You're revealing you don't know anything about biochemistry. The genetic code that's been decoded contains specific coded instructions about which amino acid to use in which order to build proteins. The coded information exists in the form of codons, consisting of three adjacent nucleic acid bases. Each combination of three bases, or codon, specifies a particular amino acid. There are also start and stop codons. Strands of RNA are run through a nanomachine called a ribosome just like tape is fed through tape reader. Except that this tape reader reads the instructions and builds a unique protein. There are thousands of unique proteins used in living things and they have up to several thousand amino acids in each. The specific sequence of amino acids is what differentiates one protein from another. That sequence needs to be exact or the protein won't fold property and won't function as its supposed to do. For example, there are 574 amino acids that make up hemoglobin. A mutation that gets only one of these wrong is what causes hemophilia.
The reading of the genetic code isn't merely a chemical reaction like oxidation. There's no reason a particular codon has to designate a particular amino acid. For example, there are some variant codes used in various living things (25 of these identified so far) which read one or more particular codon differently than is "normal". And these variants are scattered around the so-called "tree of life" in clearly unrelated organisms. These variants aren't totally different from the main code, the differences are minor BUT there is no known way how a code could change or evolve without rendering the organism unviable. That any such evolution would have to have happened convergently for some variants is another problem. The odds are insurmountable.
Though the genetic code is complex and organized, it's not JUST complex and organized. It is a true symbolic CODE, like a computer language or Morse code or naval semaphore codes ... or for that matter like human languages.
And btw, there are very likely different codes other than the one we have decoded. The genetic code we've decoded is likely a subdirectory containg recipes on how to build the proteins the living things needs. Other codes would govern when and how the subdirectory is accessed.
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What Bleeping Codes Say About Intelligent Design
by Richard W. Stevens
I first saw Gandalf in 1974. No, not the wizard of The Lord of the Rings. This Gandalf was the colorful box attached to a PDP 11-40 computer, its lights blinking almost rhythmically amid a tangle of wires in the slightly dusty lab office. It had a label in faux Olde English lettering with that whimsical brand name.
What was this device named Gandalf? It was a modem, an electronic machine that translates information from one symbolic form to another. A modem is a device that modulates (encodes) and demodulates (decodes). Modems allow computers to communicate with one another over telephone lines, cable connections, or wireless links.
The 1974 Gandalf modem converted digital data into tones to send over a telephone line, and also converted tone codes coming in via that line back into digital data. If your personal computer or e-phone connects via WiFi, then there are two modems involved to convey data over that connection.
In short, a modem is an encoder–decoder device. With a wink to J. R. R. Tolkien, let's call any device that receives information, encodes it into symbols, and can receive the same kinds of symbols and convert them into information, a Gandalf system. And let's consider this idea: the existence of a Gandalf system gives strong evidence of intelligent design.
"Houston, Captain Midnight Got Here First"
Imagine that astronauts have landed on Mars and discovered there a smooth, concrete-like pyramid, with letters engraved on its surface in two columns. The left-hand column displayed letters from the Roman alphabet, and the right-hand column displayed the corresponding letters from the Greek alphabet.
Surely such a discovery would have electrified the astronauts, and they would immediately report back to earth the exciting news that they had found clear evidence of intelligent life on Mars. And let's say that they also discovered a Captain Midnight (Ovaltine) Secret Decoder Badge, the kind used by American kids in the 1950s. Then the astronauts would report the even more astonishing news that the intrepid Captain Midnight had visited the Red Planet before them.
Either way, whether the astronauts dug up a Roman-Greek letter conversion chart or a secret decoder ring on Mars, their instincts would shout: "Intelligence found!" In fact, if a Gandalf system were discovered there, the whole world would trumpet the proof that intelligent life existed on Mars.
How could finding one Gandalf system command that unshakeable conclusion? The answer seems obvious: no undirected material forces are known that can (1) create a code, and (2) create the corresponding encoder and decoder devices. With all the scientific knowledge we command, we cannot conceive of a purposeless, undirected mechanism that can design a code and assemble the coding devices. Gandalf systems simply do not occur naturally among the non-living, non-intelligent elements of the universe.
Wizards See the Future
If Gandalf systems do not arise from undirected non-living forces, then how do they come to exist? Well, first, in order to make a Gandalf system, you need to know the code. That means, at minimum, you must know:
• The symbols that represent the incoming information;
• The outgoing symbols that correspond to the incoming symbols; and
• The techniques for receiving and sending the symbols (e.g., printed letters, audio sounds, light flashes, radio signals)
Knowing the code means recognizing that one symbol equates to another. For example, if you know Morse code, then you know that "• • •" equates to "S," and "– – –" equates to "O." Thus, if you hear "• • • – – – • • •," then you recognize "SOS," the international distress signal that regrettably did not work out so well for the Titanic.
To decode a coded message, you must know the code in advance. Before you can understand "• • • – – – • • •," you must know the Morse code for the two letters.
Knowledge of the code underlies a Gandalf system's magic: expecting the future. In building a Gandalf system, the designer implicitly expects two realities:
1. That the device will actually receive information to encode; and
2. That some other device somewhere will be waiting to receive the coded message that the Gandalf system sends out.
Every Gandalf system is set up to carry out its functions as soon as certain foreseen events occur. Gandalf #1 stands ready to receive a message in a predefined format from its host computer, and when it does, it will encode the message for transmission to Gandalf #2. When it sends its message, Gandalf #1 uses a particular outgoing code only because its designer foresaw a future reality wherein Gandalf #2 would receive and decode its symbols.
Gandalf Contra Darwin
Dressed as neo-Darwinism, secular humanism, or resurgent atheism, the "scientific" contender in the worldview wars is materialism (aka naturalism). Materialism declares that the entire universe operates by physical laws of energy and matter alone. If intelligence exists at all, it has resulted from a combination of purely impersonal, undirected, purposeless material forces.
Consider the implications of this. If a Thoughtless Thing is impersonal, undirected, and purposeless, then the Thing does not know or even care about future events. Therefore, that Thoughtless Thing cannot and does not plan for future conditions. It does not foresee its own future nor the future or even the existence of any other thing.
Such a Thoughtless Thing cannot and will not create a code, let alone an encoder–decoder device. Why not? Because to encode a message now presumes the belief that the message might be decoded later—in the future. Similarly, to build a decoder device today presumes the belief that a coded message will arrive in the future. Yet a Thoughtless Thing cannot and does not imagine any future event.
No Thoughtless Thing—no impersonal, undirected, purposeless material force—can create a Gandalf system. Neo-Darwinism's mechanisms, undirected mutation and natural selection, are Thoughtless Things. Therefore, neo-Darwinism's mechanisms cannot create a Gandalf system.
No Gandalf, No Cell
The prevailing, science-based worldview says that neo-Darwinian mechanisms produced all life on earth. On earth we notice that animals and plants are composed of cells. Their cells operate with DNA and RNA systems that both encode and decode information about building proteins. Encoder–decoder systems in cells—those are Gandalf systems.
But neo-Darwinian mechanisms cannot be the source of the cells' Gandalf systems because:
1. No known undirected material forces can produce codes with their matching encoder–decoder devices; and
2. Undirected material forces are logically incapable of creating codes and coding devices.
Chemistry and physics lack the tools to create Gandalf systems. As Dr. Hubert Yockey wrote in a 1981 article in the Journal of Theoretical Biology, "Nothing which even vaguely resembles a code exists in the physio-chemical world."
Cells Compare to Computers?
Does this Gandalf system analogy apply to systems other than computers? While this article cannot explore that entire topic, the Modest Physical Church-Turing Thesis, a thesis widely believed by philosophers of science, may be worth mentioning. (What would it be called if it were not so modest?) Gualtiero Piccinini provides a thorough discussion of this thesis in a July 2010 article in the Stanford Encyclopedia of Philosophy (online), but in simplified lay terms, it says that, if you can specify a usable translation process (a function) with a defined set of rules for converting from one set of symbols to another, then you can perform that translation using a Turing machine.
Why is the "Turing machine" important here? Because a Turing machine is defined as an extremely simple computer that itself uses a Gandalf system (encoder–decoder) to operate. That universal model of computing, the Turing machine, requires a Gandalf system.
The Turing machine conceptual model is theoretically capable of modeling any step-by-step physical process or procedure—that is, any algorithm—in the universe. Increasingly, scientists are realizing that biological systems are essentially machines executing algorithms. Executing an algorithm, as with the Turing machine, requires a Gandalf system for encoding and decoding information.
Computer scientist Corrado Priami, in a 2009 article, "Algorithmic Systems Biology," describes the logical connection between biological systems (like the cell) and computer-like functions: "The underlying metaphor is one that (1) represents biological entities as programs being executed simultaneously and that (2) represents the interactions of two entities by the exchange of messages between the programs."
Priami observed "the need for a deeper involvement of computer science in biology and the need of an algorithmic description of life." In making the connection between biology and algorithms, Priami recognizes the necessary encoder–decoder processes involved in both.
In his book Signature in the Cell, Dr. Stephen C. Meyer, a philosopher of science, shows that the "cell's information-processing system" operates using the same key elements of computer-based information processing systems, including mechanisms for digitally storing, encoding, decoding, and executing instructions for operation. In a 2000 article for the journal Computers and Chemistry, Dr. Yockey confirmed: "The genetic code is constructed to confront and solve the problems of communication and recording by the same principles found . . . in modern communication and computer codes."
Nobody would treat the finding of a Gandalf system on Mars as ho-hum. Such a discovery would signal the presence of an intelligent being on that planet who built the encoder–decoder device and specified the codes. Trillions of biological cells on earth, operating as they do with codes and coding devices mimicking computer science equivalents, likewise provide evidence of intelligent design. Now comes the real challenge: finding that designer. •
Sources Consulted
• Stephen C. Meyer, Signature in the Cell: DNA and the Evidence for Intelligent Design, pp. 367–368 (Harper Collins, 2009).
• Gualtiero Piccinini, Computation in Physical Systems, The Stanford Encyclopedia of Philosophy (July 2010), plato.stanford.edu 
• Corrado Priami, "Algorithmic Systems Biology," Communications of the ACM, 52:5, pp. 80–88 (May 2009).
• Hubert P. Yockey, "Origin of Life on Earth and Shannon's Theory of Communication," Computers and Chemistry 24:105–123 (2000).
• Hubert P. Yockey, "Self Organization Origin of Life Scenarios and Information Theory," Journal of Theoretical Biology 91:13–31 (1981).
salvomag.com
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Software: Such Is Life
Evolution News & Views July 17, 2012
"What is life?" That's a question Erwin Schrödinger tried to answer in an influential lecture at Trinity College, Dublin, in 1943. Last week the same question was addressed to pioneering synthetic geneticist Craig Venter (pictured) on the same stage, with the benefit of six decades of progress in genetics since Watson and Crick unveiled the structure of DNA in 1951. Watson was present at the lecture, according to Claire O'Connell, who reported on the event for New Scientist. So, what is life from the perspective of a genetic engineer whose team programmed DNA in a computer in the first attempt to build a synthetic organism? Venter told the packed audience in Dublin that life is DNA-software-driven machinery that operates protein robots. Here's the key passage in the article:
"All living cells that we know of on this planet are 'DNA software'-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions," said Venter. "We are now using computer software to design new DNA software."That's a remarkable statement. It has intelligent design written all through it.
O'Connell describes how Schrödinger realized 69 years ago that a living cell had to carry information. Without knowing the structure of DNA, he envisioned it as an "aperiodic crystal" that could store instructions. She quotes Luke O'Neill, a professor of biochemistry at Trinity and master of ceremonies for the July 12 lecture:
"The gene had to be stable, so it had to be a crystal, and it had to have information so it was aperiodic," he explained.
"Equally important, Schrödinger also discussed the possibility of a genetic code, stating the concept in clear physical terms."
The rest, as they say, is history: DNA did turn out to be aperiodic, stable, and the bearer of a genetic code.
It's serendipitous that the history of molecular genetics parallels the history of software engineering. Just when Schrödinger was pondering how cells might store information in a genetic code, software engineers were figuring out how to program the new computers being invented, first the clunky vacuum-tube monstrosities, followed by devices with increasing power and decreasing size as transistors (1947) and integrated circuits (1958) became available.
Software engineers faced the challenges of informational systems: How can instructions be stored and executed to command robotic devices like input-output machines and printers? How can software respond and adapt robustly to changing environments? How can hardware and software be integrated into systems and networks? Simultaneously but independently, geneticists were learning how the newly discovered DNA code stored instructions and executed them, solving the very same challenges. The timing of these discoveries was as uncanny as the similarities between them.
In Signature in the Cell (2009), Stephen Meyer used software as a simile for genetic information, quoting Microsoft founder Bill Gates: "DNA is like a computer program but far, far more advanced than any software ever created" (p. 12).
Venter's lecture essentially brings the parallel tracks together. DNA is not just likesoftware, he said: that's what it is. To prove the point, he added, "We are now using computer software to design new DNA software."
O'Connell continues,
The digital and biological worlds are becoming interchangeable, he added, describing how scientists now simply send each other the information to make DIY biological material rather than sending the material itself.Today's answer to "What is life?" therefore, is: it's software. That's a very ID-friendly idea, for numerous reasons:
Our uniform experience with software is that it is intelligently designed.
Software runs on machines, and machines are intelligently designed.
Software operates other machines (e.g., robots) that are also intelligently designed.
Systems of interconnected software and hardware are irreducibly complex.
Functional systems imply purposefully planned architecture of the whole.
Software is comprised of information, which is immaterial.
Information is independent of the storage medium bearing it (e.g., electrons, magnets, silicon chips, molecules of DNA).
Meaningful information is aperiodic; so is DNA.
As a form of information, DNA software is complex and specified.
Epigenetics regulates genetics just as computer software can regulate other software.
Software can improve over time, but only by intelligent design, not by random mutation.
Software can contain bugs and still be intelligently designed.
O'Connell told a humorous story that illustrates that last point. When Venter's team programmed their synthetic organism by running their computer-generated "DNA software" through a bacterium's "hardware," it was buggy. They had inserted some text as a watermark, including a quote by late physicist Richard Feynman -- but got it wrong. They had to go back later on and fix it.
No one sensible would claim that a mistake in the software by Venter's team counts as evidence against its being the product of intelligent design, nor should anyone look to dysteleology in life as a disproof of design. Intelligent design theory makes no claims regarding the quality of the design reflected in any phenomenon. It only points to the presence of design.
One might, of course, raise legitimate questions about the wisdom of tinkering with living software. ID theory leaves such questions in the capable hands of ethicists, philosophers, theologians, policy wonks and voters.
Nevertheless, viewing life as software represents a fundamental paradigm shift with profound implications. It's no longer a Paley-like design argument from analogy, as Stephen Meyer explained in Signature in the Cell (p. 386): it's an inference to the best explanation based on stronger premises.
The argument does not depend upon the similarity of DNA to a computer program or human language, but upon the presence of an identical feature in both DNA and intelligently designed codes, languages, and artifacts. Because we know intelligent agents can (and do) produce complex and functionally specified sequences of symbols and arrangements of matter, intelligent agency qualifies as an adequate causal explanation for the origin of this effect. Since, in addition, materialistic theories have proven universally inadequate for explaining the origin of such information, intelligent design now stands as the only entity with the causal power known to produce this feature of living systems. Therefore, the presence of this feature in living systems points to intelligent design as the best explanation of it, whether such systems resemble human artifacts in other ways or not.We might even say now, using Venter's description, that ID is not just an inference but a logical deduction. Life and software don't only contain an identical feature, but constitute an identity. They are one and the same.
evolutionnews.org
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On the splicing code:
You Won’t Believe This One: Gene Splicing Stuns and Bewilders Evolutionists
Proteins perform a wide variety of tasks in the cell and when a particular job needs to be done the right protein is quickly synthesized by unwinding the right DNA gene, making a copy, editing the transcript, and translating the transcript, according to the DNA code, into a sequence of amino acids. Evolutionists had no explanation for this incredible and profound molecular manufacturing system (which still out performs anything scientists can come up with), but they remained steadfast. Indeed they argued all of this provided yet more proofs for evolution. Why? Because the DNA code was essentially universal. As one evolutionist explained, while the genetic code is preserved across species, it would not be if the species had been created independently. [1] If that’s true then the genetic code must have somehow evolved. Is that true? It’s difficult to say because that is, as usual, a non scientific claim. But aside from the metaphysics and the unexplained molecular manufacturing system, there is another problem with this story. It has now turned out to demolish evolutionary theory and has left evolutionists staring into the headlights.
Years after the universal DNA code was discovered, several other codes were also discovered which were not only astonishingly complex, but they were not universal. One such code is the so-called splicing code.
In higher organisms many of the genes are broken up into expressed regions, or exons, which are separated by intervening regions, or introns. After the gene is copied the transcript is edited, splicing out the introns and glueing together the exons. Not only is it a fantastically complex process, it also adds tremendous versatility to how genes are used. A given gene may be spliced into alternate sets of exons, resulting in different protein machines. There are three genes, for example, that generate over 3,000 different spliced products to help control the neuron designs of the brain.
And how does the splicing machinery know where to cut and paste? There is an elaborate code that the splicing machinery uses to decide how to do its splicing. This splicing code is extremely complicated, using not only sequence patterns in the DNA transcript, but also the shape of transcript, as well as other factors.
[ It's been known for a long time gene expression is controlled by another code (in addition to the known protein-assembly code). Glad to see this is being recognized. ]
What is also complex about the new code is that it is context-dependent. In fact it even varies in different tissue types within a species. And studies of RNA binding proteins show even more complexity. These proteins are part of the molecular splicing machinery and they often regulate each other leading to an “unprecedented degree of complexity and compensatory relationships.” As one researcher explained:
We identified thousands of binding sites and altered splicing events for these hnRNP proteins and discovered that, surprisingly these proteins bind and regulate each other and a whole network of other RNA binding proteins.
Regulate each other and a whole network of other RNA binding proteins? Needless to say there is no scientific explanation for how this marvel could have evolved. And since this code is not universal but, quite the opposite, highly varying even between tissues, we can safely conclude the “universal code” prediction of evolution is falsified.
If evolution is true then we expect codes to be universal. [ I think that was always a false premise. If genetic codes could spontaneously generate, that would have happened a vast number of times and some of the surviving life forms would have very different protein-assembly codes. ] Here we have an obvious example of a code that most definitely is not universal, so the prediction is false. And if a prediction is false, then either the theory is false, or it must be modified. But with so many falsifications, and so many modifications that make no sense on evolution, it is obvious that something is very wrong with the theory. In this case we would have to say that random mutations just happened to create many different splicing codes, over and over, of unimaginable complexity.
1. Mark Ridley, Evolution. (Boston: Blackwell Scientific Publications, 1993) 49.
darwins-god.blogspot.com
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Lino D'Ischia June 23, 2012 12:33 PM
Oleg:
Nice story, but this is "apples" to evolution's "oranges."
As you state:
Einstein's relativity peacefully coexists with Newtonian mechanics. Wave theory of light agrees with geometrical optics in the appropriate limit, where both apply.
In the "limit" they are equivalent. And both Newtonian gravity, and Einstein-ian gravity, bring about correct results. You use one, or the other, given your needs. (Didn't Feynman calculate that the difference between the gravitational potential on the surface of the Sun using GR was different from Newtonian calculations by a factor of something like 1 in 10^12?)
The situation with NS is very different. It's predictions are almost nil; and most of Darwin's predictions have turned out to be wrong. Darwinism HAD to be joined to Mendelian genetics, and it was done only in a vague sort of way [R.A. Fisher, the Godfather of neo-Darwinism, used a formula (the genetical theory of evolution) which is used in statistical mechanics---so vague is it.]. And the Neutral Theory originated because of the complete failure of neo-Darwinism to explain the extremely high levels of polymorphism found in living beings (another "prediction"---this time of "neo"-Darwinism---that was wrong).
And, per the originator of Neutral Theory, Kimura, there are severe limitations to what Neutral Theory can do.
So, where does that leave us? Well, at the The Edge of Evolution! That is, NS does indeed have some applicability (Here's a prediction: in fifteen years, even the little that NS is supposed to be able to do will be shown to rely on other in vivo processes); but, it is indeed only at the 'edges', and very limited indeed.
When this limited mechanism encounters the type of problem-to-be-solved that CH is describing, no amount of NS/Neutral Theory, or whatever nonsense you want to throw at the problem, is going to even come remotely close to explaining its origins.
As CH points out, it's time to leave Darwinism on the dustbin of history, and to move on to something that makes sense: intelligent design.
BTW, Dr. Cornelius, here's a rejoinder to the argument made about the "universal" code: there are all kinds of computers, with all kind of different capabilities, running all sorts of different and very complex software programs, and they all are built on the x86 architecture. Does this prove that they evolved from one another? IOW, what limits a Designer from using the same design over and over, while building more powerful machines and software programs.
bornagain77 June 23, 2012 3:39 PM
Oleq , you mention many branches of science that have been modified as new evidence has come along. The trouble with your analogy is that at least those nascent theories had a mathematical foundation that comported somewhat roughly to reality to start off with. Darwinism never has had any such mathematical foundation;
Nobel Prize-Winning Physicist Wolfgang Pauli on the Empirical Problems with Neo-Darwinism - Casey Luskin - February 27, 2012
Excerpt: "In discussions with biologists I met large difficulties when they apply the concept of 'natural selection' in a rather wide field, without being able to estimate the probability of the occurrence in a empirically given time of just those events, which have been important for the biological evolution. Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely 'scientific' and 'rational,' they become actually very irrational, particularly because they use the word 'chance', not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word 'miracle.'" Wolfgang Pauli (pp. 27-28) -
evolutionnews.org
Murray Eden, as reported in “Heresy in the Halls of Biology: Mathematicians Question Darwinism,” Scientific Research, November 1967, p. 64.
“It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.” Murray Eden, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory,” Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, editors Paul S. Moorhead and Martin M. Kaplan, June 1967, p. 109.
creationscience.com
Michael Behe on the theory of constructive neutral evolution - February 2012
Excerpt: I don’t mean to be unkind, but I think that the idea seems reasonable only to the extent that it is vague and undeveloped; when examined critically it quickly loses plausibility. The first thing to note about the paper is that it contains absolutely no calculations to support the feasibility of the model. This is inexcusable. - Michael Behe
uncommondescent.com
Oxford University Admits Darwinism's Shaky Math Foundation - May 2011
Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. - On a 2011 Job Description for a Mathematician, at Oxford, to 'fix' the persistent mathematical problems with neo-Darwinism within two years.
evolutionnews.org
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John June 23, 2012 12:35 PM
I remember when they reverse engineered a good part of the splicing code (last year sometime wasn't it?) It would be really cool to see how the entire spliceosome moves and makes "decisions". The interesting thing is that this is a higher level code - ie. it's like C++ built upon the ASM code of DNA transcripts while the language suite itself is also built from ASM. What this means for evolution is that it somehow has to mutate the ASM level code which then has to be stable long enough to give the C++ code on top of it enough chance to evolve anything at all.
At what point can it be considered intelligently programmed? Or as they said, "When Messiah comes, will he do more miracles than these?"
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M. Holcumbrink June 23, 2012 9:28 PM
John, I think of that passage quite often, whenever the detractors of ID play the black knight. These people would ascribe intelligence to a single rune scrawled on a cave wall, but when we discover algorithmically compressed machine code regulating sophisticated compound machinery at the root of biological life, they chalk that up to a cosmic fart. So my thought becomes “you say life is not designed, but if it had been designed, would it be even more algorithmic, fully integrated, optimized and fantastic than this?”
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Claudiu Bandea June 24, 2012 5:57 AM
Elizabeth Liddle: And evolutionary theory, as you well know, Cornelius, is a scientific theory. So I ask you again: what is wrong with the theory of evolution as a explanation of "how this marvel could have evolved"?
True scientists should not just say that ‘evolution did it’, but they should present plausible models on 'how evolution did it'.
To my knowledge, no such models have been advanced by the current science establishment. Even worse, apparently, this issue has not been even been seriously raised, so we should thank Cornelius for raising it!
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