Intelligent Design

The Skeptical Zone asks: What is a code?

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Over at the Skeptical Zone, Petrushka has written a post arguing that “DNA is a template, not a code.” In today’s post, I’d like to briefly review the reasons why we claim that the genetic code is a literal reality, not a metaphor, and explain exactly what a code is.

But before I do that, I’d like to critique Petrushka’s short post, titled, What Is A Code? (October 20, 2015):

Lots of heat surrounding this question.

My take is that a code must be a system for conveying meaning.

In my view, an essential feature of a code is that it must be abstract and and able to convey novel messages.

DNA fails at he level of abstraction. Whatever “meaning” it conveys cannot be translated into any medium other than chemistry. And not just any abstract chemistry, but the chemistry of this universe.

Without implementing in chemistry, it is impossible to read a DNA message. One cannot predict what a novel DNA string will do.

DNA is a template, not a code.

Go to it.

Petrushka’s three reasons for denying that the code in our DNA is a genuine code are that: (i) its meaning can only be translated into chemistry; (ii) it cannot convey new messages; and (iii) it is impossible to predict what a novel DNA string will do.

Regarding Petrushka’s argument that whatever “meaning” DNA conveys “cannot be translated into any medium other than chemistry”: scientists have developed computer models of DNA (see also here), so the objection that DNA’s meaning is confined to the domain of chemistry is factually incorrect.

As for DNA’s ability to convey new messages: I’d like to ask Petrushka if he believes that genes have evolved over the course of time, and that one gene (call it A), which codes for a certain protein, can evolve into another gene (call it B), that codes for a different protein. Since Petrushka writes for the Skeptical Zone, I presume his answer would be yes to both questions. In that case, Petrushka’s objection that DNA cannot convey new messages falls to the ground: he himself would admit that DNA can, over the course of time, convey new messages.

Finally, Petrushka’s claim that “it is impossible to predict what a novel DNA string will do” is incorrect. There is a whole field of science, known as gene prediction, whose aim is to identify the regions of genomic DNA that encode genes. Indeed, there is a Web server that “takes a sequence, either RNA or DNA, and creates a highly probable, probability annotated group of secondary structures, starting with the lowest free energy structure and including others with varied probabilities of correctness.” For an overview of the various software tools that predict DNA structure, the reader is invited to go here.

So when Petrushka argues (in a comment in his post) that whereas “grammar, syntax and spelling make it possible to construct novel sentences that have a predictable meaning,” “you cannot construct novel sequences of DNA and know what they mean or what they will do,” he is overstating his point. It is indeed true, as we will see, that we cannot deduce with certainty what a given piece of DNA will do, but that’s because the genetic code is but one of several codes that controls what goes on inside the cell. Despite this fact, scientists can deduce quite a lot about what a piece of DNA will do, simply by examining its sequence.

Why the genetic code is a literal reality

In today’s post, I’d like to discuss four pieces of evidence that support my claim that talk of a genetic code is no mere metaphor: it is a literal reality.

My first piece of evidence is a letter by Francis Crick to his son in March 1953 (h/t kairosfocus):

I could quote Crick at further length, but I see that Mung has already done so, in an excellent post over at the Skeptical Zone, titled, Code Denialism Pt. 1 – Crick, which was written in reply to Petrushka’s post. I highly commend Mung’s post to readers, as well as his follow-up post, Code Denialism Pt. 2 – Nirenberg, in which he quotes further scientific testimony, concluding with a quote from theoretical biologist Howard H. Pattee’s paper, “Causation, Control, and the Evolution of Complexity”: “…the fact is that present life requires semiotic control by coded gene strings.”

My second piece of evidence is the sheer prevalence of usage of the term “genetic code” among scientists today. If the reader goes over to Pub Med and types “genetic code” in quotes, he/she will get nearly 9,000 matches. That number speaks for itself.

Even Intelligent Design’s most ardent foes readily admit the legitimacy of the term, “genetic code.” Larry Moran, Professor of biochemistry at the University of Toronto and a long-time critic of Intelligent Design, was asked by commentator Virgil Cain whether he accepted the reality of the genetic code, in a recent post on Uncommon Descent:

Larry Moran- Do you think the genetic code is a real code (like Morse Code is a real code)?

Professor Moran replied:

Yes. That’s how I describe it in my textbook.

Well, there you have it. That’s what an eminent professor of biochemistry and a leading critic of Intelligent Design says.

Dr. Stephen Meyer on why protein-based life requires a code

My third, and most vital. piece of evidence comes from a passage in Dr. Stephen Meyer’s best-selling book, Signature in the Cell (HarperOne, 2009, pp. 114-118), in which he explains, in pellucid prose, exactly what a code is, and what’s wrong with Petrushka’s assertion that “DNA is a template, not a code.” Meyer exposes the error in the “template” metaphor for DNA (which was first formulated by George Gamow) by contrasting it with Francis Crick’s proposal that DNA contained a code:

Deducing a Code

By the late 1950s the relationship between DNA and protein was coming into focus. By then leading molecular biologists understood that the three-dimensional specificity of proteins depended on the one-dimensional specificity of their amino acid sequences. They also suspected that the specific arrangements of amino acids in protein chains derived in turn from specific sequences of nucleotide bases on the DNA molecule. Yet the question remained: How does the sequence of bases on the DNA direct the construction of protein molecules? How do specific sequences in a four-character alphabet generate specific sequences in a twenty-character alphabet?

Francis Crick anticipated the answer: the cell is using some kind of a code. Crick first began to suspect this as he reflected on a proposal by George Gamow, a Russian-born theoretical physicist and cosmologist who had, in the post-war years, turned some of his prodigious intellectual powers to reflect on new discoveries in molecular biology.

Gamow had immigrated to the States in the 1930s to take an appointment at George Washington University after working at the famed Theoretical Physics Institute in Copenhagen. In 1953 and 1954 he proposed a model to explain how the specific sequences in DNA generate the specific sequences in proteins. According to Gamow’s “direct template model,” as it was called, protein assembly occurred directly on the DNA strand. Gamow proposed that proteins formed as amino acids attached directly to the DNA molecule at regularly spaced intervals. Gamow thought the amino acids could nestle into diamond-shaped cavities in DNA that formed in the space between the two backbones (see Fig. 5.1). In this model, a group of four nucleotide bases from two parallel strands of DNA made a specifically shaped hollow into which one and only one amino acid could fit. As each group of nucleotides acquired an amino acid partner, the amino acids would also link with each other to form a chain. According to Gamow, the nearly identical spacing of amino acids in protein and of bases in DNA enabled the direct “matching” of amino acids to nucleotide groups on the DNA template. This matching occurred because of the supposed fit between the cavities produced by the bases and the shape of the side chain of the amino acids and the chemical affinity between the bases and amino acids.

The notion that “DNA is a template” isn’t Petrushka’s; it’s George Gamow’s. But it rests on bad science. To quote Meyer again:

Francis Crick first recognized the futility of this scheme. In a famous communication to members of the “RNA Tie Club,” Crick explained that there was nothing about the chemical properties or shapes of the bases to ensure that one and only one amino acid would fit into, or attach to, the cavities created by a group of bases. In the first place, many of the amino acids were difficult to differentiate structurally, because they had similar side chains. Second, the bases themselves did not necessarily create shapes that either matched these shapes or, still less, differentiated one from another. As Crick put it, “Where are the nobby hydrophobic surfaces to distinguish valine from leucine from isoleucine? Where are the charged groups, in specific positions, to go with the acidic and basic amino acids?” As Juddson explains, “Crick was a protein crystallographer, and knew of no reason to think that Gamow’s holes in the helix could provide the variety or precision of shapes necessary to differentiate a score or more of rather similar objects.”

Yet in the absence of such spatial matching and the formation of corresponding chemical attachments, there could be no reliable transmission of information. For the direct template needed to explain the irregularity and specificity of the amino acid sequences in proteins, individual bases (or groups of bases) needed to manifest discriminating spatial geometries. Figuratively speaking, DNA bases not only needed to “zig” in a way that matched the specific “zags” of each amino acid, but DNA needed to do so at irregular intervals in order to produce the irregular sequencing of amino acids that characterizes proteins. Yeet as Crick realized, both the individual bases themselves and their various combinations lacked distinguishing physical features that could account for the specificity of amino-acid sequencing. Further, the geometry of the DNA molecule as a whole, at the level of its gross morphology, presents a highly repetitive sequence of major and minor grooves (see Fig. 5.2). Therefore, it could not function as a direct template for protein synthesis. As Crick explained, “What the DNA structure does show … is a specific pattern of hydrogen bonds, and very little else.”

If the chemical features and shapes of the DNA bases do not directly account for the specific sequencing of proteins, what does? Crick remained adamant that the specific arrangement of the nucleotide bases, not anything about their physical or chemical features per se, dictated amino acid sequencing.

Crick’s insight had profound implications. If a single protein could not copy the information in DNA directly, as the direct template model suggested, then as Jacques Monod would later explain, “you absolutely needed a code.” And so Crick postulated a third factor consistent with his original sequence hypothesis. He proposed the existence of a genetic code – a means of translating information from one chemical domain into another.

So there we have it. A code is a means of translating information from one domain into another – in this case, a chemical domain. That’s a broad, non-trivial definition.

Meyers then proceeds to describe how the genetic code works:

To envision what Crick had in mind, imagine having a human alphabet that uses four and only four distinct shapes that combine in various specific ways to form not just words, but words that correspond to individual letters in a larger alphabet roughly the size of the English alphabet; this larger alphabet then uses its letters (each of which is one of those words composed of the four shapes) to build sentences. Of course, we have a symbol system that does much the same thing. The binary code that computer programmers use has a translation key that enables programmers to produce English text from sequences of binary digits. Each letter in the English alphabet is represented by a unique combination of two character types, O’s and 1’s. For example, in ASCII code the letter A is represented by the sequence 100 0001, the letter B by the sequence 100 0010, and so on. Each of the letters of the twenty-six letter English alphabet has a corresponding representation in the two-digit numeric alphabet of this binary system (see Fig. 5.3). Crick realized that if his sequence hypothesis were true, then there must be some similar translation system in the cell – one that determined how sequences written in the four-character alphabet of DNA are converted into sequences that use a twenty-letter amino-acid alphabet. The DNA detective was now in the business of code breaking as well.

Yet in a physical system, as opposed to a social or linguistic one, a code must have a <b?physical expression. Crick postulated the existence of a third molecule, an adapter molecule functioning as a translation device that could recognize and convert the information in the sequential arrangements of the bases into specific amino-acid sequences. More specifically, he proposed the existence of twenty separate adapter molecules corresponding to each of the twenty protein-forming amino acids. Each adapter would, by the familiar mechanism of complementary base pairing, bind to a sequence of DNA text at one end and to a specific amino acid at the other. Crick also proposed the existence of specific enzymes (one for each of the twenty adapter-amino acid pairs) to connect the specific amino acids and their corresponding adapters. The set of correspondences between sections of genetic text, on the one hand, and the specific amino acid, on the other, constituted a genetic code (see Fig. 4.6).

Though these correspondences were mediated physically by adapter molecules and enzymes, this complex system, as conceived by Crick, would be governed by the functional requirements of information transfer as by rules of chemical affinity – as much by a set of chemically arbitrary conventions as by the necessary relations of physical-chemical law. Indeed, as Crick imagined this system, nothing about the physical or chemical features of the nucleotides or amino acids directly dictated any particular set of assignments between amino acids and bases in the DNA text. It had to be cracked…

That last phrase encapsulates a vital feature of the genetic code: its chemical arbitrariness: “nothing about the physical or chemical features of the nucleotides or amino acids directly dictated any particular set of assignments between amino acids and bases in the DNA text.”

So, how did Crick’s proposal withstand the test of time? Remarkably well, as Meyer describes it:

Crick’s proposal was striking in its sheer theoretical audacity. Biochemistry had not a shred of evidence for the existence of adapter molecules or their corresponding enzymes. Crick simply deduced the need for a code by thinking about what would be needed to make the cell’s communication system work…

What Crick would postulate on the grounds of functional necessity took nearly five years of intensive research and many transatlantic communications and conferences to verify and calculate…

Indeed, Crick’s adapter molecules and their corresponding enzymes functioned much as he had originally envisaged, albeit as part of a far more complex process than even he has foreseen.

Finally, I should point out that strictly speaking, DNA itself is not a code. As Meyer puts it, “The set of correspondences between sections of genetic text, on the one hand, and the specific amino acid, on the other, constituted a genetic code .”

Dr. Jonathan Wells: In addition to the genetic code, there are other codes in the cell

My fourth and final piece of evidence comes from Dr. Jonathan Wells, who has two Ph.D.s – one in Molecular and Cell Biology from the University of California at Berkeley, and one in Religious Studies from Yale – and who is the author of Icons of Evolution: Science or Myth?: Why Much of What We Teach About Evolution is Wrong, The Politically Incorrect Guide to Darwinism and Intelligent Design and The Myth of Junk DNA as well as being the co-author of The Design of Life with Dr. William A. Dembski.

Dr. Wells contends that not only is the genetic code real, but there are at least six different codes inside the cell.

In a recent podcast on ID The Future, Dr. Jonathan Wells defined a code in biology as follows:

Well, a code, generally speaking, is a pattern that conveys information. Now, what information does is it limits whatever thing that promotes a huge range of possibilities to a specific set of those possibilities. For example, if we have a long string of letters that really make no sense – they don’t delimit anything, except the letters themselves – but if the sentence actually means something in English, then it specifies the thought, out of the infinite universe of thoughts that are out there, and that’s how information works. It can be in the form of letters, it can be in the form of digital information on a CD that specifies music – say, one song – out of the infinite number of possible songs that are out there, and in biology, the code specifies, among other things, the form of an organism. And a code in biology is generally carried, not by digital information or by letters, but by molecules. So biological code is a pattern in molecules that carries information to specify features of the organism.

Dr. Wells then proceeded to describe not only the genetic code, but five other codes inside the cell:

Well, a genetic code can mean two things. To a biologist, it technically means a set of instructions whereby information in DNA and RNA is translated into protein. A certain set of sub-units in RNA specifies a certain subset of amino acids and proteins. But that’s not the only meaning of code in biology – genetic code, that is. The other meaning – somewhat less technical – is that the sequence of sub-units in DNA and RNA can carry information that specifies proteins. So, I’ll use “genetic code” in the second sense, and it certainly is such a code. It’s not as powerful as it’s sometimes made out to be, as I’ll explain in a minute, because there are other codes besides it.

One code we could call the epigenetic code. It turns out that the DNA molecules in cells are chemically altered in many cases – not in the sense that the sequences of the sub-units changes, but the sub-units are decorated, so to speak, with other molecules that affect which parts of the DNA get transcribed into RNA and therefore translated into protein. So that’s another code in the organism that’s independent of the sequence of DNA it sequences.

On top of that, there’s still another code: the RNA splicing code. It turns out that in organisms such as ourselves, when the DNA is transcribed into RNA, the RNA is then cut up and spliced back together. And it can be spliced back together in many ways. We know of one stretch of DNA in fruit flies, for example, that after RNA splicing, can produce over 18,000 different proteins – a single stretch of DNA! So there’s the RNA splicing code, about which we don’t know a whole lot. It might be partly influenced by RNAs that have been transcribed from non-protein-coding RNA, but we don’t fully understand the nature of the RNA splicing code.

On top of that is the sugar code. It turns out that almost every protein made in the cell is further modified by the addition of sugar molecules. Now sugar molecules are far more complex than DNA and RNA. DNA and RNA sequences are linear – one-dimensional – but sugar molecules are three-dimensional, and so they carry a whole lot more information than in the RNA and in the DNA. So proteins are modified by the addition of sugar molecules that add a whole new level of complexity to what’s going on here.

Now on top of the sugar code is the membrane code. It turns out that there’s a pattern in the membrane of the living cell that’s there before the DNA is transcribed, and can be inherited independently of the DNA. And the membrane pattern is that it determines[?? – audio unclear] the spatial gradient for things in the cell, and the spatial ranking is all-important – especially in the embryo.

And finally, on top of the membrane code, there’s something called the bio-electric code. There are molecules in the membranes of all our cells that generate electric fields, and these fields, once generated, form a three-dimensional pattern that is known to affect development. For example, in a frog embryo, researchers have modified the electric field that they generate, without modifying the molecules or the membrane. And just by electrically modifying the bio-electric field, they can alter development.

So there are at least six codes in biology: the genetic code and five others.… They all carry information. They all affect cellular activity, and mostly embryo development.

Readers who would like to learn more about codes in biology will enjoy perusing Dr. Wells’s latest paper, “Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA”. The “Summary and Implications” section on page 14 provides a helpful overview.

A final objection?

In a subsequent comment on his post, Petrushka writes:

My understanding of the word “code” — which may not be the only possible one — is a system of transferring information such that an arbitrary reader can discover the meaning of the message.

This applies to human languages, including encrypted ones or extinct ones.

I think it also applies to musical notation, including mechanical notations, such as music box cylinders.

One thing that distinguishes such symbol systems is grammar and syntax. The notation has elements that can be rearranged to form alternate messages, and such alternate messages can be understood.

DNA does not have anything analogous to grammar and syntax….

Contrary to what Petrushka asserts, scientists can indeed legitimately speak of the language of the cell. Dr. Don Johnson is a scientist who has worked hard to build a link between the biological sciences and information technology over the past two decades. In addition to being the author of Programming of Life and Probability’s Nature and Nature’s Probability: A Call to Scientific Integrity, Dr. Johnson has both a Ph.D. in chemistry and a Ph.D. in computer and information sciences. He has spent 20 years teaching in universities in Wisconsin, Minnesota, California, and Europe. On April 8, 2010, Dr. Johnson gave a presentation entitled Bioinformatics: The Information in Life for the University of North Carolina Wilmington chapter of the Association for Computer Machinery. Dr. Johnson’s presentation is now on-line here. Both the talk and accompanying handout notes can be accessed from Dr. Johnson’s Web page. Here’s an excerpt from his presentation blurb:

Each cell of an organism has millions of interacting computers reading and processing digital information using algorithmic digital programs and digital codes to communicate and translate information.

On a slide entitled “Information Systems In Life,” Dr. Johnson points out that:

  • the genetic system is a pre-existing operating system;
  • the specific genetic program (genome) is an application;
  • the native language has a codon-based encryption system;
  • the codes are read by enzyme computers with their own operating system;
  • each enzyme’s output is to another operating system in a ribosome;
  • codes are decrypted and output to tRNA computers;
  • each codon-specified amino acid is transported to a protein construction site; and
  • in each cell, there are multiple operating systems, multiple programming languages, encoding/decoding hardware and software, specialized communications systems, error detection/correction systems, specialized input/output for organelle control and feedback, and a variety of specialized “devices” to accomplish the tasks of life.

Petrushka’s claim that DNA lacks grammar and syntax is also incorrect, as author, business consultant and electrical engineer Perry Marshall points out on his Cosmic Fingerprints.com Website, in a thought-provoking article titled, Language and Design: Product of a Mental Process:

…DNA is not just a molecule, DNA is a language. It is actually very comparable to English and human languages in the way that it is structured. Here is a little chart and it shows the comparison between human languages and DNA. The nucleotide is the A, T, C, G.

Marshall uses a chart to illustrate his point:

DNA Language Human Language
Nucleotide Character
Codon Letter
Gene Word
Operon Sentence
Regulon Paragraph

Marshall continues:

DNA is encoding, decoding mechanism that stores and transmits the message of the living organism. Biologists have actually been using linguistic analysis to decode the human genome. Tools that we must use to analyze languages are continually being used to figure out what all of those genes actually mean.

So if you read some article in the newspaper it says we found a gene that causes Spina Bifida or something like that, some kind of linguistic analysis was used to help figure that out.

Perry Marshall’s Intelligent Design argument

Marshall also proposes an update to Paley’s design argument, which he believes makes it logically unassailable:

Perry Marshall’s Update to Paley’s Design Argument

But now I have an improvement to Paley’s design argument. This sounds audacious but I’m serious. I have an improvement that makes Paley’s argument airtight:

  • Element common to both watches and life is language
  • The essential distinction between pattern and design is language
  • Fundamental Property of all Designs: Idea precedes Implementation
  • Idea must be represented by language
  • All language comes from a mind

Life is preceded by DNA, and a watch is preceded by a plan where a blueprint or at least an idea in somebody’s mind that preceded the building of the watch.

That is true of all things that are designed, an idea comes first.

The essential distinction betweens patterns and designs is language. Patterns don’t have languages, but designs do. So the fundamental property of all designs is that an idea precedes the implementation of the idea.

The idea exists in a symbolic form before it’s physically built. An idea, in order to exist, has to be represented by a language. Even to have an idea in your mind you have to talk to yourself and have images in your mind of what you want to do before you do it. So we know this:

  • Ideas always precede implementation, always, no exceptions.
  • All languages come from a mind. No exceptions.
  • There are no languages that do not come from a mind.
  • So we know that DNA was designed.
  • A mind designed DNA, therefore God exists.

Can this be refuted? Yes, if any exceptions to this can be found. But a lot of people have tried to refute it, unsuccessfully. It’s an airtight inductive proof that life was designed by a mind. If anyone can find a flaw in the logic, it fails. Until that happens, it stands. It’s just like the laws of thermodynamics, or gravity, or conservation of matter and energy. If anyone can find an exception, the law fails to hold.

This leads to what I call The Atheist’s Riddle:

“Show me a language that does not come from a mind.

It’s so simple and a child can understand, but so complex no atheist can solve.

Conclusion

It seems to me that Petrushka’s point would be better expressed by saying that whereas the language of the cell is an artificial language, the language we use in our everyday speech is a natural language. (See here for a short exposition of these terms.) Natural languages do indeed have a richness which cannot be exhausted by their grammatical and syntactical rules. Nevertheless, it remains true that to the best of our knowledge, only a mind is capable of designing a language, whether natural or artificial. I conclude that the language of the cell warrants an inference to the existence of an Intelligent Designer.

But regardless of what readers may think of this Intelligent design argument, one point is undeniable: the genetic code is real. It is not a metaphor, but a literal reality – a point I elaborated in my 2013 post, Is the genetic code a real code?

What do readers think?

47 Replies to “The Skeptical Zone asks: What is a code?

  1. 1
    Virgil Cain says:

    The only people to object to the genetic code being a real code are the same people who realize there isn’t any way that materialism can explain a code. They will deny it is part of a communication system even after it is pointed out it is part of the intracellular communication system.

    There was a reason it is called messenger RNA-> it is carrying a message from the nucleus (in eukaryotes) that says to build a protein and here is the coding for amino acid sequence.

    The implications are too great for them to bear so they reach critical mass and either deny or say that of course natural selection could do that.

  2. 2
    bornagain says:

    Moreover, besides the coding Dr. Wells highlighted, there is also additional multiple overlapping coding within DNA itself:

    Thirty Years of Multiple Sequence Codes – Edward N. Trifonov – 2011
    How Many “Second Genetic Codes”?
    Excerpt: According to the media sympathetic to science and enthusiastic about sensational discoveries, the “Second Genetic Code” as it was called by New York Times (8) was discovered by Ya-Ming Hou and Paul Schimmel and published in Nature in 1988 (9). It was about recognition of tRNAs by respective aminoa- cyl-tRNA synthetases. Thirteen years later New Scientist announced the second Second Genetic Code (13), discovered by Jenuwein and Allis (14) and published in Science. This time it was about histone modifications. Five years later, New York Times, again, reported about “a second code in DNA in addition to the genetic code” (15). This was already the third Second Genetic Code, discovered by Segal et al (16), sug- gesting now nucleosome positioning rules. One, surely, would raise eyebrows having learned that there is also the fourth Second Genetic Code (17)—on in- teraction specificities between proteins and DNA, and the fifth Second Genetic Code, the name given by Nature magazine (18) to the set of rules governing gene splicing(19). Bewildered reader, naturally, would say “I’m done with seconds, can I have a third?” (20)
    The conclusion from the above is obvious: one has to admit that the genetic sequences carry many different codes. If we are to know what the sequences are about, we have to detect and decipher these codes. The times of surrender to “junk” and “selfish DNA” are over, and “non-coding” becomes a misnomer.,,,
    http://www.sciencedirect.com/s.....2911600016

    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

    Multiple levels of meaning in DNA sequences, and one more. – Trifonov EN, Volkovich Z, Frenkel ZM. – 2012
    Excerpt: If we define a genetic code as a widespread DNA sequence pattern that carries a message with an impact on biology, then there are multiple genetic codes. Sequences involved in these codes overlap and, thus, both interact with and constrain each other, such as for the triplet code, the intron-splicing code, the code for amphipathic alpha helices, and the chromatin code. Nucleosomes preferentially are located at the ends of exons, thus protecting splice junctions, with the N9 positions of guanines of the GT and AG junctions oriented toward the histones.,,
    http://www.ncbi.nlm.nih.gov/pubmed/22954214

    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.....08728_0006

    Moreover, there are very good mathematical reasons why overlapping coding within DNA will prevent one creature from ever being changed into another creature.

    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.....08728_0006

    A very simple way to understand the monumental brick wall any evolutionary scenario faces with the multiple overlapping coding found in DNA is with the following puzzle found on page 141 of the book ‘Genetic Entropy’ by Dr. Sanford.

    S A T O R
    A R E P O
    T E N E T
    O P E R A
    R O T A S

    Which is translated ;

    THE SOWER NAMED AREPO HOLDS THE WORKING OF THE WHEELS.

    This ancient puzzle, which dates back to at least 79 AD, reads the same four different ways, Thus, If we change (mutate) any letter we may get a new meaning for a single reading read any one way, as in Dawkins weasel program, but we will consistently destroy the other 3 readings of the message with the new mutation (save for the center).
    This is what is meant when it is said that a poly-functional genome is poly-constrained to any random mutations.
    This poly-constrained principle is why we never see the unlimited plasticity in organisms that was, and is, imagined by Darwin and his followers, and is also why random mutations, that have effects that great enough that we are able to measure them, are almost always deleterious in the effects that are measured:

    ‘It’s becoming extremely problematic to explain how the genome could arise and how these multiple levels of overlapping information could arise, since our best computer programmers can’t even conceive of overlapping codes. The genome dwarfs all of the computer information technology that man has developed. So I think that it is very problematic to imagine how you can achieve that through random changes in the code.,,, and there is no Junk DNA in these codes. More and more the genome looks likes a super-super set of programs.,, More and more it looks like top down design and not just bottom up chance discovery of making complex systems.’ –
    Dr. John Sanford – Inventor of the ‘Gene Gun’ – 31 second mark – video
    http://www.youtube.com/watch?f.....dM_s#t=31s

    Verse and Music:

    John1:1-4
    In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. In him was life, and that life was the light of all mankind.

    Casting Crowns – The Word Is Alive – Live
    https://www.youtube.com/watch?v=fXGaZn1dDOw

  3. 3
    Virgil Cain says:

    petrushka’s three “objections” are not thought out:

    (i) its meaning can only be translated into chemistry;

    Meaningless as Morse code is only translated into letters and words- same with Braille. Both are real codes.

    (ii) it cannot convey new messages;

    Is that a requirement for a code? There are many different proteins. And for DNA Venter coded in a message of sorts.

    and (iii) it is impossible to predict what a novel DNA string will do.

    Not a requirement for being a code. Good secret codes are unpredictable and yet they are still codes. And Venter new what his novel DNA would do.

  4. 4
    steveh says:

    Element common to both watches and life is language
    The essential distinction between pattern and design is language
    Fundamental Property of all Designs: Idea precedes Implementation
    Idea must be represented by language
    All language comes from a mind

    How would you code an accurate working watch in DNA?

    Too hard? Ok, what about a very simple non-functioning watch-face? You guys are experts on watches and DNA coding, so how would you implement a simple circular disc with 12 markers representing twelve hour and/or five-minute intervals from 0 to 55 arranged at regular 30 degree angles around the circumference in DNA such that a living organism of your choosing would produce such a simple artifact?

    For extra credit, add roman numerals at 0/12, 3, 6, and 9. In DNA. Where do you start?

    edit: fixed some of probably many typos

  5. 5
    Mapou says:

    This is a well-written and captivating article. Easy and informative prose that does not insult one’s intelligence. This is the kind of articles I enjoy reading on UD.

  6. 6
    Mapou says:

    So which one of the two evolved first, the code or the decoder? Oh wait, that’s abiogenesis, not evolution. I know, magicland. Like this somehow exonerates the fact that the most important aspect of the theory (its beginning) is missing and nowhere to be found.

    ahahaha…AHAHAHA…ahahaha…

  7. 7
    mike1962 says:

    Nothing impressive about The Code. After all, “it’s just chemistry.” 😀

  8. 8
    Mung says:

    I want to thank VJT for his OP. I post over at TSZ but had declined to participate in that particular thread.

    What stands out to me is that the question was raised, “What Is A Code?” – but never answered.

    Further, petrushka admits he doesn’t care:

    I’m not interested in a dictionary war. I don’t care about classifying sequences as codes or languages or whatever. I’m not a bucket person.

    But back to my roadway. the problem I’m addressing is not the definition of code. I couldn’t care less.

  9. 9
    Mapou says:

    Petrushka:

    My understanding of the word “code” — which may not be the only possible one — is a system of transferring information such that an arbitrary reader can discover the meaning of the message.

    This is not true, of course. A code is a symbol the meaning of which is must be agreed upon by both sender and receiver. Even a single bit can be enough to convey a message if it occurs at the right time or place. This is why, for example, no one could decipher ancient Egyptian hieroglyphic writings until the discovery of the Rosetta stone by one of Napoleon’s soldiers. It was the key that gave meaning to the symbols.

  10. 10
    computerist says:

    What happened to PaV’s thread?

  11. 11
    ppolish says:

    A template has a purpose. A template is a product of design. DNA as a template an example of irreducible complexity? Maybe Petrushka meant “appearance of template”.

  12. 12
    Andre says:

    2015 and there are still people in denial?

    Denial is a river in Africa……

  13. 13
    gpuccio says:

    I am really amazed at Petrushka’s “arguments”. Even if I usually disagree with him, I have usually found that his objections are somewhat reasonable, and to the point.

    That seems not to be the case here.

    The necessity to deny that the genetic code is a code seems to be really strong for our interlocutors, but it’s obviously a folly.

    OK, I suppose they need to exercise, so that tomorrow they can start denying that the many epigenetic codes are codes… 🙂

  14. 14
    awstar says:

    DNA Language | Human Language | Chemistry
    Nucleotide | Character | atoms
    Codon | Letter | element
    Gene | Word | molecule
    Operon | Sentence | amino acid (left handed)
    Regulon | Paragraph | protein

    I think I see a pattern (template?) here. All these words represent stuff.

  15. 15
    Virgil Cain says:

    gpuccio:

    Even if I usually disagree with him, I have usually found that his objections are somewhat reasonable, and to the point.

    Strange, I have never seen a reasonable argument from petrushka. petrushka is on the same level of insipidity as Zachriel.

  16. 16
    gpuccio says:

    Virgil Cain:

    OK, it’s probably a question of personal taste.

    I have good respect of both Zachriel and Petrushka, even if for different reasons. They are both interlocutors that I appreciate.

    Obviously, I strongly disagree with them on almost everything! 🙂

  17. 17
    bornagain says:

    “You don’t have a soul. You are a soul. You have a body.”
    George MacDonald – Annals of a Quiet Neighborhood – 1892

    As Jonathan Wells mentioned, the bioelectric code cannot be reduced, like the membrane code cannot be reduced, to information in the DNA.
    Moreover, the bioelectric code is said to be a ‘jaw dropper’.

    The (Electric) Face of a Frog – video
    https://www.youtube.com/watch?v=0VULjzX__OM

    The face of a frog: Time-lapse video reveals never-before-seen bioelectric pattern – July 2011
    Excerpt: For the first time, Tufts University biologists have reported that bioelectrical signals are necessary for normal head and facial formation in an organism and have captured that process in a time-lapse video that reveals never-before-seen patterns of visible bioelectrical signals outlining where eyes, nose, mouth, and other features will appear in an embryonic tadpole.,,, “When a frog embryo is just developing, before it gets a face, a pattern for that face lights up on the surface of the embryo,”,,, “We believe this is the first time such patterning has been reported for an entire structure, not just for a single organ. I would never have predicted anything like it. It’s a jaw dropper.”,,,
    http://www.physorg.com/news/20.....-seen.html

    Dr Hunter comments:

    “The video suggests that bioelectric signals presage, (i.e. foreshadow), the morphological development of the face. It also, in an instant, gives a peak at the phenomenal processes at work in biology. As the lead researcher said, “It’s a jaw dropper.””
    Cornelius Hunter – An Electric Face: A Rendering Worth a Thousand Falsifications – September 2011

    The bioelectric code adds to the growing list of empirical evidences that the ‘form’ of an organism is not reducible to DNA, nor to any other material particulars in the cell for that matter, in any conceivable way:
    http://www.uncommondescent.com.....ent-584055

    In fact Jonathan Wells comments that, in direct contradiction to the molecular reductionism that undergirds neo-Darwinian thought, it is the organism controlling the DNA, not the DNA controlling the organism:

    Ask an Embryologist: Genomic Mosaicism – Jonathan Wells – February 23, 2015
    Excerpt: humans have a “few thousand” different cell types. Here is my simple question: Does the DNA sequence in one cell type differ from the sequence in another cell type in the same person?,,,
    The simple answer is: We now know that there is considerable variation in DNA sequences among tissues, and even among cells in the same tissue. It’s called genomic mosaicism.
    In the early days of developmental genetics, some people thought that parts of the embryo became different from each other because they acquired different pieces of the DNA from the fertilized egg. That theory was abandoned,,,
    ,,,(then) “genomic equivalence” — the idea that all the cells of an organism (with a few exceptions, such as cells of the immune system) contain the same DNA — became the accepted view.
    I taught genomic equivalence for many years. A few years ago, however, everything changed. With the development of more sophisticated techniques and the sampling of more tissues and cells, it became clear that genetic mosaicism is common.
    I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It’s the organism controlling the DNA, not the DNA controlling the organism.
    http://www.evolutionnews.org/2.....93851.html

    The human body is conservatively made up of a billion-trillion protein molecules.

    One Body – XVIVO Scientific Animation – video
    http://www.youtube.com/watch?v=pDMLq6eqEM4

    HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE – Stephen L. Talbott – May 2012
    Excerpt: “If you think air traffic controllers have a tough job guiding planes into major airports or across a crowded continental airspace, consider the challenge facing a human cell trying to position its proteins”. A given cell, he notes, may make more than 10,000 different proteins, and typically contains more than a billion protein molecules at any one time. “Somehow a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places”. And further: “It’s almost as if every mRNA [an intermediate between a gene and a corresponding protein] coming out of the nucleus knows where it’s going” (Travis 2011),,,
    Further, the billion protein molecules in a cell are virtually all capable of interacting with each other to one degree or another; they are subject to getting misfolded or “all balled up with one another”; they are critically modified through the attachment or detachment of molecular subunits, often in rapid order and with immediate implications for changing function; they can wind up inside large-capacity “transport vehicles” headed in any number of directions; they can be sidetracked by diverse processes of degradation and recycling… and so on without end. Yet the coherence of the whole is maintained.
    The question is indeed, then, “How does the organism meaningfully dispose of all its molecules, getting them to the right places and into the right interactions?”
    The same sort of question can be asked of cells, for example in the growing embryo, where literal streams of cells are flowing to their appointed places, differentiating themselves into different types as they go, and adjusting themselves to all sorts of unpredictable perturbations — even to the degree of responding appropriately when a lab technician excises a clump of them from one location in a young embryo and puts them in another, where they may proceed to adapt themselves in an entirely different and proper way to the new environment. It is hard to quibble with the immediate impression that form (which is more idea-like than thing-like) is primary, and the material particulars subsidiary.
    Two systems biologists, one from the Max Delbrück Center for Molecular Medicine in Germany and one from Harvard Medical School, frame one part of the problem this way:
    “The human body is formed by trillions of individual cells. These cells work together with remarkable precision, first forming an adult organism out of a single fertilized egg, and then keeping the organism alive and functional for decades. To achieve this precision, one would assume that each individual cell reacts in a reliable, reproducible way to a given input, faithfully executing the required task. However, a growing number of studies investigating cellular processes on the level of single cells revealed large heterogeneity even among genetically identical cells of the same cell type. (Loewer and Lahav 2011)”,,,
    And then we hear that all this meaningful activity is, somehow, meaningless or a product of meaninglessness. This, I believe, is the real issue troubling the majority of the American populace when they are asked about their belief in evolution. They see one thing and then are told, more or less directly, that they are really seeing its denial. Yet no one has ever explained to them how you get meaning from meaninglessness — a difficult enough task once you realize that we cannot articulate any knowledge of the world at all except in the language of meaning.,,,
    http://www.netfuture.org/2012/May1012_184.html#2

    But since the ‘form’ of an organism is not reducible to DNA in any conceivable way, what in blue blazes is making the approx. billion-trillion protein molecules of the human body cohere as a single unified whole, i.e. a ‘form’, for precisely a lifetime, and not a moment longer?

    picture – What power holds off that moment — precisely for a lifetime, and not a moment longer?
    http://cdn-4.spiritscienceandm.....ardd-2.jpg

    The Unbearable Wholeness of Beings – Stephen L. Talbott – 2010
    Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary.
    ,,, the question, rather, is why things don’t fall completely apart — as they do, in fact, at the moment of death. What power holds off that moment — precisely for a lifetime, and not a moment longer?
    Despite the countless processes going on in the cell, and despite the fact that each process might be expected to “go its own way” according to the myriad factors impinging on it from all directions, the actual result is quite different. Rather than becoming progressively disordered in their mutual relations (as indeed happens after death, when the whole dissolves into separate fragments), the processes hold together in a larger unity.
    http://www.thenewatlantis.com/.....-of-beings

    Indeed, the reductive materialistic framework that neo-Darwinists rely on is grossly inadequate as to providing any sensible explanation for how it is possible for a billion-trillion protein molecules to cohere as a single unified whole, i.e. a ‘form’, for precisely a lifetime, and not a moment longer.
    In fact, until recently it was naively thought that the communication of information in the cell was accomplished primarily when diffusing molecules randomly collided with each other:

    “We have always underestimated cells. Undoubtedly we still do today. But at least we are no longer as naive as we were when I was a graduate student in the 1960s. Then, most of us viewed cells as containing a giant set of second-order reactions: molecules A and B were thought to diffuse freely, randomly colliding with each other to produce molecule AB—and likewise for the many other molecules that interact with each other inside a cell. This seemed reasonable because, as we had learned from studying physical chemistry, motions at the scale of molecules are incredibly rapid. … But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered. Proteins make up most of the dry mass of a cell. But instead of a cell dominated by randomly colliding individual protein molecules, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines,,,
    – Bruce Alberts, “The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists,” Cell, 92 (February 6, 1998): 291-294) Editor-in-Chief of Science (2009-2013) served two six-year terms as the president of the National Academy of Sciences

    To say that randomly diffusing molecules are grossly inadequate as an explanation for how it is possible for a billion-trillion protein molecules to cohere for a single unified whole, i.e. a ‘form’, for precisely a lifetime, and not a moment longer, is to insult the fact that smoke signals are grossly inadequate as a means of communication for the internet. (i.e. ‘Grossly inadequate’ is to understate the severity of the shortfall in the explanation for how it is possible for a billion-trillion molecules to cohere as a single unified whole.)

    Indeed, far from communication in the cell being accomplished mainly via randomly diffusing molecules, (as was apparently presupposed for decades by reductive materialists), we now know that extremely sophisticated biophotonic communication is being accomplished within the cell and even between the cells.

    Strange! Humans Glow in Visible Light – Charles Q. Choi – July 22, 2009
    Schematic illustration of experimental setup that found the human body, especially the face, emits visible light in small quantities that vary during the day. B is one of the test subjects. The other images show the weak emissions of visible light during totally dark conditions. The chart corresponds to the images and shows how the emissions varied during the day. The last image (I) is an infrared image of the subject showing heat emissions.
    http://i.livescience.com/image.....1296086873

  18. 18
    bornagain says:

    The Puzzling Role Of Biophotons In The Brain – Dec. 17, 2010
    Excerpt: In recent years, a growing body of evidence shows that photons play an important role in the basic functioning of cells. Most of this evidence comes from turning the lights off and counting the number of photons that cells produce. It turns out, much to many people’s surprise, that many cells, perhaps even most, emit light as they work.
    In fact, it looks very much as if many cells use light to communicate. There’s certainly evidence that bacteria, plants and even kidney cells communicate in this way. Various groups have even shown that rats brains are literally alight thanks to the photons produced by neurons as they work.,,,
    ,,, earlier this year, one group showed that spinal neurons in rats can actually conduct light.
    ,, Rahnama and co point out that neurons contain many light sensitive molecules, such as porphyrin rings, flavinic, pyridinic rings, lipid chromophores and aromatic amino acids. In particular, mitochondria, the machines inside cells which produce energy, contain several prominent chromophores.
    The presence of light sensitive molecules makes it hard to imagine how they might not be not influenced by biophotons.,,,
    They go on to suggest that the light channelled by microtubules can help to co-ordinate activities in different parts of the brain. It’s certainly true that electrical activity in the brain is synchronised over distances that cannot be easily explained. Electrical signals travel too slowly to do this job, so something else must be at work.,,,
    (So) It’s a big jump to assume that photons do this job.
    http://www.technologyreview.co.....the-brain/

    Cellular Communication through Light – 2009
    Excerpt: Information transfer is a life principle. On a cellular level we generally assume that molecules are carriers of information, yet there is evidence for non-molecular information transfer due to endogenous coherent light. This light is ultra-weak, is emitted by many organisms, including humans and is conventionally described as biophoton emission.
    http://www.plosone.org/article.....ne.0005086

    Paramecium caudatum can communicate with neighbors using a non-molecular method, probably photons. The cell populations were separated either with glass allowing photon transmission from 340 nm to longer waves, or quartz being transmittable from 150 nm, i.e. from UV light to longer waves. Energy uptake, cell division rate and growth correlation were influenced.
    http://en.wikipedia.org/wiki/Paramecium_caudatum

    Biophoton Communication: Can Cells Talk Using Light? – May 2012
    Excerpt: The question he aims to answer is whether the stream of photons has any discernible structure that would qualify it as a form of communication.,, Biophoton streams consist of short quasiperiodic bursts, which he says are remarkably similar to those used to send binary data over a noisy channel.
    http://www.technologyreview.co.....alk-using/

    The Real Bioinformatics Revolution – Proteins and Nucleic Acids ‘Singing’ to One Another?
    Excerpt: the molecules send out specific frequencies of electromagnetic waves which not only enable them to ‘see’ and ‘hear’ each other, as both photon and phonon modes exist for electromagnetic waves, but also to influence each other at a distance and become ineluctably drawn to each other if vibrating out of phase (in a complementary way).,,, More than 1,000 proteins from over 30 functional groups have been analysed. Remarkably, the results showed that proteins with the same biological function share a single frequency peak while there is no significant peak in common for proteins with different functions; furthermore the characteristic peak frequency differs for different biological functions.,,, The same results were obtained when regulatory DNA sequences were analysed.
    http://www.i-sis.org.uk/TheRea.....lution.php

    Bioactive peptide design using the Resonant Recognition Model – 2007
    Excerpt: There is evidence that proteins and DNA have certain conducting properties [12]. If so, then charges would be moving through the backbone of the macromolecule and passing through different energy stages caused by the different side groups of various amino acids or nucleotides. This process provides sufficient conditions for the emission of electromagnetic waves.
    http://www.ncbi.nlm.nih.gov/pm.....MC1997124/

    Symphony of Life, Revealed: New Imaging Technique Captures Vibrations of Proteins, Tiny Motions Critical to Human Life – Jan. 16, 2014
    Excerpt: To observe the protein vibrations, Markelz’ team relied on an interesting characteristic of proteins: The fact that they vibrate at the same frequency as the light they absorb.
    This is analogous to the way wine glasses tremble and shatter when a singer hits exactly the right note. Markelz explained: Wine glasses vibrate because they are absorbing the energy of sound waves, and the shape of a glass determines what pitches of sound it can absorb. Similarly, proteins with different structures will absorb and vibrate in response to light of different frequencies.
    So, to study vibrations in lysozyme, Markelz and her colleagues exposed a sample to light of different frequencies and polarizations, and measured the types of light the protein absorbed.
    This technique, , allowed the team to identify which sections of the protein vibrated under normal biological conditions. The researchers were also able to see that the vibrations endured over time, challenging existing assumptions.
    “If you tap on a bell, it rings for some time, and with a sound that is specific to the bell. This is how the proteins behave,” Markelz said. “Many scientists have previously thought a protein is more like a wet sponge than a bell: If you tap on a wet sponge, you don’t get any sustained sound.”
    http://www.sciencedaily.com/re.....084838.htm

    Indeed, this electromagnetic energy in the cell that proteins, (and DNA), are using to communicate with each other in such a precisely controlled way is more than merely a random by-product of metabolic processes, (i.e. ‘classical’ light), but this biophotonic light is, in fact, ‘quantum light’ that is generated ‘purposely’ via some type of quantum process (i.e. similar to how laser light is generated)

    Photocount distribution of photons emitted from three sites of a human body – 2006
    Excerpt: Signals from three representative sites of low, intermediate and high intensities are selected for further analysis. Fluctuations in these signals are measured by the probabilities of detecting different numbers of photons in a bin. The probabilities have non-classical features and are well described by the signal in a quantum squeezed state of photons. Measurements with bins of three sizes yield same values of three parameters of the squeezed state.
    http://www.ncbi.nlm.nih.gov/pubmed/16520060

    The absorbed energy in the Shroud body image formation appears as contributed by discrete values – Giovanni Fazio, Giuseppe Mandaglio – 2008
    Excerpt: This result means that the optical density distribution,, can not be attributed at the absorbed energy described in the framework of the classical physics model. It is, in fact, necessary to hypothesize a absorption by discrete values of the energy where the ‘quantum’ is equal to the one necessary to yellow one fibril.
    http://cab.unime.it/journals/i.....802004/271

  19. 19
    bornagain says:

    Quantum criticality in a wide range of important biomolecules
    Excerpt: “Most of the molecules taking part actively in biochemical processes are tuned exactly to the transition point and are critical conductors,” they say.
    That’s a discovery that is as important as it is unexpected. “These findings suggest an entirely new and universal mechanism of conductance in biology very different from the one used in electrical circuits.”
    The permutations of possible energy levels of biomolecules is huge so the possibility of finding even one that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,,
    “what exactly is the advantage that criticality confers?”
    https://medium.com/the-physics-arxiv-blog/the-origin-of-life-and-the-hidden-role-of-quantum-criticality-ca4707924552

    Biophotons – The Light In Our Cells – Marco Bischof – March 2005
    Excerpt page 2: The Coherence of Biophotons: ,,, Biophotons consist of light with a high degree of order, in other words, biological laser light. Such light is very quiet and shows an extremely stable intensity, without the fluctuations normally observed in light. Because of their stable field strength, its waves can superimpose, and by virtue of this, interference effects become possible that do not occur in ordinary light. Because of the high degree of order, the biological laser light is able to generate and keep order and to transmit information in the organism.
    http://www.international-light.....hotons.pdf

    Finding proteins and DNA of the human body to be communicating via ‘quantum laser light’, (and even emitting ‘quantum laser light’ from the human body), goes a long way towards explaining how it is possible for a billion-trillion protein molecules to cohere as single unified whole, i.e. a ‘form’, for precisely a lifetime and not a moment longer.
    It goes a long way, but does not quite get us home yet as to providing an adequate explanation as to explaining how it is possible for a billion-trillion protein molecules to cohere as single unified whole, i.e. a ‘form’, for precisely a lifetime and not a moment longer.
    Jim Al-Khalili, who is an atheist by the way, comments on famed quantum physicist Erwin Schrödinger’s approach to the ‘billion-trillion’ coherence problem:

    Jim Al-Khalili, at the 2:30 minute mark of the following video states,
    “Biologists, on the other hand have got off lightly in my view. They are very happy with their balls and sticks models of molecules. The balls are the atoms. The sticks are the bonds between the atoms. And when they can’t build them physically in the lab nowadays they have very powerful computers that will simulate a huge molecule.,, It doesn’t really require much in the way of quantum mechanics in the way to explain it.”
    At the 6:52 minute mark of the video, Jim Al-Khalili goes on to state:
    “To paraphrase, (Erwin Schrödinger in his book “What Is Life”), he says at the molecular level living organisms have a certain order. A structure to them that’s very different from the random thermodynamic jostling of atoms and molecules in inanimate matter of the same complexity. In fact, living matter seems to behave in its order and its structure just like inanimate cooled down to near absolute zero. Where quantum effects play a very important role. There is something special about the structure, about the order, inside a living cell. So Schrodinger speculated that maybe quantum mechanics plays a role in life”.
    Jim Al-Khalili – Quantum biology – video
    https://www.youtube.com/watch?v=zOzCkeTPR3Q

    Schrodinger would be very happy to know that his theory that quantum principles govern life at the molecular level has recently been verified. i.e. Quantum coherence, as Shrodinger predicted, was just recently verified in protein molecules:

    Quantum coherent-like state observed in a biological protein for the first time – October 13, 2015
    Excerpt: If you take certain atoms and make them almost as cold as they possibly can be, the atoms will fuse into a collective low-energy quantum state called a Bose-Einstein condensate. In 1968 physicist Herbert Fröhlich predicted that a similar process at a much higher temperature could concentrate all of the vibrational energy in a biological protein into its lowest-frequency vibrational mode. Now scientists in Sweden and Germany have the first experimental evidence of such so-called Fröhlich condensation (in proteins).,,,
    The real-world support for Fröhlich’s theory (for proteins) took so long to obtain because of the technical challenges of the experiment, Katona said.
    http://phys.org/news/2015-10-q.....otein.html

    Classical and Quantum Information Channels in Protein Chain – Dj. Koruga, A. Tomi?, Z. Ratkaj, L. Matija – 2006
    Abstract: Investigation of the properties of peptide plane in protein chain from both classical and quantum approach is presented. We calculated interatomic force constants for peptide plane and hydrogen bonds between peptide planes in protein chain. On the basis of force constants, displacements of each atom in peptide plane, and time of action we found that the value of the peptide plane action is close to the Planck constant. This indicates that peptide plane from the energy viewpoint possesses synergetic classical/quantum properties. Consideration of peptide planes in protein chain from information viewpoint also shows that protein chain possesses classical and quantum properties. So, it appears that protein chain behaves as a triple dual system: (1) structural – amino acids and peptide planes, (2) energy – classical and quantum state, and (3) information – classical and quantum coding. Based on experimental facts of protein chain, we proposed from the structure-energy-information viewpoint its synergetic code system.
    http://www.scientific.net/MSF.518.491

    As well, quantum information is now also found to ‘hold DNA together’:

    Quantum entanglement holds together life’s blueprint – 2010
    Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours. “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford.
    http://neshealthblog.wordpress.....blueprint/

    In fact, the entire DNA molecule can be looked at as quantum information which has classical information embedded within it:

    Classical and Quantum Information in DNA – Elisabeth Rieper – video (Longitudinal Quantum Information along the entire length of DNA discussed at the 19:30 minute mark; at 24:00 minute mark Dr Rieper remarks that practically the whole DNA molecule can be viewed as quantum information with classical information embedded within it)
    https://youtu.be/2nqHOnVTxJE?t=1176

    Moreover, in quantum mechanics, it is information, not matter-energy, that is 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/20.....tally.html

    Will Human Teleportation Ever Be Possible?
    As experiments in relocating particles advance, will we be able to say, “Beam me up, Scotty” one day soon? By Corey S. Powell – Monday, June 16, 2014
    Excerpt: Note a fascinating common thread through all these possibilities. Whether you regard yourself as a pile of atoms, a DNA sequence, a series of sensory inputs or an elaborate computer file, in all of these interpretations you are nothing but a stack of data. According to the principle of unitarity, quantum information is never lost. Put them together, and those two statements lead to a staggering corollary: At the most fundamental level, the laws of physics say you are immortal.
    http://discovermagazine.com/20.....eportation

  20. 20
    bornagain says:

    Besides providing direct empirical falsification of neo-Darwinian claims as to the generation of information from a material basis, the implication of finding ‘non-local’, beyond space and time, and ‘conserved’ quantum information in molecular biology on a massive scale is fairly, and pleasantly, obvious:

    Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff – video
    https://www.youtube.com/watch?v=iIyEjh6ef_8

    The Case for the Soul (Near-Death Experiences) – video (Quantum Entangled consciousness and conservation of quantum information discussed at 9:00 minute mark of the video)
    https://www.youtube.com/watch?v=rlBO0Y9GJhk

    So where does our conserved quantum information, and our quantum biophotons, go upon the death of our temporal/material bodies? Well there are ‘rumors’ of a higher heavenly dimension above this temporal dimension.
    Moreover, in contrast to the multiverse conjectures of atheists, for which we have no empirical evidence, we actually do have very good empirical and observational evidence for a higher ‘eternal’ dimension above this one:

    For instance: Moving away from the face of a clock at the speed of light, and thus ‘freezing’ the hands of the clock at a specific moment in time, happens to be the ‘thought experiment’ that gave Einstein his breakthrough insight into e=mc2.

    Einstein: Einstein’s Miracle Year (Thought Experiment 55 second mark) – video
    http://www.history.com/topics/.....racle-year

    “I’ve just developed a new theory of eternity.”
    Albert Einstein – The Einstein Factor – Reader’s Digest – 2005

    “..the distinction between past, present, and future is only an illusion, however tenacious this illusion may be.”
    – Albert Einstein – March 1955 (of note: he passed away in April of that year)

    “The laws of relativity have changed timeless existence from a theological claim to a physical reality. Light, you see, is outside of time, a fact of nature proven in thousands of experiments at hundreds of universities. I don’t pretend to know how tomorrow can exist simultaneously with today and yesterday. But at the speed of light they actually and rigorously do. Time does not pass.”
    Richard Swenson – More Than Meets The Eye, Chpt. 12

    And we do indeed have observational evidence from Near Death Experiences for this ‘eternal’ dimension of light:

    ‘Earthly time has no meaning in the spirit realm. There is no concept of before or after. Everything – past, present, future – exists simultaneously.’
    – Kimberly Clark Sharp – NDE Experiencer

    ‘There is no way to tell whether minutes, hours or years go by. Existence is the only reality and it is inseparable from the eternal now.’
    – John Star – NDE Experiencer

    It is also very interesting to point out that the ‘light at the end of the tunnel’, reported in many Near Death Experiences(NDEs), is also corroborated by Special Relativity when considering the optical effects for traveling at the speed of light. Please compare the similarity of the optical effect, noted at the 3:22 minute mark of the following video, when the 3-Dimensional world ‘folds and collapses’ into a tunnel shape around the direction of travel as a ‘hypothetical’ observer moves towards the ‘higher dimension’ of the speed of light, with the ‘light at the end of the tunnel’ reported in very many Near Death Experiences: (Of note: This following video was made by two Australian University Physics Professors with a supercomputer.)

    Approaching The Speed Of Light – Optical Effects – video
    https://www.youtube.com/watch?v=JQnHTKZBTI4

    “Very often as they’re moving through the tunnel, there’s a very bright mystical light … not like a light we’re used to in our earthly lives. People call this mystical light, brilliant like a million times a million suns…”
    – Jeffrey Long M.D. – has studied NDE’s extensively

    “I started to move toward the light. The way I moved, the physics, was completely different than it is here on Earth. It was something I had never felt before and never felt since. It was a whole different sensation of motion. I obviously wasn’t walking or skipping or crawling. I was not floating. I was flowing. I was flowing toward the light. I was accelerating and I knew I was accelerating, but then again, I didn’t really feel the acceleration. I just knew I was accelerating toward the light. Again, the physics was different – the physics of motion of time, space, travel. It was completely different in that tunnel, than it is here on Earth. I came out into the light and when I came out into the light, I realized that I was in heaven.”
    Barbara Springer – Near Death Experience – The Tunnel – video
    https://www.youtube.com/watch?v=gv2jLeoAcMI

    “I was in a body, and the only way that I can describe it was a body of energy, or of light. And this body had a form. It had a head, it had arms and it had legs. And it was like it was made out of light. And it was everything that was me. All of my memories, my consciousness, everything.”,,, “And then this vehicle formed itself around me. Vehicle is the only thing, or tube, or something, but it was a mode of transportation that’s for sure! And it formed around me. And there was no one in it with me. I was in it alone. But I knew there were other people ahead of me and behind me. What they were doing I don’t know, but there were people ahead of me and people behind me, but I was alone in my particular conveyance. And I could see out of it. And it went at a tremendously, horrifically, rapid rate of speed. But it wasn’t unpleasant. It was beautiful in fact. I was reclining in this thing, I wasn’t sitting straight up, but I wasn’t lying down either. I was sitting back. And it was just so fast. I can’t even begin to tell you where it went or whatever it was just fast!” –
    Vicki’s NDE – Blind since birth –
    https://www.youtube.com/watch?v=e65KhcCS5-Y

    The following video gives us a small insight as to what it would be like to exist in a higher dimension:

    Dr. Quantum in Flatland – video
    https://www.youtube.com/watch?v=B5yxZ5I-zsE&feature=player_detailpage#t=25
    of note: The preceding video happens to be the lead off video on the outreach page of Dr. Anton Zeilinger’s quantum group in Vienna:
    https://vcq.quantum.at/outreach/multimedia/videos.html

    Verses and Music:

    Psalm 139:13-16
    For you created my inmost being; you knit me together in my mother’s womb. I will give thanks to You, for I am fearfully and wonderfully made; Wonderful are Your works, And my soul knows it very well. My frame was not hidden from You, When I was made in secret, And skillfully wrought in the depths of the earth; Your eyes have seen my unformed substance; And in Your book were all written The days that were ordained for me, When as yet there was not one of them.

    Matthew 16:26
    And what do you benefit if you gain the whole world but lose your own soul? Is anything worth more than your soul?

    Evanescence – My Heart Is Broken
    https://www.youtube.com/watch?v=f1QGnq9jUU0

  21. 21
    kairosfocus says:

    VJT: You may find it useful to add to the post, Yockey’s diagram on the communication-coded system, which is in the set of images for UD. KF

  22. 22
    Mung says:

    So there we have it. A code is a means of translating information from one domain into another – in this case, a chemical domain. That’s a broad, non-trivial definition.

    Pretty good.

    Thank you for reminding me that Meyer’s book is a potential resource, though he could be in large part summarizing from The Eighth Day of Creation

    I’ll need to look up that Jacques Monod quote. Excellent!

    Jacques Monod would later explain, “you absolutely needed a code.

  23. 23
    Mung says:

    bornagain, thanks for the links, as always!

  24. 24
    bornagain says:

    No problem Mung, and thank you for all your insightful input. Always fun to read your concise, and humorous, rebuttals.

    You ought to write a book, “How to completely devastate an atheist in 50 words or less” 🙂

    of related note:

    Perry Marshall – Download 3 Free Chapters of “Evolution 2.0”.
    http://cosmicfingerprints.com/

    Shannon
    http://cosmicfingerprints.com/.....system.jpg

    Yockey
    http://cosmicfingerprints.com/.....orphic.jpg

  25. 25
    Mapou says:

    What is truly amazing about all this is that Francis Crick turned out to be one of the most boneheaded materialists on the planet. In spite of his discovery of the DNA code with Watson, he eventually hooked up with another clueless materialist named Christof Koch on a mission to find the “neural correlates of consciousness.” Koch is the guy who concluded after decades of work that consciousness was just another property of matter, not unlike mass or charge. The cluelessness of materialists is painful to watch.

  26. 26
    Mung says:

    Well, thanks to the post by VJT, you all are going to see some things here before they appear at TSZ. So be sure to thank Dr. Torley.

    A mathematician considers the problem of how genetic information is encoded for transmission from parent to offspring,. by Solomon W. Golomb. 1962.

    Genetic Coding (pdf)

    See also:

    Genetic Codes in the 1950s

  27. 27
    Mung says:

    From the OP:

    Crick realized that if his sequence hypothesis were true, then there must be some similar translation system in the cell – one that determined how sequences written in the four-character alphabet of DNA are converted into sequences that use a twenty-letter amino-acid alphabet.

    Definition. Let the set of symbols comprising a given alphabet be called S = {s1, s2, …sq}. Then we define a code as a mapping of all possible sequences of symbols of S into sequences of symbols of some other alphabet X = {x1, x2, …, xr}. We call S the source alphabet and X the code alphabet.

    – Norman Abramson. Information Theory and Coding. 1963.

  28. 28
    Mapou says:

    I wonder how and where the “non-coding” regulatory sequences are decoded.

  29. 29
    kairosfocus says:

    Mung,

    I like a very familiar diagram on p 10, by Golomb.

    Likewise, here is Webster’s:

    Full Definition of CODE

    3
    a : a system of signals or symbols for communication
    b : a system of symbols (as letters or numbers) used to represent assigned and often secret meanings

    There is no good reason to object to the understanding that the genetic code is machine code, used in NC molecular scale machinery to build proteins.

    And yes, that is inherently linguistic.

    Face it.

    KF

  30. 30
    kairosfocus says:

    Mapou, that is indeed a big set of questions. Starting with how so much string is indexed, unzipped, templated off [mRNA], rezipped, kept from tangling, indexed, regulated in how much of protein X is made, then how the cell’s internal delivery system sends the right protein to the right place at the right time and more. As one who fishes, I can assure one and all that the tangling-twisting issue is not to be underestimated. KF

  31. 31
    Mung says:

    Organic codes
    Barbieri introduced the concept of ”organic codes” as a semiotic framework to explain the sign usage in biological systems. His definition of code requires three propositions to be met: There have to exist (1) two independent molecular worlds that (2) are connected by a system of adapters that realise a (3) relation between elements of the two worlds. Independent molecular worlds, here, are characterised by chemically different molecular species, as for example in the genetic code where DNA is chemically different from the amino acids

    A Formal Model of Molecular Codes with Respect to Chemical Reaction Networks (pdf)

  32. 32
    gpuccio says:

    Mapou:

    Non coding sequences are non coding only in the sense that they are not protein coding genes, IOWs they do not work according to the genetic code. However, they often work according to some other kind of code, implicit in their interactions in complex regulation networks. Those codes are absolutely real, but they do not configure a strictly repetitive semiotic code, like the genetic code, and therefore their recognition and interpretation is more difficult.

  33. 33
    bFast says:

    “DNA fails at he level of abstraction. Whatever “meaning” it conveys cannot be translated into any medium other than chemistry. And not just any abstract chemistry, but the chemistry of this universe.”

    Patently False. The sequence information from DNA is regularly translated to paper using a simple four digit code: CGTA. It has also been “dumped” into computers, taken from the computer rendition to generate a new DNA, then the DNA has been installed into organisms, and works.

    If you say, well, it only works if its in DNA, there is some truth in that. But the machine language for one type of CPU does not work on another type. The code is bound to run in an engine that uses that particular code. Such is the nature of codes. However, as has been mentioned elsewhere, DNA sequences are run through electronic simulators that are fairly effective (and increasing in effectiveness) at simulating the resultant protein shape. Hmmm.

  34. 34
    bFast says:

    If the skeptics need to believe that DNA sequence is not a code then their position is painfully untenable.

  35. 35
    Mung says:

    I call it Code Denialism.

    The fear that Code = Goddidit leading to the foregone conclusion that there can’t be any real codes (other than those that are human generated).

  36. 36
    Mung says:

    If you say, well, it only works if its in DNA, there is some truth in that.

    These same people though probably believe that RNA came before DNA.

  37. 37
    mike1962 says:

    Mung: I call it Code Denialism.

    That one’s a keeper

  38. 38
    bFast says:

    Mung, “I call it Code Denialism. The fear that Code = Goddidit” I like it. However, whenever I see that word “fear”, I think we need a “phobia”. I think it’s codophobia. What do you think?

  39. 39
    Mapou says:

    Code denialism is no different than free will denialism or consciousness denialism or duality denialism. It’s evident that all humans are innately religious (you got to believe in something) whether they like it or not. But there is no need to fear. The correct religion will win in the end.

  40. 40
    Mung says:

    kf, I hadn’t fully read that paper by Golomb (@26) before, but it’s pretty neat. I came across him as a source in the Abramson book I quoted from.

    Mapou, I think code denialism is much more difficult to defend though. That the genetic code is a real code is consensus science, after all. 😉

  41. 41
    Mung says:

    Looking far into the future, I envision a keyboard with the symbols A, C, G, and U. An operator will type out any sequence of his liking, feed it into a “tape-reader” for processing, and out will crawl the newly designed organism.

    😀

  42. 42
    Mung says:

    If codes only come from humans, and thus the existence of a code is indicative of intelligence, then even if the genetic code (and other biological codes) are not real codes, treating them as if they are has advanced the cause of science.

    It would seem that ID is science after all.

  43. 43
    Mapou says:

    It should be, in principle, possible to simulate an entire organism and its development in a sufficiently powerful computer starting from a complete genome. So the claim that the DNA code is only useful in a chemical context is bogus.

    It is only logical to suppose that the original designers had all sorts of powerful virtual simulators to play with.

  44. 44
    Mung says:

    bfast, I think it’s a phobia of the divine foot. Apparently they are afraid of foot kissing. Got a name for that? 😉

  45. 45
    gpuccio says:

    I would invite all to have a look at UB’s new post and to his linked websites. I believe that what he says has a lot of connections with the discussion here.

  46. 46
    Mung says:

    New thread at TSZ with mathematical definitions of what a code is. More confirmation that the genetic code is a real code.

    What A Code Is – Code Denialism Part 3

    Of particular interest, is continuing from the Abramson text cited above from 1963:

    Note 2. One of the most interesting applications of the ideas discussed in Chapter 3 is that of genetic coding (Golomb, 1961, 1962). It has been determined that the vast amount of information necessary to specify the structure of a biological system is contained in the chromosomes of the parent system. More precisely it is the deoxyribonucleic acid (DNA) contained in the chromosomes which transmits the genetic information. In 1953 Crick and Watson showed that DNA existed in the form of a double helix. These helices may be thought of as being connected by sequences of four nucleotides which comprise the genetic message. The nucleotides, usually designated A, C, G, and T (for adenine, cytosine, guanine, and thymine), correspond to the code symbols discussed in Chapter 3. Experimental evidence therefore indicates that nature operates with a four-symbol code alphabet. These code symbols are combined in some manner to represent about twenty amino acids which must be manufactured by the new biological system. The manner in which nucleotides (A, C, G, T) are coded to represent the different amino acids is the primary problem in genetic coding.

  47. 47
    Mung says:

    Over at TSZ they have gone into full meltdown. Now they see codes everywhere.

    Bicodalism: From there are no codes to everything is a code.

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