ID Foundations 15(c) — A FAQ on Front-Loading, thanks to Genomicus

_{kairosfocus

February 1, 2012

Cell biology, Genetics, ID Foundations, Origin Of Life}

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Onlookers, Geno concludes for the moment with FAQ’s:

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Geno: >>

A Testable ID Hypothesis: Front-loading, part C

In the last two articles on front-loading, I explained what the front-loading hypothesis is all about and some research questions we can ask from a front-loading perspective. This article will be an FAQ about the front-loading hypothesis. So, without further introduction, let’s begin (note: some of the content of this FAQ can be found in the previous two articles).

What is front-loading?

“Front-loading is the investment of a significant amount of information at the initial stage of evolution (the first life forms) whereby this information shapes and constrains subsequent evolution through its dissipation. This is not to say that every aspect of evolution is pre-programmed and determined. It merely means that life was built to evolve with tendencies as a consequence of carefully chosen initial states in combination with the way evolution works.” Mike Gene, The Design Matrix: A Consilience of Clues, page 147

In short, this ID hypothesis proposes that the earth was, at some point in its history, seeded with unicellular organisms that had the necessary genomic information to shape future evolution. Necessarily, this genomic information was designed into their genomes.

How is front-loading different from directed panspermia?

In a paper published in the journal Icarus, Francis Crick and Leslie Orgel proposed the hypothesis of directed panspermia. According to this hypothesis, the earth was intentionally seeded with life forms by some intelligence. The front-loading hypothesis goes a step further and proposes that these life forms contained the necessary genomic information to shape the course of future evolution. For example, the origin of metazoan complexity would have been planned and anticipated by the genomic information in the first genomes. Thus, the front-loading hypothesis is inherently teleological and an ID hypothesis.

Does front-loading propose that all the genes found in life were in the first life forms?

No, it does not. Front-loading does not suggest that all genes were there from the start. Indeed, many genes found in modern life forms are probably the result of purely unplanned mechanisms (gene duplication and subsequent divergence, for example). Nevertheless, genes essential for the origin and development of the metazoan body plan would be present in the first genomes (or have homologs in the first genomes).

If genes necessary for the origin of metazoan life forms were placed, then random mutation would have destroyed them and they would decay, right?

This is a common objection to the front-loading hypothesis, but it can be easily answered. These genes would be given an important function in the first life forms, such that they would be preserved across deep time. Front-loading doesn’t involve much of simply turning genes (that were previously unexpressed) on at some given time.

How could sophisticated molecular systems be front-loaded?

There are two basic solutions to the problem of front-loading sophisticated molecular systems, but more research is needed so that we can find out exactly how these solutions would work in practice. In theory, however, there’s the “bottom up” approach and the “top down” approach to front-loading molecular systems. In the “bottom up” approach, the original cells would contain the components of the molecular machine we want to front-load, but these components would be carrying out functions not related to the function of the molecular machine. Then, somehow (here’s where we need research), something causes them to associate such that they fit nicely with each other, forming a novel molecular machine.

The “top down” approach proposes that the first cells had a highly complex molecular machine, composed of, say, components A, B, C, D, E, F, G, H, and J. If we want to front-load a molecular machine composed of components A, B, C, and D, then this highly complex molecular machine contains a functional subset of A, B, C, and D. In other words, components E, F, G, H, and J would simply have to be deleted from the highly complex molecular machine, resulting in a molecular machine composed of A, B, C, and D. This model is actually testable. Under this model, we would tentatively predict that a homologous system of a molecular machine will be more complex if it is more ancient than the molecular machine.

What testable predictions does the front-loading hypothesis make?

There are several testable predictions the front-loading hypothesis makes:

Cytosine deamination. Of the three bases in DNA (adenine, guanine, and cytosine) that are prone to deamination, cytosine is the most likely to undergo deamination. This ultimately results in a C –> T transition. Cytosine deamination often causes severe genetic diseases in humans, so why would a front-loader choose cytosine as a base in DNA? It has been observed that C –> T transitions result in a pool of strongly hydrophobic amino acids, which leads to the following prediction from a front-loading perspective: a designer would have chosen cytosine because it would facilitate front-loading in that mutations could be channeled in the direction of increased hydrophobicity. This prediction would be confirmed if key protein sequences in metazoan life forms were the result of numerous C –> T transitions.
The genetic code. The front-loading hypothesis proposes that the universal optimal genetic code was present at the dawn of life: in other words, we won’t find precursors of sub-optimal genetic codes, because the genetic code was optimal from the start. Further, the front-loading hypothesis predicts that all 20 amino acids would have been used in the first life forms, and that the transcription, translation, and proof-reading machinery would have all been present at the start of life on earth.
Biological complexity. Front-loading predicts that the last universal common ancestor (LUCA) was quite complex, complete with genes necessary for the origin and development of metazoan life forms.
Protein sequence conservation. In eukaryotes, there are certain proteins that are extremely important. For example, tubulin is an important component of cilia; actin plays a major role in the cytoskeleton and is also found in sarcomeres (along with myosin), a major structure in muscle cells; and the list could go on. How could such proteins be front-loaded? Of course, with some of these proteins they could be designed into the initial life forms, but some of them are specific to eukaryotes, and for a reason: they don’t function that well in a prokaryotic context. For these proteins, how would a designer front-load them? Let’s say X is the protein we want to front-load. How do we go about doing this? Well, firstly, we can design a protein, Y, that has a very similar fold to X, the future protein we want to front-load. Thus, a protein with similar properties to X can be designed into the initial life forms. But what is preventing random mutations from basically destroying the sequence identity of Y, over time, such that the original fold/sequence identity of Y is lost? To counter this, Y can also be given a very important function so that its sequence identity will be well conserved. Thus, we can make this prediction from a front-loading perspective: proteins that are very important to eukaryotes, and specific to them, will share deep homology (either structurally or in sequence similarity) with prokaryotic proteins, and importantly, that these prokaryotic proteins will be more conserved in sequence identity than the average prokaryotic protein. Darwinian evolution only predicts the first part of that: it doesn’t predict that part that is in bold text. This is a testable prediction made exclusively by the front-loading hypothesis.

Does the front-loading hypothesis suggest that evolution was programmed?

No. Front-loading does not propose that all biological innovations were the result of planning and teleology.

Conclusion

The more I discuss front-loading with its opponents and proponents, the more I will add to this FAQ. Please add any questions, comments, etc., below.

About me

Over the years, I have become quite interested in the discussion over biological origins, and I think there is “something solid” behind the idea that teleology has played a role in the history of life on earth. When I’m not doing multiple sequence alignments, I’m thinking about ID and writing articles on the subject, which can be found on my website, The Genome’s Tale.

I am grateful to UD member kairosfocus for providing me with this opportunity to make a guest post on UD. Many thanks to kairosfocus.

Also see The Design Matrix, by Mike Gene. >>

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So, here we have one specific model for how ID could possibly have been done. Obviously, not the only possibility, but a significant one worthy of investigations. END

Comments

champignon, I would like to hear your explanation. What I was told in college was that evolution is not a violation of the 2nd law because earth is constantly bathed in high ordered energy. So earth has the resources to slowly evolve life utilizing that high ordered energy. What causes me to doubt is that many celestial objects are bathed in high ordered energy but don't seem to exhibit anything near as complex and interconnected as life. Indeed, ultraviolet radiation seems to destroy life rather than foster it despite ultraviolet radiation being high ordered energy. Why don't we see life or something just as complex on mercury, venus mars or elsewhere (so far)?Collin_{February 2, 2012
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Maus, as far as I can see, a demonstrated gain in functional prescriptive, information, not merely shannon information, by neo-Darwinian processes would be, for all practical purposes of empirical science, the same thing as a violation of the second law:
“Is there a real connection between entropy in physics and the entropy of information? ….The equations of information theory and the second law are the same, suggesting that the idea of entropy is something fundamental…” Siegfried, Dallas Morning News, 5/14/90, [Quotes Robert W. Lucky, Ex. Director of Research, AT&T, Bell Laboratories & John A. Wheeler, of Princeton & Univ. of TX, Austin] “Bertalanffy (1968) called the relation between irreversible thermodynamics and information theory one of the most fundamental unsolved problems in biology.” Charles J. Smith – Biosystems, Vol.1, p259. “Gain in entropy always means loss of information, and nothing more.” Gilbert Newton Lewis – preeminent Chemist of the first half of last century Klimontovich’s S-theorem, an analogue of Boltzmann’s entropy for open systems, explains why the further an open system gets from the equilibrium, the less entropy becomes. So entropy-wise, in open systems there is nothing wrong about the Second Law. S-theorem demonstrates that spontaneous emergence of regular structures in a continuum is possible.,,, The hard bit though is emergence of cybernetic control (which is assumed by self-organisation theories and which has not been observed anywhere yet). In contrast to the assumptions, observations suggest that between Regularity and Cybernetic Systems there is a vast Cut which cannot be crossed spontaneously. In practice, it can be crossed by intelligent integration and guidance of systems through a sequence of states towards better utility. No observations exist that would warrant a guess that apart from intelligence it can be done by anything else. Eugene S – UD Blogger
You see maus, I consider not only equilibrium, but also I consider the entropy as defined by the randomness that may be inherent in a system,,,
Thermodynamics – 3.1 Entropy Excerpt: Entropy – A measure of the amount of randomness or disorder in a system. http://www.saskschools.ca/curr_content/chem30_05/1_energy/energy3_1.htm
,,, to be completely insufficient to generate functional information. As Eugene S pointed out, it is simply an assumption that 'S-theorem demonstrates that spontaneous emergence of regular structures in a continuum is possible'. An assumption that, as Eugene S pointed out again, has not one shred of empirical support that natural processes can 'spontaneously' generate cybernetic systems as such. Whereas I hold that the correspondence of the equations of Entropy and Information are so tightly correlated, and that functional, prescriptive, information is so distinct from mere Shannon information, That indeed the more randomness a system has, then the more propensity that that random system, (no matter how many isolated pockets are away from equilibrium in that system), will have to destroy the functional, prescriptive, information within that system. Thus, though you may say in purely theoretical mathematical honesty, it is possible for neo-Darwinian evolution to occur without violating the second law, I may also equally hold against you, from a purely empirical standpoint, since indeed empirical evidence has the final word in the scientific method, that to find 'natural' material processes generating functional, prescriptive, information would be, for all practical purposes, equivalent to breaking the second law. You may say that I am not being true to the math, yet I would equally hold that the math is not fully developed yet to the point of a rightful consideration and inclusion of functional, prescriptive, information. And thus, once again, since empirical evidence has final say in the scientific method, then it is on the one who contests my claim to demonstrate, empirically, that it is otherwise! i.e. more to the point, why is the assumption that randomness can possibly generate functional information, though no one has ever seen this (Abel) given precedence over the fact that randomness, as far as the evidence can tell us, consistently destroys functional information??? Of note:
Blackholes - The neo-Darwinian ‘god of entropic randomness’ which can create all things (at least according to them) https://docs.google.com/document/d/1fxhJEGNeEQ_sn4ngQWmeBt1YuyOs8AQcUrzBRo7wISw/edit?hl=en_US
bornagain77_{February 1, 2012
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ba77:
You state that second law principles are not violated by ‘work’, perhaps not violated by ‘work’, I never said work did violate it, but OOL and neo-Darwinian evolution is certainly a flagrant violation of the second law.
I've said it before and I'll say it again: Do not do this. There is no violation of the 2nd by having localized areas out of equilibrium. With any chaotic system involved it is not simply not a violation, it is an expectation. See: Weather forecasting. If it helps: Your error comes in when trying to apply 'work', I assume qua Carnot, to a system defined as the entire universe. The 2nd only requires that photons zinging off this way and that go happily off to nowhere on a very long trip at the end of the day. It doesn't require that their disallowed from making bank shots for a while.Maus_{February 1, 2012
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Well Champ, apparently you are too smart to bother with empirical evidence. It must be nice to not ever have to demonstrate what you claim to be true is actually true:
"Is there a real connection between entropy in physics and the entropy of information? ....The equations of information theory and the second law are the same, suggesting that the idea of entropy is something fundamental..." Siegfried, Dallas Morning News, 5/14/90, [Quotes Robert W. Lucky, Ex. Director of Research, AT&T, Bell Laboratories & John A. Wheeler, of Princeton & Univ. of TX, Austin] “Bertalanffy (1968) called the relation between irreversible thermodynamics and information theory one of the most fundamental unsolved problems in biology.” Charles J. Smith – Biosystems, Vol.1, p259. "Gain in entropy always means loss of information, and nothing more." Gilbert Newton Lewis - preeminent Chemist of the first half of last century Klimontovich’s S-theorem, an analogue of Boltzmann’s entropy for open systems, explains why the further an open system gets from the equilibrium, the less entropy becomes. So entropy-wise, in open systems there is nothing wrong about the Second Law. S-theorem demonstrates that spontaneous emergence of regular structures in a continuum is possible.,,, The hard bit though is emergence of cybernetic control (which is assumed by self-organisation theories and which has not been observed anywhere yet). In contrast to the assumptions, observations suggest that between Regularity and Cybernetic Systems there is a vast Cut which cannot be crossed spontaneously. In practice, it can be crossed by intelligent integration and guidance of systems through a sequence of states towards better utility. No observations exist that would warrant a guess that apart from intelligence it can be done by anything else. Eugene S - UD Blogger
bornagain77_{February 1, 2012
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Sorry, BA, but I just don't think it's worth the effort to try to explain to you why evolution and the second law are perfectly compatible. Perhaps you could ask one of your fellow ID supporters for an explanation. But if someone else -- even Granville himself -- asks me to explain what's wrong with his arguments, I will, and you're welcome to listen in.champignon_{February 1, 2012
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Get back to me after you’ve read and understood the Thornton paper that inspired this comment.
I'm not sure you understand it yourself. (Did you think that you were the first to post it?) What you call the 'gain of function' is the addition of a protein to a component which adds no known functionality at all. Thornton himself expressed that it runs counter to the expectations of natural selection because it has no apparent benefit. This is about as exciting as a four-leaf clover. I don't know which is more astonishing - the degree of hyperbole or that anyone at all buys it. Apparently people go into a trance when they see the words "evolution" and "complexity." When describing the paper you used the exact words "net gain of function." And yet Thornton explicitly states that it demonstrates an increase in complexity "without the apparent evolution of novel functions." And you're asking me if I've read it? The problem isn't the paper. The sales job is disgraceful. It's insulting.ScottAndrews2_{February 1, 2012
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You don’t find it the least bit odd to propose that “the accumulation of simple, degenerative changes over long periods of times could have created many of the complex molecular machines present in organisms today?”
Get back to me after you've read and understood the Thornton paper that inspired this comment. Be sure you understand why Thornton calls it counterintuitive and why he proposes it anyway. I am aware that Behe has made a habit of mocking mutations as loss of function, so be prepared to defend the position that loss of function can't lead to a net gain of function. This has always been a key point in the ID quiver, so I expect to see a vigorous defense. Just as an aside, when I wrote my word evolving game, I noticed it got stuck on local hills of function, just as folks predicted. So I flip a coin every few generations and kill off the most fit individual. The net effect is the ability to navigate over valleys. It's just a toy, but it amuses me. I'm amused that a blind process that decreases function can in itself be functional.Petrushka_{February 1, 2012
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Well Champ, perhaps you can humble yourself and condescend to humor ignorant ole me on the second law by actually demonstrating the generation of functional complexity/information over and above what was already present. How about passing the fitness test??? that should be easy enough for a process claimed to have built the undreamt complexity of all life on earth with no help from a Mind whatsoever???;
Is Antibiotic Resistance evidence for evolution? - 'The Fitness Test' - video http://www.metacafe.com/watch/3995248 Thank Goodness the NCSE Is Wrong: Fitness Costs Are Important to Evolutionary Microbiology Excerpt: it (an antibiotic resistant bacterium) reproduces slower than it did before it was changed. This effect is widely recognized, and is called the fitness cost of antibiotic resistance. It is the existence of these costs and other examples of the limits of evolution that call into question the neo-Darwinian story of macroevolution. http://www.evolutionnews.org/2010/03/thank_goodness_the_ncse_is_wro.html
or how about falsifying this null hypothesis?:
Three subsets of sequence complexity and their relevance to biopolymeric information - Abel, Trevors Excerpt: Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,, Testable hypotheses about FSC What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses: Null hypothesis #1 Stochastic ensembles of physical units cannot program algorithmic/cybernetic function. Null hypothesis #2 Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function. Null hypothesis #3 Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function. Null hypothesis #4 Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time. We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified. http://www.tbiomed.com/content/2/1/29 Is Life Unique? David L. Abel - January 2012 Concluding Statement: The scientific method itself cannot be reduced to mass and energy. Neither can language, translation, coding and decoding, mathematics, logic theory, programming, symbol systems, the integration of circuits, computation, categorizations, results tabulation, the drawing and discussion of conclusions. The prevailing Kuhnian paradigm rut of philosophic physicalism is obstructing scientific progress, biology in particular. There is more to life than chemistry. All known life is cybernetic. Control is choice-contingent and formal, not physicodynamic. http://www.mdpi.com/2075-1729/2/1/106/ "Nonphysical formalism not only describes, but preceded physicality and the Big Bang Formalism prescribed, organized and continues to govern physicodynamics." http://www.mdpi.com/2075-1729/2/1/106/ag The Law of Physicodynamic Insufficiency - Dr David L. Abel - November 2010 Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.” http://www-qa.scitopics.com/The_Law_of_Physicodynamic_Insufficiency.html The Law of Physicodynamic Incompleteness - David L. Abel - August 2011 Summary: “The Law of Physicodynamic Incompleteness” states that inanimate physicodynamics is completely inadequate to generate, or even explain, the mathematical nature of physical interactions (the purely formal laws of physics and chemistry). The Law further states that physicodynamic factors cannot cause formal processes and procedures leading to sophisticated function. Chance and necessity alone cannot steer, program or optimize algorithmic/computational success to provide desired non-trivial utility. http://www.scitopics.com/The_Law_of_Physicodynamic_Incompleteness.html
Or how about proving the 'First Rule' is wrong?:
“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.(that is a net 'fitness gain' within a 'stressed' environment i.e. remove the stress from the environment and the parent strain is always more 'fit') http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/
You see champ it doesn't matter what you claim is true in science, with big 25 cent words, it matters what you can actually demonstrate to be true in science!!! which reminds me of this demonstration in science that you apparently are to smart to pay attention to:
Falsification Of Neo-Darwinism by Quantum Entanglement/Information https://docs.google.com/document/d/1p8AQgqFqiRQwyaF8t1_CKTPQ9duN8FHU9-pV4oBDOVs/edit?hl=en_US
bornagain77_{February 1, 2012
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You don't find it the least bit odd to propose that "the accumulation of simple, degenerative changes over long periods of times could have created many of the complex molecular machines present in organisms today?" Don't get me wrong. It works. I can create a functional Lexus with 4/70 air conditioning if you give me a Lexus and a sledgehammer. I don't want to explain what's wrong with this. At this point I'm really wondering if you can see what's wrong with this without me telling you. From my standpoint this is no longer a debate. It's a curiosity. It's like something you pay $.25 to see even though you know it might not be real.ScottAndrews2_{February 1, 2012
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Well pet, you believe in degenerative possesses, over long periods of time, that can build undreamt of complexity in cells? Perhaps you leave you door open on your house for a year and it will build itself into a Castle! :) If you ever decide to come back to the real world, there are some notes in this video description for you to chew on; The Digital Code of DNA and the Unimagined Complexity of a 'Simple' Bacteria - Rabbi Moshe Averick - video (notes on unimagined complexity of DNA and 'simple' life in video description) http://vimeo.com/35730736bornagain77_{February 1, 2012
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BA77:
You claim, with a lot of rhetoric, that it [the 2nd law] can be violated, Fine show me!
No, BA, I don't claim that the 2nd law can be violated. Slow down and think, man! You and Granville are the ones who say that evolution violates the 2nd law, not me. And I'll repeat my offer. If there is anyone out there besides you and Granville who actually believes that evolution violates the 2nd law, and if they post a comment indicating this, I'll explain why Granville is wrong. Otherwise, it's not worth the effort.champignon_{February 1, 2012
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Moreover, the harder they are pressed the more convoluted they lie!
Have you ever noticed that when you are angry you engage in name calling?Petrushka_{February 1, 2012
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It’ll be like Cope and Marsh more like Laurel and Hardy!!! :)bornagain77_{February 1, 2012
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(I’m not commenting on it. I’m just quoting it.)
No need to comment when one instance has been demonstrated and every young gun in the west will be trying to top it. It'll be like Cope and Marsh.Petrushka_{February 1, 2012
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Well Pet, I have no curriculum vitae, in fact I am nothing and nobody in particular except a sinner saved by the grace of God. I do have just a few years of watching neo-Darwinists lie through their teeth on these blogs and never proving anything that they claim. Moreover, the harder they are pressed the more convoluted they lie! Perhaps it doesn't bother you that supposed scientists could be so deceptive in what they tell the public, but it bugs the crap out of me that this should be so! Intelligent Design - The Anthropic Hypothesis http://lettherebelight-77.blogspot.com/2009/10/intelligent-design-anthropic-hypothesis_19.htmlbornagain77_{February 1, 2012
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Which do you think will happen first: the ID movement produces a theory of design, or someone like Szostak figures out how it can bootstrap?
Szostak is trying to engineer life. So heads I win, tails you lose.ScottAndrews2_{February 1, 2012
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,,,All I can say is that if you believe that, You guys are insane!
Have you ever noticed,,,,,,,, that when you get angry;;;; you tend!!!!! to insert superfluous,,,, punctuation marks??????????????????? Personally, I just tend to overlook spelling mistakes. To each his own.Petrushka_{February 1, 2012
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Thornton proposes that the accumulation of simple, degenerative changes over long periods of times could have created many of the complex molecular machines present in organisms today.
(I'm not commenting on it. I'm just quoting it.)ScottAndrews2_{February 1, 2012
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In contrast to the assumptions, observations suggest that between Regularity and Cybernetic Systems there is a vast Cut which cannot be crossed spontaneously.
Nor by design, in the absence of a theory of design. So I await a theory of how the designer did it, so we can see which process best fits the data. Which do you think will happen first: the ID movement produces a theory of design, or someone like Szostak figures out how it can bootstrap?Petrushka_{February 1, 2012
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This is cutting edge research???
Well yes. Perhaps you'll grace us with your curriculum vitae, so we can compare.Petrushka_{February 1, 2012
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pet you quote this; 'Thornton proposes that the accumulation of simple, degenerative changes over long periods of times could have created many of the complex molecular machines present in organisms today.' ,,,All I can say is that if you believe that, You guys are insane!bornagain77_{February 1, 2012
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look in the mirror champ! You are the one claiming that processes which overwhelmingly and relentless degrade can be build complexity the likes of which man has never dreamed of in his most advanced machines. Moreover, evolution is the only 'science' that is at complete variance with this law. You claim, with a lot of rhetoric, that it can be violated, Fine show me! Produce a molecular machine by neo-Darwinian processes and I will believe you! “There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject.” James Shapiro – Molecular Biologist Perhaps you have an example of one these following molecular machines being ‘self designed’ by a cell? Bacterial Flagellum – A Sheer Wonder Of Intelligent Design – video http://www.metacafe.com/watch/3994630 The ATP Synthase Enzyme – exquisite motor necessary for first life – video http://www.youtube.com/watch?v=W3KxU63gcF4 Powering the Cell: Mitochondria – video http://www.youtube.com/watch?v=RrS2uROUjK4 Molecular Machine – Nuclear Pore Complex – Stephen C. Meyer – video http://www.metacafe.com/watch/4261990 Programming of Life – Protein Synthesis – video http://www.youtube.com/user/Pr.....5Z3afBdxB0 Kinesin Linear Motor – Video http://www.youtube.com/watch?v=kOeJwQ0OXc4 DNA – Replication, Wrapping & Mitosis http://vimeo.com/33882804 or if you can’t find an example of ‘self design’ for one of those molecular machines there are several more here that you can look for examples for: The following article has a list of 40 (yes, 40) irreducibly complex molecular machines in the cell: Molecular Machines in the Cell - http://www.discovery.org/a/14791 and after you get done producing any evidence whatsoever that cells can ‘self design’ any molecular machine from scratch, then you can work on refuting this falsification of neo-Darwinism: Falsification Of Neo-Darwinism by ‘non-local’ Quantum Entanglement/Information https://docs.google.com/document/d/1p8AQgqFqiRQwyaF8t1_CKTPQ9duN8FHU9-pV4oBDOVs/edit?hl=en_USbornagain77_{February 1, 2012
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One thought has struck me - you write "Front-loading predicts that the last universal common ancestor (LUCA) was quite complex, complete with genes necessary for the origin and development of metazoan life forms.", which made me wonder about complex non-metazoans (e.g. plants). Did the LUCA have all the necessary genes for them too? But then it struck me that there doesn't seem to be any necessity for a single LUCA - who or what ever seeded the earth might have seeded it with more than one organism, so there doesn't have to be a LUCA. This raises some questions about why the genetic code is so similar across organisms, but if the seeding was done by a single entity or group, this might not be so unreasonable. I do wonder - does the front-loading hypothesis would have anything to say about variation in the genetic code?Heinrich_{February 1, 2012
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More from Thornton: http://www.eurekalert.org/pub_releases/2012-01/uocm-eoc010512.php
"The mechanisms for this increase in complexity are incredibly simple, common occurrences," Thornton said. "Gene duplications happen frequently in cells, and it's easy for errors in copying to DNA to knock out a protein's ability to interact with certain partners. It's not as if evolution needed to happen upon some special combination of 100 mutations that created some complicated new function." Thornton proposes that the accumulation of simple, degenerative changes over long periods of times could have created many of the complex molecular machines present in organisms today. Such a mechanism argues against the intelligent design concept of "irreducible complexity," the claim that molecular machines are too complicated to have formed stepwise through evolution. "I expect that when more studies like this are done, a similar dynamic will be observed for the evolution of many molecular complexes," Thornton said.
Petrushka_{February 1, 2012
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Think, BA.champignon_{February 1, 2012
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champignon, You got a violation of the second law to show??? Well shoot man, if you actually have a violation of the second law why don't you build a perpetual motion machine??? LOLbornagain77_{February 1, 2012
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Petrushka, You are right. Klimontovich's S-theorem, an analogue of Boltzmann's entropy for open systems, explains why the further an open system gets from the equilibrium, the less entropy becomes. So entropy-wise, in open systems there is nothing wrong about the Second Law. S-theorem demonstrates that spontaneous emergence of regular structures in a continuum is possible. The hard bit though is emergence of cybernetic control (which is assumed by self-organisation theories and which has not been observed anywhere yet). In contrast to the assumptions, observations suggest that between Regularity and Cybernetic Systems there is a vast Cut which cannot be crossed spontaneously. In practice, it can be crossed by intelligent integration and guidance of systems through a sequence of states towards better utility. No observations exist that would warrant a guess that apart from intelligence it can be done by anything else.Eugene S_{February 1, 2012
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This is cutting edge research??? LOL you have got to be kidding me!!! They did not even empirically demonstrate anything, they merely conjectured a semi-plausible route for a very minor adjustment of a already existing system!!! If this is the 'best cutting edge research' thus far from neo-Darwinists, you guys are hopelessly lost in a fantasy world and are definitely not practicing science with any sort of rigor of integrity that I can see!!!bornagain77_{February 1, 2012
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Whoops, I messed up the formatting. Perhaps I can get a Thornton quote right.
"It's counterintuitive but simple: complexity increased because protein functions were lost, not gained," Thornton said. "Just as in society, complexity increases when individuals and institutions forget how to be generalists and come to depend on specialists with increasingly narrow capacities."
And having demonstrated that such an evolutionary sequence of mutations has taken place it would be interesting to recall this quote:
Therefore to the same natural effects we must, as far as possible, assign the same causes. and The qualities of bodies, which admit neither intensification nor remission of degrees, and which are found to belong to all bodies within the reach of our experiments, are to be esteemed the universal qualities of all bodies whatsoever.
Petrushka_{February 1, 2012
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BA77:
...OOL and neo-Darwinian evolution is certainly a flagrant violation of the second law.
Besides BA77 and Granville Sewell, is there anyone out there who actually believes this? I'm trying to gauge whether it's worth spending the time to post a refutation.champignon_{February 1, 2012
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