James Shapiro’s Evolution: A View from the 21st Century free on Kindle!

My comment 6.1.2.2, which is a quote from the book, and your response, 6.1.2.2.1, in which you argue with me, rather than with Shapiro. Throughout this thread I have done little else but cite quotations from the book. At several points I have characterized his understanding as mainstream and have praised him for outlining lines of research to support his conjectures. I do find this statement to be oddly worded.

The fact that future adaptive needs are unknowable does not mean that filling those needs has to be a blind process.

I would characterize evolution as an effective search, but if it doesn't know future needs, it is blind. I think what he is saying is that evolution has an effective way of generating variations, not that it knows in advance which variants will prove useful. Petrushka

Test HouseStreetRoom

Petrushka, since you seem to agree that Shapiro is wrong also, as I do, when you state;,,,

I think your disagreement is with Shapiro, not with me.

,,,Please point out the unfounded presumptions in the statement you cited. bornagain77

I think your disagreement is with Shapiro, not with me.

Evolution is life’s way of dealing with the unpredictable. We have seen that principle most clearly at work in the adaptive immune system, where antibodies have to be synthesized that can recognize unknown invaders. The fact that future adaptive needs are unknowable does not mean that filling those needs has to be a blind process. In immune system natural genetic engineering, and in evolutionary change in general, we have been able to discern regular features of genome restructuring that facilitate the production of novel molecular tools with an enhanced likelihood of real-world utility. A measure of success for the more informational perspective sketched out in this book will be the extent of future research into the cognitive cellular operations that have led to successful evolutionary inventions. We have a great deal to learn in this respect. Shapiro, James A. (2011-06-08). Evolution: A View from the 21st Century (FT Press Science) (Kindle Locations 2679-2684). FT Press. Kindle Edition.

Petrushka

Perhaps this song is more fitting for the 'perfectionist' ability of ribosomes to hit the bullseye:

Sara Groves performs "Eyes On The Prize" http://www.youtube.com/watch?v=BmrTvDoqvMM

bornagain77

Petrushka, Well actually there is no hint of such a highly choreographed 'search and find' mechanism, as employed in the immune system, for making proteins i.e. the proteins hit the target first time, every time, to sequence dictated by 'natural genetic engineering', or else they are immediately destroyed by the ever finicky ribosomes;

The Ribosome: Perfectionist Protein-maker Trashes Errors Excerpt: The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist...the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products... To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is "shocking" and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis. http://www.sciencedaily.com/releases/2009/01/090107134529.htm

Whereas searching for correct novel functional protein sequences, out of astronomical amounts of non-functional protein sequences, would look much more akin to this:

How Proteins Evolved - Cornelius Hunter - December 2010 Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function. http://darwins-god.blogspot.com/2010/12/how-proteins-evolved.html

,,,which, regardless of the neo-Darwinists severe distortion of the immune system for propaganda purposes, to 'sell the lie' of neo-Darwinism, the fact is that the immune system still severely begs the question, because the immune system is in fact another stunningly elegant example of Intelligent Design:

Falk’s fallacy - Feb. 2010 Excerpt: This (the immune system) is one of the most amazing processes ever described.,,, Whatever may be said about it, it is a highly regulated, specified, directed and choreographed process. It is obviously the product of overwhelmingly brilliant design,,, https://uncommondescent.com/intelligent-design/falks-falacy/ Response to Kathryn Applegate - Caroline Crocker PhD.- cell biologist and immunologist - October 2010 Excerpt: Diversity of antibodies generated by B cells is due to deliberate, cell-engineered changes in the DNA sequence, not random mutations. In fact, I have never before heard the process whereby functional antibodies are formed (before they encounter antigen) described as mutation. And it is well-known that the appearance of functionality as a result of a mistake-mutation is extremely rare. Of course, after encountering antigen the hypervariable regions of the antibody DNA do undergo somatic hypermutation, but again this is in particular places and is controlled by enzymes.,,, https://uncommondescent.com/intelligent-design/comments-on-kathryn-applegate%E2%80%99s-may-posts-on-biologos/#more-15176 Generation of Antibody Diversity is Unlike Darwinian Evolution - microbiologist Don Ewert - November 2010 Excerpt: The evidence from decades of research reveals a complex network of highly regulated processes of gene expression that leave very little to chance, but permit the generation of receptor diversity without damaging the function of the immunoglobulin protein or doing damage to other sites in the genome. http://www.evolutionnews.org/2010/11/response_to_edward_max_on_talk040661.html "A Masterful Feat of Courtroom Deception": Immunologist Donald Ewert on Dover Trial - audio http://intelligentdesign.podomatic.com/player/web/2010-12-20T15_01_03-08_00

In this following podcast, Casey Luskin interviews microbiologist and immunologist Donald Ewert about his previous work as associate editor for the journal Development and Comparative Immunology, where he realized that the papers published were comparative studies that had nothing to do with evolution at all.

What Does Evolution Have to Do With Immunology? Not Much - April 2011 http://intelligentdesign.podomatic.com/entry/2011-04-06T11_39_03-07_00

note: As well, the 'protein factory' of the ribosome, which is, as far as I know, the only machine in the universe capable of making proteins, is far more complicated than first thought:

Honors to Researchers Who Probed Atomic Structure of Ribosomes - Robert F. Service Excerpt: "The ribosome’s dance, however, is more like a grand ballet, with dozens of ribosomal proteins and subunits pirouetting with every step while other key biomolecules leap in, carrying other dancers needed to complete the act.” http://www.creationsafaris.com/crev200910.htm#20091015a

Music:

Sara Groves – Something Changed – music video http://www.vimeo.com/28076423

bornagain77

It’s very well likely that ‘natural genetic engineering’, completely by random accident of course , stumbled upon functional proteins, out of astronomically large numbers of non-functional protein sequences, that are uniquely tailored for each person;

He compares it to the operation of the immune system, which rather quickly finds antibodies through such a process. If you think it isn't possible, you should write to him. I'm just reporting what he says. Petrushka

a few notes:

Most Detailed Annotation of Fruit-Fly Genome Points Way to Understanding All Organisms’ Genomes – December 2010 Excerpt: “We also found an order-of-magnitude increase in the ways that genes are spliced and edited to produce alternate forms of known proteins, thus significantly increasing the complexity of the proteome.”,,, Despite the scrutiny to which the Drosophila genome has been subjected, the researchers found new or altered exons or splice forms in almost three-quarters of Drosophila’s previously annotated genes,,, http://www.sciencedaily.com/releases/2010/12/101222131131.htm

And it gets better:

New level of genetic diversity in human RNA sequences uncovered Excerpt: A detailed comparison of DNA and RNA in human cells has uncovered a surprising number of cases where the corresponding sequences are not, as has long been assumed, identical. The RNA-DNA differences generate proteins that do not precisely match the genes that encode them.,,, Nearly half of the RDDs uncovered in the new study cannot be explained by the activity of deaminase enzymes, however, indicating that unknown processes must be modifying the RNA sequence, either during or after transcription. ,,, Although all of the individuals analyzed in the study had a large number of RDDs, there was a great deal of variability in the specific RDDs found in each person's genetic material." http://www.physorg.com/news/2011-05-genetic-diversity-human-rna-sequences.html

i.e. It's very well likely that 'natural genetic engineering', completely by random accident of course :) , stumbled upon functional proteins, out of astronomically large numbers of non-functional protein sequences, that are uniquely tailored for each person; i.e. each human being is very likely to have fairly unique protein sequences, that were 'naturally engineered' on the fly, that no one else, or living thing, possesses!!! How astonishing is that???

Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681

further note:

Human Genome “Infinitely More Complex” Than Expected - April 2010 Excerpt: Hayden acknowledged that the “junk DNA” paradigm has been blown to smithereens. “Just one decade of post-genome biology has exploded that view,” she said,,,, Network theory is now a new paradigm that has replaced the one-way linear diagram of gene to RNA to protein. That used to be called the “Central Dogma” of genetics. Now, everything is seen to be dynamic, with promoters and blockers and interactomes, feedback loops, feed-forward processes, and “bafflingly complex signal-transduction pathways.” http://www.creationsafaris.com/crev201004.htm#20100405a

bornagain77

There's one other weird thing about the book. I've searched through the whole thing without finding any reference to information loss during mutation. What I did find is this:

This book gives solid biological evidence on the origin of variation and evolutionary change. That evidence will surprise those who still think that variation is random. Cells and organisms sense their environment and transmit that information to their genomes. Brilliant.” Shapiro, James A. (2011-06-08). Evolution: A View from the 21st Century (FT Press Science) (Kindle Locations 24-26). FT Press. Kindle Edition.

The exact mechanism by which information is conveyed to the genome is controversial, to say the least, but the fact that it happens is something evolutionist have been saying for a long time. Elizabeth Liddle has repeated it over and over in the last month or so. But there is no controversy about the fact that Shapiro disagrees with those who claim evolution can't produce information gain. He just thinks genomes learn in much the same way brains learn. I believe he even invokes consciousness. Petrushka

This thread is about Shapiro's book, so I'll limit myself to summarizing what hes says. If anyone thinks I've misquoted or misrepresented him him, I'll respond. My summary of the relevant points is found at 2.1.1.1.1 What he says about protein evolution is:

So the capacity of living cells to carry out the requisite natural genetic engineering operations for protein evolution by domain swapping is unequivocally established.

He neither asks nor answers where the ability comes from, but the does note that after genome duplication, the duplicate genes are free to change without damaging the organism. He does not invoke any outside agency. It sounds pretty materialistic to me. Feel free to examine the book and tell me where he appeals to intervention. Petrushka

Petrushka, well by-golly just use a 'engineered process', call it natural, (as if that question does not beg the question of where this 'natural' engineering process came from all day long), and then claim that these 'natural engineered processes' where proteins are custom made for very specific molecular needs in the cell, by the unmatched, extremely sophisticated, intensively parallel, distributed programming of the cell, then claim that this jaw-dropping feat, of manufacturing exactly correct proteins on the fly, is a completely 'random' event, that somehow arose by completely random 'material' processes, and WA LA, that somehow explains the 'random' evolution of exactly the correct amino acid sequences for proteins out of astronomical possibilities?????? Excuse me please!!!,, By chance, is the world you live in down a rabbit hole somewhere? Perhaps you would like to come back to reality and actually demonstrate that ANY protein can be had by a purely random material processes instead of severely begging the question by appealing to the 'natural engineering' of the cell. After you have done that you can work on refuting A.Aspect, and company's, falsification of local realism and the finding of non-local quantum information in molecular biology!! But then again that would require you being honest with the evidence, so I guess I can count that out!!! bornagain77

Since this thread is about Shapiro, I'll quote him:

My late colleague Malcolm Casadaban developed a generalized in vivo technique using a DNA transposon that could fuse any E. coli protein coding sequence to the enzymatically active domains of LacZ beta-galactosidase [748]. Mammalian tissue culture experiments have demonstrated the domain-swapping capabilities of non-LTR retrotransposons through retrotransduction, either of upstream sequences (SVA elements) or downstream sequences (LINE elements) [522, 749, 750]. In addition to domain swapping by retrotransduction, genome sequences in plants and animals have begun to document protein-coding regions where new exons have been incorporated by different classes of DNA transposons (so-called “Pack-MULEs” in rice and helitrons in maize [213, 751–754]). So the capacity of living cells to carry out the requisite natural genetic engineering operations for protein evolution by domain swapping is unequivocally established. Shapiro, James A. (2011-06-08). Evolution: A View from the 21st Century (FT Press Science) (Kindle Locations 1776-1784). FT Press. Kindle Edition.

Petrushka

Moreover, as you well know Petruska, the dispute between IDists and Darwinists has, thus far, not focused on quantum information so much, if at all, but has instead focused on ‘classical information’,

“LIFE’S CONSERVATION LAW: Why Darwinian Evolution Cannot Create Biological Information”: http://evoinfo.org/publications/lifes-conservation-law/

Yet, though the dispute between Darwinists and IDist has been over ‘classical information,, classical information is shown to be a subset of quantum information by the following method:

This following research provides solid falsification for Rolf Landauer?’s contention that information encoded in a computer is merely physical (“Information is physical!” – Rolf Landauer) (merely ‘emergent’ from a material basis) since he believed it always required energy to erase it; Quantum knowledge cools computers: New understanding of entropy – June 2011 Excerpt: No heat, even a cooling effect; In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy. Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.” http://www.sciencedaily.com/releases/2011/06/110601134300.htm

And transcendent quantum information is shown, empirically, to be ‘conserved’ here:

Quantum no-hiding theorem experimentally confirmed for first time – March 2011 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. http://www.physorg.com/news/2011-03-quantum-no-hiding-theorem-experimentally.html

I would like to reiterate just how 'spooky', to use Einstein's word, it is to find something that blatantly defies our concepts of time and space, on a massive scale, within our bodies

Light and Quantum Entanglement Reflect Some Characteristics Of God - video http://www.metacafe.com/watch/4102182

Further note:

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 (Functional Sequence Complexity). 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

verse and music:

John 1:1-3 In the beginning was the Word, and the Word was with God, and the Word was God. 2 He was with God in the beginning. 3 Through him all things were made; without him nothing was made that has been made. Brooke Fraser - Lord of Lords(Legendado Português) - http://www.youtube.com/watch?v=rkF3iVjOZ1I

bornagain77

Petruska, please feel free to cite, with actual references, the origination of any novel gene/protein by purely neo-Darwinian (i.e. random material) processes using whatever source of 'purely random' variation, epigenetic or point mutations, that you care to postulate.,,, Moreover, I did not state 'falsify evolution', I said it was 'devastating' to the genetic reductionism model of the modern synthesis of neo-Darwinism!!,,, But if you are interested a actuall Falsification for the reductive materialistic framework of neo-Darwinism, then that is achieved by the following method:

Here is a clip of a talk in which Alain Aspect talks about the failure of ‘local realism’, or the failure of materialism, to explain reality since quantum entanglement/information is now conclusively shown to be ‘non-local’ (i.e. instantaneous, as well as completely transcendent of any space-time (material) constraints): Quantum Entanglement – The Failure Of Local Realism – Materialism – Alain Aspect – video http://www.metacafe.com/w/4744145 This falsification for local realism (materialism), discussed by Aspect in the preceding video, was recently greatly strengthened: Physicists close two loopholes while violating local realism – November 2010 Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview. http://www.physorg.com/news/2010-11-physicists-loopholes-violating-local-realism.html Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009 Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables. http://www.sciencedaily.com/releases/2009/07/090722142824.htm

Quantum entanglement is shown to be related to ‘functional information’ by the following evidence;

Quantum Entanglement and Information Excerpt: A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. http://plato.stanford.edu/entries/qt-entangle/

And yet Quantum Entanglement/Information, which falsified ‘local realism (reductive materialism), is found to be intertwined in the molecular basis life on a massive scale:

Quantum Information/Entanglement In DNA & Protein Folding – short video http://www.metacafe.com/watch/5936605/

Indeed the ‘computation’ accomplished by the non-local quantum entanglement/information within DNA is very impressive:

Quantum Dots Spotlight DNA-Repair Proteins in Motion – March 2010 Excerpt: “How this system works is an important unanswered question in this field,” he said. “It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.” Dr. Bennett Van Houten – of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. http://www.sciencedaily.com/releases/2010/03/100311123522.htm

Anton Zeilinger?, a leading researcher in Quantum mechanics, relates how quantum entanglement is related to quantum teleportation in this following video;

Quantum Entanglement and Teleportation – Anton Zeilinger – video http://www.metacafe.com/watch/5705317/

And quantum teleporation showed that atoms, which are suppose to be the basis from which functional information ‘emerges’, in the neo-Darwinian framework, are now shown to be, in fact, reducible to the transcendent functional quantum information that the atoms are suppose to be the basis of!

Ions have been teleported successfully for the first time by two independent research groups Excerpt: In fact, copying isn’t quite the right word for it. In order to reproduce the quantum state of one atom in a second atom, the original has to be destroyed. This is unavoidable – it is enforced by the laws of quantum mechanics, which stipulate that you can’t ‘clone’ a quantum state. In principle, however, the ‘copy’ can be indistinguishable from the original (that was destroyed),,, http://www.rsc.org/chemistryworld/Issues/2004/October/beammeup.asp Atom takes a quantum leap – 2009 Excerpt: Ytterbium ions have been ‘teleported’ over a distance of a metre.,,, “What you’re moving is information, not the actual atoms,” says Chris Monroe, from the Joint Quantum Institute at the University of Maryland in College Park and an author of the paper. But as two particles of the same type differ only in their quantum states, the transfer of quantum information is equivalent to moving the first particle to the location of the second. http://www.freerepublic.com/focus/news/2171769/posts

Petrushka please tell me how quantum information/entanglement can ‘emerge’ from any material basis of atoms when atoms are now shown to reduce to a transcendent basis of quantum information in the first place? i.e. It is IMPOSSIBLE for the 'cause' for functional quantum information to reside in material particles!!! bornagain77

I'm really confused by your assertion that materialism has been devastated. I'd like to see a reference to anything in Shapiro that asserts that the algorithms he sees in cellular machinery are carried out by anything other than physical processes. Just because a machine executes algorithms doesn't mean it isn't physical. Computers do it. Petrushka

If epigenetic changes aren't very important for long-term evolution, how does epigenetics falsify evolution? I don't see that Shapiro's book falsifies anything. He asserts that organisms can respond to environmental stress by producing various kinds of genomic changes, and he asserts that some are not random with respect to fitness, but he doesn't offer proof. He offers some ideas for research. The word mutation includes point mutations and other kinds of changes. there are at least 20 kinds of changes. Petrushka

Petrushka states at September 27, 2011 at 8:59 am in response to the devastating critique of the genetic reductionism model of the modern synthesis that Dr. Shapiro levels,

I’d like to point out that neither Darwin nor subsequent biologists have ever assumed that point mutations are the only source of variation.

Yet in this other thread at September 26, 2011 at 6:08 pm, Petrushka, without reference, hinted at no such trouble for the modern synthesis of neo-Darwinism:

That’s simply untrue. Both in theory and in the data. Most fixed mutations are neutral or nearly neutral. This has been known since before 1950 and has been mainstream for well over 50 years. It depends on population size. In large populations, favorable mutations tend to get fixed. In small populations, neutral mutations predominate. This fits both observation and simulations of population genetics. https://uncommondescent.com/intelligent-design/science-and-freethinking/comment-page-1/#comment-400865

Petrushka is corrected, with several references, here, at September 26, 2011 at 7:35 pm, that observation, nor the modern synthesis of population genetics, offers any support, whatsoever, for his claim that proteins and/or genes can arise by random point mutations!

https://uncommondescent.com/intelligent-design/science-and-freethinking/comment-page-1/#comment-400866

Petrushka does not respond to this cited refutation; yet just this morning, at September 27, 2011 at 6:29 am, he again, without reference, falsely asserts:

Neutral theory is well established. It is fairly easy to demonstrate in software. It is fairly easy to demonstrate in living things by tracing the lineage of neutral or neutral alleles. https://uncommondescent.com/intelligent-design/science-and-freethinking/comment-page-1/#comment-400893

So, shortly after that this morning, when Petrushka states, at September 27, 2011 at 8:59 am, that;,,,

I’d like to point out that neither Darwin nor subsequent biologists have ever assumed that point mutations are the only source of variation.

,,,One if left to wonder if Petrushka is even paying attention to the many lies and rationalizations that he repeats over and over, or if he is merely a Darwinbot programmed to spew the same refuted garbage over and over not caring that he has contradicted himself:?!?! I would also like to point out that even though atheistic neo-Darwinists would very much love to get away from the whole genetic reductionism/point mutation gambit, since it is such a complete failure for them as far as actual empirical evidence is concerned, they are inextricably wed to the scenario to explain the origination of the novel sequences in novel genes and/or proteins. Moreover I would like to point out that whatever relief for finding a alternate source of 'random' variation, from the many epigenetic mechanisms listed by Dr. Shapiro, was recently been dealt a severe blow by this following study: notes

And though epigentics falsifies the modern synthesis of neo-Darwinism (Genetic Reductionism), epigentics also provides no 'escape hatch' for a 'extended' materialistic theory of evolution which may have been postulated to explain body plan morphogenesis, which, of course, the modern synthesis had completely failed to explain in the first place: Epigenetic changes don't last - September 2011 Excerpt: They found that epigenetic changes are many orders of magnitude more frequent than conventional DNA mutations, but also often short lived. They are therefore probably much less important for long-term evolution than previously thought. http://www.physorg.com/news/2011-09-epigenetic-dont.html

bornagain77

Yeah, read the whole book first and then get back to us. Chris Doyle

Perhaps we are having trouble with different readings of the term "mechanistic." Shapiro contrast it with "informational." I find that distinction unfortunate. Computers are machines that process information. They are entirely mechanistic. If cells can modify their genome in response to environmental stress, it's still a mechanism. This books suggests but does not produce evidence, that the change mechanism has foresight. He proposes research to demonstrate this. That's all good stuff. Conjectures that can be tested. Petrushka

Have I read the whole thing. No. I just got it this morning. At the moment I don't have access to it. I've read enough to know that my rather lengthy excerpts are representative of his thinking. I see arguments that some variation is algorithmic in the sense that certain events may be triggered by environmental stress, and some kinds of change may have a statistically better than random chance of being useful. Environmental triggers are mainstream. The non-random nature of changes is not mainstream, but he proposes specific, targeted research to settle the issue. I also see suggestions for research to verify these conjectures. I don't see any invocation of intervention or of non-naturalistic events or processes. I think he rather handily disposes of certain kinds of assertions. 1. He dismisses any challenge to common descent (Microbes are a special case, because they exchange genetic material.) 2. He invokes no intervention, even for the invention of complex functions. 3. He describes a naturalistic process for speciation and invention of new body plans. It's pretty mainstream: gene or whole genome duplication followed by evolution of the duplicated genetic material. 5. He does not see the Cambrian explosion as an unexpected event. 6. He asserts that mammals share nearly all of their protein genes, and that most of the differences lie in developmental pathways. 7. All of his mechanisms are known and supported in mainstream biology. Feel free to find one that doesn't come directly from mainstream biology. So what he proposes -- and it's not entirely new -- is evolvability. A concept that has been tossed around for decades. He has an extreme interpretation. I do not intend "extreme" as a pejorative, just a description. Petrushka

Have you read any of the book yet, Petrushka? Shapiro repeatedly points out that a 'mechanistic' view of biology is wrong. Chris Doyle

Please point out where "natural genetic engineering" is not "mechanistic." I must have missed it. Perhaps Sahpiro assumes, like Michael Denton, that the game was set up at creation. I don't know what he thinks about origins. But he proposes no interventions and is quite explicit in attributing evolution to natural processes. Petrushka

For some reason I'm having trouble posting. the responses are not showing up as replies. I'd like to point out that neither Darwin nor subsequent biologists have ever assumed that point mutations are the only source of variation. The mechanisms discussed in this book all come from mainstream biology. The book is a review of current knowledge, plus suggestions for research. Petrushka

Depends on what you mean by random mutations. All the processes he describes are natural processes, and all of them are part of mainstream biology. He suggests research targeted to determine randomness with regard to fitness. He does not say the research has been done. He suggests Lenski-like experiments and seems to predict outcomes quite different from what Behe would expect. All in all, he is well within the mainstream in that he makes hypotheses and suggests ways of testing them. Petrushka

Who needs the book when you can just keep posting snippets!? Genomes are sophisticated data storage organelles integrated into the cellular and multicellular life cycles of each distinct organism. Thinking about genomes from an informatic perspective, it is apparent that systems engineering is a better metaphor for the evolutionary process than the conventional view of evolution as a selection-biased random walk through the limitless space of possible DNA configurations. So far, it seems to me as though James Shapiro is trying to reconcile the overwhelming evidence for design with his a priori commitment to evolution and the first thing to be jettisoned in the process is the idea that natural selection acting upon random mutations can provide any significant, or indeed empirically-supported, explanations for the world we live in. Chris Doyle

Some research proposals (one of them sounds like Lenski):

Besides fitting within the currently defined boundaries of biology, the concept of functionally targeted and coordinated natural genetic engineering is open to experimental test. The problem can be approached from two directions. The bottom-up approach is to design experimental systems in which cells have to produce two or more targeted changes to pass through a particular selection regime (such as growth on a medium that lacks a particular nutrient or that uses a novel growth substrate). The frequencies of single and multiple change events can be determined, and the roles of particular natural genetic engineering systems, such as transposons and retrotransposons, can be evaluated. In this way, we can develop an appreciation of the potential for coordinated genomic changes. The successful isolation of bacterial mutants containing multiple related mutations within periods as short as a month is a promising indicator that the experiments can prove successful [1122, 1123]. The top-down approach to investigating targeted changes in the genome is to utilize our rapidly growing ability to obtain and interpret whole genome sequences [1124]. We can subject various organisms to particular kinds of “genome shocks” known to activate complex genome restructuring (Tables II.7 and II.8) and then carry out complete genome sequencing of the survivors that display novel heritable characteristics. The results will indicate the nature of the genome changes that have produced the new traits, and we can see how many of them have involved coordinated changes in network function. This method should be particularly applicable in well-studied plant species, such as Arabidopsis thaliana, where evidence already exists for morphological, chromosomal, and transcriptional changes following interspecific hybridization [1083, 1125–1128]. Shapiro, James A. (2011-06-08). Evolution: A View from the 21st Century (FT Press Science) (Kindle Locations 2520-2535). FT Press. Kindle Edition.

Petrushka

Here is another interesting snippet which undermines the entire neo-Darwinian framework:

Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf

Thus in one fell swoop Shapiro topples the major cornerstone of the non-teleological 'randomness' required to be at the base of the atheistic form of neo-Darwinian reductive materialism!!! Another interesting snippet:

These discoveries contradict atomistic pre-DNA ideas of genome organization and violate the central dogma at multiple points. In place of the earlier mechanistic understanding of genomics, molecular biology has led us to an informatic perspective on the role of the genome. The informatic viewpoint points towards the development of novel concepts about cellular cognition, molecular representations of physiological states, genome system architecture, and the algorithmic nature of genome expression and genome restructuring in evolution.

It cannot be understated how devastating the removal of genetic reductionism is for the atheistic/materialistic model of neo-Darwinism that is still predominately taught in schools with no mention of the severe problems that Dr. Shapiro has made clear!!!! bornagain77

More interesting snippets:

It is important to note that selection has never led to formation of a new species, as Darwin postulated. No matter how morphologically and behaviorally different they become, all dogs remain members of the same species, are capable of interbreeding with other dogs, and will revert in a few generations to a common feral dog phenotype if allowed to go wild. Shapiro, James A. (2011-06-08). Evolution: A View from the 21st Century (FT Press Science) (Kindle Locations 2250-2252). FT Press. Kindle Edition. Where did these extra Hox complexes come from? The answer comes from noting that duplications, triplications, tetraplications, and even octaplications are not limited to Hox complexes. They also are observed for other important genetic loci, such as those encoding surface receptors and components of signal transduction circuits [1070]. The sources of such widespread amplifications are now seen to be the result of “whole genome duplications” (WGDs). In his prescient 1970 book Evolution by Gene Duplication, Susumu Ohno predicted two successive WGD events in the evolution of vertebrates [1071]. These two WGD events-—the first preceding appearance of the first vertebrates, and the second preceding appearance of jawed vertebrates—produced the required four copies of the Hox complexes and other genome components [1072–1074]. Rigorously speaking, genomic evidence alone is insufficient to establish that a WGD has occurred. What is observed in cases where we believe that a WGD has occurred is the presence of a significant number of duplicated syntenic regions throughout the genome. Technically, this can only be termed a large-scale duplication (LSD) event, conceivably having arisen through a series of independent or even coordinated segmental duplications in different parts of the genome. Nonetheless, geneticists, genomicists, and evolutionists are confident that WGD is the correct explanation for these dispersed duplications, because we can actually observe WGD and its direct role in speciation in real time. Shapiro, James A. (2011-06-08). Evolution: A View from the 21st Century (FT Press Science) (Kindle Locations 2248-2249). FT Press. Kindle Edition. In addition to flowering plants and vertebrates, we know that WGDs have played a role in the evolution of fungi and protozoa [1093–1096]. It is likely that even more instances of WGD at major evolutionary junctures will be documented as more eukaryotic genomes are sequenced. One of the most significant features of WGD events is that they produce two copies of the dispersed genome regions that encode complex networks [1097, 1098]. Having an extra copy of the entire network means that no functionality is lost if one copy of the network is modified to change its inputs, outputs, and/or internal operation. The fact that intracellular signaling networks, for example, have been adapted to many different cellular and developmental functions indicates that, in the course of evolution, they have been duplicated and modified to meet new adaptive needs [1099, 1100]. It makes sense to believe that this kind of whole-network adaptation is significantly easier to execute in an organism that has a recently duplicated genome than in one where every network is unique and fulfills an important functional requirement. Shapiro, James A. (2011-06-08). Evolution: A View from the 21st Century (FT Press Science) (Kindle Locations 2275-2284). FT Press. Kindle Edition.

Petrushka

Another interesting snippet:

Comparing mice and men, the “genes” stay largely the same, but their deployment differs. The bones, ligaments, muscles, skin, and other tissues are similar, but their morphogeneses and growth follow distinct patterns. In other words, humans and mice share most of their proteins, and the most obvious differences in morphology and metabolism can be attributed to distinct regulatory patterns in late embryonic and postnatal development. Shapiro, James A. (2011-06-08). Evolution: A View from the 21st Century (FT Press Science) (Kindle Locations 2224-2227). FT Press. Kindle Edition.

Petrushka

Seems to cover much of the same ground as the Koonin book. Possibly with a different slant. It's far more technical than Koonin. But here's a readable snippet:

Descent with modification provides the overall context for this book, whose main theme is to illustrate how many exciting facts we have learned about the processes that lead to evolutionary inventions. Analyzing the fossil record is somewhat outside the scope of this book, but the correlation of paleontological novelties and genome organization is a fascinating question addressed by the branch of science now called Evo-Devo, the study of the evolutionary basis of morphogenetic processes [1014] [1015–1018]. Evo-Devo attempts to integrate the results of molecular developmental biology, genomics, and paleontology. Molecular development tells us about the networks and component molecules that guide the morphogenesis of contemporary organisms. Genomics permits us to infer phylogenies of those morphogenetic circuits, and paleontology tells us about the historical record. As the three areas of study become more fully integrated, our confidence grows in the solidity of our understanding of the evolutionary process. Shapiro, James A. (2011-06-08). Evolution: A View from the 21st Century (FT Press Science) (Kindle Locations 2145-2153). FT Press. Kindle Edition.

Petrushka