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A Dog is a Chien is a Perro is a Hund

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File:RNA-codons.png

Photo courtesy of Wikipedia

In his “UB Sets It Out Step-By-Step” UprightBiped argued that the transfer of recorded information in the genome is like any other form of recorded information – i.e., it is an arbitrary relationship instantiated in matter.

After several months and over 1,400 combox comments, UB’s argument has withstood a barrage of attacks from our materialist friends.  This post is a response to one such attack.

UB’s opponents argue they cannot understand what he means by “arbitrary” in his argument.  Of course, UB has good responses to this objection, and I invite you to read them in the combox.  But as I was thinking about the matter this morning, it occurred to me that there is a very simple definition of “arbitrary” that, I think, makes the matter so clear that only the willfully obtuse could deny it.  Here it is:  An arrangement of signs is arbitrary when the identical purpose could be accomplished through a different arrangement of signs if the rules of the semiotic code were different.  [“Semiotics” is the study of how signs are used to represent things, such as how a word in a language represents a particular object.]

Here’s an example of an arbitrary arrangement of signs:  DOG.  This is the arrangement of signs English speakers use when they intend to represent Canis lupus familiaris. In precise semiotic parlance, the word “dog” is a “conventional sign” for Canis lupus familiaris among English speakers.  Here, “conventional” is used in the sense of a “convention” or an agreement.  In other words, English speakers in a sense “agree” that “dog” means Canis lupus familiaris.

Now, the point is that there is nothing inherent in a dog that requires it to be represented in the English language with the letters “D” followed by “O” followed by “G.”  If the rules of the semiotic code (i.e., the English language) were different, the identical purpose could be accomplished through a different arrangement of signs.  We know this because in other codes the same purpose is accomplished with vastly different signs.  In French the purpose is accomplished with the following arrangement of signs:  C H I E N.  In Spanish the purpose is accomplished with the following arrangement of signs:  P E R R O.  In German the purpose is accomplished with the following arrangement of signs:  H U N D.

In each of the semiotic codes the purpose of signifying an animal of the species Canis lupus familiaris is accomplished through an arbitrary set of signs.  If the rules of the code were different, a different set of signs would accomplish the identical purpose.  For example, if, for whatever reason, English speakers were collectively to agree that Canis lupus familiaris should be represented by “B L I M P,” then “blimp” would accomplish the purpose of representing Canis lupus familiaris just as well as “dog.”

How does this apply to the DNA code?  The arrangement of signs constituting a particular instruction in the DNA code is arbitrary in the same way that the arrangement of signs for representing Canis lupus familiaris is arbitrary.  For example, suppose in a particular strand of DNA the arrangement “AGC” means “add amino acid X.”  There is nothing about amino acid X that requires the instruction “add amino acid  X” to be represented by  “AGC.”  If the rules of the code were different the same purpose (i.e, instructing the cell to “add amino acid  X”) could be accomplished using “UAG” or any other combination.  Thus, the sign AGC is “arbitrary” in the sense UB was using the word.

Why is all of this important to ID?  It is important because it shows that the DNA code is not analogous to a semiotic code.  It is isometric with a semiotic code.  In other words, the digital code embedded in DNA is not “like” a semiotic code, it “is” a semiotic code.  This in turn is important because there is only one known source for a semiotic code:  intelligent agency.  Therefore, the presence of a semiotic code embedded within the cells of every living thing is powerful evidence of design, and the burden is on those who would deny design to demonstrate how a semiotic code could be developed though blind chance or mechanical law or both.

Comments
BA77:
Mr. Fox, claims...
Wrong! Mr Fox asked you to support your assertion that Mr Fox denies that design happens in living organisms. Please produce the evidence or withdraw the assertion. It's the honest thing to do one or the other.Alan Fox
February 14, 2013
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StephenB
In this context, I define “information” as the substance of the message communicated to the cell that tells it what role it is to play and how to carry it out. I define “instruction” as the relevant set of directions. Do we agree that those two elements reside in the DNA molecule? If we do not agree on the use of the words “information” and “instruction,” what words would you use?
I'm no expert, so this is idle speculation, but I don't think that a distinction between "information" and "instructions" is necessary or accurate with regard to the process that results in adult organism from zygote. However I can agree that the information necessary for development of the organism must reside in the genes and the cytoplasm of the oocyte (mitochondria, for example). Although I should add that some external influences (maternal control being a major example) occur. Sex determination in some reptiles (turtles and crocodiles is controlled by temperature for instance.
You mean the zygote does not unfold according to a pre-existent plan? If no plan orders its development and outcome, what does? If no plan determines its traits and features, what does? We understand that chemical and physical processes are involved, but what, if not a plan, determines the way in which they are ordered. You can’t say that the chemical and physical elements are the cause of the form they take–they are the thing being formed.
I was being literal. Development proceeds by cell division and differentiation. A lot of this depends on cascades of gene switches that control how sheets of cells fold and turn into specific cell types. I am sure you have heard of Hox genes. The instructions for growing a human being are not read off a blueprint. It is a dynamic process and a rapidly expanding field of knowledge generally referred to as evo-devo. But, essentially, it is all chemistry!
Why would you expect to “find” a plan? The plan is a conception that shapes the reality of an ordered outcome. We infer the conception from the outcome. I realize that you don’t accept that proposition, but the point is that an ordering principle is, by definition, an abstract concept. It has no physical parts. There is nothing there to find. We can only know it exists by observing its effects.
I can't recall that I ever expected that genetic material would contain a plan and I don't think that now. I used to think that penetrating the mysteries of how DNA sequences that only represented RNA and amino-acid sequences (there are no nonsense codes, any possible triplet codes for an amino-acid or "stop") could notwithstanding cause an organism to develop as necessary would be impossible but progress has been astonishing.
What is inexcusable, as it wastes everyone’s time and marks some as dishonest, is to continue to equivocate over meanings when a misunderstanding over use of words occurs.
I agree and I share your frustration when people do that.
Thanks and I appreciate that. I like to argue but abhor violence! ;)Alan Fox
February 14, 2013
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Joe and BA77 your recent comments are noted.Alan Fox
February 14, 2013
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@ ciphertext I am unsure whether you are highlighting or falling into the trap of anthropomorphism in your comment 235. All the issues you raise fade away if people explain what they mean when asked.Alan Fox
February 14, 2013
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RSCO/I is an integral part of the challenge presented to your arguments/worldview
Rubbish, William. It's the invention of one commenter here.Alan Fox
February 14, 2013
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StephenB
Alan Fox, I realize that you are trying to play chess with several people at once, so I will economize my points as best I can.
Appreciated, Stephen. I seem to have defaulted into the rôle of resident token ID sceptic for which I am not at all well qualified but there is a tide in the affairs of men which taken at the flood... Detailed response in preparation...Alan Fox
February 14, 2013
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Moreover,, More from Ann Gauger on why humans didn’t happen the way Darwin said - July 2012 Excerpt: Each of these new features probably required multiple mutations. Getting a feature that requires six neutral mutations is the limit of what bacteria can produce. For primates (e.g., monkeys, apes and humans) the limit is much more severe. Because of much smaller effective population sizes (an estimated ten thousand for humans instead of a billion for bacteria) and longer generation times (fifteen to twenty years per generation for humans vs. a thousand generations per year for bacteria), it would take a very long time for even a single beneficial mutation to appear and become fixed in a human population. You don’t have to take my word for it. In 2007, Durrett and Schmidt estimated in the journal Genetics that for a single mutation to occur in a nucleotide-binding site and be fixed in a primate lineage would require a waiting time of six million years. The same authors later estimated it would take 216 million years for the binding site to acquire two mutations, if the first mutation was neutral in its effect. Facing Facts But six million years is the entire time allotted for the transition from our last common ancestor with chimps to us according to the standard evolutionary timescale. Two hundred and sixteen million years takes us back to the Triassic, when the very first mammals appeared. One or two mutations simply aren’t sufficient to produce the necessary changes— sixteen anatomical features—in the time available. At most, a new binding site might affect the regulation of one or two genes. https://uncommondescent.com/intelligent-design/more-from-ann-gauger-on-why-humans-didnt-happen-the-way-darwin-said/ If that wasn't bad enough,, Haldane's Dilemma Excerpt: Haldane was the first to recognize there was a cost to selection which limited what it realistically could be expected to do. He did not fully realize that his thinking would create major problems for evolutionary theory. He calculated that in man it would take 6 million years to fix just 1,000 mutations (assuming 20 years per generation).,,, Man and chimp differ by at least 150 million nucleotides representing at least 40 million hypothetical mutations (Britten, 2002). So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (40 million divided by 2), yet natural selection could only have selected for 1,000 of those. All the rest would have had to been fixed by random drift - creating millions of nearly-neutral deleterious mutations. This would not just have made us inferior to our chimp-like ancestors - it surely would have killed us. Since Haldane's dilemma there have been a number of efforts to sweep the problem under the rug, but the problem is still exactly the same. ReMine (1993, 2005) has extensively reviewed the problem, and has analyzed it using an entirely different mathematical formulation - but has obtained identical results. John Sanford PhD. - "Genetic Entropy and The Mystery of the Genome" - pg. 159-160 Kimura's Quandary Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in responce to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most 'evolution' must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom's (neo-Darwinism's) very validity. John Sanford PhD. - "Genetic Entropy and The Mystery of the Genome" - pg. 161 - 162 A graph featuring 'Kimura's Distribution' is shown in the following video: Evolution Vs Genetic Entropy - Andy McIntosh - video http://www.metacafe.com/watch/4028086 The Frailty of the Darwinian Hypothesis "The net effect of genetic drift in such (vertebrate) populations is “to encourage the fixation of mildly deleterious mutations and discourage the promotion of beneficial mutations,” http://www.evolutionnews.org/2009/07/the_frailty_of_the_darwinian_h.html Thou Shalt Not Put Evolutionary Theory to a Test - Douglas Axe - July 18, 2012 Excerpt: "For example, McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time (i.e. the mutations cannot be 'neutral'). Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (>100 million years). My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that did the trick, but rather a list of mutations that can do it. Otherwise they're in the position of insisting that something is a scientific fact without having the faintest idea how it even could be." Doug Axe PhD. http://www.evolutionnews.org/2012/07/thou_shalt_not062351.htmlbornagain77
February 14, 2013
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Inconsistent Nature: The Enigma of Life's Stupendous Prodigality - James Le Fanu - September 2011 Excerpt: Many species that might seem exceptionally well adapted for "the survival of the fittest" are surprisingly uncommon. The scarce African hunting dog has the highest kill rate of any predator on the savannah, while cheetahs may have no difficulty in feeding themselves thanks to their astonishing speediness -- but are a hundred times less common than lions. http://www.evolutionnews.org/2011/09/inconsistent_nature051281.htmlbornagain77
February 14, 2013
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Alan Fox:
That’s what natural selection is – a process of design by the environment.
So you keep sayin' yet never can support.
Now by “environment” I mean all the various effects that environment, including but not exclusively, weather, climate, catastrophe, prey, predators, parasites, etc. that contribute to differential survival.
Except differential survival doesn't design anything. It relies on existing designs. You lose, again.Joe
February 14, 2013
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Mr. Fox, claims "where have I denied that design happens in living organisms? That’s what natural selection is – a process of design by the environment. Now by “environment” I mean all the various effects that environment, including but not exclusively, weather, climate, catastrophe, prey, predators, parasites, etc. that contribute to differential survival." Yet, Mr. Fox is severely deluded in what he imagines his proposed 'designer substitute' of Natural Selection can actually do: Darwin proven wrong, again! Experimental Evolution Reveals Resistance to Change (Fruit Flies) Excerpt: Our work provides a new perspective on the genetic basis of adaptation. Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. https://uncommondescent.com/intelligent-design/darwin-proven-wrong-again-experimental-evolution-reveals-resistance-to-change/ At Why Evolution Is True, the Chewbacca Defense – David Klinghoffer – December 13, 2012 Excerpt: “There is no compelling empirical or theoretical evidence that complexity, modularity, redundancy or other features of genetic pathways are promoted by natural selection….Mmany aspects of complexity at the genomic, molecular and cellular levels in multicellular species are likely to owe their origins to these non-adaptive forces, representing little more than passive outcomes.” (Lynch, “The evolution of genetic networks by non-adaptive processes,” Nature Rev. Gen., 8:803-13, (October, 2007)) So if the “complexity, modularity, redundancy or other features of genetic pathways” and “many aspects of complexity at the genomic, molecular and cellular levels in multicellular species” aren’t easily explained by natural selection, that’s a lot. http://www.evolutionnews.org/2012/12/at_why_evolutio_5067451.html Evidence for Creation now banned from UK religious education classes - July 2012 Excerpt: (In 2008) Professor Massimo Piattelli-Palmarini spoke for a number (of top university academics) in stating simply that natural selection ‘is not the way new species and new classes and new phyla originated.’ http://creation.com/creation-religious-education Darwin’s Legacy – Donald R. Prothero – February 2012 Excerpt: In four of the biggest climatic-vegetational events of the last 50 million years, the mammals and birds show no noticeable change in response to changing climates. No matter how many presentations I give where I show these data, no one (including myself) has a good explanation yet for such widespread stasis despite the obvious selective pressures of changing climate. http://www.skeptic.com/eskeptic/12-02-15/#feature “Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection.,,, The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection.” Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79 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. http://www.evolutionnews.org/2011/05/oxford_university_admits_darwi046351.html Are We Reaching a Consensus that Evolution is Past its Prime? By Doug Axe - October 2012 Excerpt: By this classically Darwinian view (of natural selection), all that was needed for our ape ancestors to evolve the intellectual capabilities that distinguish us so dramatically from apes was the right “conditions of life.” It follows that any ape population of today, if placed in those conditions, should evolve in the same way—not becoming human per se, but rather human-like in every respect that we benefit from being un-ape-like. And similarly, all it should take for one member of a protein family to transition to a new function is the right selective environment. As old-fashioned as this classical view sounds in a day when very few biologists are proudly waving the flag of natural selection, it did at least have its place in the time-honored scientific tradition of making claims that can be tested today. So, to Moran I say, regale us with heroic stories of magically evolvable apes and magically evolvable enzymes if you must, but when you’re finished with the stories, be sure to join us in doing the science that should convince everyone one way or the other as to their plausibility. It’s the same challenge I put to James Shapiro at the beginning of the year:,,, http://www.biologicinstitute.org/post/34190339725/are-we-reaching-a-consensus-that-evolution-is-past-its This following study is very interesting for the researcher surveyed 130 DNA-based evolutionary trees to see if the results matched what 'natural selection' predicted for speciation and found: Accidental origins: Where species come from - March 2010 Excerpt: If speciation results from natural selection via many small changes, you would expect the branch lengths to fit a bell-shaped curve.,,, Instead, Pagel's team found that in 78 per cent of the trees, the best fit for the branch length distribution was another familiar curve, known as the exponential distribution. Like the bell curve, the exponential has a straightforward explanation - but it is a disquieting one for evolutionary biologists. The exponential is the pattern you get when you are waiting for some single, infrequent event to happen.,,,To Pagel, the implications for speciation are clear: "It isn't the accumulation of events that causes a speciation, it's single, rare events falling out of the sky, so to speak." http://www.newscientist.com/article/mg20527511.400-accidental-origins-where-species-come-from.html?page=2 Did Natural Selection Construct Metazoan Developmental Sequences? - Paul Nelson - July 2011 The necessary and sufficient conditions of the process of natural selection (Endler, Natural Selection in the Wild, 1986) are (1) variation, (2) selection or fitness differences, and (3) inheritance. These conditions impose evidential demands on any investigator who wishes to employ natural selection in evolutionary (i.e., historical) explanation. Data from model systems (e.g., C. elegans, Drosophila, and Danio), as well as theoretical analyses, raise challenges for the use of natural selection as the causal process responsible for the origin of developmental sequences. In particular, the conditions of (2) selection differences and (3) inheritance have not been adequately described in current theories of the evolution of the Metazoa. http://www.evolutionnews.org/2011/07/paul_nelson_jonathan_wells_tak048301.html Lynn Margulis Criticizes Neo-Darwinism in Discover Magazine (Updated) Casey Luskin April 12, 2011 Excerpt: This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn't create....[N]eo-Darwinists say that new species emerge when mutations occur and modify and organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change-led to new species. I believed it until I looked for evidence. http://www.evolutionnews.org/2011/04/lynn_margulis_criticizes_neo-d045691.htmlbornagain77
February 14, 2013
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Alan Fox:
How many times do you get told that science advances by the testing of competing hypotheses?
And we are still waiting for your position to produce a testable hypothesis.
Had I a position and you were able to shred it by wielding your mighty intellect, it would not improve the strength of any alternative hypothesis.
Perhaps not. But in this case SCIENCE mandates that we eliminate necessity and chance before even considering design. So it is part of the process.
ID proponents need to start advancing testable hypotheses of their own if they want to be taken seriously.
We have. You just don't know what a testable hypothesis is as your position can't muster one. Alan Fox:
However, when someone proposes a new idea like, say, complex specified information, the onus is on the proposer to make it clear what he means by the phrase.
We have. That you choose to be obtuse is not our problem.Joe
February 14, 2013
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as to: " if one could simulate the simplest single cell lifeform of an adequately sized population," To Model the Simplest Microbe in the World, You Need 128 Computers - July 2012 Excerpt: Mycoplasma genitalium has one of the smallest genomes of any free-living organism in the world, clocking in at a mere 525 genes. That's a fraction of the size of even another bacterium like E. coli, which has 4,288 genes.,,, The bioengineers, led by Stanford's Markus Covert, succeeded in modeling the bacterium, and published their work last week in the journal Cell. What's fascinating is how much horsepower they needed to partially simulate this simple organism. It took a cluster of 128 computers running for 9 to 10 hours to actually generate the data on the 25 categories of molecules that are involved in the cell's lifecycle processes.,,, ,,the depth and breadth of cellular complexity has turned out to be nearly unbelievable, and difficult to manage, even given Moore's Law. The M. genitalium model required 28 subsystems to be individually modeled and integrated, and many critics of the work have been complaining on Twitter that's only a fraction of what will eventually be required to consider the simulation realistic.,,, http://www.theatlantic.com/technology/archive/2012/07/to-model-the-simplest-microbe-in-the-world-you-need-128-computers/260198/bornagain77
February 14, 2013
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Alan Fox, I realize that you are trying to play chess with several people at once, so I will economize my points as best I can. [“Do we agree that the “instructions” providing the necessary “information” for the organism’s development reside in the cell’s nucleus as a DNA molecule? If the words “instruction” and “information” are too strong (too anthropomorphic) to express that relationship, what words would you use?”]’
I think you should be able to work out what my answer is here. Years ago there was a BBC radio program called “The Brains Trust” where a panel of experts answered question from the audience. One panel member, Professor C. M. Joad, was noted for often prefacing his answers with “It all depends what you mean by [some key word in the question]“. So, in any discussion where the intent is to communicate effectively and honestly, first define your terms.
In this context, I define “information” as the substance of the message communicated to the cell that tells it what role it is to play and how to carry it out. I define “instruction” as the relevant set of directions. Do we agree that those two elements reside in the DNA molecule? If we do not agree on the use of the words “information” and “instruction,” what words would you use? [“Do we agree that a DNA molecule “encodes” a detailed set of plans for building different parts of the cell. If “encode” is too strong (human-like) of a verb, what verb would you use?”]
Most assuredly, not! Talking of “building plans” is a total misunderstanding in what goes on when a zygote develops into an adult organism (though there is no reason to limit this to sexually reproducing eukaryotes).
You mean the zygote does not unfold according to a pre-existent plan? If no plan orders its development and outcome, what does? If no plan determines its traits and features, what does? We understand that chemical and physical processes are involved, but what, if not a plan, determines the way in which they are ordered. You can’t say that the chemical and physical elements are the cause of the form they take--they are the thing being formed.
There is nowhere in the genetic material where anything resembling an overall plan can be found.
Why would you expect to “find” a plan? The plan is a conception that shapes the reality of an ordered outcome. We infer the conception from the outcome. I realize that you don’t accept that proposition, but the point is that an ordering principle is, by definition, an abstract concept. It has no physical parts. There is nothing there to find. We can only know it exists by observing its effects.
What is inexcusable, as it wastes everyone’s time and marks some as dishonest, is to continue to equivocate over meanings when a misunderstanding over use of words occurs.
I agree and I share your frustration when people do that.StephenB
February 14, 2013
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It seems to me, from reading through the postings, that each "camp" (for lack of a better term) has "staked out" their positions based upon perceived strategies associated with the use of the english lexicon. The one camp sees a strategy to the use of "code" as indicative of an external intelligence to the system. The other camp sees a strategy to downplay the use of "code" to something more benign, like simply an"abbreviation" or "shortcut" for a more complex process. I know, that is a huge over-simplification of the "camps'" respective positions, but that is how I (an interested onlooker, sometimes participator to a degree) have come to understand the arguments. I also understand that depending on the camp, there are particular merits/demerits to each use of the various words. Here is the Merriam-Websters definitions of "genetic code" and "code" respectively. <a href="http://www.merriam-webster.com/dictionary/genetic+code?show=0&t=1360861037"genetic code: the biochemical basis of heredity consisting of codons in DNA and RNA that determine the specific amino acid sequence in proteins and appear to be uniform for nearly all known forms of life code: a system of signals or symbols for communication (there are several definitions, here I am using #3a.) In studying the history of the genetic code, what is useful to remember (at least for me) is that most likely the operational definition that I list for "code" was the one being used during the time during which the relevant research was being conducted. This is because the definition of "genetic code" as we have it defined, didn't exist prior to its (the genetic code) discovery and subsequent refinement. So at the very least, the "code" in "genetic code" owes its existence to the definition which "includes a system of signals or symbols for communication". Now, we should probably also include definitions for the term communication. That, also, seems to be a loaded term with respect to the various "camps". Here are three definitions (four technically), all from Merriam Websters, which are most likely the ones being used by the different camps. It should be obvious which ones based upon the idea being proposed by each camp. communication: 1) an act or instance of transmitting 2a) information transmitted or conveyed 2b) a verbal or written message 3) a process by which information is exchanged between individuals through a common system of symbols, signs, or behavior ; also : exchange of information What I find curious, is that the definition of "genetic code" (from Merriam Websters at least) makes no mention of communication, which typically goes hand-in-glove with the use of code. If no communication takes place, then shouldn't we rename the genetic code? If for no other reason than to avoid the issues of lexicon we experience here? Though the names "Genetic Abbreviations", "Genetic Shorthand", "Genetic Symbols" (which is really a "code" in another word) don't seem to fit as a representation of what "it" is. I find it interesting that the history of the research indicate that the scientists themselves did in fact believe the DNA to be "communicating" or part of a larger "communication" apparatus associated with heredity. Which is likely why they chose the word "code" as opposed to "representative" or some other category descriptor. They could have made one for their own purposes it seems. Yet they chose "code". The term "communication" to most persons implies an intelligence does it not? Though the act of communication as defined above in definition "1" doesn't necessarily require one. It is the physical process of transmission. That definition occurs every day millions of times a second. Both in the biological world (as evidenced by my participation in the prior posts about B-Cells and antibodies) and in the physical world (financial transactions for instance). The question is then begged, the transmission of what? That question itself, won't definitively "prove" the existence of an intelligent, external (to the system being viewed) agent, but it could strengthen a case for such a position. Another question that I have about communication is "why"? I like the question "the transmission of what?". It is much more interesting to me than the "how". Though, how is interesting in its own right. That is where another word with a polymeaning enters into the discussion. Rather than clarifying, the word causes each camp to sharpen their swords, insure the reinforcement of their barricades, and "circle the wagons". Usually, it boils down to a difference of opinion as to what definition of such a word should be applied. The word in question here is information. I, once again, return to Merriam Websters and have selected the following definition as appropriate. You may disagree, but you must provide another definition for use. It is definition #2b. information: the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something (as nucleotides in DNA or binary digits in a computer program) that produce specific effects In light of these definitions, it would seem to me that the genetic code is the total of all "codes" (def #3a); which are representatives of information (inherent attributes per above definition) that is "communicated" (def #1, or act of transmission) between cellular systems. Notice, I haven't described the communication system (the RNA, tRNA, ribosomes, etc...). Nor have I described the information being communicated (the amino acids etc...). Interesting questions that follow are "what" is being communicated? The answer being simply "nucleotides". Though a longer, more technical discussion could take place about that. Seemingly, the nucleotides are themselves "codes" that represent an instruction set are they not? Specifically instructions to the cell on which amino acids to use in constructing a specific protein, correct? My question is what leads "us" to believe that heredity and natural selection would be sufficient to generate the "codes", "information", and "communication" as I have them defined? I understand that the codes could be preserved through the mechanism of inheritance. That is loosely the equivalent of obtaining an ability to parse an ASC EDI X12 purchase order specification from a "library" class. I'm less confident that natural selection would be the genesis of such specifications (i.e. the ASC EDI X12 or metaphorical equivalent in biology) or even of the metaphorical equivalent to the library class (though that would seem to be an easier hurdle than the specification). I'm not unwilling to entertain the hypothesis, however. It is easy to relate the concept of "intelligence" to cellular automata, once you use terms like "code", "information", and "communication". The reason being, is that there are, I argue, default assumptions about those particular words; which are held by the general public. Namely, the computer technology we enjoy today are almost always associated with those words. The general populace will make an implicit assumption about topics that use "code", "information", and "communication" regularly as descriptors. The assumption is that an intelligent agent defined those systems. The information systems employed today were designed by mankind, so that association is made (design association at least). The hard question for the "design hypothesis" camp is how do you associate a more "abstract" intelligence to the "codes", "information", and "communication" exhibited by the biological machinery? The approach you are "stuck with" will be a hard sell to the scientist community that uses the a materialistic (Popper?) Philosophy of Science, rather than meta-physical (Aristotelian?) Philosophy of Science. Though, the individuals who dislike the study of Philosophy, will no doubt not enjoy that the prominence of their position rests upon the philosophical foundation of their choosing. Which, at base, is largely a matter of preference.ciphertext
February 14, 2013
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Answer a simple question if you will, G. Is functional sequence complexity the same concept as your FSCO/I (what do these initials stand for, BTW)?
Really? This far into several debates where RSCO/I is an integral part of the challenge presented to your arguments/worldview ... and you haven't even bothered to find out what it means? Like so many others, AF is not serious about any debate here, he's only serious about preserving his own worldview via willful ignorance and denial.William J Murray
February 14, 2013
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PS @ KF And until you can show that functional proteins are rare in sequence space, there is no possible way to calculate CSI or it's imaginative variants.Alan Fox
February 14, 2013
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Answer a simple question if you will, G. Is functional sequence complexity the same concept as your FSCO/I (what do these initials stand for, BTW)? If so, why use a different acronym? If not why is Durston's paper relevant?Alan Fox
February 14, 2013
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JWT, shoot me an email (follow the link) and I will pass to you a PDF. Sorry on eqn formats, I did that in part to get around the formatting headaches that crop up in so many situations and to avoid the problem of using GIFs (which are actually just displayed in the page, they "live" elsewhere). KFkairosfocus
February 14, 2013
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AF: Playing at the "let's object on style (one can ALWAYS do that . . . ) if we cannot answer on substance" game I see; sadly. And, trying the switcheroo that Durston et al were not speaking about functionally specific bits, and providing a metric of complexity for same. (Perhaps, you need to be aware of this earlier work (observe the diagram) by them and what FSC -- functional sequence complexity -- stands for, which is what the paper is providing a metric for with specific application to protein sequences, which is what they report. Note, that the nodes-arcs analysis means that anything that has functionally specific organisation can be reduced to strings, so this is WLOG. Remember, too, H is a metric of avg info per symbol in light of the observed statistics for a given system, where any real world system will have some redundancy. KFkairosfocus
February 14, 2013
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...had AF bothered to simply scan down...
Hey, don't blame me for your inadequacies in blog layout! ;) Durston doesn't cut it. Firstly its not FCSI in his paper. FCSI is not referred to anywhere. Secondly Durston's "fits" produce no new insight into protein structure. I note there are zero citations showing on Google Scholar for this paper.Alan Fox
February 14, 2013
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@kairosfocus: Is there any way you could make your paper "On Information, Design, Science, Creation & Evolutionary Materialism" available as a nice-looking (tex-based) pdf-file one could read on an e-book (Btw. have you ever thought about printing your article as a book? :-) I'd buy it.)? Maybe it's just me, but the website is really hard to read, especially with the unfriendly formatting of equations.JWTruthInLove
February 14, 2013
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So Mr. Fox are you really that self deceived to see that you are directly refuted by empirical evidence, or are you just being purposely dishonest to the evidence that was presented to you because you don’t like the implications of admitting design in biology?
But Phil, where have I denied that design happens in living organisms? That's what natural selection is - a process of design by the environment. Now by "environment" I mean all the various effects that environment, including but not exclusively, weather, climate, catastrophe, prey, predators, parasites, etc. that contribute to differential survival.Alan Fox
February 14, 2013
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* If evolution is true!Alan Fox
February 14, 2013
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Can the simplest structure possible that copies itself, while being able to take in/accumulate changes (probably necessarily of a truly random, stochastic nature initially), transition to a state where both the copying and updating/modifying functions rely on/utilize a coded system, without disrupting the process along the way?
There are* upper and lower limits for any population of replicators. If copying is too perfect, there is nothing for natural selection to work on and if copying results in too many mutations the population will become extinct with natural selection too slow to eliminate the deleterious changes. There are many on-line resources and communities who can be of help in getting more information than I as a layman can provide. Talkorigins.org is a good starting point.
I was wondering if you had a chance to check out the link to the more recently discovered spider...
Yes. Most impressive! The evolutionary explanation involves the assumption that the innate behaviour patterns that result in decoy building (and, essentially, all other innate behaviour that occurs in metazoans) must exist in the fertilized egg. I happen to think the only possible candidate is DNA sequences (though I have no idea remotely how this happens precisely) and thus this is passed on as "alleles" (different versions of the genetic sequences) which will then be subject to natural selection. Each spider builds its decoys to according to its programmed behaviour. Where a variation gives a survival advantage, that allele will proliferate. I'm not sure I'm convincing myself here but there is no better competing hypothesis that I am aware of.Alan Fox
February 14, 2013
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Correction/Update @221: Of course, if one could simulate the simplest single cell lifeform of an adequately sized population, along with an adequately sophisticated/detailed environment, one would be tasked with demonstrating that a code/dialect in use could transform to a different code/dialect- as obviously the cell requires that an initial code already exist. So this would address a different but related question: Can codes change "naturally", as opposed to can codes arise "naturally"? (Or for that matter, can codes in living systems be engineered to change by human minds, and if so, what types of changes are possible?)MrMosis
February 14, 2013
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Onlookers, another couple of dodges. First, the burden of proof game is appropriate to courtrooms where since the Govt has overwhelming resources it is safer to have the defendant presumed innocent. In scientific matters, everyone who makes a claim, has a burden of evidence-based warrant, even if the claim is negative. As one experienced with machine code and its use in discrete state control context, and communication contexts, I state that I find that the coded information that fits on the Codon table and commonly appears in mRNA is an obvious and well known INSTANCE of a control tape; one using prong height as coding mechanism. There has been no cogent, empirically based answer. If AF wants to reject that evidence, let him bring forth his evidence based reasons, and while he is at it, correct from Crick on down. Similarly, had AF bothered to simply scan down and notice the indented list (never mind, actually attending to the relevant chain of reasoning, which inter alia gives in outline what info measured in bits is about), he would have observed the following information measured in functional bits (which should itself have been a clue), the basis of which has been in the peer-reviewed literature for some five years:
Using Durston’s Fits values -- functionally specific bits -- from his Table 1, to quantify I, so also accepting functionality on specific sequences as showing specificity giving S = 1, we may apply the simplified Chi_500 metric of bits beyond the threshold:
RecA: 242 AA, 832 fits, Chi: 332 bits beyond SecY: 342 AA, 688 fits, Chi: 188 bits beyond Corona S2: 445 AA, 1285 fits, Chi: 785 bits beyond
This is in the end based on the view of informational entropy as specifying the average information per symbol [cf discussion here], which is linked to thermodynamic entropy from an informational view as measuring the average missing information on the specific microstate facing us if we only have the state info that gives the macrostate of a system. I highlight this, to underscore that the quantifiable concepts of information we are dealing with are now embedded in a serious school of thought in thermodynamics. KFkairosfocus
February 14, 2013
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Mr. Fox states: "Argument from incredulity! You must skip Joe’s and BA77?s comments!" Yet Mr. Fox was the one who originally 'incredulously' claimed: ”It is not fine to assume that merely by using a convenient descriptive, this somehow gives credence that there is more than analogy between the genetic code and, say, computer language.” And yet Mr. Fox was shown that, among other things such as storing massive amounts of 'digital' information directly on DNA, that,, Passing the baton of life – from Schrödinger to Venter – July 2012 Excerpt: “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.” – Craig Venter http://www.newscientist.com/blogs/culturelab/2012/07/passing-the-baton-of-life---from-schrodinger-to-venter.html So Mr. Fox are you really that self deceived to see that you are directly refuted by empirical evidence, or are you just being purposely dishonest to the evidence that was presented to you because you don't like the implications of admitting design in biology?bornagain77
February 14, 2013
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Alan Fox: Thank you for the reply. I gathered that some were disputing the adequacy of the descriptor altogether. I suppose the real disagreement concerns whether or not anything meaningful can be said about whether or not such systems (those using codes as defined here) can arise “naturally”. I would think a rigorous mathematical system/model that tightly corresponds with reality and has a limited set of assumptions could address this- similar but not identical to the matter of FSCO/I. Can the simplest structure possible that copies itself, while being able to take in/accumulate changes (probably necessarily of a truly random, stochastic nature initially), transition to a state where both the copying and updating/modifying functions rely on/utilize a coded system, without disrupting the process along the way? (putting aside for the moment the issue of how the original system came to be) This may not be practical, in large part because to my [limited] knowledge, the only known, imagined, or contemplated system that is capable of doing this is the cell, which is still too big and complicated to model with enough specificity. ALSO slightly OT: I was wondering if you had a chance to check out the link to the more recently discovered spider I posted @145. It is mind boggling to consider what form of mutation could have facilitated the spider’s “knowing” how to model itself in its web. Stochastic point mutations at random locations do not seem to be up to the task. But if that is true, what would that entail? What if the spider’s web making-related knowledge is stored in such a manner that it is oriented towards enabling some form of change? Such that the spider and its instincts have a predisposition towards taking in “suggestions” for how to do web decoys “better”. And even if so, it is hard to imagine how the spider could wind up putting legs on its decoys. At the very least, the appearance of purposes seems to emerge from some very strange places of late.MrMosis
February 14, 2013
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Eric Anderson:
It is hard to imagine a more clueless statement.
Argument from incredulity! You must skip Joe's and BA77's comments! :)Alan Fox
February 14, 2013
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...real world cases on measuring FSCI...
As I am sure many here will agree, I am not the most assiduous reader. However can anyone else spot a "real world case" in the piece KF links to?Alan Fox
February 14, 2013
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