Dawkins: DNA is Encoded Digital Information in the “Strong Sense”

_{Barry Arrington

September 14, 2016

Intelligent Design}

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From time to time materialists come into these pages and argue that DNA is not a true “code.” This proves nothing other than that materialists are often quite shameless in the arguments they make to prop up their religious views. We would do well to remind that that arch-materialist Richard Dawkins did not get the memo. Testifying against interest he writes:

After Watson and Crick, we know that genes themselves, within their minute internal structure, are long strings of pure digital information. What is more, they are truly digital, in the full and strong sense of computers and compact disks, not in the weak sense of the nervous system. The genetic code is not a binary code as in computers, nor an eight-level code as in some telephone systems, but a quaternary code, with four symbols. The machine code of the genes is uncannily computerlike. Apart from differences in jargon, the pages of a molecular-biology journal might be interchanged with those of a computer-engineering journal. . . .

Our genetic system, which is the universal system of all life on the planet, is digital to the core. With word-for-word accuracy, you could encode the whole of the New Testament in those parts of the human genome that are at present filled with “junk” DNA – that is, DNA not used, at least in the ordinary way, by the body. Every cell in your body contains the equivalent of forty-six immense data tapes, reeling off digital characters via numerous reading heads working simultaneously. In every cell, these tapes – the chromosomes – contain the same information, but the reading heads in different kinds of cells seek out different parts of the database for their own specialist purposes. . . .

Genes are pure information – information that can be encoded, recoded and decoded, without any degradation or change of meaning. Pure information can be copied and, since it is digital information, the fidelity of the copying can be immense. DNA characters are copied with an accuracy that rivals anything modern engineers can do.

Richard Dawkins, River out of Eden, 16-19

Comments

TheBestSchools:
Why do you think the interpretation of evolutionary biology raises such passion, and even anger?
Denis Noble:
Two opposing sides became entrenched into dogmatism [...] [...] dogmatic science shouldn’t exist. When it does it becomes a faith rather than a science.

TheBestSchools blog Professor Denis Noble interview http://www.thebestschools.org/dialogues/evolution-denis-noble-interview/Dionisio_{September 15, 2016
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TheBestSchools:
Do you find it fruitful to interact with philosophers? What do you think they have to bring to the table in important scientific disputes like the one surrounding the adequacy of the neo-Darwinian explanatory framework? Would you recommend more collaborations of this sort between scientists and philosophers?
Denis Noble:
Such interaction used to be much more common. The world of science today makes it very difficult. This is unfortunate. As the great French physicist and polymath Henri Poincaré (1854–1912) remarked a century ago, those who claim they are not philosophers make the worst conceptual errors. They don’t even see the conceptual holes into which they fall.

TheBestSchools blog Professor Denis Noble interview http://www.thebestschools.org/dialogues/evolution-denis-noble-interview/Dionisio_{September 15, 2016
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TheBestSchools:
Would you say that your criticism of neo-Darwinism (the Modern Synthesis) is primarily conceptual [...]?
Denis Noble:
One of the problems with the hardening of the Modern Synthesis during the mid-twentieth century is that it made it difficult both to think that certain experiments [...] were worth doing and, even if one thought they were, there wouldn’t be funding to do so. Many of the problems with neo-Darwinism arise from the misuse of language and the influence that has on our thought patterns. [...] many of my other papers deal with the empirical evidence for changing our ideas on evolutionary biology.

TheBestSchools blog Professor Denis Noble interview http://www.thebestschools.org/dialogues/evolution-denis-noble-interview/Dionisio_{September 15, 2016
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TheBestSchools:
What is the best way to think about the relationship between genes and organisms?
Denis Noble:
The sequencing of the genomes [...] has not led to much success in enabling the development of new therapies. Even the leaders of the Project admit that the outcome has been disappointing. In fact it has been disastrous. [...] genes do not fit what was expected of them. Very few ailments indeed depend on a single gene. Most are complex interactions involving many components in networks that extend in the body well beyond the genome.

TheBestSchools blog Professor Denis Noble interview http://www.thebestschools.org/dialogues/evolution-denis-noble-interview/Dionisio_{September 15, 2016
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TheBestSchools:
What about the role of genes in life? Nowadays, many people are saying that the word “gene” has acquired so many senses as to be almost meaningless. What is your own working definition of a “gene”?
Denis Noble:
I agree that we now have so many definitions of “gene” that some even question the utility of the concept. I try to distinguish clearly between the various definitions to avoid the pitfalls of confusing them.

TheBestSchools blog Professor Denis Noble interview http://www.thebestschools.org/dialogues/evolution-denis-noble-interview/Dionisio_{September 15, 2016
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TheBestSchools:
What is your definition of “neo-Darwinism” (or “Modern Synthesis”)? Isn’t it enough to talk of “extending” it? Why do you speak of its needing to be “replaced”?
Denis Noble:
The main ideas in the original formulation of neo-Darwinism are the following: 1. All changes in the genetic material are random [...] This is the “blind chance” part of the theory with no room for teleology. 2. The germ line cells are completely isolated from the rest of the organism. Dawkins encapsulated this view in The Selfish Gene: “Sealed off from the outside world.” [...] I am very sympathetic to the extension idea in science. But when neo-Darwinism goes so far as to accept the inheritance of acquired characteristics and of non-random functional variations, I think we are talking more about a replacement. [...] I am saying that neo-Darwinism is incomplete.

TheBestSchools blog Professor Denis Noble interview http://www.thebestschools.org/dialogues/evolution-denis-noble-interview/ The 3rd way of evolution attacking the establishment? No one can threaten professor Denis Noble with losing his job. That's why he can afford to rebel against the Neo-Darwinian empire. Also, who's going to argue with him and his "3rd way" colleagues, who know as much or more biology than the establishment folks? :) I don't want to miss the future episodes of this debate between the establishment and the 3rd way rebels. :) Meanwhile, many seriously dedicated scientists continue to work passionately in wet and dry labs trying to figure out how exactly the amazingly complex information-processing biological systems work.Dionisio_{September 15, 2016
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TheBestSchools:
A machine is a goal-directed system (it has a “function”), in which the goal state of the system is determined by an outside observer/agent. A living organism is very different. The functionality—that is, the teleology—of the system as a whole arises as a result of purely inherent, internal, or intrinsic processes. Do you agree with this characterization of the essential difference between machines and organisms? That is, do you agree with the proposition that organisms are not machines—that machines and organisms belong to fundamentally different ontological categories?
Denis Noble:
I don’t think they arise as a result of “purely inherent, internal, or intrinsic processes.” They [their functioning?] arise because organisms are open systems interacting extensively with their environment, including the behavior of other organisms.

TheBestSchools blog Professor Denis Noble interview http://www.thebestschools.org/dialogues/evolution-denis-noble-interview/Dionisio_{September 15, 2016
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TheBestSchools:
[...] if we must understand teleology in biology as objectively real, how can we do so without bringing in unwanted theological or similar baggage?
Denis Noble:
[...] explaining purpose in organisms can be complete at any level, without having to go further to higher levels. The rhythm of the heart is explained at a cellular level. Its function is explained at the level of the cardiovascular system. That doesn’t mean that there could not be a theological explanation. It does mean that the theological explanation is not necessary.

TheBestSchools blog Professor Denis Noble interview http://www.thebestschools.org/dialogues/evolution-denis-noble-interview/ Obviously, the actual functioning can be explained as more information comes out research. In some areas of biology the complete picture is still missing, but gradually being filled up. The problem is explaining how we got all that complex functionality. In order to explain how biological systems work, all we have to do is get more information from research. The overwhelming volume of information coming out of both wet and dry labs seems to indicate that many serious dedicated scientists are passionately working on trying to figure out how exactly biological systems work in different scenarios. Generally they seem heading in the right direction, though sometimes taking 'long and winding' paths based on wrong assumptions and false presuppositions, incorrectly following reductionist bottom-up approaches to describe complex information-processing systems that obviously appear to be the result of top-down design. However, understanding exactly how things work is not the same as understanding exactly how we got them to begin with. The former may be required for the latter, but they are separate issues that demand different kinds of investigative approaches. I may know exactly how my bike works, hence I can maintain it in good condition. However, don't ask me how exactly it was produced. PS. Emphasis mine. Note the bold text: unwanted? why? Also, professor Noble leaves the door open with the bold sentence. :)Dionisio_{September 15, 2016
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semi OT:
Evolution Just Got Harder to Defend By Eric Metaxas | September 14, 2016 Excerpt: These life forms came into existence virtually overnight,, “[g]enetic code, proteins, photosynthesis, the works.” This appearance of fully-developed life forms so early in the fossil record led Dr. Abigail Allwood of Caltech to remark that “life [must not be] a fussy, reluctant and unlikely thing.” Rather, “[i]t will emerge whenever there’s an opportunity.” Pardon me? If life occurs so spontaneously and predictably even under the harshest conditions, then it should be popping up all over the place! Yet scientists still cannot come close to producing even a single cell from raw chemicals in the lab. Dr. Stephen Meyer explains in his book “Signature in the Cell” why this may be Darwinism’s Achilles heel. In order to begin evolution by natural selection, you need a self-replicating unit. But the cell and its DNA blueprint are too complicated by far to have arisen through chance chemical reactions. The odds of even a single protein forming by accident are astronomical. So Meyer and other Intelligent Design theorists conclude that Someone must have designed and created the structures necessary for life. Meanwhile Darwinists, faced with a fossil record that theoretically pushes the origin of life back further into the past, are forced to assume the metaphorical can opener. They just don’t know how these early cells came into existence, and the more we dig up, the more improbable—rather than likely—life becomes. - Eric Metaxas http://cnsnews.com/commentary/eric-metaxas/evolution-just-got-harder-defend
bornagain77_{September 15, 2016
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TheBestSchools:
[...] the most striking thing about living things, in comparison with non-living systems, is their teleological organization—meaning the way in which all of the local physical and chemical interactions cohere in such a way as to maintain the overall system in existence. Moreover, it is virtually impossible to speak of living beings for any length of time without using teleological and normative language—words like “goal,” “purpose,” “meaning,” “correct/incorrect,” “success/failure,” etc.
Denis Noble:
My work on heart rhythm taught me that the rhythm simply doesn’t exist at the molecular level. If I placed all the molecular components in a nutrient solution, but without being constrained by a living cell, the rhythm would not exist. By the usual ontological criteria the rhythm doesn’t exist at a molecular level but does exist at a cellular level.

TheBestSchools blog Professor Denis Noble interview http://www.thebestschools.org/dialogues/evolution-denis-noble-interview/Dionisio_{September 15, 2016
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jimmontg @11: That's a good point. Thank you. But let's remember there are friends -including some ID proponents who comment and even write OPs in this blog- who may not have the saving faith either. Let's pray for them too. God loves them. One day every knee will bow and every tongue will confess that Christ is Lord, but by then it might be too late for many nice folks in this world. The moment is now. Rev. 22:21Dionisio_{September 15, 2016
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I wonder, how many of us pray that Dawkins comes to see the Truth and believes in Christ? Prayer has been proven to work in double blind studies. Pray for Dawkins, maybe, just maybe...jimmontg_{September 14, 2016
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Dawkins: Cells are transitory, and DNA is not. Denis Noble: This is a common mantra, copied from Dawkins’s The Selfish Gene. It is linguistically incoherent and factually incorrect.
Professor Denis Noble interview by TBS http://www.thebestschools.org/dialogues/evolution-denis-noble-interview/Dionisio_{September 14, 2016
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[...] organisms have been demonstrated to use stochasticity in effective functional ways. The best example is the immune system.
Professor Denis Noble interview by TBS http://www.thebestschools.org/dialogues/evolution-denis-noble-interview/Dionisio_{September 14, 2016
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Randomness versus functionality of inherited variations. This is perhaps the biggest question of all. How does functionality, and hence teleology, arise in random processes? My short answer is that viewed from the level of molecules we may never see it.
Professor Denis Noble interview by TBS http://www.thebestschools.org/dialogues/evolution-denis-noble-interview/Dionisio_{September 14, 2016
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I argue that if large, already-functional sequences are moved around the genome, then potentially existing or new functions travel with the sequences. The Modern Synthesis was built on the idea of the gradual accumulation of point mutations. I explain the significance of moving large sequences in the next item.
Professor Denis Noble interview by TBS http://www.thebestschools.org/dialogues/evolution-denis-noble-interview/Dionisio_{September 14, 2016
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Finding one code in DNA was bad enough for Darwinists:
The Origin of Information: How to Solve It - Perry Marshall Where did the information in DNA come from? This is one of the most important and valuable questions in the history of science. Cosmic Fingerprints has issued a challenge to the scientific community: “Show an example of Information that doesn’t come from a mind. All you need is one.” “Information” is defined as digital communication between an encoder and a decoder, using agreed upon symbols. To date, no one has shown an example of a naturally occurring encoding / decoding system, i.e. one that has demonstrably come into existence without a designer. A private equity investment group is offering a technology prize for this discovery (up to 3 million dollars). We will financially reward and publicize the first person who can solve this;,,, To solve this problem is far more than an object of abstract religious or philosophical discussion. It would demonstrate a mechanism for producing coding systems, thus opening up new channels of scientific discovery. Such a find would have sweeping implications for Artificial Intelligence research. http://cosmicfingerprints.com/solve/ Ode to the Code – Brian Hayes The few variant codes known in protozoa and organelles are thought to be offshoots of the standard code, but there is no evidence that the changes to the codon table offer any adaptive advantage. In fact, Freeland, Knight, Landweber and Hurst found that the variants are inferior or at best equal to the standard code. It seems hard to account for these facts without retreating at least part of the way back to the frozen-accident theory, conceding that the code was subject to change only in a former age of miracles, which we’ll never see again in the modern world. https://www.americanscientist.org/issues/pub/ode-to-the-code/4
As I said, finding one code in DNA was bad enough for Darwinists, its origin belonging to 'the former age of miracles' according to one Darwinist, but now we know that there are multiple overlapping codes in DNA which makes the 'former age of miracles', a far, far, far, worse problem for Darwinists:
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 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 - May 2013 Conclusions: Our analysis confirms mathematically what would seem intuitively obvious - multiple overlapping codes within the genome must radically change our expectations regarding the rate of beneficial mutations. As the number of overlapping codes increases, the rate of potential beneficial mutation decreases exponentially, quickly approaching zero. Therefore the new evidence for ubiquitous overlapping codes in higher genomes strongly indicates that beneficial mutations should be extremely rare. This evidence combined with increasing evidence that biological systems are highly optimized, and evidence that only relatively high-impact beneficial mutations can be effectively amplified by natural selection, lead us to conclude that mutations which are both selectable and unambiguously beneficial must be vanishingly rare. This conclusion raises serious questions. How might such vanishingly rare beneficial mutations ever be sufficient for genome building? How might genetic degeneration ever be averted, given the continuous accumulation of low impact deleterious mutations? http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006 Dynamic Genomes in Bacteria Argue for Design By Ann Gauger "Codes within codes within codes – highly efficient and highly intelligent systems – don’t happen by accident and/or selection. The cell might begin with one code, which is incredible in itself. To layer another code in the opposite direction is far and away beyond that. Then to add a third layer of structural dynamics is simply awe-inspiring." http://www.biologicinstitute.org/post/128798433944/dynamic-genomes-in-bacteria-argue-for-design
At the 10:30 minute mark of the following video, Dr. Trifonov states that Dawkin's idea of the selfish gene 'inflicted an immense damage to biological sciences', for over 30 years:
Second, third, fourth… genetic codes - One spectacular case of code crowding - Edward N. Trifonov - video https://www.youtube.com/watch?v=fDB3fMCfk0E
In the preceding video, Trifonov elucidates codes that are, simultaneously, in the same sequence, coding for DNA curvature, Chromatin Code, Amphipathic helices, and NF kappaB. In fact, at the 58:00 minute mark he states, "Reading only one message, one gets three more, practically GRATIS!". And please note that this was just an introductory lecture in which Trifinov just covered the very basics and left many of the other codes out of the lecture. Codes which code for completely different, yet still biologically important, functions. In fact, at the 7:55 mark of the video, there are 13 codes that are listed on a powerpoint, although the writing was too small for me to read. Concluding powerpoint of the lecture (at the 1 hour mark):
"Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages." Edward N. Trifonov - 2010
Verse:
John 1:1-4 1 In the beginning was the Word, and the Word was with God, and the Word was God. 2 The same was in the beginning with God. 3 All things were made through him; and without him [a]was not anything made that hath been made. 4 In him was life; and the life was the light of men.
bornagain77_{September 14, 2016
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Lynn had killer lines.
Dawkins: “It [neo-Darwinism] is highly plausible, it’s economical, it’s parsimonious, why on earth would you want to drag in symbiogenesis when it’s such an unparsimonious, uneconomical [theory]?” Margulis: “Because it’s there.”
That’s it in a nutshell. What is there, what exists, is the starting point of all science.
Professor Denis Noble interview by TBS http://www.thebestschools.org/dialogues/evolution-denis-noble-interview/Dionisio_{September 14, 2016
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Lateral transfer of DNA. The Modern Synthesis was based on Darwin’s idea of the tree of life, radiating from a common ancestor. We now know that the tree is more like a network, particularly in the early branches. DNA is not just transferred vertically from generation to generation; it can also be transferred laterally between organisms, even between different species.
Professor Denis Noble interview by TBS http://www.thebestschools.org/dialogues/evolution-denis-noble-interview/Dionisio_{September 14, 2016
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In a landmark study in 2008 all 6000 genes in yeast were studied using individual knockouts. Eighty percent of the knockouts were silent in the sense that no change in metabolic or reproductive activity was observed. That does not mean that those genes have no function. It means simply that the organisms are extremely well buffered against changes in their own genomes. Once the organisms were stressed by depriving them of various nutrients, it was possible to reveal that most of the 80 percent have functional roles. At the least, such experiments and calculations force one to think deeply about the basis of [Dawkins'?] gene-centric views of biology. What followed was like a falling domino cascade. Once one central issue in gene-centrism comes into question, others inevitably also come under suspicion. I will now list some of the dominoes that fell in the wake of questioning the gene-centric view of genome-phenotype relationships. 1. The Central Dogma of Molecular Biology. The idea of a one-way determinate read-out of genome sequences (if that is taken as the meaning of the Central Dogma) doesn’t make much sense to a physiologist. The 200 or so cell types in a vertebrate organism all have the same genome. Each cell clearly controls its genome to produce a pattern of gene expression that is unique to that type. Moreover, the environment of each cell type, formed by the tissues and organs the cells find themselves in, also contributes to control of the genome. As a mechanism contributing to the rare process of speciation, rare transgenerational inheritance of epigenetic changes could clearly occur. In a recent study of Darwin’s finches, this is what seems to have happened.
Professor Denis Noble interview by TBS http://www.thebestschools.org/dialogues/evolution-denis-noble-interview/Dionisio_{September 14, 2016
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Yea know, Dawkins is mostly, well, wrong. However, he has spoken good truth a couple of times. This is one of them. The other time that comes to mind is that he sees creationism, even young earth creationism, as an hypothesis that is within the scope of scientific inquiry. He doesn't think it is a correct hypothesis, but he does see it as falsifiable, therefore within the scope of scientific inquiry.bFast_{September 14, 2016
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Yet another excellent post. "This proves nothing other than that materialists are often quite shameless in the arguments they make to prop up their religious views." Priceless!Truth Will Set You Free_{September 14, 2016
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