: Design intuition in children, which is beaten out of us, suppressed, as we grow older. Design intuition: observation -> question -> deduction Dr. Axe referred to The Wall Street Journal article "See Jane Evolve: Picture Books Explain Darwin". The word 'intuition' according to Merriam-Webster dictionary:

the power or faculty of attaining to direct knowledge or cognition without evident rational thought and inference Simple Definition of intuition 1 : a natural ability or power that makes it possible to know something without any proof or evidence : a feeling that guides a person to act a certain way without fully understanding why 2 : something that is known or understood without proof or evidence

Interestingly Dr. Axe said he wants to take the message to a wide audience, i.e. as many people as possible. @45:30 truth can be counterintuitive ? Darwin proposed two things: the so-called tree of life random variation (mutation) and natural selection as the cause of the tree of life @47:30 ID does not take side in the debate between CD and UD? @50 arguments from probability can be vulnerable ? @1:00:00 relativism vs. realism debate? @1:03:20 2-yo child does science? @1:06:10 creativity associated with some kind of intuition ? moment of inspiration? Dionisio

KF Thank you for posting this. BTW, @4:

But don’t you unnner-stand? SCIENCE is the only begetter of truth, and all right-thinking people know that SCIENCE is evolutionary materialistic.

Apparently that's how it goes these days and we have no choice but accept it. Pathetic. Dionisio

PS: I added a 4th screen shot, which surfaces the isolated islands of function search challenge issue. kairosfocus

News: I added a clip with a cite of the key thesis from the blurb. [I ended up with a trio.] (News, I also put the vid link back up top using the embed widget again -- I hope it is visible to all.) D: But don't you unnner-stand? SCIENCE is the only begetter of truth, and all right-thinking people know that SCIENCE is evolutionary materialistic. KF kairosfocus

Then maybe D. Axe's new book seriously addressing fundamental scientific issues will be in the 'Religion/Philosophy' sections of some bookstores while R. Dawkins' pseudoscience books mocking and whining against belief in God are displayed in the 'Science' sections? Welcome to this world! :) Dionisio

I added embed code so the vid shows on this page Also note #1 in developmental biology as of this morning, which I have swatched in. - News News

The report for the general public on 25 years of technical research on whether blind chance and mechanical necessity can credibly create significantly novel complex proteins and genes. kairosfocus