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It’s Official: Lamarckism has Now Joined the Narrative, July 1, 2015 !

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It is often said that all truth passes through three stages. First, it is ridiculed. Second, it is violently opposed. Third, it is accepted as being self-evident. Yesterday with the publishing of a new paper out of Israel, and two centuries later, Lamarck’s pre Darwinian theory of evolution, sometimes referred to as the inheritance of acquired characteristics, prophetically completed the cycle.  Read more

What is truly ridiculous is that Neo-Darwinism is assumed as some kind of sacrosanct 'default' position that must be disproved. It has never been well-supported by evidence, but largely assumed, (and laughably so) as the process that drove all of biodiversity. lifepsy
Soon Lamarckian mechanisms will be self-evident. Evolutionists have already begun to prepare the way for this tectonic shift in their thinking.
Prepare for? A tectonic shift? To quote from "The Beginning of Infinity"....
“Some have considered [Lamarckism] a pretty vision. But it bears hardly any resemblance to the facts. Its most glaring mismatch is that, in reality, evolutionary adaptations are of a wholly different character from the changes that take place in an individual during its lifetime. The former involve the creation of new knowledge; the latter happen only when there is already an adaptation for making that change. For instance, the tendency of muscles to become stronger or weaker with use and disuse is controlled by a sophisticated (knowledge-laden) set of genes. The animal’s distant ancestors did not have those genes. Lamarckism cannot possibly explain how the knowledge in them was created." [...] “The fundamental error being made by Lamarck has the same logic as inductivism. Both assume that new knowledge (adaptations and scientific theories respectively) is somehow already present in experience, or can be derived mechanically from experience. But the truth is always that knowledge must be first conjectured and then tested. That is what Darwin’s theory says: first, random mutations happen (they do not take account of what problem is being solved); then natural selection discards the variant genes that are less good at causing themselves to be present again in future generations.”
So, yes. You can call Lamarckism evolution, if you like, and bring it into the fold. But that would hardly represent a tectonic shift worth celebrating. Rather, it merely muddies the water. Popperian
semi OT: Jennifer Doudna (UC Berkeley / HHMI): Genome Engineering with CRISPR-Cas9 - video https://www.youtube.com/watch?v=SuAxDVBt7kQ Frank Huguenard: Do you know what CRISPRS are? Look up CRISPR. It’s an acronym without the ‘e’. C-R-I-S-P-R. ,,, Check this out. This is mind blowing.,,, So they’re looking at Ebola bacteria and they’re just looking at Epigenetics and they’re trying to understand what’s happening outside of the chromosome–the methylation, demethylation, turning genes on and off. And they observed there are these other sequences showing up outside. And they didn’t know anything about it. They just published it and here’s the report. So other people started looking into this. And what they realize is that the E. coli got infected with a virus and the bacteria’s 50 times larger than a virus. The DNA in the E. coli with the kind of sophistication that the NSA would be proud of hacks into genome of the virus; uses the RNA to create a duplicate strand of the virus DNA–a segment of the virus; attaches it to an enzyme and converts it to a protein that then attaches itself hand-and-glove to the right sequence of the virus and slices it in half and kills it.,, It’s one of the most amazing things in nature. If you look at the sophistication, how does an E. coli bacteria know how to replicate the exact sequence and in the right portion of the DNA of this virus to kill the virus? It’s amazing stuff. http://www.skeptiko.com/277-frank-huguenard-beyond-mindbrain/ OT: Dr. Michael Nahm on Terminal Lucidity and Near-Death Experience - interview http://www.skeptiko.com/278michael-nahm-terminal-lucidity/ Join Skeptiko host Alex Tsakiris for an interview with Dr. Michael Nahm to discuss his reports on patients who experience brief periods of unexplainable lucidity before death: Alex Tsakiris: The end result of those experiments [on terminal lucidity and near-death experience] is — this really happened. bornagain77
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
Neo-Darwinism is based on classical physics/information and therefore cannot explain protein fold entanglement as described. Darwinism is linear and sequential - like analog recording. A single point-mutation affects DNA but does not explain the changed relationships that result. Silver Asiatic
Well, where does the biological information, specifically the quantum information, that was keeping the organism alive for ‘precisely a lifetime’, suddenly go upon the death of an organism? Reductive materialists would hold that the biological/quantum information simply ceases to exist upon the death of an organism, (since they hold information to be ’emergent’ from a material basis). But the fact of the matter is that the quantum information, the information that was/is in fact ‘holding life together’ for precisely a life time, is ‘conserved’, and does not simply disappear from reality:
Black holes don’t erase information, scientists say – April 2, 2015 Excerpt: The research marks a significant step toward solving the “information loss paradox,” a problem that has plagued physics for almost 40 years, since Stephen Hawking first proposed that black holes could radiate energy and evaporate over time. This posed a huge problem for the field of physics because it meant that information inside a black hole could be permanently lost when the black hole disappeared—a violation of quantum mechanics, which states that information must be conserved. http://phys.org/news/2015-04-black-holes-dont-erase-scientists.html+/ Quantum no-hiding theorem experimentally confirmed for first time Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment. http://www.physorg.com/news/2011-03-quantum-no-hiding-theorem-experimentally.html Quantum no-deleting theorem Excerpt: A stronger version of the no-cloning theorem and the no-deleting theorem provide permanence to quantum information. To create a copy one must import the information from some part of the universe and to delete a state one needs to export it to another part of the universe where it will continue to exist. http://en.wikipedia.org/wiki/Quantum_no-deleting_theorem#Consequence Information Conservation and the Unitarity of Quantum Mechanics Excerpt: “In more technical terms, information conservation is related to the unitarity of quantum mechanics. In this article, I will explain what unitarity is and how it’s related to information conservation.” http://youngsubyoon.com/QMunitarity.htm
Besides providing direct empirical falsification of neo-Darwinian claims as to the generation of information, the implication of finding ‘non-local’, beyond space and time, and ‘conserved’ quantum information in molecular biology on a massive scale is fairly, and pleasantly, obvious. That pleasant implication being the strong validation of the Theist’s contention that we, as distinct ‘persons’, are ‘souls’ that merely live in a material body and that we are not ‘persons’ who are co-terminus with our material bodies:
“You don’t have a soul. You are a soul. You have a body.” George MacDonald – Annals of a Quiet Neighborhood – 1892 Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff – video https://www.youtube.com/watch?v=iIyEjh6ef_8
Verse, Picture, and Music:
Psalm 139:13-16 For you created my inmost being; you knit me together in my mother’s womb. I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well. My frame was not hidden from you when I was made in the secret place, when I was woven together in the depths of the earth. Your eyes saw my unformed body; all the days ordained for me were written in your book before one of them came to be. “What power holds off that moment — precisely for a lifetime, and not a moment longer?” - picture – http://cdn-4.spiritscienceandmetaphysics.com/wp-content/uploads/2014/12/harvardd-2.jpg MATT MAHER - Because He Lives (Amen): Song https://www.youtube.com/watch?v=PBvU7arNhQs
Supplemental note: As to the question of where does this ‘conserved’ quantum information go upon death, well there are ‘theories’ in that regards as well. ‘Theories’ that happen to far better supported, evidence-wise, than the present multiverse conjectures of atheists that try to 'explain away' the fine-tuning of the universe:
Special Relativity, General Relativity, Heaven and Hell https://docs.google.com/document/d/1_4cQ7MXq8bLkoFLYW0kq3Xq-Hkc3c7r-gTk0DYJQFSg/edit
As well, RNA molecules also lack a correspondence betweem sequence and shape:
The Strange Inevitability of Evolution – Philip Ball – Jan. 2015 Excerpt: Naively, you might expect RNAs with a similar shape, and thus presumably phenotype, to share a similar sequence, so that a map of the possible sequences—the sequence space, which can be represented as a many-dimensional space where each grid point corresponds to a particular sequence—is divided up into various “shape kingdoms” (See Not a Patch, a). But that wasn’t what Schuster found. Instead, RNAs with the same shape could vary very widely in sequence: You could get the same shape, and therefore potentially the same kind of catalytic function, from very different sequences. http://nautil.us/issue/20/creativity/the-strange-inevitability-of-evolution
In the following article, Dr. Wells comments that, 'It’s the organism controlling the DNA, not the DNA controlling the organism.'.
Ask an Embryologist: Genomic Mosaicism – Jonathan Wells – February 23, 2015 Excerpt: humans have a “few thousand” different cell types. Here is my simple question: Does the DNA sequence in one cell type differ from the sequence in another cell type in the same person?,,, The simple answer is: We now know that there is considerable variation in DNA sequences among tissues, and even among cells in the same tissue. It’s called genomic mosaicism. In the early days of developmental genetics, some people thought that parts of the embryo became different from each other because they acquired different pieces of the DNA from the fertilized egg. That theory was abandoned,,, ,,,(then) “genomic equivalence” — the idea that all the cells of an organism (with a few exceptions, such as cells of the immune system) contain the same DNA — became the accepted view. I taught genomic equivalence for many years. A few years ago, however, everything changed. With the development of more sophisticated techniques and the sampling of more tissues and cells, it became clear that genetic mosaicism is common. I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It’s the organism controlling the DNA, not the DNA controlling the organism. http://www.evolutionnews.org/2015/02/ask_an_embryolo093851.html
Here is an article that strongly supports Dr. Wells's contention that, 'It’s the organism controlling the DNA, not the DNA controlling the organism.'.
Neurons constantly rewrite their DNA - Apr. 27, 2015 Excerpt: They (neurons) use minor "DNA surgeries" to toggle their activity levels all day, every day.,,, "We used to think that once a cell reaches full maturation, its DNA is totally stable, including the molecular tags attached to it to control its genes and maintain the cell's identity," says Hongjun Song, Ph.D.,, "This research shows that some cells actually alter their DNA all the time, just to perform everyday functions.",,, ,,, recent studies had turned up evidence that mammals' brains exhibit highly dynamic DNA modification activity—more than in any other area of the body,,, http://medicalxpress.com/news/2015-04-neurons-constantly-rewrite-dna.html
Another method that clearly demonstrates that form/shape is not reducible to ‘bottom up’ materialistic explanations is by noting that it is the ‘bioelectric code’, not the genetic code, that dictates what the basic ‘form/shape’ of an organism will be during its embryological development:
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 An Electric Face: A Rendering Worth a Thousand Falsifications – Cornelius Hunter – September 2011 Excerpt: The video suggests that bioelectric signals presage the morphological development of the face. It also, in an instant, gives a peak at the phenomenal processes at work in biology. As the lead researcher said, “It’s a jaw dropper.” https://www.youtube.com/watch?v=0VULjzX__OM The face of a frog: Time-lapse video reveals never-before-seen bioelectric pattern – July 2011 Excerpt: For the first time, Tufts University biologists have reported that bioelectrical signals are necessary for normal head and facial formation in an organism and have captured that process in a time-lapse video that reveals never-before-seen patterns of visible bioelectrical signals outlining where eyes, nose, mouth, and other features will appear in an embryonic tadpole.,,, “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.physorg.com/news/2011-07-frog-time-lapse-video-reveals-never-before-seen.html
Here is another fascinating method by which it was clearly demonstrated that form/shape is not reducible to ‘bottom up’ materialistic explanations:
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
But perhaps the best demonstration that ‘form/shape’ is not reducible to the ‘bottom up’ material explanations is by noting the fact that the ‘form/shape’ of an organism is almost immediately lost upon the death of an organism:
Rabbit decomposition time-lapse (higher resolution) – video https://www.youtube.com/watch?v=C6sFP_7Vezg
In the following article, Stephen Talbott asks this very important question about the relatively sudden loss of 'form' at the death of an organism. Specifically Talbott asks, “What power holds off that moment — precisely for a lifetime, and not a moment longer?”
The Unbearable Wholeness of Beings – Stephen L. Talbott Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary. ,,, the question, rather, is why things don’t fall completely apart — as they do, in fact, at the moment of death. What power holds off that moment — precisely for a lifetime, and not a moment longer? Despite the countless processes going on in the cell, and despite the fact that each process might be expected to “go its own way” according to the myriad factors impinging on it from all directions, the actual result is quite different. Rather than becoming progressively disordered in their mutual relations (as indeed happens after death, when the whole dissolves into separate fragments), the processes hold together in a larger unity. http://www.thenewatlantis.com/publications/the-unbearable-wholeness-of-beings
Noble lists several presuppositions of neo-Darwinism that have now been falsified,,,
"Physiology Is Rocking the Foundations of Evolutionary Biology": Another Peer-Reviewed Paper Takes Aim at Neo-Darwinism - Casey Luskin March 31, 2015 Excerpt: Noble doesn't mince words: "It is not only the standard 20th century views of molecular genetics that are in question. Evolutionary theory itself is already in a state of flux (Jablonka & Lamb, 2005; Noble, 2006, 2011; Beurton et al. 2008; Pigliucci & Muller, 2010; Gissis & Jablonka, 2011; Shapiro, 2011). In this article, I will show that all the central assumptions of the Modern Synthesis (often also called Neo-Darwinism) have been disproved." Noble then recounts those assumptions: (1) that "genetic change is random," (2) that "genetic change is gradual," (3) that "following genetic change, natural selection leads to particular gene variants (alleles) increasing in frequency within the population," and (4) that "inheritance of acquired characteristics is impossible." He then cites examples that refute each of those assumptions,,, He then proposes a new and radical model of biology called the "Integrative Synthesis," where genes don't run the show and all parts of an organism -- the genome, the cell, the body plan, everything -- is integrated. http://www.evolutionnews.org/2015/03/physiology_is_r094821.html
And although, as Dr. Hunter pointed out in his article, Nobel would like to make Darwinism more Lamarckian in its foundational theoretical make-up, I would like to point out one more presupposition that Nobel did not examine in his critique of the modern synthesis. An unexamined presupposition that falsifies both the neo-Darwinian view, and his preferred Lamarckian view, of reality. Namely, both the neo-Darwinian and the Lamarckian view of reality are ultimately based on reductive materialism.
Jean-Baptiste Lamarck Excerpt: As a rather typical eighteenth-century materialist, Lamarck believed that the universe and the Earth were as eternal as matter. http://hsmt.history.ox.ac.uk//staff/documents/Lamarck-MIT-1_Oct2011_000.pdf
That is to say, both the neo-Darwinian and Lamarckian view of reality presuppose that 'plasticity of form', and 'form' itself, of any organism can ultimately be explained solely by reference to particular arrangements, and/or rearrangements, of material. That reductive materialistic presupposition simply is not true. The insurmountable problem of ‘form/shape’ for reductive materialistic explanations has now been demonstrated by a few different methods. That proteins have ‘non-sequential’ information determining the primary ‘form/shape’ of a protein, (information that resides 'holistically', as opposed to discretely, along the entirety of the protein chain), was demonstrated by the following:
Proteins with cruise control provide new perspective: Excerpt: “A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.” http://www.princeton.edu/main/news/archive/S22/60/95O56/
Moreover, the profound mystery of how a protein folds so quickly is now found to belong to the world of quantum information, not to the world of classical information. (of note: I personally hold that quantum computation is obviously heavily implicated in protein folding).
Physicists Discover Quantum Law of Protein Folding – February 22, 2011 Quantum mechanics finally explains why protein folding depends on temperature in such a strange way. Excerpt: First, a little background on protein folding. Proteins are long chains of amino acids that become biologically active only when they fold into specific, highly complex shapes. The puzzle is how proteins do this so quickly when they have so many possible configurations to choose from. To put this in perspective, a relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows.,,, Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins. That’s a significant breakthrough. Luo and Lo’s equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics. http://www.technologyreview.com/view/423087/physicists-discover-quantum-law-of-protein/
As well, it is found that the ‘form/shape’ of DNA itself is determined, in large measure, by quantum information, not by sequential, discrete, classical information:
Quantum entanglement holds together life’s blueprint – 2010 Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours. “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford. http://neshealthblog.wordpress.com/2010/09/15/quantum-entanglement-holds-together-lifes-blueprint/
In the following video, Longitudinal Quantum Information running along the entire length of DNA is discussed at the 19:30 minute mark. At the 24:00 minute mark, Dr Rieper remarks that practically the whole DNA molecule can be viewed as quantum information that has classical information embedded within it.
Classical and Quantum Information in DNA – Elisabeth Rieper – video https://youtu.be/2nqHOnVTxJE?t=1176
The following study found both quantum and classical information to be within proteins:
Classical and Quantum Information Channels in Protein Chain – Dj. Koruga, A. Tomi?, Z. Ratkaj, L. Matija – 2006 Abstract: Investigation of the properties of peptide plane in protein chain from both classical and quantum approach is presented. We calculated interatomic force constants for peptide plane and hydrogen bonds between peptide planes in protein chain. On the basis of force constants, displacements of each atom in peptide plane, and time of action we found that the value of the peptide plane action is close to the Planck constant. This indicates that peptide plane from the energy viewpoint possesses synergetic classical/quantum properties. Consideration of peptide planes in protein chain from information viewpoint also shows that protein chain possesses classical and quantum properties. So, it appears that protein chain behaves as a triple dual system: (1) structural – amino acids and peptide planes, (2) energy – classical and quantum state, and (3) information – classical and quantum coding. Based on experimental facts of protein chain, we proposed from the structure-energy-information viewpoint its synergetic code system. http://www.scientific.net/MSF.518.491
Another method of determining that the ‘form/shape’ of an organism is not reducible to ‘bottom up’ materialistic explanations is by noting that the ‘form/shape’ of many proteins is determined, not by its sequential information, but by the overall context in which the protein is residing:
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 disoredered 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 per Darwin's God Biology’s Quiet Revolution – Jonathan Wells – September 8, 2014 Excerpt: In 1996, biologists discovered a protein that does not fold into a unique shape but can assume different shapes when it interacts with other molecules. Since then, many such proteins have been found; they are called “intrinsically disordered proteins,” or IDPs. IDPs are surprisingly common, and their disordered regions play important functional roles.,,, So it is not true that biologists know all the basic features of living cells and are merely filling in the details. Nor is it true that Darwinian evolution is a settled scientific “fact,” as its defenders claim. Huge unanswered questions remain, and they will only be answered by going beyond the discredited myth that “DNA makes RNA makes protein makes us.” http://www.evolutionnews.org/2014/09/biologys_quiet_089651.html podcast – Dr. Jonathan Wells: Biology’s Quiet Revolution – September 17, 2014 “We are talking about 1/3 of the proteins in our body, (could be Intrinsically Disordered Proteins)” – Jonathan Wells http://www.discovery.org/multimedia/audio/idtf/2014/09/dr-jonathan-wells-biologys-quiet-revolution/
While "Lamarckism" today is usually simply meant to mean the idea of inherited characteristics, in Darwin's time the term implied far more than that. Darwin disagreed with Lamarckism on the idea of an innate tendency of progression, spontaneous generation, recapitulation, etc, the only thing he agreed on was the idea use and disuse, which was an idea accepted by many non-Lamarckists, and did not originate with Lamarck. Hunter is right that Darwin did ridicule Lamarck and Lamarckism - but he never ridiculed the idea of acquired characteristics. Hunter is fascinated by the recent change in attitude regarding acquired characteristics among evolutionists. I'm equally fascinated in seeing the change in attitude from ID proponents regarding acquired characteristics, and in particular Darwin's remarkable change from warmly embracing the idea to suddenly "hating" the idea in the past few years. :-) It wasn't long ago that Creationists and ID proponents regularly mocked Darwin for his enthusiastic support of inherited characteristics. Here's an article from the Discovery Institute - from just 2 years ago! - arguing that if not for Darwin that Lamarckism "would likely have died a quicker and more merciful death." The article also praises Wallace for his "prescience in rejecting the inheritance of acquired characteristics." It's interesting now that evidence how mounted that (at least to a certain extent), in some circumstances, that the phenomena occurs, how Darwin is suddenly viewed as "hating" the idea of inherited characteristics. Here's a list of examples of Darwin (from a Creationist site) talking about acquired characteristics/use and disuse in Origin: http://www.creationbc.org/index.php?option=com_content&view=article&id=118&Itemid=54 Judge for yourselves how much he "hated" the idea. And he would later incorporate it into his theory of Pangenesis. And far from wanting to rid of the idea inheritance of acquired characteristics, when Galton did an experiment that many believed put a death knell to the idea, Darwin still refused to give it up. goodusername
Of related note, the 'Lamarckians' still have an gargantuan unbridged gap to cross in that they, like the neo-Darwinians, do not have any real time empirical evidence that proteins can be created 'naturally' but have to rely on sequence comparisons. Here is James Shapiro commenting on the problem:
How Natural Genetic Engineering Solves Problems in Protein Evolution - James Shapiro - May 2012 Excerpt: When I pointed out the potential of domain shuffling by natural genetic engineering to Intelligent Design advocates who claimed protein evolution by natural mechanisms was impossible, they refused to recognize genomic data as irrefutable evidence and insisted on real-time experiments. I disagree with them strongly on the DNA sequence data. http://www.huffingtonpost.com/james-a-shapiro/genetic-engineering_b_1541180.html
Thus, like neo-Darwinists, Lamarckians must rely on sequence data to try to make their case. The problem being, of course, that the conclusion of evolution is assumed to as being true from the outset when evolutionists compare sequences, i.e. the fallacy of 'assuming your conclusion' into your premise. Shapiro did refer to 'domain shuffling' to try to give 'natural genetic engineering' a leg up on neo-Darwinian explanations. Yet domain shuffling is found to be far harder than Shapiro had originally led people to believe:
Exon Shuffling, and the Origins of Protein Folds - Jonathan M. - July 15, 2013 Excerpt: A frequently made claim in the scientific literature is that protein domains can be readily recombined to form novel folds. In Darwin’s Doubt, Stephen Meyer addresses this subject in detail (see Chapter 11). http://www.evolutionnews.org/2013/07/exon_shuffling074401.html Exon Shuffling: Evaluating the Evidence - Jonathan M. - July 16, 2013 The Problems with Domain Shuffling as an Explanation for Protein Folds Excerpt: The domain shuffling hypothesis in many cases requires the formation of new binding interfaces. Since amino acids that comprise polypeptide chains are distinguished from one another by the specificity of their side-chains, however, the binding interfaces that allow units of secondary structure (i.e. ?-helices and ?-strands) to come together to form elements of tertiary structure is dependent upon the specific sequence of amino acids. That is to say, it is non-generic in the sense that it is strictly dependent upon the particulars of the components. Domains that must bind and interact with one another can't simply be pieced together like LEGO bricks. In his 2010 paper in the journal BIO-Complexity Douglas Axe reports on an experiment conducted using ?-lactamase enzymes which illustrates this difficulty (Axe, 2010). http://www.evolutionnews.org/2013/07/an_evaluation_o074441.html Why Proteins (Protein Domains) Aren't Easily Recombined - Ann Gauger - May 2012 Excerpt: each particular helix or sheet has a distinct set of side chains sticking out from it, requiring a distinct set of chemical interactions with any nearby protein sequence. Thus, helices and sheets are sequence-dependent structural elements within protein folds. You can’t swap them around like lego bricks. This necessarily means that when you bring new secondary structure elements into contact by some sort of rearrangement, they will be unlikely to form a stable three dimensional fold without significant modification. http://www.biologicinstitute.org/post/22595615671/why-proteins-arent-easily-recombined "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 Two Domain Protein - video (several novel binding sites required) http://www.facebook.com/photo.php?v=421708024519477

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