Key prediction of Darwinian evolution falsified?

_{Denyse O'Leary

July 29, 2015

Culture, Darwinism, Evolution}

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Biological life requires thousands of different protein families, about 70% of which are ‘globular’ proteins, each with a 3-dimensional shape that is unique to each family of proteins. An example is shown in the picture at the top of this post. This 3D shape is necessary for a particular biological function and is determined by the sequence of the different amino acids that make up that protein. In other words, it is not biology that determines the shape, but physics. Sequences that produce stable, functional 3D structures are so rare that scientists today do not attempt to find them using random sequence libraries. Instead, they use information they have obtained from reverse-engineering biological proteins to intelligently design artificial proteins.

Indeed, our 21st century supercomputers are not powerful enough to crunch the variables and locate novel 3D structures. Nonetheless, a foundational prediction of neo-Darwinian theory is that a ploddingly slow evolutionary process consisting of genetic drift, mutations, insertions and deletions must be able to ‘find’ not just one, but thousands of sequences pre-determined by physics that will have different stable, functional 3D structures. So how does this falsifiable prediction hold up when tested against real data? As ought to be the case in science, I have made available my program so that you can run your own data and verify for yourself the kinds of probabilities these protein families represent. More.

Readers? Sensible responses wanted. (It’s getting so Darwin’s tenured trolls have nothing to offer but sneers, persecution, and—in the case of those afflicted with religiosity—Jesus-hollers in response.)

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Comments

daveS
given a quantum system (such as a molecule)
If I give you a system then you'll be starting with something that shows evidence of design - and therefore non-randomness - as all systems do. As I said elsewhere, you can't start with a system and then claim no-design. There needs to be evidence that chaos can produce a quantum system. Failing that, we have indisputable evidence of Design.Silver Asiatic_{July 31, 2015
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jerry: But that is the debate, the origin of proteins or new alleles. jerry: provide the evidence for the origin of a new protein family. Is there a reason you moved the goalposts? Silver Asiatic: Random, Non-Random (Design) Non-random Design, so that's a false dichotomy.Zachriel_{July 31, 2015
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Silver Asiatic, Well, ppolish was responding specifically to Zachriel's statement that the movement of molecules is random, and from context it's clear that the list of equations/phenomena that he posted was meant to contradict Zachriel. The Born Rule tells you, given a quantum system (such as a molecule) and an observable (for example position or momentum), what the possible outcomes and corresponding probabilities are for measurements of this observable. Under the Copenhagen interpretation, the outcomes are determined randomly by the above data.daveS_{July 31, 2015
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as to Zach at 41:
"ppolish: Along with 2nd Law of Thermodynamics. Zach: Which is due to the law of large numbers, not guided by a conscious agent."
HUH? If anything ever gave overwhelming evidence as being the product of intelligent design, specifically God in this case, it is the second law of thermodynamics. The second law, i.e. entropy, is, by a wide margin, the most finely tuned of initial conditions of the Big Bang:
“The time-asymmetry is fundamentally connected to with the Second Law of Thermodynamics: indeed, the extraordinarily special nature (to a greater precision than about 1 in 10^10^123, in terms of phase-space volume) can be identified as the “source” of the Second Law (Entropy).” Roger Penrose - The Physics of the Small and Large: What is the Bridge Between Them? How special was the big bang? – Roger Penrose "This now tells us how precise the Creator’s aim must have been: namely to an accuracy of one part in 10^10^123." (from the Emperor’s New Mind, Penrose, pp 339-345 – 1989) Roger Penrose discusses initial entropy of the universe. – video http://www.youtube.com/watch?v=WhGdVMBk6Zo Multiverse and the Design Argument - William Lane Craig Excerpt: Roger Penrose of Oxford University has calculated that the odds of our universe’s low entropy condition obtaining by chance alone are on the order of 1 in 10^10(123), an inconceivable number. If our universe were but one member of a multiverse of randomly ordered worlds, then it is vastly more probable that we should be observing a much smaller universe. For example, the odds of our solar system’s being formed instantly by the random collision of particles is about 1 in 10^10(60), a vast number, but inconceivably smaller than 1 in 10^10(123). (Penrose calls it “utter chicken feed” by comparison [The Road to Reality (Knopf, 2005), pp. 762-5]). Or again, if our universe is but one member of a multiverse, then we ought to be observing highly extraordinary events, like horses’ popping into and out of existence by random collisions, or perpetual motion machines, since these are vastly more probable than all of nature’s constants and quantities’ falling by chance into the virtually infinitesimal life-permitting range. Observable universes like those strange worlds are simply much more plenteous in the ensemble of universes than worlds like ours and, therefore, ought to be observed by us if the universe were but a random member of a multiverse of worlds. Since we do not have such observations, that fact strongly disconfirms the multiverse hypothesis. On naturalism, at least, it is therefore highly probable that there is no multiverse. — Penrose puts it bluntly “these world ensemble hypothesis are worse than useless in explaining the anthropic fine-tuning of the universe”. http://www.reasonablefaith.org/multiverse-and-the-design-argument The Fine Tuning of the Universe - drcraigvideos - video https://www.youtube.com/watch?v=UpIiIaC4kRA A Matter of Considerable Gravity: On the Purported Detection of Gravitational Waves and Cosmic Inflation - Bruce Gordon - April 4, 2014 Excerpt: Thirdly, at least two paradoxes result from the inflationary multiverse proposal that suggest our place in such a multiverse must be very special: the "Boltzmann Brain Paradox" and the "Youngness Paradox." In brief, if the inflationary mechanism is autonomously operative in a way that generates a multiverse, then with probability indistinguishable from one (i.e., virtual necessity) the typical observer in such a multiverse is an evanescent thermal fluctuation with memories of a past that never existed (a Boltzmann brain) rather than an observer of the sort we take ourselves to be. Alternatively, by a second measure, post-inflationary universes should overwhelmingly have just been formed, which means that our existence in an old universe like our own has a probability that is effectively zero (i.e., it's nigh impossible). So if our universe existed as part of such a multiverse, it would not be at all typical, but rather infinitely improbable (fine-tuned) with respect to its age and compatibility with stable life-forms. http://www.evolutionnews.org/2014/04/a_matter_of_con084001.html
Moreover, in regards to establishing the relation of agent causality to thermodynamics, there is the quantum zeno effect:
Quantum Zeno Effect The quantum Zeno effect is,, an unstable particle, if observed continuously, will never decay. http://en.wikipedia.org/wiki/Quantum_Zeno_effect Quantum Zeno effect “It has been experimentally confirmed,, that unstable particles will not decay, or will decay less rapidly, if they are observed. Somehow, observation changes the quantum system. We’re talking pure observation, not interacting with the system in any way.” Douglas Ell – Counting to God – pg. 189 – 2014 – Douglas Ell graduated early from MIT, where he double majored in math and physics. He then obtained a masters in theoretical mathematics from the University of Maryland. After graduating from law school, magna cum laude, he became a prominent attorney. Interaction-free measurements by quantum Zeno stabilization of ultracold atoms – 14 April 2015 Excerpt: In our experiments, we employ an ultracold gas in an unstable spin configuration, which can undergo a rapid decay. The object—realized by a laser beam—prevents this decay because of the indirect quantum Zeno effect and thus, its presence can be detected without interacting with a single atom. http://www.nature.com/ncomms/2015/150414/ncomms7811/full/ncomms7811.html?WT.ec_id=NCOMMS-20150415
This is just fascinating! Why in blue blazes should conscious observation put a freeze on entropic decay, unless consciousness was/is more foundational to reality than entropy is? And seeing as how entropy is VERY foundational to reality, then I think the Theistic implications of all this are fairly obvious: Verses, Quote, and Music:
Romans 8:18-21 I consider that our present sufferings are not worth comparing with the glory that will be revealed in us. The creation waits in eager expectation for the sons of God to be revealed. For the creation was subjected to frustration, not by its own choice, but by the will of the one who subjected it, in hope that the creation itself will be liberated from its bondage to decay and brought into the glorious freedom of the children of God. Psalm 102:25-27 Of old You laid the foundation of the earth, And the heavens are the work of Your hands. They will perish, but You will endure; Yes, they will all grow old like a garment; Like a cloak You will change them, And they will be changed. But You are the same, And Your years will have no end. "We have the sober scientific certainty that the heavens and earth shall ‘wax old as doth a garment’.... Dark indeed would be the prospects of the human race if unilluminated by that light which reveals ‘new heavens and a new earth.’" Sir William Thomson, Lord Kelvin (1824 - 1907) - pioneer in many different fields, particularly electromagnetism and thermodynamics. Evanescence – The Other Side (Lyric Video) http://www.vevo.com/watch/evanescence/the-other-side-lyric-video/USWV41200024?source=instantsearch
bornagain77_{July 31, 2015
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The options are: Random Non-Random (Design) "We don't know" is not an option when it comes to arriving at the best explanation with the evidence we have.Silver Asiatic_{July 31, 2015
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Yes. There is evidence that new proteins have evolved. And there is evidence that random sequences can fold into simple functional proteins.
But I understand it all minimal. Even Brosius, the main one pushing new usable sequences, provides only simple changes. If not, provide the evidence for the origin of a new protein family.jerry_{July 31, 2015
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Zachriel:
Yes. There is evidence that new proteins have evolved
No, there isn't any evidence any proteins evolved by natural selection and/ or drift
And there is evidence that random sequences can fold into simple functional proteins.
Yet there isn't any evidence that natural selection and/ or drift can produce those random sequencesVirgil Cain_{July 31, 2015
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ppolish: Along with 2nd Law of Thermodynamics. Which is due to the law of large numbers, not guided by a conscious agent. ppolish: "The movement of molecules is random." Perhaps we should have included the definite article. "The movement of the molecules is random, like the roll of dice are random," but it was clear from context that we were referring to a gas filling a chamber. Box: We all know that there is nothing random about protein folding, so your weather analogy fails miserably. Weather isn't random either. jerry: But that is the debate, the origin of proteins or new alleles. Yes. There is evidence that new proteins have evolved. And there is evidence that random sequences can fold into simple functional proteins.Zachriel_{July 31, 2015
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Box
We all know that there is nothing random about protein folding, so your weather analogy fails miserably.
That's it, simply put. Weather has somewhat random inputs and therefore produces hard to predict, non-functional outputs. Protein-folds are systems that produce specific, functional outputs. Non-ordered, chaotic, randomness supposedly created an ordered, functional system. You have to start with no-process, non-system, nothing-ordered (because processes, systems and ordered elements are evidence of Design) and produce the fully precise, specified system. This can't even be done with a pseudo-random (designed) simulations trying to produce the most primitive level of order. No, wait ... I just gave away far too much. It can't be done at all. Theoretically it's impossible. If randomness produces ordered systems, then it wasn't randomness. That's just true by definition. So, materialism fails before it can even evaluate anything. To claim that chaos produced processes and ordered systems is to say something contradictory - intellectually incoherent. It's in the nature of randomness that it cannot produce systemic processes. Keeping in mind that the nature of the variables (molecules, forces) have to be non-ordered (therefore no evidence of having been designed) in their properties, motions, powers.Silver Asiatic_{July 31, 2015
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For those interested in the actual discussion by Durston go here http://p2c.com/students/blogs/kirk-durston/2015/07/computing-best-case-probability-proteins-actual-data-and-falsification http://p2c.com/sites/default/files/documents/blogs/kirk/Devious-Distortions-Durston-or-Myers_.pdf Apparently all the storms from the beginning of the universe would not have enough resources to form one significant protein let alone the thousands of protein families needed for life if the elements of the storm were amino acids. Of course they're not. But that is the debate, the origin of proteins or new alleles. If they arose naturally, then there should be evidence in the genomes of existing organisms and this is testable with the ever diminishing cost of sequencing a genome and analyzing them.jerry_{July 31, 2015
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daveS
Are you familiar with the meanings of all those equations and their derivations, ppolish?
It's not the outputs of those equations that is important, but their origin and why supposed chance elements are measurable by such things. The point to that listing is that it's abundant evidence of Design.Silver Asiatic_{July 31, 2015
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Steveh: However, the comments you quoted make no sense to me. Our most powerful 21st century computers struggle to simulate the weather conditions we will experience in any part of the world with any accuracy more than a few days into the future, but the weather just happens continuously without doing any computations.
Proteins cannot come into existence without "computations".
Steveh: Similarly a protein may fold in a fraction of a second, but a supercomputer may take several weeks to simulate it.
We all know that there is nothing random about protein folding, so your weather analogy fails miserably.Box_{July 31, 2015
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OT: 90 Minutes In Heaven - In Theaters September 11 - trailer http://90minutesinheaventhemovie.com/bornagain77_{July 31, 2015
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steveh
So how can you design the protein sequences needed to achieve a novel new function if you can’t simulate the evolution of protein folding sequences?
If you're designing something, then it's not evolution. You don't need evolutionary mechanisms to create new designs. As mentioned, evolution searches random sequence libraries, but a design approach can reverse engineer to extract and use information.
designers using universe-sized computers – if such a thing were possible – would be doomed to an eternity of waiting and error (See also: “Waterloo”).
If the evolution of protein folds could be observed in real-time then you'd have something here. But nobody has observed such a thing.Silver Asiatic_{July 30, 2015
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KF, Feynman's 1965 "Messenger Series" lectures are up on YouTube. I've been listening to them as I fall asleep at night. Wonderful stuff. One of these days I'll watch them to see what he's writing on the blackboard:) And thanks for that link.ppolish_{July 30, 2015
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No, DaveS, but I did stay at a Holiday Inn Express last night. And that makes me smart enough to realize the shape of 3D Protein Folds are about as random as the shape of the free breakfast waffles. Although turning molecules into waffles is much simpler than folding 3D Proteins.ppolish_{July 30, 2015
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Have fun: http://www.feynmanlectures.caltech.edu/kairosfocus_{July 30, 2015
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PS: I'd like to know your rationale for including the Born Rule to support your argument.daveS_{July 30, 2015
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Are you familiar with the meanings of all those equations and their derivations, ppolish?daveS_{July 30, 2015
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"The movement of molecules is random." Funny, Zachriel, real funny:) • F=ma • Newton’s law of gravity • The Maxwell equations • The laws of thermodynamics • Entropy and state-counting • Black body formula • Lorentz transformation • Mass energy conversion • Einstein’s field law • Expansion of the universe (homogeneous cosmology) • Schr ?odinger equation • Commutation relations and uncertainty principle • Born rule • Dirac equation • Yang-Mills equation • Renormalization group; running of couplings • Band Structure • Gap equation • Josephson effects • Bell’s inequality • Bekenstein-Hawking entropy formula http://frankwilczek.com/2015/princetonCompanionProposal08.pdfppolish_{July 30, 2015
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But the difference is, we can simulate the origin of rain clouds and lightning and wind in lab conditions. But we can’t simulate the evolution of protein folding processes.
So how can you design the protein sequences needed to achieve a novel new function if you can't simulate the evolution of protein folding sequences? And even if you could, how would you simulate all of the difficult to predict knock-on effects? Biology, Chemistry and Physics just get on with it in real time but designers using universe-sized computers - if such a thing were possible - would be doomed to an eternity of waiting and error (See also: "Waterloo").steveh_{July 30, 2015
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Law of Gravity, Zach. Along with 2nd Law of Thermodynamics. Unless you spill on the International Space Station. Then it's mostly 2nd Law. Atoms guided through the void. Guided.ppolish_{July 30, 2015
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ppolish: It’s why spilt milk doesn’t jump back in the bowl. Thought that was due to gravity.Zachriel_{July 30, 2015
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Zachriel, the motion of atoms is most definitely guided. Guided by many Laws. It's why spilt milk doesn't jump back in the bowl. In fact, guided motion gives the impression that "time is passing". But time is an illusion - guided motion is real. Guidance with a capital G.ppolish_{July 30, 2015
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BA77 #14 “It proves that measurement is everything. ... which means the person, the observer is everything.Axel_{July 30, 2015
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ppolish #3 '“Unguided” and “Purposeless” is not real science.' The best it can be is a blotting pad.Axel_{July 30, 2015
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Zachriel:
The movement of molecules is random.
In what way are they "random"?Virgil Cain_{July 30, 2015
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BA77 (8), thanks for the link: Eugene Wigner Quantum Physics Debunks Materialism – video playlist This is profound! He is not saying that "materialism is not enough to explain it", he is saying "materialism doesn't exist at all." Without mind, without consciousness, well, nothing.bFast_{July 30, 2015
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Silver Asiatic: The gas fills nooks and crannies because of ordered, non-random physical forces. No. The movement of molecules is random. It's the law of large numbers that results in the gas acting as if it were moving methodically to fill the nooks and crannies of the chamber. Silver Asiatic: The gas does not change the boundaries of the nook. The gas doesn’t shape it’s own niche. Sure it can. Silver Asiatic: But they also cannot be modeled because the variables cannot be defined – they’re continually changing by entry or exit of organisms in or out of the niche and the full range of environmental conditions that create and destroy the niche. There are plenty of simple examples, even in nature, such as exposure of a bacteria to antibiotics.Zachriel_{July 30, 2015
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Z
A gas will fill the nooks and crannies of an enclosure even though the molecular movement is random. Indeed, the gas acts as if it were flowing into the empty spaces.
In a pure sense, the molecular movement is also bounded, ordered by certain properties and therefore predictable. The gas fills nooks and crannies because of ordered, non-random physical forces. Ordered, predictable systems are evidence of design. But beyond that, even calling the molecules random, the nooks and crannies are observable and definable. The gas does not change the boundaries of the nook. The gas doesn't shape it's own niche. Biological niches are imaginary, in the first place - they could be a physical space or a relationship or a process (bees fill the niche of organisms that use pollen) or something else. But they also cannot be modeled because the variables cannot be defined - they're continually changing by entry or exit of organisms in or out of the niche and the full range of environmental conditions that create and destroy the niche. The organisms themselves create and shape the niche in unpredictable ways.
http://www.nature.com/news/does-evolutionary-theory-need-a-rethink-1.16080 Volcanic eruptions are idiosyncratic events, independent of organisms’ actions. By contrast, termites construct and regulate their homes in a repeatable, directional manner that is shaped by past selection and that instigates future selection. Similarly, mammals, birds and insects defend, maintain and improve their nests — adaptive responses to nest building that have evolved again and again7. This ‘niche construction’, like developmental bias, means that organisms co-direct their own evolution by systematically changing environments and thereby biasing selection7.
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