James Shapiro on “dangerous oversimplifications” about the cell

_{Denyse O'Leary

August 6, 2013

Cell biology, News}

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From non-Darwinian Shapiro’s “How Life Changes Itself: The Read-Write (RW) Genome”

It is essential for scientists to keep in mind the astonishing reliability and complexity of living cells. Even the smallest cells contain millions of different molecules combined into an integrated set of densely packed and continuously changing macromolecular structures.

Depending upon the energy source and other circumstances, these indescribably complex entities can reproduce themselves with great reliability at times as short as 10-20 minutes. Each reproductive cell cycle involves literally hundreds of millions of biochemical and biomechanical events. We must recognize that cells possess a cybernetic capacity beyond our ability to imitate. Therefore, it should not surprise us when we discover extremely dense and interconnected control architectures at all levels. Simplifying assumptions about cell informatics can be more misleading than helpful in understanding the basic principles of biological function.

Two dangerous oversimplifications have been (i) to consider the genome as a mere physical carrier of hypothetical units called “genes” that determine particular cell or organismal traits, and (ii) to think of the genome as a digitally encoded Read-Only Turing tape that feeds instructions to the rest of the cell about individual characters [4].

See also these illustrations.

Comments

The post about information was intriguing. I suppose you could use the synonym "knowledge". Even though it has no weight, or volition, it has the capacity to change the world, and could conceivably be more powerful than the world's armies.mjazzguitar_{August 7, 2013
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I am wondering if they have become words to avoid in a scientific paper, tainted by association with creationist dogma.
That is a pretty good observation. All these scientific papers which actually support the ID position but are unable to say the obvious. It is like if the term is used, Zeus will throw a thunderbolt and strike the author dead. Actually, if a scientist says "intelligent design" in a scientific paper, an even worse fate will happen. He/she will loose all his/her dinner invitations.jerry_{August 7, 2013
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That’s encouraging, Jerry! You’re asking scientific questions.!
Ever since I first commented on this site in 2006 I have been driven by the science of the issue. I have only seen one anti-ID person who was also driven by science, logic and reason. Plenty of the ID people are driven by the science but certainly not all. Because of my interest in science, I realized quickly that Darwinian processes were science but essentially equivalent to what is modern day genetics. I also realized that Darwin's ideas had nothing to do with the evolution debate. I identified at the beginning that the debate was about new alleles which is what Douglas Axe and Kirk Durston's work is all about. I was one of the first ones here to read Eva Jablonka's book which Allen MacNeill highly recommended. Nothing to support Darwin there. I have explored Hazen's ideas on the origin of life. I have read Dawkins, Gee and Coyne. I have Futuyama's book on evolution. I have read some of Pigliucci who says they don't have a clue about macro-evolution. Not one pro Darwinian visitor to this site since 2006 has been able to back up their contention that Darwinian processes had anything to do with evolution. There does not exist any examples in the published literature which supports Darwinian processes for anything more than genetics. That is a fairly good sample. Right now I have been watching a brand new Teaching Company Course on the history of life. Just passed the Cambrian and the Burgess Shales and so far nothing to justify a naturalistic explanation for life and life's changes. So as I keep sampling the urn of various scientific explanation, I only get ID balls. Still looking for those Darwinian balls in the urn. My guess is Biochemistry for Dummies will still come up ID. I asked the questions about development a few years ago and no one answered them. Some of the answers are in Meyer's book but this is almost completely unexplored territory and it is where the evolution debate will probably turn to quickly. One of the three main virtues of Christianity is hope. Keep the faith and maybe someday your hope will prove out. If it does, I will be the first one to recognize it and support it. That is part of Christian charity.jerry_{August 7, 2013
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Jerry:
What determines the switching patterns? Where is that? What determines the sequencing of cell division and their placement? It must be somewhere and wherever it is, it and the content of the information is probably the key to evolution.
That's encouraging, Jerry! You're asking scientific questions. My out-of-date undergraduate biochemistry is not up to the task of answering you. Indeed, I struggle (and fail) to keep up with progress in the field. What answers currently exist are unlikely to be found at UD. Amazingly, there is even Biochemistry for Dummies which gets good reviews from purchasers. Also your enquiry overlaps into evolutionary developmental biology and into the fascinating field of HOX genes. With the internet, information is at your fingertips!Alan Fox_{August 7, 2013
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Interstingly the words “intelligent” and “design” do not appear in the linked paper!
So?
Well, as you point out, I managed to use both words in a sentence. I am wondering if they have become words to avoid in a scientific paper, tainted by association with creationist dogma.Alan Fox_{August 7, 2013
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Jerry @ 5 said .... "Finally, would Darwin have published his Origin of Species if he knew what Shapiro knows about the complexity and preciseness of the interactions in the cell or would he have thought what a fool he was to think it could happen naturally." I think Charles Darwin would have no doubt been an IDest. Here is quoted from his book "The Autobiography of Charles Darwin 1809-1892" pages 92-3 The same Darwin quote also found in Antony Flew's book "There Is A God" page106 "Reason tells me of the extreme difficulty or rather impossibility of conceiving this immense and wonderful universe, including man with his capability of looking far backwards and far into futurity, as the result of blind chance and necessity. When thus reflecting I feel compelled to look to a First Cause having an intelligent mind in some degree analogous to that of man; and I deserve to be called a Theist." Was Charles Darwin an Intelligent Design theist!!!!!!!!!!!!!!!Johnnyfarmer_{August 6, 2013
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Alan Fox:
Interstingly the words “intelligent” and “design” do not appear in the linked paper!
But they do appear in your post. Does that mean you're a fan?
Interstingly the words “intelligent” and “design” do not appear in the linked paper!
So?Mung_{August 6, 2013
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of semi related note: JonathanM, who likes to get into the nitty gritty of the complexity of the cell, has a new article up on ENV: The Cell's Surveillance System: Introducing the Cell Cycle Checkpoint Pathways Jonathan M. August 6, 2013 Conclusion: My discussion thus far of the molecular mechanisms underpinning cell cycle progression has barely scratched the surface, and indeed entire books have been written on the subject (such as this one). The more deeply you explore the cell cycle, however, the more you come to the realization that it represents one of the most remarkable evidences of design in the biological universe. http://www.evolutionnews.org/2013/08/the_cells_surve075151.htmlbornagain77_{August 6, 2013
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as to this comment from Dr. Shapiro,,,
" Each reproductive cell cycle involves literally hundreds of millions of biochemical and biomechanical events. We must recognize that cells possess a cybernetic capacity beyond our ability to imitate. Therefore, it should not surprise us when we discover extremely dense and interconnected control architectures at all levels."
,,,It is interesting to note what the father of cybernetics said:
"The mechanical brain does not secrete thought "as the liver does bile," as the earlier materialists claimed, nor does it put it out in the form of energy, as the muscle puts out its activity. Information is information, not matter or energy. No materialism which does not admit this can survive at the present day." Norbert Weiner - MIT Mathematician -(Cybernetics, 2nd edition, p.132) Norbert Wiener created the modern field of control and communication systems, utilizing concepts like negative feedback. His seminal 1948 book Cybernetics both defined and named the new field.
Also it is interesting to note what Dr. Stephen Meyer has said in regards to information:
“One of the things I do in my classes, to get this idea across to students, is I hold up two computer disks. One is loaded with software, and the other one is blank. And I ask them, ‘what is the difference in mass between these two computer disks, as a result of the difference in the information content that they posses’? And of course the answer is, ‘Zero! None! There is no difference as a result of the information. And that’s because information is a mass-less quantity. Now, if information is not a material entity, then how can any materialistic explanation account for its origin? How can any material cause explain it’s origin? And this is the real and fundamental problem that the presence of information in biology has posed. It creates a fundamental challenge to the materialistic, evolutionary scenarios because information is a different kind of entity that matter and energy cannot produce. In the nineteenth century we thought that there were two fundamental entities in science; matter, and energy. At the beginning of the twenty first century, we now recognize that there’s a third fundamental entity; and its ‘information’. It’s not reducible to matter. It’s not reducible to energy. But it’s still a very important thing that is real; we buy it, we sell it, we send it down wires. Now, what do we make of the fact, that information is present at the very root of all biological function? In biology, we have matter, we have energy, but we also have this third, very important entity; information. I think the biology of the information age, poses a fundamental challenge to any materialistic approach to the origin of life.” -Dr. Stephen C. Meyer earned his Ph.D. in the History and Philosophy of science from Cambridge University for a dissertation on the history of origin-of-life biology and the methodology of the historical sciences.
Well do we have actual physical evidence of this 'weightless' information, which is not matter or energy, in the cell? Yes we do. Quantum entanglement/information, which is now conclusively shown to be completely transcendent of any space-time matter/energy constraints, is now shown to be in the molecular biology of living organisms, on a massive scale, in every protein and DNA molecule.
Quantum Information/Entanglement In DNA – short video http://www.metacafe.com/watch/5936605/ DNA Can Discern Between Two Quantum States, Research Shows – June 2011 Excerpt: — DNA — can discern between quantum states known as spin. – The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team’s results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property. http://www.sciencedaily.com/releases/2011/03/110331104014.htm Coherent Intrachain energy migration at room temperature - Elisabetta Collini & Gregory Scholes - University of Toronto - Science, 323, (2009), pp. 369-73 Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state. http://www.scimednet.org/quantum-coherence-living-cells-and-protein/
Moreover, it is very interesting to get a small glimpse what is being accomplished by this quantum information in the cell:
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
Of note: DNA repair machines ‘Fixing every pothole in America before the next rush hour’ is analogous to the traveling salesman problem. The traveling salesman problem is a NP-hard (read: very hard) problem in computer science; The problem involves finding the shortest possible route between cities, visiting each city only once. ‘Traveling salesman problems’ are notorious for keeping supercomputers busy for days.
NP-hard problem - Examples http://en.wikipedia.org/wiki/NP-hard#Examples
Yet, quantum computation is now shown to excel exactly in this traveling salesman area which bogs 'classical' supercomputers down for days:
Speed Test of Quantum Versus Conventional Computing: Quantum Computer Wins - May 8, 2013 Excerpt: quantum computing is, "in some cases, really, really fast." McGeoch says the calculations the D-Wave excels at involve a specific combinatorial optimization problem, comparable in difficulty to the more famous "traveling salesperson" problem that's been a foundation of theoretical computing for decades.,,, "This type of computer is not intended for surfing the internet, but it does solve this narrow but important type of problem really, really fast," McGeoch says. "There are degrees of what it can do. If you want it to solve the exact problem it's built to solve, at the problem sizes I tested, it's thousands of times faster than anything I'm aware of. If you want it to solve more general problems of that size, I would say it competes -- it does as well as some of the best things I've looked at. At this point it's merely above average but shows a promising scaling trajectory." http://www.sciencedaily.com/releases/2013/05/130508122828.htm
Since it is obvious that there is not a material CPU (central processing unit) in the DNA, or cell, busily computing answers to this monster logistic problem, in a purely ‘material’ fashion, i.e. crunching bits, then it is readily apparent that this monster ‘traveling salesman problem’, for DNA repair, must somehow be computed by ‘non-local’ quantum computation within the cell; It is also interesting to note how miniscule is man's progress in quantum computation compared to the quantum computation being accomplished within the cell. Man, using all his ingenuity and resources, has accomplished a mere 128 qubit entanglement for quantum computation,,
D-Wave quantum computer solves protein folding problem - 17 Aug 2012 Excerpt: The D-Wave One quantum computer (which bears more than a passing resemblance to the monolith) consists of 128 superconducting quantum bits or ‘qubits’. - per: nature blog
Whereas in the cell, as highlighted in the Rieper DNA entanglement video I listed, quantum entanglement is maintained along the entirety of a DNA molecule which, I would guess, involves at least millions upon millions of molecules. It is also interesting to note that encoded ‘classical’ information, such as what Dembski and Marks demonstrated the conservation of, and such as what we find encoded in computer programs, and yes, as we find encoded in DNA, is found to be a subset of this ‘transcendent’ (beyond space and time) quantum entanglement/information by the following method:,,,
,,,This following research provides solid falsification for the late Rolf Landauer’s decades old contention that the information encoded in a computer is merely physical (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 here is supporting evidence that quantum information is in fact ‘conserved’;,,,
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
Music and Verse:
ROYAL TAILOR – HOLD ME TOGETHER – music video http://www.youtube.com/watch?v=vbpJ2FeeJgw Acts 17:28 For in him we live and move and have our being.' As some of your own poets have said, 'We are his offspring.'
bornagain77_{August 6, 2013
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Methylation patterns are only symbolic if we use the word in a different sense to the way that Alan and I are using it.
Does anyone really care? What determines the switching patterns? Where is that? What determines the sequencing of cell division and their placement? It must be somewhere and wherever it is, it and the content of the information is probably the key to evolution. Sean Carroll said it would take several thousand pages to write out the switching patterns for a human. Is it all CSI? My guess most of it is.jerry_{August 6, 2013
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Interstingly the words “intelligent” and “design” do not appear in the linked paper!
They should be present but he would never get another grant if he used them but he seems to be saying intelligent design by default unless he can point to something else. He also would not get anymore dinner or cocktail party invitations. I don't know which would be more devastating to him.jerry_{August 6, 2013
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Epigenetics appears to involve more than just methyl tags on DNA
Meyer in his book discusses all sorts of epigenetic information. The methylation process is just one form of it. But something has to determine the methylation patterns and where is that. I have been reading Nessa Carey's book on Epigenetics and it has a lot of interesting examples, probably mostly due to methylation patterns. DNA is information. Whatever determines the methylation patterns is also information. Information is everywhere in the cell and zygote.jerry_{August 6, 2013
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Methylation patterns are only symbolic if we use the word in a different sense to the way that Alan and I are using it. I'd say they are more like switches. It's true that a switch can "symbolise" "on" and "off", but it's more useful if they actually turn things on and off.Elizabeth B Liddle_{August 6, 2013
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Jerry @5, Epigenetics appears to involve more than just methyl tags on DNA. You might be interested in the following video beginning at about the 25 minute mark, where Denis Noble discusses an instance of cross-species cloning. Actually the entire presentation deserves to be watched, more than once. Physiology and the Revolution in Biology I think that methylation patterns could be said to be symbolic. At the least, they contribute to the symbolic content of DNA. If you found that interesting, you might also like the "Homage to Darwin" series linked on the same page (right side, under "Margulis-Dawkins debate").Chance Ratcliff_{August 6, 2013
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A question, is all this information, symbolic?
No.Alan Fox_{August 6, 2013
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Interstingly the words "intelligent" and "design" do not appear in the linked paper!Alan Fox_{August 6, 2013
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Some comments. Another simplification is to think of the genome as the total source of information about the organism especially during development. We are now well aware of the epigenetic information attached to the DNA in each cell which determines what type of cell it will be come and which genes will be expressed. But where does the information come from that determines the methylation patterns during cell division during development? And where does information come from that determines the exact sequence and location for all these cell types during gestation and later during the various changes of life. A question, is all this information, symbolic? Or is just some other type of information? Or does anybody care? Finally, would Darwin have published his Origin of Species if he knew what Shapiro knows about the complexity and preciseness of the interactions in the cell or would he have thought what a fool he was to think it could happen naturally.jerry_{August 6, 2013
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John Witton, I sent the reply with the requested info. I'll trust you received it unless you say otherwise.bornagain77_{August 6, 2013
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To some, being realistic is more dangerous than to over-simplify.bw_{August 6, 2013
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@bornagain77 I sent you an email with a kind request to your yahoo account. Please review. Thanks, JohnJohn Witton_{August 6, 2013
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Excellent find News!bornagain77_{August 6, 2013
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