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Are Darwinian claims for evolution consistent with the 2nd law of thermodynamics?

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A friend wrote to ask because he came across a 2001 paper, Entropy and Self-Organization in Multi-Agent Systems by H. Van Dyke Parunak and Sven Brueckner Proceedings of the International Conference on Autonomous Agents (Agents 2001), 124-130:

Emergent self-organization in multi-agent systems appears to contradict the second law of thermodynamics. This paradox has been explained in terms of a coupling between the macro level that hosts self-organization (and an apparent reduction in entropy), and the micro level (where random processes greatly increase entropy). Metaphorically, the micro level serves as an entropy “sink,” permitting overall system entropy to increase while sequestering this increase from the interactions where selforganization is desired. We make this metaphor precise by constructing a simple example of pheromone-based coordination, defining a way to measure the Shannon entropy at the macro (agent) and micro (pheromone) levels, and exhibiting an entropybased view of the coordination.

The thought seems to be that entropy decreases here but somehow increases somewhere where we can’t see it.

I’ve (O’Leary for News) always thought that a fishy explanation, especially because I soon discovered that even raising the question is considered presumptive evidence of unsound loyalties. The sort I am long accustomed to hearing from authoritarians covering up a scandal.

So not only do I not believe it, but after that sort of experience I get the sense I shouldn’t believe it. Depending on where I am working, I might need to parrot it to keep my job, of course, but it would be best not to actually believe it.

Dr Sheldon
Rob Sheldon

Rob Sheldon told us both,

What you read is the “standard” physics response. It is misleading on many levels.

a) Physicists really, really can’t explain what goes on in biology. Neither their definition of entropy, nor their definition of information (Shannon, etc) work. Rather than admit that they don’t know what is going on, they simply extrapolate what they do know (ideal gasses) to biology and make pronouncements.

b) While it is true that “open” systems may allow energy and matter to flow through them, which would change the information in the system, this does not nor cannot explain biology. The best treatment of this is Granville Sewell’s articles on different types of entropy. Truly excellent. It explains why sunlight does not carry enough information to create life out of precursor molecules. And people who claim this are either: (i) deluded that physics entropy = biology entropy, or (ii) equivocating on the use of the word “entropy”, or (iii) unable to handle basic math, or most likely, (iv) all the above.

c) This paper suggests that the cell has machinery for converting sunlight to information–e.g. photosynthesis. While true, this machine must be even more complicated than the carbohydrates it produces. Ditto for self-replicating machinery, etc. So if we permit some high level of information to enter the system, then low-level information can be created from energy sources. This argument really is indistinguishable from ID, though they may not realize it.

In conclusion, the violation of the 2nd Law remains true for biology, and there still is no good physics explanation for it.

It’s a good thing they didn’t realize it. They won’t have to issue some embarrassing repudiation of their work.

And I don’t have to believe something for which we have no evidence just to protect the tenurebots’ theory.

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Comments
Zachriel:
With a refrigerator, it’s not ‘information’ that enters, but electrical energy.
So electrical energy cools?
In any case, adding intelligence, as in Intelligent Design, does not allow one to violate the 2nd Law of Thermodynamics.
It allows there to be order out of disorder. It allows for the order to be maintained longer than if nature operated freely.
Are you claiming that the intelligence somehow rearranges matter to “inject information”?
That seems to be what we do.Joe
March 4, 2015
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Box: Yes it is indeed consistent, because the information enters from the outside. With a refrigerator, it's not 'information' that enters, but electrical energy. In any case, adding intelligence, as in Intelligent Design, does not allow one to violate the 2nd Law of Thermodynamics. Are you claiming that the intelligence somehow rearranges matter to inject 'information'? If so, there is cost measured in work. What is the origin of the requisite energy?Zachriel
March 4, 2015
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Hangonasec:
Fine, GAs don’t model unguided evolution AND they demonstrate that unguided evolution leads to genetic entropy.
Wrong. They CAN be used to demonstrate unguided evolution leads to genetic entropy.Joe
March 4, 2015
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Zachriel: Life and evolution are consistent with the 2nd Law of Thermodynamics, as are refrigerators and designer genes.
Yes it is indeed consistent, because the information enters from the outside.
Sewell: (...) we conclude that the fact that order can increase in an open system does not mean that tornados can turn rubble into houses and cars without violating the second law. And it does not mean that computers can appear on a barren planet as long as the planet receives solar energy. Something must be entering from outside which makes the appearance of computers not extremely improbable, for example, computers.
Box
March 4, 2015
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Adding intelligence, as in Intelligent Design, does not allow one to violate the 2nd Law of Thermodynamics. Life and evolution are consistent with the 2nd Law of Thermodynamics, as are refrigerators and designer genes.Zachriel
March 4, 2015
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Biological Information - Entropy, Evolution and Open Systems, 11-15-2014 by Paul Giem - at youtube. I notice some silly 'arguments' in this thread. E.g. Gordon Davisson who seems to argue that there is a meaningful relationship between gravity and the organizational order that Granville Sewell is talking about - humans, cars, high-speed computers, libraries full of science texts and encyclopedias, TV sets, airplanes and spaceships. One has to wonder if by "Oh good grief, not this nonsense again." Gordon really addresses his own drivel.Box
March 4, 2015
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Hey Joe, if you don't mind being logically inconsistent ... what am I saying? You're Joe! Fine, GAs don't model unguided evolution AND they demonstrate that unguided evolution leads to genetic entropy. That's logic, that is!Hangonasec
March 4, 2015
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Hangonasec:
If they don’t model unguided evolution, Sanford’s GA cannot be used to support the contention that unguided evolution leads to ‘genetic entropy’
Cuz you say so?Joe
March 4, 2015
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Joe - and therefore ... ? If they don't model unguided evolution, Sanford's GA cannot be used to support the contention that unguided evolution leads to 'genetic entropy'. That thing with a hole in it - that's your foot, Joe. :DHangonasec
March 4, 2015
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Hangonasec:
As for Sanford – too funny; GAs suddenly work just fine, with no accusations of ‘smuggling’, when one appears to dismantle evolution.
GAs do work fine. They just do not model unguided evolution.Joe
March 4, 2015
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Of related note, entropy is the ultimate cause of the death for our temporal, i.e. material, bodies:
Entropy Explains Aging, Genetic Determinism Explains Longevity, and Undefined Terminology Explains Misunderstanding Both - 2007 Excerpt: There is a huge body of knowledge supporting the belief that age changes are characterized by increasing entropy, which results in the random loss of molecular fidelity, and accumulates to slowly overwhelm maintenance systems [1–4].,,, http://www.plosgenetics.org/article/info%3Adoi/10.1371/journal.pgen.0030220 John Sanford on (Genetic Entropy) - Down, Not Up - 2-4-2012 (at Loma Linda University) - video http://www.youtube.com/watch?feature=player_detailpage&v=PHsu94HQrL0#t=1040s Notes from John Sanford's preceding video: *3 new mutations every time a cell divides in your body * Average cell of 15 year old has up to 6000 mutations *Average cell of 60 year old has 40,000 mutations Reproductive cells are 'designed' so that, early on in development, they are 'set aside' and thus they do not accumulate mutations as the rest of the cells of our bodies do. Regardless of this protective barrier against the accumulation of slightly detrimental mutations still we find that,,, *60-175 mutations are passed on to each new generation.
This following video brings the point personally home to us about the effects of genetic entropy:
Aging Process - 85 years in 40 seconds - video http://www.youtube.com/watch?v=A91Fwf_sMhk
Also of interest is where the greatest source of entropy is found in the universe:
Entropy of the Universe – Hugh Ross – May 2010 Excerpt: Egan and Lineweaver found that supermassive black holes are the largest contributor to the observable universe’s entropy. They showed that these supermassive black holes contribute about 30 times more entropy than what the previous research teams estimated. http://www.reasons.org/entropy-universe “Einstein’s equation predicts that, as the astronaut reaches the singularity (of the black-hole), the tidal forces grow infinitely strong, and their chaotic oscillations become infinitely rapid. The astronaut dies and the atoms which his body is made become infinitely and chaotically distorted and mixed-and then, at the moment when everything becomes infinite (the tidal strengths, the oscillation frequencies, the distortions, and the mixing), spacetime ceases to exist.” Kip S. Thorne – “Black Holes and Time Warps: Einstein’s Outrageous Legacy” pg. 476
Also of note, Christ's overcame gravity, and thus entropy, in his resurrection from death:
A Quantum Hologram of Christ’s Resurrection? by Chuck Missler Excerpt: “You can read the science of the Shroud, such as total lack of gravity, lack of entropy (without gravitational collapse), no time, no space—it conforms to no known law of physics.” The phenomenon of the image brings us to a true event horizon, a moment when all of the laws of physics change drastically. Dame Piczek created a one-fourth size sculpture of the man in the Shroud. When viewed from the side, it appears as if the man is suspended in mid air (see graphic, below), indicating that the image defies previously accepted science. The phenomenon of the image brings us to a true event horizon, a moment when all of the laws of physics change drastically. http://www.khouse.org/articles/2008/847 THE EVENT HORIZON (Space-Time Singularity) OF THE SHROUD OF TURIN. – Isabel Piczek – Particle Physicist Excerpt: We have stated before that the images on the Shroud firmly indicate the total absence of Gravity. Yet they also firmly indicate the presence of the Event Horizon. These two seemingly contradict each other and they necessitate the past presence of something more powerful than Gravity that had the capacity to solve the above paradox. http://shroud3d.com/findings/isabel-piczek-image-formation Turin shroud – (Particle Physicist explains event horizon) – video https://www.youtube.com/watch?v=HHVUGK6UFK8 The Center Of The Universe Is Life (Jesus) - General Relativity, Quantum Mechanics, Entropy and The Shroud Of Turin - video http://vimeo.com/34084462
Verses and Music:
John 8:23-24 But he continued, “You are from below; I am from above. You are of this world; I am not of this world. I told you that you would die in your sins; if you do not believe that I am he, you will indeed die in your sins. Matthew 10:28 “Do not fear those who kill the body but are unable to kill the soul; but rather fear Him who is able to destroy both soul and body in hell. Colossians 1:15-20 The Son is the image of the invisible God, the firstborn over all creation. For in him all things were created: things in heaven and on earth, visible and invisible, whether thrones or powers or rulers or authorities; all things have been created through him and for him. He is before all things, and in him all things hold together. And he is the head of the body, the church; he is the beginning and the firstborn from among the dead, so that in everything he might have the supremacy. For God was pleased to have all his fullness dwell in him, and through him to reconcile to himself all things, whether things on earth or things in heaven, by making peace through his blood, shed on the cross. Evanescence – The Other Side (Music-Lyric Video) http://www.vevo.com/watch/evanescence/the-other-side-lyric-video/USWV41200024?source=instantsearch
bornagain77
March 4, 2015
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LoL!@ Me Think- Read MoranJoe
March 4, 2015
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Bob O'H as to this question,,,
As a layman, if there truly is no conflict between evolution and thermodynamics, then why did Dr. Behe formulate the first rule,
you state in responce to that question:
Because what Behe wrote doesn’t involve thermodynamics.
Really??? and yet Dr. Behe states that ' that even the great majority of helpful mutations degrade the genome to a greater or lesser extent' :
Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.
So Bob O'H in your book, this tendency towards degradation, i.e. disorder, instead of towards order that Behe found, for laboratory evolution experiments of microbes going back four decades no less, does not reflect the Second Law's tendency to drive everything in the universe towards disorder??? What, pray tell, is this 'other' law operating in the universe besides the second law that is driving living systems towards disorder? And why can't we separate that unknown law's overall effect from the second law's overall effect to drive everything in the universe towards disorder?
A 'flat universe', which is actually another very surprising finely-tuned 'coincidence' of the universe, means this universe, left to its own present course of accelerating expansion due to Dark Energy, will continue to expand forever, thus fulfilling the thermodynamic equilibrium of the second law to its fullest extent (entropic 'Heat Death' of the universe). The Future of the Universe (Heat Death) Excerpt: After all the black holes have evaporated, (and after all the ordinary matter made of protons has disintegrated, if protons are unstable), the universe will be nearly empty. Photons, neutrinos, electrons and positrons will fly from place to place, hardly ever encountering each other. It will be cold, and dark, and there is no known process which will ever change things. --- Not a happy ending. http://spiff.rit.edu/classes/phys240/lectures/future/future.html Shining Light on Dark Energy – October 21, 2012 Excerpt: It (Entropy) explains time; it explains every possible action in the universe;,, Even gravity, Vedral argued, can be expressed as a consequence of the law of entropy. ,,, The principles of thermodynamics are at their roots all to do with information theory. Information theory is simply an embodiment of how we interact with the universe —,,, http://crev.info/2012/10/shining-light-on-dark-energy/ "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.’" Lord Kelvin 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.
Bob O'H, as to this question,,,
and why are mutations overwhelming detrimental,
you answer:
because (a) most of the fitness effects are tiny, so their effects are too small to notice,
Really??? Better inform these guys of that:
Unexpectedly small effects of mutations in bacteria bring new perspectives - November 2010 Excerpt: Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness. And this is the case regardless whether they lead to changes in the bacterial proteins or not.,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed. http://www.physorg.com/news/2010-11-unexpectedly-small-effects-mutations-bacteria.html
and as to this question Bob,,,
and why does all evidence support Dr. Sanford’s contention of Genetic Entropy?
you answer
(b) it doesn’t.
Really??? Man you Darwinists really ought to share some of the evidence that only you guys seem privy to! , The evidence for the detrimental nature of mutations in humans is overwhelming for scientists have already cited over 100,000 mutational disorders.
Inside the Human Genome: A Case for Non-Intelligent Design - Pg. 57 By John C. Avise Excerpt: "Another compilation of gene lesions responsible for inherited diseases is the web-based Human Gene Mutation Database (HGMD). Recent versions of HGMD describe more than 75,000 different disease causing mutations identified to date in Homo-sapiens." I went to the mutation database website cited by John Avise and found: Mutation total (as of 2014-05-02) - 148,413 http://www.hgmd.cf.ac.uk/ac/ Human Genetic Variation Recent, Varies Among Populations - (Nov. 28, 2012) Excerpt: Nearly three-quarters of mutations in genes that code for proteins -- the workhorses of the cell -- occurred within the past 5,000 to 10,000 years,,, "One of the most interesting points is that Europeans have more new deleterious (potentially disease-causing) mutations than Africans,",,, "Having so many of these new variants can be partially explained by the population explosion in the European population. However, variation that occur in genes that are involved in Mendelian traits and in those that affect genes essential to the proper functioning of the cell tend to be much older." (A Mendelian trait is controlled by a single gene. Mutations in that gene can have devastating effects.) The amount variation or mutation identified in protein-coding genes (the exome) in this study is very different from what would have been seen 5,000 years ago,,, The report shows that "recent" events have a potent effect on the human genome. Eighty-six percent of the genetic variation or mutations that are expected to be harmful arose in European-Americans in the last five thousand years, said the researchers. The researchers used established bioinformatics techniques to calculate the age of more than a million changes in single base pairs (the A-T, C-G of the genetic code) that are part of the exome or protein-coding portion of the genomes (human genetic blueprint) of 6,515 people of both European-American and African-American decent.,,, http://www.sciencedaily.com/releases/2012/11/121128132259.htm Scientists Discover Proof That Humanity Is Getting Dumber, Smaller And Weaker By Michael Snyder, on April 29th, 2014 Excerpt: An earlier study by Cambridge University found that mankind is shrinking in size significantly. Experts say humans are past their peak and that modern-day people are 10 percent smaller and shorter than their hunter-gatherer ancestors. And if that’s not depressing enough, our brains are also smaller. The findings reverse perceived wisdom that humans have grown taller and larger, a belief which has grown from data on more recent physical development. The decline, said scientists, has happened over the past 10,000 years. http://thetruthwins.com/archives/scientists-discover-proof-that-humanity-is-getting-dumber-smaller-and-weaker Human mutation rate slower than thought - Moms and dads not equal in passing down genetic typos - June 2011 Excerpt: the rate indicates that, on average, about one DNA chemical letter in every 85 million gets mutated per generation through copying mistakes made during sperm and egg production. The new rate means each child inherits somewhere in the neighborhood of 30 to 50 new mutations.,,, http://www.sciencenews.org/view/generic/id/331194/title/Human_mutation_rate_slower_than_thought
Interestingly, this ‘slightly detrimental’ mutation rate of 30 per generation is far greater than what even evolutionists agree is an acceptable mutation rate since detrimental mutations will accumulate far faster than ‘selection’ can eliminate them in any given genome:
Human evolution or extinction - discussion on acceptable mutation rate per generation (with clips from Dr. John Sanford) - video http://www.youtube.com/watch?v=aC_NyFZG7pM
bornagain77
March 4, 2015
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BA77 @5
As a layman, if there truly is no conflict between evolution and thermodynamics, then why did Dr. Behe formulate the first rule, and why are mutations overwhelming detrimental, and why does all evidence support Dr. Sanford’s contention of Genetic Entropy?
Why on earth would anyone think detrimental mutations involve more entropy change than beneficial ones? Apart, that is, from people with barely a clue what entropy is. I'll let Behe off; as a biochemist, he probably does know what entropy is, and therefore wisely steers clear of this most bogus of arguments, BA's co-option of his name notwithstanding. As for Sanford - too funny; GAs suddenly work just fine, with no accusations of 'smuggling', when one appears to dismantle evolution.Hangonasec
March 4, 2015
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Joe @ 12
Darwinian claims for evolution are consistent with astrology’s claims for the future. Astrology is science :-) Read Behe
Me_Think
March 4, 2015
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rvb8: You say you are not a maths and science major (which was no secret to anyone here, given the way you've always avoided detailed discussion of anything close to science), but you also say that you like Gordon Davisson's presentation because it's written in a way that you can understand. Really? So you understood this?: "calculate the X-entropy change as a block of X is compressed by 0.1% (i.e. compressed to 0.999 of its original volume." and this?: "If you integrate the final X-entropy over the original volume of the block, you’ll find that the change in X-entropy in the 0.1% that no longer contains X … diverges to negative infinity. If you integrate only over the final volume, the X-entropy change depends on a constant of integration … which is undefined." I'm not knocking Gordon's presentation, which seems to me to be pretty good (which is not to say I entirely agree with his conclusions, but only to give credit where it's due); I am questioning why you would agree with paragraphs which, given your self-admitted lack of training in the area, it is very unlikely that you comprehend. Or do you automatically agree with anything that seems to denounce ID, whether you understand it or not? It certainly *looks* as if you have read only the refutations of Sewell, and not Sewell's argument which is being refuted. If so, you have made up your mind without first hearing both sides. Charles Darwin directly stated that in order to get a fair intellectual result, one must hear both sides of any controversy. So you operate against the spirit of Darwin himself. (Which is not uncommon, for modern Darwinians.)Timaeus
March 4, 2015
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Darwinian claims for evolution are consistent with astrology's claims for the future. ;)Joe
March 4, 2015
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As a layman, if there truly is no conflict between evolution and thermodynamics, then why did Dr. Behe formulate the first rule,
Because what Behe wrote doesn't involve thermodynamics.
and why are mutations overwhelming detrimental, and why does all evidence support Dr. Sanford’s contention of Genetic Entropy?
because (a) most of the fitness effects are tiny, so their effects are too small to notice, and (b) it doesn't.Bob O'H
March 4, 2015
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RVB8 If you're hanging onto the words of Nick Matzke, you're not in very good company, we are still waiting for his book that proves macro-evolution. You might want to reconsider what you consider a trustworthy source.....Andre
March 3, 2015
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F/N: Sewell's core point -- never mind the many dismissals -- is right. Per Clausius' formulation, how we get the expression ds >/= d'Q/T, is that we consider two interacting bodies A and B within an isolated overall system; with A hotter than B. On passing increment of heat d'Q, and taking the ratio and adding up, the heat-importing body INCREASES its entropy by an amount sufficient to over-compensate for the loss of entropy in A on giving up the increment of heat. Crossing over into an informational, microscopic view (objectors tend to denigrate or dismiss this perspective) the added increment allows mass and energy in B to be distributed and arranged in more possible ways. This effectively means that the average missing information to specify the particular microstate of B consistent with its macro-scale [P,V, T etc] state, has increased sharply. That can be measured as string length of the chain of Y/N q's to describe the state. This means, in effect (and in first approximation terms), that a body that imports raw, uncorrelated energy not coupled to mechanisms that perform work, will tend to move towards a less ordered state. The notion that we may reasonably expect functionally specific, complex organisation and associated information [FSCO/I] relevant to cell based life to spontaneously emerge from such a raw energy injection, fails. Fails, because of the very premise of the statistical form of the 2nd law of thermodynamics: the probability (rooted in statistical weights] of special ordered -- much less, organised -- states on blind undirected needle in haystack search, is vanishingly small relative to the bulk of configurational possibilities. In short, on first principles, it is not reasonable to expect a warm sun-irradiated and lightning struck pond or the like to spontaneously open the gateway to C-chemistry, aqueous medium, encapsulated, gated, code and algorithm using cell based life. But, we live in an age where to say such is ever so politically incorrect and it will be denounced and attacked. In answer I say the same as I say to string theorists, multiverse aficionados and the like: SHOW me. I can readily show how raw e=nergy importation tends to ADD to entropy and to disorganise, starting with impacts of diffusion and destructive chemistry etc. If you want to argue for a successful Darwin's pond or the like and insist that thermodynamics and its underlying considerations have no constraining relevance, SHOW us empirically. I guarantee that once the exaggerated headlines and hype are set aside, it will be seen that it's froth not mauby. KF PS: Interested onlookers may wish to look here http://www.angelfire.com/pro/kairosfocus/resources/Info_design_and_science.htm#shnn_info . . . and here in my always linked briefing note: http://www.angelfire.com/pro/kairosfocus/resources/Info_design_and_science.htm#thermodkairosfocus
March 3, 2015
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Holy moley, BA77!! You're like Mr. Universe in the movie "Serenity". You have access to ALL the information! Those are some great links.William J Murray
March 3, 2015
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All of the tired 2nd Law nonsense is beautifully exposed at a new science friendly site compiled by the very smart, James Downard. It is Trouble In Paradise (TIP), and is available at http://tortucan.wordpress.com. Described by Matzke as a voluminous history of all forms of creationism, its contents covers all shannanigins upto 2004 and the eve of Dover. Apparently he is currently compiling 2004 to today soon. Downard has culled over 30,000 documents and all the embarassing missteps of the past are easily, and glaringly available; a new and uneditable resource for science history.rvb8
March 3, 2015
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Sewell's papers have been discussed at TSZ a number of times. Here are technical threads: A Second Look at the Second Law… Granville Sewell vs Bob Lloyd Granville Sewell Doubles Down The bottom line: Sewell does not understand statistical physics and thermodynamics all that well.skram
March 3, 2015
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As a layman, if there truly is no conflict between evolution and thermodynamics, then why did Dr. Behe formulate the first rule, and why are mutations overwhelming detrimental, and why does all evidence support Dr. Sanford's contention of Genetic Entropy?
“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/ Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - May 2013 Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11]. 1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696. 2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19. 3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358. 4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144. 5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47. 6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. 7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117. 8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526. 9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685. 10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079. 11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006 Genetic Entropy - Dr. John Sanford - Evolution vs. Reality - video (Notes in description) http://vimeo.com/35088933 "Moreover, there is strong theoretical reasons for believing there is no truly neutral nucleotide positions. By its very existence, a nucleotide position takes up space, affects spacing between other sites, and affects such things as regional nucleotide composition, DNA folding, and nucleosome building. If a nucleotide carries absolutely no (useful) information, it is, by definition, slightly deleterious, as it slows cell replication and wastes energy.,, Therefore, there is no way to change any given site without some biological effect, no matter how subtle." - John Sanford - Genetic Entropy and The Mystery of The Genome - pg. 21 - Inventor of the 'Gene Gun' "The neo-Darwinians would like us to believe that large evolutionary changes can result from a series of small events if there are enough of them. But if these events all lose information they can’t be the steps in the kind of evolution the neo-Darwin theory is supposed to explain, no matter how many mutations there are. Whoever thinks macroevolution can be made by mutations that lose information is like the merchant who lost a little money on every sale but thought he could make it up on volume." Lee Spetner (Ph.D. Physics - MIT - Not By Chance)
Now you may still insist there is no conflict between thermodynamics and evolution, but the empirical evidence itself tells me otherwise! Myself, not being versed in math, I think I will follow the evidence instead of you. Hope you don't mind.
The Scientific Method - Richard Feynman - video Quote: 'If it disagrees with experiment, it’s wrong. In that simple statement is the key to science. It doesn’t make any difference how beautiful your guess is, it doesn’t matter how smart you are who made the guess, or what his name is… If it disagrees with experiment, it’s wrong. That’s all there is to it.” https://www.youtube.com/watch?v=OL6-x0modwY
Of related note: Classical Information in the cell has now been physically measured and is shown to correlate to the thermodynamics of the cell:
Maxwell’s demon demonstration (knowledge of a particle’s position) turns information into energy – November 2010 Excerpt: Scientists in Japan are the first to have succeeded in converting information into free energy in an experiment that verifies the “Maxwell demon” thought experiment devised in 1867.,,, In Maxwell’s thought experiment the demon creates a temperature difference simply from information about the gas molecule temperatures and without transferring any energy directly to them.,,, Until now, demonstrating the conversion of information to energy has been elusive, but University of Tokyo physicist Masaki Sano and colleagues have succeeded in demonstrating it in a nano-scale experiment. In a paper published in Nature Physics they describe how they coaxed a Brownian particle to travel upwards on a “spiral-staircase-like” potential energy created by an electric field solely on the basis of information on its location. As the particle traveled up the staircase it gained energy from moving to an area of higher potential, and the team was able to measure precisely how much energy had been converted from information. http://www.physorg.com/news/2010-11-maxwell-demon-energy.html Demonic device converts information to energy – 2010 Excerpt: “This is a beautiful experimental demonstration that information has a thermodynamic content,” says Christopher Jarzynski, a statistical chemist at the University of Maryland in College Park. In 1997, Jarzynski formulated an equation to define the amount of energy that could theoretically be converted from a unit of information2; the work by Sano and his team has now confirmed this equation. “This tells us something new about how the laws of thermodynamics work on the microscopic scale,” says Jarzynski. http://www.scientificamerican.com/article.cfm?id=demonic-device-converts-inform
Moreover, Dr. McIntosh, who is the Professor of Thermodynamics Combustion Theory at the University of Leeds, holds that regarding information as independent of energy and matter ‘resolves the thermodynamic issues and invokes the correct paradigm for understanding the vital area of thermodynamic/organisational interactions’.
Information and Thermodynamics in Living Systems – Andy C. McIntosh – 2013 Excerpt: ,,, information is in fact non-material and that the coded information systems (such as, but not restricted to the coding of DNA in all living systems) is not defined at all by the biochemistry or physics of the molecules used to store the data. Rather than matter and energy defining the information sitting on the polymers of life, this approach posits that the reverse is in fact the case. Information has its definition outside the matter and energy on which it sits, and furthermore constrains it to operate in a highly non-equilibrium thermodynamic environment. This proposal resolves the thermodynamic issues and invokes the correct paradigm for understanding the vital area of thermodynamic/organisational interactions, which despite the efforts from alternative paradigms has not given a satisfactory explanation of the way information in systems operates.,,, http://www.worldscientific.com/doi/abs/10.1142/9789814508728_0008
Here is a recent video by Dr. Giem, that gets the main points of Dr. McIntosh’s paper over very well, in an easy to understand manner, for the lay person:
Biological Information – Information and Thermodynamics in Living Systems 11-22-2014 by Paul Giem (A. McIntosh) – video https://www.youtube.com/watch?v=IR_r6mFdwQM
bornagain77
March 3, 2015
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Thank you Gordon. Not being a scientist or maths major, it's always pleasant when explanations are given in a way I can follow. Like you, I exclaimed, 'this hoary old chestnut again, hasn't it been refuted, proved wrong, laughed at and then spanked for presumption dozens of times?' I knew it had, but couldn't be bothered with their tired reclamation of barren thought. Cheers!rvb8
March 3, 2015
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Oh good grief, not this nonsense again. Look, I know it's tempting to think there should be a conflict between evolution and thermodynamics, but nobody's actually been able to point one out. That certainly includes Granville Sewell: in the first place, he doesn't even claim to have found a conflict with the second law, only that he thinks there's some sort of conflict (that he can't precisely point out) and what he sees as the fundamental principle behind the second law (which is to say, not the second law itself). In the second place, his attempts to explain this fundamental principle are pretty obviously wrong. Let me point out two examples of how he gets it wrong, specifically problems with his X-Entropies (see e.g. section 2 of his article "Entropy, Evolution and Open Systems" in "BIO-Complexity and Biological Information: New Perspectives"). Essentially, he defines a family of entropy functions for each diffusing substance (e.g. the carbon-entropy), and winds up claiming:
Furthermore, equation (5) does not simply say that the X-entropy cannot decrease in an isolated system; it also says that in a non-isolated system, the X-entropy cannot decrease faster than it is exported through the boundary, because the boundary integral there represents the rate at which X-entropy is exported across the boundary.Furthermore, equation (5) does not simply say that the X-entropy cannot decrease in an isolated system; it also says that in a non-isolated system, the X-entropy cannot decrease faster than it is exported through the boundary, because the boundary integral there represents the rate at which X-entropy is exported across the boundary.
This is true in the situation he considered, but not true in general. I gave a simple counterexample back in 2011, and I'll repeat it here:
Consider a jar containing nitrogen gas and some powdered graphite (a form of carbon). Let me start with the jar’s contents thoroughly mixed: the graphite is uniformly scattered throughout the volume inside the jar, and it and the gas is all at the same temperature. What happens if the jar is isolated (except for gravity), and just left to sit for a while? All of the graphite will settle to the bottom; its arrangement is then more ordered, and in fact the carbon entropy within the jar has decreased. This does not, however, violate the second law of thermodynamics (as I’ll explain in a bit).
So what's happening in this example is what Sewell claims to have shown is impossible: a carbon-entropy decrease in an isolated system. Apparently, gravity is all it takes to violate his version of the second law. Now, you could complain that I'm talking about gasses and powders, while Sewell's calculations only apply to diffusion through a solid, but the same basic thing'll happen in solids as well (denser components diffusing toward the bottom, lighter ones toward the top). And besides, if Sewell's calculations only apply to solids, they're pretty thoroughly irrelevant to life, aren't they? Now, the next bit of my earlier post is also relevant, because it turns out that this is actually an example of what Denyse thinks is fishy: an entopy decrease of one sort being compensated for by an increase of another sort of entropy:
Something even more interesting happened to the distribution of thermal energy within the jar. As the graphite particles settle to the bottom, their gravitational energy is converted to kinetic energy (their downward motion), and then that’s converted to heat (both by friction as they fall, and the inelastic collisions when they hit the bottom of the jar). More of this heat is released near the bottom of the jar than the top, so the jar’s contents will become warmer at the bottom than the top. Intuitively (to me at least), this means that the heat has become more ordered. But the thermal entropy went up because there is more heat than at the beginning, and this outweighs the entropy decrease from nonuniformity. (As with human vs. bacterium, it seems to be that the best way to think of this is that since there’s more heat than there was at the beginning, it’s not a contradiction that the heat can be both more ordered and more disordered than it was at the beginning.) (BTW, the heat will eventually even out, removing the thermal order and increasing the thermal entropy even further.) So how does this fit with the second law of thermodynamics? It turns out that the increase in thermal entropy is larger than the decrease in carbon entropy, so the total entropy has increased, and the second law is satisfied. Sewell claims that the second law applies separately to each different kind of entropy, but this is not true in general. The only reason it works out that way in Sewell’s math is that there’s no coupling between the distribution of heat and carbon when they’re diffusing through a solid; anytime there’s any coupling between them, you can have conversion from one form of entropy to another.
I haven't read the Parunak and Brueckner paper yet, but from the abstract this seems to be the same sort of coupling they're talking about (although my example is certainly a lot simpler). I promised to point out two examples of problems with Sewell's analysis, so here's another. Well, actually, let me phrase this as a challenge for anyone who things his definition X-entropy makes mathematical sense: calculate the X-entropy change as a block of X is compressed by 0.1% (i.e. compressed to 0.999 of its original volume). This'll obviously require some knowledge of calculus, but anyone with the requisite expertise is welcome to take a stab at it (Sewell? Rob Sheldon? I'd suggest Sal Cordova, but he knows enough physics to realize the entropy arguments are bogus). The problem you're going to run into if you try to run the calculation is that the math falls apart. I don't mean it gives wrong answers, I mean it doesn't give meaningful answers. If you integrate the final X-entropy over the original volume of the block, you'll find that the change in X-entropy in the 0.1% that no longer contains X ... diverges to negative infinity. If you integrate only over the final volume, the X-entropy change depends on a constant of integration ... which is undefined. Either way, Sewell's math falls apart even for this very simple situation. Actually, I'll add a third problem (which also shows up in Jim Smith's comment #2): he misunderstands the relationship between entropy and probability. There's a direct relationship between entropy and probability only in the case of an isolated system fluctuating around thermodynamic equilibrium. In open systems fluctuating around equilibrium there's a more complicated relationship, and for non-equilibrium systems (e.g. pretty much everything relating to life) the relationship breaks down entirely.Gordon Davisson
March 3, 2015
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Entropy is a fancy word for probability. Even in an open system, you have to add up the probabilities to prove your point, you can't just wave your hands or make a declaration. For example, the fact that the earth is an open system does not allow tornadoes to turn rubble into buildings. You may find this relevant: http://bio-complexity.org/ojs/index.php/main/article/download/BIO-C.2013.2/BIO-C.2013.2 Entropy and Evolution Granville Sewell Mathematics Department, University of Texas, El Paso, Texas, USA Abstract It is widely argued that the spectacular local decreases in entropy that occurred on Earth as a result of the origin and evolution of life and the development of human intelligence are not inconsistent with the second law of thermodynamics, because the Earth is an open system and entropy can decrease in an open system, provided the decrease is compensated by entropy increases outside the system. I refer to this as the compensation argument, and I argue that it is without logical merit, amounting to little more than an attempt to avoid the extraordinary probabilistic difficulties posed by the assertion that life has originated and evolved by spontaneous processes. To claim that what has happened on Earth does not violate the fundamental natural principle behind the second law, one must instead make a more direct and difficult argument.Jim Smith
March 3, 2015
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OT: Stephen Meyer Talks ID on New Zealand's Leighton Smith Show, pt. 1 (February 2015) https://www.youtube.com/watch?v=bhsVUMvMAvM part 2 https://www.youtube.com/watch?v=yvHBSC5RYc4bornagain77
March 3, 2015
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