James Shapiro on intelligence in nature

BA77 So, you can't show that someone in the ID community is doing research into a physical mechanism for dictating mutations? ellazimm

claims open mindedness and then directly proceeds to demonstrate close mindedness! case closed! I'm done with this drivel! bornagain77

BA77

Promises, Promises. I seriously doubt you, as an atheist, will ever really completely ‘change your tune’ and ever truly and honestly admit that the unguided material processes of Darwinian evolution, that you have put your blind faith in, are grossly inadequate to explain the astonishing interlocking coding we find in life.

You have no idea what my beliefs are. Or how many times I have already changed my mind. You are closed minded to my ability to acknowledge truth. Thanks.

The ignorance reflected in this line of questioning is astonishing. There are several hundred, if not several thousand, scientists involved in ENCODE, epigenetic research, and Systems biology that are ‘trying to answer those questions’. And as stated previously, the problem is not that there is not coding found in life, the fact that there is coding found in life is as well established as the law of gravity, the problem is that the coding in life is much more sophisticated than anything man has ever dealt with. And researchers are having a extremely difficult time deciphering that coding.

Are you saying the ENCODE researchers are considering looking for 'coding' that directs mutations or are you just hoping that's what they find? Just because it's all complicated and hard to tease out doesn't mean a) it was designed or b) that there is anything directing mutations. Let's consider a system hardwired to mutate along proscribed lines; i.e. the end goal was known. Why wouldn't an intelligent designer just create the end goal life form in the first place along with all the necessary environmental support life forms? And, if the system is so designed, why is there so much cancer suffered by humans? Why are there occasional devastating swathes of nasty diseases which killed lots of people? Why can some humans digest lactose while others can't? Is the prostate gland really good design? Why can't we photosynthesise? There are lots and lots and lots of issues arising from a completely dictated and designed system which no one can answer. And hoping current research turns up something which upholds your view is NOT being scientific. It's just living on a prayer. So, again, is anyone specifically looking for coding that directs mutations? Not reduces their frequency or over-lapping levels of programming or any other topic. Is any ID research trying to establish a mechanism whereby mutations are guided? ellazimm

"I’ll change my tune." Promises, Promises. I seriously doubt you, as an atheist, will ever really completely 'change your tune' and ever truly and honestly admit that the unguided material processes of Darwinian evolution, that you have put your blind faith in, are grossly inadequate to explain the astonishing interlocking coding we find in life. Full context of Eugene's cited quote from ella:

ella: "Where would this programming be stored? How would it be stored? How is the programming ‘encoded’ in biological structures? How is it ‘read’ and implemented? No one has been even trying to answer those questions." EugeneS: "What ignorance!"

The ignorance reflected in this line of questioning is astonishing. There are several hundred, if not several thousand, scientists involved in ENCODE, epigenetic research, and Systems biology that are 'trying to answer those questions'. And as stated previously, the problem is not that there is not coding found in life, the fact that there is coding found in life is as well established as the law of gravity, the problem is that the coding in life is much more sophisticated than anything man has ever dealt with. And researchers are having a extremely difficult time deciphering that coding. To re-quote Vidal

"Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. “Combine all this and you can start to think that maybe some of the information flow can be captured,” he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. “The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent,” he says." “The simple pathway models are a gross oversimplification of what is actually happening.” - per Nature - Systems biology: Untangling the protein web – July 2009

Moreover, the massive and well funded ENCODE project is aiming to identify all functional elements in the human genome. Here is what the lead ENCODE researcher said:

“It's just been an incredible surprise for me. You say, ‘I bet it's going to be complicated', and then you are faced with it and you are like 'My God, that is mind blowing.'” Ewan Birney - senior scientist - ENCODE 2012 "It's very hard to get over the density of information,,, The data says it’s like a jungle of stuff out there. There are things we thought we understood and yet it is much, much, more complex. And then (there are) places of the genome we thought were completely silent and (yet) they're (now found to be) teeming with life, teeming with things going on. We still really don't understand that." Ewan Birney - senior scientist - ENCODE

Here is another ENCODE researcher:

Bits of Mystery DNA, Far From ‘Junk,’ Play Crucial Role - September 2012 Excerpt: The system, though, is stunningly complex, with many redundancies. Just the idea of so many switches was almost incomprehensible, Dr. Bernstein said. There also is a sort of DNA wiring system that is almost inconceivably intricate. “It is like opening a wiring closet and seeing a hairball of wires,” said Mark Gerstein, an Encode researcher from Yale. “We tried to unravel this hairball and make it interpretable.” There is another sort of hairball as well: the complex three-dimensional structure of DNA. Human DNA is such a long strand — about 10 feet of DNA stuffed into a microscopic nucleus of a cell — that it fits only because it is tightly wound and coiled around itself. When they looked at the three-dimensional structure — the hairball — Encode researchers discovered that small segments of dark-matter DNA are often quite close to genes they control. In the past, when they analyzed only the uncoiled length of DNA, those controlling regions appeared to be far from the genes they affect. http://www.nytimes.com/2012/09/06/science/far-from-junk-dna-dark-matter-proves-crucial-to-health.html?_r=1&pagewanted=all

That there is 'interlocking' coding outside the DNA is also now a well established fact

podcast - Dr. Jonathan Wells explains the concept of codes in living things, and how they affect the debate over neo-Darwinism and intelligent design. (at least 5 different codes outside DNA are discussed) - Oct. 2015 http://www.discovery.org/multimedia/audio/2015/10/id-inquiry-jonathan-wells-on-codes-in-biology/#more-31141 Bioelectric code - Not in the Genes: Embryonic Electric Fields - Jonathan Wells - December 2011 Excerpt: although the molecular components of individual sodium-potassium channels may be encoded in DNA sequences, the three-dimensional arrangement of those channels -- which determines the form of the endogenous electric field -- constitutes an independent source of information in the developing embryo. http://www.evolutionnews.org/2011/12/not_in_the_gene054071.html 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 Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA - Jonathan Wells – 2014 Excerpt: According to evolutionary biologist Thomas Cavalier-Smith, the idea that the genome contains all the information needed to make an organism “is simply false. Membrane heredity, by providing chemically specific two-dimensional surfaces with mutually conserved topological relationships in the three spatial dimensions, plays a key role in the mechanisms that convert the linear information of DNA into the three-dimensional shapes of single cells and multicellular organisms” [403]. In embryo development, however, membrane heredity cannot be the whole story. During ontogeny many new membrane patterns arise that cannot be traced back to patterns in pre-existing membranes. The new patterns do not arise haphazardly; they are highly specified. Yet there is no evidence that they—any more than the patterns that precede them—are determined by a program in the organism’s DNA.,,, http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2014.2/BIO-C.2014.2

And,,,

Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - published online May 2013 Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43]. 38. Sanford J (2008) Genetic Entropy and the Mystery of the Genome. FMS Publications, NY. Pages 131–142. 39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432. 40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654. 41. Kapranov P, et al (2005) Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997. 42. Birney E, et al (2007) Encode Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816. 43. Itzkovitz S, Hodis E, Sega E (2010) Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006 Extreme Information: Biocomplexity of Interlocking Genome Languages - Jeffrey P. Tomkins - 2015 (loss of gene in part 1) Abstract: People most often think of the genome as containing only the embedded protein-coding information carried in the DNA of chromosomes. However, there are a variety of other codes and language systems active in the genome that are only now beginning to be deciphered. This paper will discuss the amazing internetworked biocomplexity of these language systems that interactively control the way the genome functions. The systems that will be discussed are gene structure complexities, RNA transcript splicing codes, the microRNA binding code, circular RNAs, dual-use codons, antisense transcripts, and epigenetic language systems. The now debunked myth of junk DNA will also be briefly addressed in light of the ENCODE project and new research in genome-wide COT-1 DNA functionality. The interworking and interdependence of these complex and dynamic language systems unequivocally points towards an omnipotent and wise Creator. https://docs.google.com/document/d/1mZWJ8P3y2QDmykF7Ljs212t3JzvQPUKbl7fAOOxWOX4/edit?usp=sharing

etc.. etc.. etc.. I could go on and on citing even more evidence for extreme complex interlocking coding within the cell, such as quantum computation, that far exceeds anything man has ever built, but the main point is that no matter how much extra coding is shown to ellaz he will never really ever truly 'change his tune' since to do so would basically require him to change his anti-theistic Darwinian religion that he has adopted as his worldview. bornagain77

EugeneS

What ignorance!

If you would kindly point me to any ongoing research by members of the ID community regarding Dr Shapiro's proposed extra programming I'll change my tune. ellazimm

Ellazimm, "No one has been even trying to answer those questions." What ignorance! EugeneS

ellazimm, you are the one blatantly ignoring overwhelming evidence that contradicts your anti-religious Darwinian belief. Appealing to personal opinions of other atheists is certainly NOT science! bornagain77

BA77

ellazimm quoting wikipedia?? (insert laugh tract here) What a friggin joke! Your other responses were almost as bad.

There are outside references to the quote I gave from Wikipedia. Reviews of Dr Shapiro's book. Did you read them? I bet not. You pick and choose, you do NOT consider all the available data, only that which you agree with. That's not how science works. Robert

the point of the dna and all cells is that is fantastic mysterious and complicated. hidden things easily could be encoded. The dna is so glorious that to read it must remain a future thing.

Well then, why isn't there any ID researchers trying to find the extra programming which is supposedly dictating mutations? Lots of talk and no work.

Yet can one see it written out? no. So why not loads of info is encoded and ready for use.

Maybe so but you have to find it first.

Including using or making instant mutations. Possibly chance mutations are a minority in the genetic system. Possibly mutations are a major used mechanism for change. Healthy speculation.

Speculation is fine, an important part of science in fact. But after that one has to do some research to see what's true. Is anyone doing that work? Are you? ellazimm

Ellazimm the point of the dna and all cells is that is fantastic mysterious and complicated. hidden things easily could be encoded. The dna is so glorious that to read it must remain a future thing. Looking at a woman one wopuld never know how much her body would change in order to hold the child within. Yet in those female genes is that great deed. Yet can one see it written out? no. So why not loads of info is encoded and ready for use. Including using or making instant mutations. Possibly chance mutations are a minority in the genetic system. Possibly mutations are a major used mechanism for change. Healthy speculation. Robert Byers

further notes on Bennett's reversible computation: Life Leads the Way to Invention - Feb. 2010 Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale. http://creationsafaris.com/crev201002.htm#20100226a the integrated coding between the DNA, RNA of the cell apparently seem to be ingeniously programmed along the very stringent guidelines laid out in Landauer’s principle, (by Charles Bennett from IBM of Quantum Teleportation fame), for ‘reversible computation’ in order to achieve such amazing energy/metabolic efficiency as it does. Logical Reversibility of Computation* - C. H. Bennett - 1973 Excerpt from last paragraph: The biosynthesis and biodegradation of messenger RNA may be viewed as convenient examples of logically reversible and irreversible computation, respectively. Messenger RNA. a linear polymeric informational macromolecule like DNA, carries the genetic information from one or more genes of a DNA molecule. and serves to direct the synthesis of the proteins encoded by those genes. Messenger RNA is synthesized by the enzyme RNA polymerase in the presence of a double-stranded DNA molecule and a supply of RNA monomers (the four nucleotide pyrophosphates ATP, GTP, CTP, and UTP) [7]. The enzyme attaches to a specific site on the DNA molecule and moves along, sequentially incorporating the RNA monomers into a single-stranded RNA molecule whose nucleotide sequence exactly matches that of the DNA. The pyrophosphate groups are released into the surrounding solution as free pyrophosphate molecules. The enzyme may thus be compared to a simple tape-copying Turing machine that manufactures its output tape rather than merely writing on it. Tape copying is a logically reversible operation. and RNA polymerase is both thermodynamically and logically reversible.,,, http://www.cs.princeton.edu/courses/archive/fall04/cos576/papers/bennett73.html Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon - Charles H. Bennett - September 2003 Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus, dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,, http://www.sciencedirect.com/science/article/pii/S135521980300039X further notes on reversible computation in general: The amazing energy efficiency possible with ‘reversible computation’ has been known about since Charles Bennett laid out the principles for such reversible programming in 1973, but as far as I know, due to the extreme level of complexity involved in achieving such ingenious ‘reversible coding’, has yet to be accomplished in any meaningful way for our computer programs even to this day: Reversible computing is a model of computing where the computational process to some extent is reversible, i.e., time-invertible.,,, Although achieving this goal presents a significant challenge for the design, manufacturing, and characterization of ultra-precise new physical mechanisms for computing, there is at present no fundamental reason to think that this goal cannot eventually be accomplished, allowing us to someday build computers that generate much less than 1 bit's worth of physical entropy (and dissipate much less than kT ln 2 energy to heat) for each useful logical operation that they carry out internally. Can reversible computing really dissipate absolutely zero energy? Of course not. Any non-equilibrium physical system (whether a computer or a rock) dissipates energy at some rate,,, Okay, then can reversible computing really make the energy dissipation of a computation be an arbitrarily small non-zero amount? Only insofar as the computer can be arbitrarily well isolated from unwanted interactions, errors, and energy leakage,,, But, despite all these caveats, it may yet be possible to set up reversible computations that dissipate such amazingly tiny amounts of energy that the dissipation is not a barrier to anything that we might wish to do with them - I call such computations ballistic. We are a long way from achieving ballistic computation, but we do not yet know of any fundamental reasons that forbid it from ever being technically possible. http://www.cise.ufl.edu/research/revcomp/faq.html#zeroenergy bornagain77

ellazimm quoting wikipedia?? (insert laugh tract here) What a friggin joke! Your other responses were almost as bad. I'm really not going to argue what is blatantly obvious with you, a Darwinian troll, but for the unbiased reader I will restate the fact that there IS programming in life and that it is orders of magnitude more advanced than anything man has ever programmed.

Wetware: A Computer in Every Living Cell - book - Dennis Bray Description - In clear, jargon-free language, Dennis Bray taps the findings of the new discipline of systems biology to show that the internal chemistry of living cells is a form of computation. Cells are built out of molecular circuits that perform logical operations, as electronic devices do, but with unique properties. http://www.amazon.com/dp/0300167849 Dennis Bray - Amazon Description of Author Dennis Bray is an active emeritus professor at University of Cambridge. His group is also part of the Oxford Centre for Integrative Systems Biology. After a first career in Neurobiology, working on cell growth and movement, Dennis Bray moved in Cambridge to develop computational models of cell signaling, in particular in relation to bacterial chemotaxis. On November 3, 2006, he was awarded the Microsoft European Science Award for his work on chemotaxis of E. coli. Mere Biochemistry: Cell Division Involves Thousands of Complex, Interacting Parts - September 2010 http://www.creationsafaris.com/crev201009.htm#20100925a Logically and Physically Reversible Natural Computing: A Tutorial - 2013 Excerpt: This year marks the 40th anniversary of Charles Bennett’s seminal paper on reversible computing. Bennett’s contribution is remembered as one of the first to demonstrate how any deterministic computation can be simulated by a logically reversible Turing machine. Perhaps less remembered is that the same paper suggests the use of nucleic acids to realise physical reversibility. In context, Bennett’s foresight predates Leonard Adleman’s famous experiments to solve instances of the Hamiltonian path problem using strands of DNA — a landmark date for the field of natural computing — by more than twenty years. http://link.springer.com/chapter/10.1007%2F978-3-642-38986-3_20 How we could create life: The key to existence will be found not in primordial sludge, but in the nanotechnology of the living cell - Paul Davies - 2002 Excerpt: Instead, the living cell is best thought of as a supercomputer – an information processing and replicating system of astonishing complexity. DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code. Most of the workings of the cell are best described, not in terms of material stuff – hardware – but as information, or software. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won’t work because it addresses the problem at the wrong conceptual level. - Paul Davies http://www.guardian.co.uk/education/2002/dec/11/highereducation.uk

That man has barely begun to decipher how life is programmed is not due to the fact that there is not programming in life, as you apparently, in your self-imposed Darwinian ignorance, are trying to believe, but is due to the fact that the programming in life is much more advanced than anything man has ever dealt with before.

Systems biology: Untangling the protein web - July 2009 Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. "Combine all this and you can start to think that maybe some of the information flow can be captured," he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. "The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent," he says. "The simple pathway models are a gross oversimplification of what is actually happening." http://www.nature.com/nature/journal/v460/n7253/full/460415a.html Learning from Bacteria about Social Networking (Information Processing) - video Excerpt: I will show illuminating movies of swarming intelligence of live bacteria in which they solve optimization problems for collective decision making that are beyond what we, human beings, can solve with our most powerful computers. http://www.youtube.com/watch?v=yJpi8SnFXHs

bornagain77

From the Wikipedia article about Dr James A Shapiro:

He has proposed the term natural genetic engineering to account for how novelty is created in the course of biological evolution. It has been widely criticized

Again, instead of just quoting things that you think support your view you must consider all the relevant and pertinent data, research and opinions. ellazimm

BA77 Again, I asked for physical evidence of Dr Shapiro's contention that "[c]ells are acting on their own genomes in a large variety of well-defined non-random ways to bring about change." That is I'd like to know: where are these extra instructions, how are they encoded and how are they interpreted and implemented. No one has answered that. I also made a comment that there is no real research indicating that mutations are guided or directed or programmed.

David Snoke*, Systems Biology as a Research Program for Intelligent Design – 2014

doesn't really addressed the issues and is not even considered research by Bio-Complexity which lists it as a review.

How the Burgeoning Field of Systems Biology Supports Intelligent Design – July 2014

Even worse, a blog post from The Discovery Institute written by Casey Luskin who is neither a researcher nor a biologist. And who no longer works for The Discovery Institute. Also, those two 2014 sources haven't seemed to have generated any real research from ID proponents. Just talking doesn't count.

How life changes itself: The Read–Write (RW) genome – James A. Shapiro – 2013

I'm not familiar with this particular work and it's behind a pay wall. I know that other work by Dr Shapiro has been sharply criticised but, again, I haven't looked into this particular publication.

Failed Darwinian Prediction – Mutations are not adaptive – Cornelius Hunter – 2015

Oh please, Dr Cornelius Hunter. He has a huge axe to grind AND this is, again, not a research paper. I have looked into similar claims before and usually the papers cited still insist that mutations are NOT guided by some kind of intelligence.

Duality in the human genome – November 28, 2014

The text you bolded does NOT prove your case. It doesn't make them directed. You can't just copy and paste things with sentences you think prove your case. You have to look at things in context and consider ALL the research and data regarding an issue. ellazimm

"Please pay attention." Take your own advice. re-reference:

“It has become clear in the past ten years that the concept of design is not merely an add-on meta-description of biological systems, of no scientific consequence, but is in fact a driver of science. A whole cohort of young scientists is being trained to “think like engineers” when looking at biological systems, using terms explicitly related to engineering design concepts: design, purpose, optimal tradeoffs for multiple goals, information, control, decision making, etc. This approach is widely seen as a successful, predictive, quantitative theory of biology.” David Snoke*, Systems Biology as a Research Program for Intelligent Design – 2014 http://bio-complexity.org/ojs/index.php/main/article/viewArticle/BIO-C.2014.3 How the Burgeoning Field of Systems Biology Supports Intelligent Design – July 2014 Excerpt: Snoke lists various features in biology that have been found to function like goal-directed, top-down engineered systems: *”Negative feedback for stable operation.” *”Frequency filtering” for extracting a signal from a noisy system. *Control and signaling to induce a response. *”Information storage” where information is stored for later use. In fact, Snoke observes: “This paradigm [of systems biology] is advancing the view that biology is essentially an information science with information operating on multiple hierarchical levels and in complex networks [13]. ” *”Timing and synchronization,” where organisms maintain clocks to ensure that different processes and events happen in the right order. *”Addressing,” where signaling molecules are tagged with an address to help them arrive at their intended target. *”Hierarchies of function,” where organisms maintain clocks to ensure that cellular processes and events happen at the right times and in the right order. *”Redundancy,” as organisms contain backup systems or “fail-safes” if primary essential systems fail. *”Adaptation,” where organisms are pre-engineered to be able to undergo small-scale adaptations to their environments. As Snoke explains, “These systems use randomization controlled by supersystems, just as the immune system uses randomization in a very controlled way,” and “Only part of the system is allowed to vary randomly, while the rest is highly conserved.”,,, Snoke observes that systems biology assumes that biological features are optimized, meaning, in part, that “just about everything in the cell does indeed have a role, i.e., that there is very little ‘junk.'” He explains, “Some systems biologists go further than just assuming that every little thing has a purpose. Some argue that each item is fulfilling its purpose as well as is physically possible,” and quotes additional authorities who assume that biological systems are optimized.,,, http://www.evolutionnews.org/2014/07/when_biologists087871.html

as to this patently false claim:

"Nothing at all to indicate that mutations are directed or guided or programmed."

is this:

How life changes itself: The Read–Write (RW) genome - James A. Shapiro - 2013 Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). http://www.sciencedirect.com/science/article/pii/S1571064513000869 Failed Darwinian Prediction – Mutations are not adaptive – Cornelius Hunter – 2015 Excerpt: In the twentieth century, the theory of evolution predicted that mutations are not adaptive or directed. In other words, mutations were believed to be random with respect to the needs of the individual.,,, But that assumption is now known to be false.,,, (References on site) https://sites.google.com/site/darwinspredictions/mutations-are-not-adaptive Duality in the human genome - November 28, 2014 Excerpt: The results show that most genes can occur in many different forms within a population: On average, about 250 different forms of each gene exist. The researchers found around four million different gene forms just in the 400 or so genomes they analysed. This figure is certain to increase as more human genomes are examined. More than 85 percent of all genes have no predominant form which occurs in more than half of all individuals. This enormous diversity means that over half of all genes in an individual, around 9,000 of 17,500, occur uniquely in that one person - and are therefore individual in the truest sense of the word. The gene, as we imagined it, exists only in exceptional cases. "We need to fundamentally rethink the view of genes that every schoolchild has learned since Gregor Mendel's time.,,, According to the researchers, mutations of genes are not randomly distributed between the parental chromosomes. They found that 60 percent of mutations affect the same chromosome set and 40 percent both sets. Scientists refer to these as cis and trans mutations, respectively. Evidently, an organism must have more cis mutations, where the second gene form remains intact. "It's amazing how precisely the 60:40 ratio is maintained. It occurs in the genome of every individual – almost like a magic formula," says Hoehe. http://medicalxpress.com/news/2014-11-duality-human-genome.html

bornagain77

BA77

And exactly how does finding programming in life that is proving itself to be orders of magnitude more advanced than anything man has ever designed remotely help your Darwinian claims that life is the result of unguided material processes?

Sigh. Please pay attention. I was asking where Dr Shapiro's proposed extra programming is to be found, how is it encoded and how is it interpreted and implemented by a living thing's system. I hear lots of talk but no research or results. Nothing at all to indicate that mutations are directed or guided or programmed. Kind of like saying there's a designer without being able to produce one or their workshop, tools, plans, rubbish heap, documentation, etc. ellazimm

ellazimm, And exactly how does finding programming in life that is proving itself to be orders of magnitude more advanced than anything man has ever designed remotely help your Darwinian claims that life is the result of unguided material processes? For example:

Amoeba-inspired computing system outperforms conventional optimization methods - June 1, 2015 Excerpt: Researchers have designed and implemented an algorithm that solves computing problems using a strategy inspired by the way that an amoeba branches out to obtain resources. The new algorithm, called AmoebaSAT, can solve the satisfiability (SAT) problem—a difficult optimization problem with many practical applications—using orders of magnitude fewer steps than the number of steps required by one of the fastest conventional algorithms.The researchers predict that the amoeba-inspired computing system may offer several benefits, such as high efficiency, miniaturization, and low energy consumption, that could lead to a new computing paradigm for nanoscale high-speed problem solving. Led by Masashi Aono, Associate Principal Investigator at the Earth-Life Science Institute, Tokyo Institute of Technology, and at PRESTO, Japan Science and Technology Agency, the researchers have published a paper on the amoeba-inspired system in a recent issue of Nanotechnology. "We demonstrated a way to harness the huge computational power of natural phenomena in terms of complexity and energy," Aono told Phys.org. http://phys.org/news/2015-06-amoeba-inspired-outperforms-conventional-optimization-methods.html The Law of Physicodynamic Incompleteness - David L. Abel Excerpt: "If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise." If only one exception to this null hypothesis were published, the hypothesis would be falsified. Falsification would require an experiment devoid of behind-the-scenes steering. Any artificial selection hidden in the experimental design would disqualify the experimental falsification. After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: "No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone." https://www.academia.edu/Documents/in/The_Law_of_Physicodynamic_Incompleteness

of related note:

"It has become clear in the past ten years that the concept of design is not merely an add-on meta-description of biological systems, of no scientific consequence, but is in fact a driver of science. A whole cohort of young scientists is being trained to “think like engineers” when looking at biological systems, using terms explicitly related to engineering design concepts: design, purpose, optimal tradeoffs for multiple goals, information, control, decision making, etc. This approach is widely seen as a successful, predictive, quantitative theory of biology." David Snoke*, Systems Biology as a Research Program for Intelligent Design - 2014 http://bio-complexity.org/ojs/index.php/main/article/viewArticle/BIO-C.2014.3 How the Burgeoning Field of Systems Biology Supports Intelligent Design - July 2014 Excerpt: Snoke lists various features in biology that have been found to function like goal-directed, top-down engineered systems: *"Negative feedback for stable operation." *"Frequency filtering" for extracting a signal from a noisy system. *Control and signaling to induce a response. *"Information storage" where information is stored for later use. In fact, Snoke observes: "This paradigm [of systems biology] is advancing the view that biology is essentially an information science with information operating on multiple hierarchical levels and in complex networks [13]. " *"Timing and synchronization," where organisms maintain clocks to ensure that different processes and events happen in the right order. *"Addressing," where signaling molecules are tagged with an address to help them arrive at their intended target. *"Hierarchies of function," where organisms maintain clocks to ensure that cellular processes and events happen at the right times and in the right order. *"Redundancy," as organisms contain backup systems or "fail-safes" if primary essential systems fail. *"Adaptation," where organisms are pre-engineered to be able to undergo small-scale adaptations to their environments. As Snoke explains, "These systems use randomization controlled by supersystems, just as the immune system uses randomization in a very controlled way," and "Only part of the system is allowed to vary randomly, while the rest is highly conserved.",,, Snoke observes that systems biology assumes that biological features are optimized, meaning, in part, that "just about everything in the cell does indeed have a role, i.e., that there is very little 'junk.'" He explains, "Some systems biologists go further than just assuming that every little thing has a purpose. Some argue that each item is fulfilling its purpose as well as is physically possible," and quotes additional authorities who assume that biological systems are optimized.,,, http://www.evolutionnews.org/2014/07/when_biologists087871.html

bornagain77

Robert

Not chance but inbuilt programs to react to problems.

Where would this programming be stored? How would it be stored? How is the programming 'encoded' in biological structures? How is it 'read' and implemented? No one has been even trying to answer those questions. Joe used to say: it's in the cell . . . somewhere. But he couldn't find it. ellazimm

semi related:

Can Darwinian Evolutionary Theory Be Taken Seriously? - Stephen L. Talbott - May 16, 2016 Excerpt: Evolutionary biologists today find themselves in a troubled relationship with the American public. Their great source of discomfort and wonder lies in the fact that the theory of evolution is “still under siege”1 by a substantial and sometimes aggressively disbelieving population — this despite being “an established and accepted scientific theory for 150 years”.2 “What are we doing wrong?” asks Jason Wiles, a biologist and educator at Syracuse and McGill Universities. His answer: “We do not know”.3 And, in light of the vast institutional support undergirding evolutionary science, another educator wonders why “those exposed to evolution education do not generally demonstrate mastery of the concept”.4,,, The influential Dutch botanist and geneticist, Hugo de Vries, framed the matter this way during the first decade of the twentieth century: Natural selection is a sieve. It creates nothing, as is so often assumed; it only sifts. It retains only what variability puts into the sieve. Whence the material comes that is put into it, should be kept separate from the theory of its selection. How the struggle for existence sifts is one question; how that which is sifted arose is another.34 It was de Vries who formulated the catchy phrasing that has since been repeated many times: “Natural selection may explain the survival of the fittest, but it cannot explain the arrival of the fittest”.35 It’s not a concern easily dismissed. Over subsequent decades other biologists have added their own accents: “The function of natural selection is selection and not creation. It has nothing to do with the formation of new variation”. (Reginald Punnett [1911], British geneticist who cofounded the Journal of Genetics; quoted in Stoltzfus 2006) Regarding specific traits, natural selection “might afford a reason for their preservation, but never provide the cause for their origin”. (Adolf Portmann [1967, p. 123], preeminent zoologist of the middle of the twentieth century) “Natural selection is the editor, rather than the composer, of the genetic message”. (Jack King and Thomas Jukes [1969], key developers of the idea of “neutral evolution”) “In evolution, selection may decide the winner of a given game but development non-randomly defines the players”. (Pere Alberch [1980], Spanish naturalist and embryologist, sometimes spoken of as the founder of Evo-Devo — evolutionary developmental biology) “Natural selection eliminates and maybe maintains, but it doesn’t create”. (Lynn Margulis [2011], microbiologist and botanist, pioneer in exploring the role of symbiosis in evolution, and co-developer of the Gaia hypothesis) The objection these estimable biologists were raising has never gained the traction it deserves. ,,, On the other hand, it would have been hard to find even a slight blush of embarrassment when Stephen Jay Gould, countering the sort of doubt voiced above by his peers, asked, “Why was natural selection compared to a composer by Dobzhansky; to a poet by Simpson; to a sculptor by Mayr; and to, of all people, Mr. Shakespeare by Julian Huxley?” The answer, according to Gould, is that the allusions to poetry, musical composition, and sculpture helpfully underscore the “creativity of natural selection”: "The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies the raw material only. Natural selection directs the course of evolutionary change. It preserves favorable variants and builds fitness gradually".36 And so it is possible for leading theorists of evolution to declare an abstract algorithm — natural selection — a capable artist, even though the only place where we observe an actual creative and artistic activity going on is in the organism itself. And even though the explanatory appeal to natural selection simply hides the fact, as we saw above, that the explanation assumes this very same creative activity in the organism. ,,, What we do have is a god-like power of natural selection whose miracle-working activity in creating ever-new organisms is vividly clear to eyes of faith, but frustratingly obscure to mere empirical investigators. This is not a science ready for submission to a larger public along with a demand for acquiescence. Not if this public has yet to dull its sensitivity to fundamental questions in the way that the research community seems to have done. http://natureinstitute.org/txt/st/org/comm/ar/2016/teleology_30.htm

bornagain77

This is interesting. It could , like Hunters thread, be showing there is a trigger or directional agenda for genes to use mutations. Not chance but inbuilt programs to react to problems. Its all a rejection that the only option is that genes change by chance. There could be other options for built in mechanisms for genes to create sudden;y genes. Genes are mysterious things. Sure they are. Robert Byers

Yes ellazimm, the Designer can be elusive. Not of this world. Oh well, at least you can appreciate Design. It's the least you can do. Ingrate:) ppolish

But how is it inbuilt? Shapiro is certain to find much more evidence for his observations than anyone can handle, but unless the source of information can be accounted for, they will remain at the level of observations.

Interesting that no one else has found 'much more' evidence yet. You'd think Douglas Axe would be pursuing this eh? And no source found . . . that designer is very elusive. ellazimm