Time for serious pursuit of post-Darwinian theory, says new BIO-Complexity paper

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December 15, 2014

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From Ann Gauger at the Biologic Institute new BIO-Complexity paper:

Five family members from the GabT-like protein family. The first three are very similar. These enzymes are considered by current standards to be homologous, that is, evolutionarily derived.

The five enzymes shown above are clearly related in structure, especially the three on the left. Yet none of the others can replace BioF2’s function in the cell, even when mutated and made in large amounts. Why is that? Probably because each enzyme is a structural whole, whose sequence is made to work together as a whole. Substituting or changing little bits doesn’t work.

Here are the concluding paragraphs of our recent paper where we explain the problem and propose a new way of thinking about it:

“Although there is as yet no satisfactory theory of biology to take the place of Darwinism, we believe the time has come for serious pursuit of such a theory. To quote one of our previous papers [45]:

The insights we gain from the critique of neo-Darwinism can and should inform the construction of a new theory to take its place. That is, in pinpointing the key problems with the old theory we are identifying crucial respects in which its replacement must differ from it. We ourselves have become convinced that intelligent causation is essential as a starting point for any successful theory of biological innovation. If this is so, what is needed now is an elaboration of the general principles by which living things have been designed.

To that end, one of our inferred principles of design is this [45]:

The substantial reworking of a homologous structure needed to give it a genuinely new function is more suggestive of reapplication of a concept than adjustment of a physical thing.

And another is this [45]: … More. (Reeves MA, Gauger AK, Axe DD (2014) Enzyme families—Shared evolutionary history or shared design? A study of the GABA-aminotransferase family. BIO-Complexity 2014 (4):1-16. doi:10.5048/BIO-C.2014.4.)

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Comments

Evolution assumes the existence of a system capable of evolution. Is this the most news-worthy item we've seen yet today or what? Any robust theory of evolution should be able to describe the requirements that such a system must meet. Yet another in the long list of reasons why there is no coherent theory of evolution. kairosfocus has his challenge that remains unmet, and so does Upright Biped. Mine is similar. What are the minimal requirements for a system capable of Darwinian evolution? Where's the theory that ought to be fundamental to the entire evolutionary edifice?Mung_{December 15, 2014
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Zachriel, please help me to understand your view about "motifs". I would presume that you are saying that within a particular "gene" (codes for a protein) there are, well, subroutines. When I look at pictures of proteins, I often see patterns, twisty coiley things that look like hair that has been curled, for instance. A twisty coily would be a "motif", correct?Moose Dr_{December 15, 2014
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Poof Meister:
That’s not part of word evolution, which presupposes reproduction.
And that, ladies and gentlemen, is the biggest unsolvable problem of evolution: it never started in the first place. Unless, of course, you believe in poofery.Mapou_{December 15, 2014
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Mapou: how did your single individual evolve the ability to reproduce? That's not part of word evolution, which presupposes reproduction. Keep in mind, we didn’t introduce word evolution. That was Gauger.Zachriel_{December 15, 2014
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So, Poof Meister, how did your single individual evolve the ability to reproduce? And how does it know about "box, off, etc?" It poofed its knowledge into existence? And again, what's with the "we" shit? Did you poof it into existence too?Mapou_{December 15, 2014
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Mapou: And how do you get to a population when ... you have to start with a single individual? Reproduction with variation. Let's say you start with a single letter word, o. Given moderate rates of mutation, most of its offspring will be identical to the original, but some will mutate. Offspring such as q, xo, fo die, but some mutants will form new words, so we end up with o, or, a, of, ox, to and so on. After that, we might have box, ore, at, off. Then add recombination for the real fun. http://www.zachriel.com/mutagenation/Sea.htmZachriel_{December 15, 2014
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Zacky, what's with the "we" shit, huh? And how do you get to a population when anybody with 2 neurons between their ears knows you have to start with a single individual? Did an entire population suddenly poof itself into existence? PS. I'm gonna call you the poof meister from now on.Mapou_{December 15, 2014
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Mapou: Not true. It's self-evidently true. We provided an example. Mapou: Because, as every programmer knows, the number of deleterious mutations is far greater than the number of viable mutations by many orders of magnitude. In the example we provided, 100% of the mutations were deleterious. Mapou: Even if one sequence survived (and I’m being infinitely generous), the next mutation will kill it dead. Unlikely in the example we provided. Given a reasonable population of variants, it won't ever happen. Mapou: Before the organism can even get to the point of selection, it must evolve a reproductive capability. We didn't introduce word evolution. That was Gauger.Zachriel_{December 15, 2014
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zacky the magician:
gobbledygoop gobbledygook The first child is, unfortunately, stillborn. The second child, however, is a clone and survives just fine. Unless the mutation rate is very high, at least some of the offspring will be clones.
Not true. Nothing survives because it never gets to that point. Why? Because, as every programmer knows, the number of deleterious mutations is far greater than the number of viable mutations by many orders of magnitude. Even if one sequence survived (and I'm being infinitely generous), the next mutation will kill it dead. There is an even bigger problem than the above. Before the organism can even get to the point of selection, it must evolve a reproductive capability. I repeat: unless there is mechanism in place that protects sequences from deleterious mutations, all you got is crass pseudoscience and superstition. It does not matter if you jump up and down, foam at the mouth and recite 1000 Hail Marys. In conclusion, it is obvious that Darwinian evolution and naturalism are stupid, stupid, stupid, STUPID, STUPID...Mapou_{December 15, 2014
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As to:
"The five enzymes shown above are clearly related in structure, especially the three on the left. Yet none of the others can replace BioF2’s function in the cell, even when mutated and made in large amounts. Why is that? Probably because each enzyme is a structural whole, whose sequence is made to work together as a whole. Substituting or changing little bits doesn’t work."
As to the problem that 'working together as a whole', i.e. context dependency, presents for neo-Darwinism, I highly recommend Wiker & Witt’s book “A Meaningful World” in which they show, using the “Methinks it is like a weasel” phrase that Dawkins used from Shakespeare’s play Hamlet to try to illustrate the feasibility of Evolutionary Algorithms, that the problem is much worse for Darwinists than just finding the “Methinks it is like a weasel” phrase by a unguided search. This is because the “Methinks it is like a weasel” phrase doesn't makes any sense at all unless the entire context of the play of Hamlet is taken into consideration so as to give the “Weasel” phrase its proper 'meaning'. Moreover the context in which the weasel phrase finds its meaning is derived from several different levels of the play. i.e. The ENTIRE play, and even nuances of the Elizabethan culture, who said it, why was it said, where was it said, etc,,, provides the contextual meaning for providing the meaning for the individual “Weasel” phrase.
A Meaningful World: How the Arts and Sciences Reveal the Genius of Nature – Book Review Excerpt: They focus instead on what “Methinks it is like a weasel” really means. In isolation, in fact, it means almost nothing. Who said it? Why? What does the “it” refer to? What does it reveal about the characters? How does it advance the plot? In the context of the entire play, and of Elizabethan culture, this brief line takes on significance of surprising depth. The whole is required to give meaning to the part. http://www.thinkingchristian.net/C228303755/E20060821202417/
Dr. Gauger has also shown that the problem of context dependency, i.e. 'working together as a whole', extends past the primary sequence of a protein and is also present for the secondary structure and for protein domains as well:
“Why Proteins Aren’t Easily Recombined, Part 2? – Ann Gauger – May 2012 Excerpt: “So we have context-dependent effects on protein function at the level of primary sequence, secondary structure, and tertiary (domain-level) structure. This does not bode well for successful, random recombination of bits of sequence into functional, stable protein folds, or even for domain-level recombinations where significant interaction is required.” http://www.biologicinstitute.org/post/23170843182/why-proteins-arent-easily-recombined-part-2
Moreover, even the entire protein structure themselves are found to be 'context dependent, in that many proteins are now found to be multifunctional depending on the overall context (i.e. position in cell, cell type, tissue type, etc..) that the protein happens to be involved in. Thus, the sheer astronomical brick wall that Darwinian processes face in finding ANY novel functional sequence for any protein to perform any specific single task in a cell in the first place, (Axe; Sauer), is only exponentially exasperated by the fact that many proteins are multifunctional and, serendipitously, perform several different ‘context dependent’ functions within the cell:
Human Genes: Alternative Splicing (For Proteins) Far More Common Than Thought: Excerpt: two different forms of the same protein, known as isoforms, can have different, even completely opposite functions. For example, one protein may activate cell death pathways while its close relative promotes cell survival. http://www.sciencedaily.com/releases/2008/11/081102134623.htm The Gene Myth, Part II - August 2010 Excerpt: “It was long believed that a protein molecule’s three-dimensional shape, on which its function depends, is uniquely determined by its amino acid sequence. But we now know that this is not always true – the rate at which a protein is synthesized, which depends on factors internal and external to the cell, affects the order in which its different portions fold. So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape (Intrinsically Disordered Proteins), taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous (very weak or slight) influence over their functions. ,,,,So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used. Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent. Stuart A. Newman, Ph.D. – Professor of Cell Biology and Anatomy http://darwins-god.blogspot.com/2010/08/gene-myth-part-ii.html podcast - Dr. Jonathan Wells: Biology’s Quiet Revolution - September 17, 2014 "We are talking about 1/3 of the proteins in our body, (may be Intrinsically Disordered Proteins)" - Jonathan Wells http://www.discovery.org/multimedia/audio/idtf/2014/09/dr-jonathan-wells-biologys-quiet-revolution/
Context dependency, and the problem it presents for ‘bottom up’ Darwinian evolution is perhaps most dramatically illustrated by the following examples in which ‘form’ dictates how the parts are used:
What Do Organisms Mean? Stephen L. Talbott – Winter 2011 Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: “Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements … take unique meaning from their context.[3]“,,, http://www.thenewatlantis.com/publications/what-do-organisms-mean Timelapse Video Reveals Electric Face in Embryonic Tadpole - July 2011 Excerpt: "When a frog embryo is just developing, before it gets a face, a pattern for that face lights up on the surface of the embryo. We believe this is the first time such patterning has been reported for an entire structure, not just for a single organ. I would never have predicted anything like it. It's a jaw dropper." http://www.sciencespacerobots.com/timelapse-video-reveals-electric-face-in-embryonic-tadpole-718111
In the following podcast and article, Dr. Jonathan Wells reveals that the 'bioelectric code', which is what is apparently dictating the 'form' of the organism in the preceding video, is not reducible to sequences of DNA as is presupposed in neo-Darwinism:
podcast - Jonathan Wells: Is There Biological Information Outside of the DNA?, pt. 3 - Bioelectric code http://intelligentdesign.podomatic.com/entry/2014-06-11T16_35_52-07_00 Not in the Genes: Embryonic Electric Fields - Jonathan Wells - December 2011 Excerpt: although the molecular components of individual sodium-potassium channels may be encoded in DNA sequences, the three-dimensional arrangement of those channels -- which determines the form of the endogenous electric field -- constitutes an independent source of information in the developing embryo. http://www.evolutionnews.org/2011/12/not_in_the_gene054071.html
bornagain77_{December 15, 2014
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Mapou: Unless there is a system in place that prevents existing good sequences from being destroyed by random mutations, all that is left is gobbledygook. That is incorrect. Consider replication with occasional mutation, say one mutation per hundred letter copies. Start with the string "gobbledygook". Let's say it has the following two offspring: gobbledygoop gobbledygook The first child is, unfortunately, stillborn. The second child, however, is a clone and survives just fine. Unless the mutation rate is very high, at least some of the offspring will be clones.Zachriel_{December 15, 2014
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The mammalian middle ear is a canonical example.
Imagination is neither an example nor evidence. BTW, remixing existing information is not required for evolutionJoe_{December 15, 2014
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Zacky:
Silver Asiatic: The problem in building the first “sentences” letter by letter remains. The analogous case in English is easy if the sequences are selected for length and meaningfulness.
This is a lie. Unless there is a system in place that prevents existing good sequences from being destroyed by random mutations, all that is left is gobbledygook. Such a sequence repair mechanism would have to be highly complex and would have to know in advance which sequence is good and which is bad. Evolution is a gigantic lie. It is a relentless fraud perpetrated on the public by a-holes with an agenda of imposing their one true state religion on the world. Like all lies, it will not succeed.Mapou_{December 15, 2014
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Silver Asiatic: The problem in building the first “sentences” letter by letter remains. The analogous case in English is easy if the sequences are selected for length and meaningfulness. humbled: Could you please provide an example where a larger structure has evolved from a simpler structure? The mammalian middle ear is a canonical example.Zachriel_{December 15, 2014
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"Larger structures can evolve from simpler structures." Could you please provide an example where a larger structure has evolved from a simpler structure? Thanks.humbled_{December 15, 2014
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gpuccio:
However, neo darwinists always overstate that point, especially when they have difficulties in even trying to explain how those motifs, domains or exons got there in the beginning.
Yes, it's interesting. They often know it is overstating, so they try to disguise that with understated language. That's NDE in itself - an enormous claim, understated in terms of minor, tiny, easily accepted changes.
Re-mixing existing information is just that: re-mixing what already exists. What already exists had to come into existence by random variation, according to your theory, and that means usually by single bit variation, or by multibit variation which has nothing to do with existing structures.
Exactly again. The problem in building the first "sentences" letter by letter remains. But I noticed how that was avoided by moving to the idea that evolution merely swaps functions.
Even re-mixing existing exons or whatever requires much more than random combinatorics: object oriented programming is not done by simply re-mixing objects, and requires careful engineering.
Very well said. I would hope that point would be strikingly obvious to anyone who read the responses thus far. The notion that evolution moves from one function to another, as a means of avoiding the problem of how to build the components of modular design (so to speak) was left standing as an explanation.Silver Asiatic_{December 15, 2014
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gpuccio: Re-mixing existing information is just that: re-mixing what already exists. Both are required in evolution. There has to be a source of novelty as well as shuffling of existing motifs. Larger structures can evolve from simpler structures.Zachriel_{December 15, 2014
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Z:
Not even sure your point.
I just clarified your point. Just observing the process of restatements and linguistic engineering was interesting enough. Eventually, what you were actually saying became clear.Silver Asiatic_{December 15, 2014
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Silver Asiatic: So, in response to Ann Gauger’s paper, there should be no concern about “alteration” because evolution can just recombine functions. Not even sure your point. As for Gauger, she has a conclusion, but no evidence other than a failed experiment.Zachriel_{December 15, 2014
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Zachriel: "Motifs", especially if simple, are usually not functional in themselves. A function must be there to be selected. It must be implemented at biochemical, molecular level. It is certainly possible that similar motifs, or domains, or exons, can be shuffled or re-utilized in different proteins. That is often seen in all forms of modular design, and especially in Object Oriented Programming. However, neo darwinists always overstate that point, especially when they have difficulties in even trying to explain how those motifs, domains or exons got there in the beginning. Re-mixing existing information is just that: re-mixing what already exists. What already exists had to come into existence by random variation, according to your theory, and that means usually by single bit variation, or by multibit variation which has nothing to do with existing structures. Even re-mixing existing exons or whatever requires much more than random combinatorics: object oriented programming is not done by simply re-mixing objects, and requires careful engineering. Gauger's paper is a new important step in trying a top down analysis of protein functional space: a much needed understanding, which is strangely overlooked by official academic researchers. Strange that those people who are so sure that the functional protein space is so filled with functional states of all kinds are not trying to demonstrate that that is the case.gpuccio_{December 15, 2014
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Silver Asiatic: No – evolution moves directly from one functional idea to another, supposedly, as it has been said. Z: What we were pointing out is that evolution doesn’t work merely through simple letter changes, but through recombination as well.
Yes, I understood what you already said. Motifs. You were pointing out (claiming) that evolution moves directly from one functional structure to another. So, in response to Ann Gauger's paper, there should be no concern about "alteration" because evolution can just recombine functions.Silver Asiatic_{December 15, 2014
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What we were pointing out is that evolution doesn’t work merely through simple letter changes, but through recombination as well.
The debate is about whether or not evolution is blind, mindless and without goals. How was it determined that recombination is a blind watchmaker mechanism?Joe_{December 15, 2014
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Silver Asiatic: Through a recombination of existing functional ideas. Well, functional structures at least. Silver Asiatic: No – evolution moves directly from one functional idea to another, supposedly, as it has been said. What we were pointing out is that evolution doesn't work merely through simple letter changes, but through recombination as well.Zachriel_{December 15, 2014
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A motif is an idea. "And through recombination of existing motifs." Therefore: "Through a recombination of existing functional ideas." Therefore: Silver Asiatic: Evolution supposedly moves from one functional idea to another by changing the letters in each sentence. No - evolution moves directly from one functional idea to another, supposedly, as it has been said.Silver Asiatic_{December 15, 2014
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Silver Asiatic: Evolution supposedly moves from one functional idea to another by changing the letters in each sentence. And through recombination of existing motifs.Zachriel_{December 15, 2014
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Sentences that convey different ideas may have similar structures, but when we write a sentence we start with the idea, not the sentence structure. We never take a sentence that conveys some other idea and ask which letters can be changed to make it better suited for our present purpose.
Good analogy. Evolution supposedly moves from one functional idea to another by changing the letters in each sentence.Silver Asiatic_{December 15, 2014
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News: Very interesting paper. Thank you.gpuccio_{December 15, 2014
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