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When Darwinism infects popular culture, confusion follows as well as nonsense

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File:Nostradamus prophecies.jpg

Every so often, one reads a sentence that just takes one’s breath away from an otherwise intelligent writer who uses Darwinism to help explain the world: This from Colin Dickey’s “Quack Prophet” (Lapham’s Quarterly):

Whether it’s the Dead Sea Scrolls or Finnegan’s Wake, there’s a long literary history of taking the garbled and the fragmented and looking for lucid meaning beneath. The science writer and professional skeptic Michael Shermer has gone so far as to argue that we’re hard-wired, from an evolutionary perspective, to look for such hidden meanings. “From sensory data flowing in through the senses the brain naturally begins to look for and find patterns, and then infuses those patterns with meaning,” Shermer writes. “We can’t help it. Our brains evolved to connect the dots of our world.” By adjusting the signal-to-noise ratio, Nostradamus introduced enough static into his Prophecies that they could be all things to all readers, poetic Rorschach blots of detail and blur.

Excuse us, but: The Dead Sea Scrolls are a remarkable 1947 find (since augmented) of a group of manuscript fragments and artifacts that everyone knew had lucid meaning, but awaited translation and clarification. You didn’t need to be “hard-wired” to notice any of that. Finnegan’s Wake is a deliberately obscure novel written by Irish novelist James Joyce, pored over by generations of academic dullards – to Joyce’s huge amusement, had he lived to see that entire circus play out. Much of it probably did have some meaning; it was written in English by an already successful novelist. Again, no “hardwiring” required to suppose that, though a certain amount of denseness for spending a lot of time on the problem.

It’s not like seeing patterns in the clouds, which might actually be evidence for Shermer’s thesis if not pressed too far – which it nearly always is.

Conflating the Scrolls and Finnegan’s Wake, spiced up with some Shermerite nonsense about how our brains evolved to … whatever, is an appalling but telling example of cultural Darwinism at work.

Those who don’t believe in meaning corrupt and confound it.

Note: The ostensible subject of the piece is that reliable checkout counter tabloid icon, the “prophet” Nostradamus, who was obscure for an entirely unrelated reason – to avoid falsification. Reminds one of something, no … ?

Comments
Dr Liddle: Perhaps, it has not been recognised by you that once the alphabet is discrete state, it is perforce digital?
No, it has not been recognised by me, kf, because it is not true. "Discrete" does not mean the same as "digital". Letters as used in words are discrete, that does not mean they are digital.
You appear to have a fixed confusion about what defines a digital system.
Well, my view is that the "fixed confusion" is on your side, kf. :)
I am therefore simply pointing out (again) that it is discrete stateness that defines a digital system, and that the system of alphabetic spelling — a digital conversion of speech BTW — is such that words carry the string data structure *-*-*-*- . . ., where the *’s denote valid positions. The symbol *, takes values from the set A, B, C . . . (with extensions) and between any two neighbouring letters such as A and B there is no third valid letter-value.
Well, obviously if you define any system with discrete parts as "digital" then, yes. But then why single out DNA? Any molecule is "digital" by that definition, because it is composed of "discrete" parts. And quantum physics tells us that the whole world is "digital" because is is quantized. If you define "digital" simply to mean "discrete" then you lose all meaning from the term, and it still doesn't allow you describe it as being in "base 4" because however you idiosyncratically you define "digital", "base 4" is a description of a positional numeric system, which DNA is not. It's neither numeric (as Charles says, no one base has a higher or lower "value" than any other) nor positional (it's not the absolute position that determines the "meaning" of a base, but its place in a sequence).
Insistence on such a basic error as though force of will and novel terms like “graphemes,” can change the basic definition and why it is made (the key distinction is that we have a fundamental PHYSICAL and conceptual contrast: discrete/continuous . . . ), does your position no good.
"Grapheme" is not a "novel term" kf. And using it doesn't alter the fact that in normal English usage "discrete" and "digital" are not synonyms.
When we convert one digital thing to another, we can do so without data loss, but for continuous state — analogue — systems, we have to accept a certain level of error, throwing away things beyond a certain precision. But once we accept that conversion error, we can then take steps to essentially eliminate further noise, within limits. (Notice how digital TV is usually very good, then beyond a certain limit utterly broken up into horrible distortions?)
Yes, indeed, kf, but that is entirely off point, as at no time have a suggested that DNA is a analog system. But there are more kinds of systems in heaven and earth Horatio than analog and digital systems. One of them is alphabetic.
And, yes, I am entirely correct to speak of “values,” as the old RION set of scales reminds us: ratio, interval, ordinal, NOMINAL.
And letters are nominal. Because they don't have [quantitative] values. That's why they are called "nominal" from the Latin for "name", not "numerical" from the Latin for "number".
This inherent digitalness is why the alphabetic system was so easily represented in the old 5-bit Baudot code, then onward to 7/8-bit ASCII [and EBCDIC etc]and now 16-bit Unicode.
Sure, but that doesn't make it a digital system, just because it can be rendered on one. Recall: I do not dispute that alphabetical letters are discrete. Indeed they are a way of rendering discrete the continuous sounds we utter as speech. But they are not "digital" in any normal sense of the word, and certainly not in a "base".
Building on this, I have always been struck by the very direct comparison of 8-bit punched paper tape and how mRNA works in the ribosome. Of course the tape used punched holes, vs non punched, but that is of no great consequence. I have similarly highlighted how Braille used a 6-bit raised dot code, and how von Neumann’s original description of the self replicator, used bars of differing height to encode information. (For that matter, Yale type keys do much the same and bars of cams are again similar.)
Sure, but none of that makes it "digital" in the sense of being a "base N" system. Some cam systems are analog and some digital (music boxes for instance). Some systems in the cell act like cams. Doesn't make them Base N digital. Though at least one system arguably is, IMO, i.e. the regulatory network.
DNA, again, uses a 4-state per digit string data structure. Alphabetic writing, uses a 26 state [or extended to 128 or more depending] system.
Well, no. Not unless you define "digital" as "discrete", and even then you don't get to call it "base N" unless your code depends on changing the state of some position. If your code depends on changing the sequence of symbols then it could still be a discrete system, but it isn't a digital base N system.
Maybe, the key thing is to note that digital is not to be equated to binary digital, which happens to be a very convenient base to use in technology.
No indeed. But nor is it, IMO, to be equated to "discrete" without serious loss of meaning. And "Base N" does not mean "a code that uses N different symbols". But if it makes you happy I am happy to stipulate that DNA is a code that uses permutations of 4 discrete entities. Now, will you place take back the implication that I am rejecting the notion that DNA is a "base 4 digital" system because I fear the ID implications?Elizabeth Liddle
November 2, 2011
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Thanks William J Murray, at least I can take comfort in the fact that you have read it and have understood.bornagain77
November 2, 2011
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F/N: Cams (and I believe Yale locks), of course are actually ANALOGUE.
In what sense - that 'locked' and 'unlocked' are not discrete states but exist on a continuum of effectively infinite resolution, or that setting the lock into one of two discrete states requires the operation of a mechanical system? Logic gates are analogue - they consist of very high gain amplifiers with hysteresis. Does that make all computers analogue?DrBot
November 2, 2011
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Elizabeth Liddle:
A “string of digits” is a string. The elements of a string are not digits (though they may be alphanumeric).
Wrong. Each element of a string is a "digit" where its value is any of the possible states allowed by the system upon which the string is built. In the case of binary systems that is any of two states "up down", "on off" "0 1"; in trinary systems "up flat down", "0 1 2"; and similary adenine uracil guanine and cytosine are the four allowed "states" of an RNA "digit"
DNA is not a positional numeral system.
As I already stipulated, but you knew that and yet blew right past it.
Please let me have a definition for "base 4 digital" that refers to systems other than positional numeral systems, or, alternatively, define "position" for me in the context of a DNA base pair, with reference to the examples I gave in 1.2.2.2.2.
Again I already explained that but either in intransigence or inexperience you blew right past that too.
I doubt if any symposium would accept a paper that made the perfectly obvious point that a system based on strings made up of permutations of four discrete units, and varied by deletion, insertion, duplication and substitution, is not a “base 4 digital” system.
I too doubt your paper would be accepted, because you would be confronted with refutations from reviewers of your premises and novel conceptual conflations.Charles
November 2, 2011
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Dunsinane, thank you for your cool responses :) Things are getting a little steamy in here, and I appreciate your objective tone :)
There are 4 possible values TCAG, therefore N=4. Given a word of length 3, position 1 can contain T, C, A, or G, position 2 can contain T, C, A, or G, position 3 can contain T, C, A, or G. What am I missing here? Do you think because the way the “memory” works is different that that means it’s not base 4?
All you are "missing" is the fact that we are not "given a word length 3". What we have are long sequences of variable length, but similar "meaning" (e.g. produce comparable proteins). Comparing variants, then, "place" has no meaning. If you insert or delete a multiple of three bases, you radically change the "place" of the basepairs either side of the change, but they retain the same "meaning" in terms of their amino acids. To give an example: these three alphabetic sentences all mean roughly the same thing: I am very happy to hear your exciting news. I am very happy to hear your news. I am very very happy to hear your exciting news. even though, in the second, the value of every "position" after the word "your" is radically altered, and in the third, after the first "very". Contrast this with three digital items: 100110001 10011001 1001110001 In text, the "meaning" of a letter sequence depends on the order of the letters, regardless of their "place" or "position" relative to some absolute location, whereas in a digital system, the meaning depends on the state of a given "place" or position. There is simply no equivalent to "place value" in text, so there is nothing that can "take one of 27 states", nor is there in DNA. Both are sequence systems not positional systems, and when DNA varies, there is no "position" to change state, but plenty of "sequence" to change order. Not that it makes the slightest difference to ID either way!Elizabeth Liddle
November 2, 2011
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Joseph
All we know about the designers of Stonehenge we got from studying the evidence left behind.
Er...no. We already had considerable knowledge of human capabilities, evidence of local human habitation, previous examples of human stone monument building, etc. that all helped determine Stonehenge was made by humans. But thanks for your usual blithering fact-free inputs.GinoB
November 2, 2011
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Simply incredible Ms. Liddle, instead of clearly seeing that a base 4 DNA based computer greatly exceeds our best base 2 silicon based 'super-computers' you act as if you are being reasonable. Simply completely unbelievable!!! No arrogance in all that denial is there??? here are more notes for you to ignore Ms. Liddle:
Biophysicist Hubert Yockey determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the optimal universal genetic code that is found in nature. The maximum amount of time available for it to originate is 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that is optimal. Put simply, natural selection lacks the time necessary to find the optimal universal genetic code we find in nature. (Fazale Rana, -The Cell's Design - 2008 - page 177) Deciphering Design in the Genetic Code Excerpt: When researchers calculated the error-minimization capacity of one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution where the naturally occurring genetic code's capacity occurred outside the distribution. Researchers estimate the existence of 10 possible genetic codes possessing the same type and degree of redundancy as the universal genetic code. All of these codes fall within the error-minimization distribution. This finding means that of the 10 possible genetic codes, few, if any, have an error-minimization capacity that approaches the code found (semi) universally in nature. http://www.reasons.org/biology/biochemical-design/fyi-id-dna-deciphering-design-genetic-code Ode to the Code - Brian Hayes The few variant codes known in protozoa and organelles are thought to be offshoots of the standard code, but there is no evidence that the changes to the codon table offer any adaptive advantage. In fact, Freeland, Knight, Landweber and Hurst found that the variants are inferior or at best equal to the standard code. It seems hard to account for these facts without retreating at least part of the way back to the frozen-accident theory, conceding that the code was subject to change only in a former age of miracles, which we'll never see again in the modern world. https://www.americanscientist.org/issues/pub/ode-to-the-code/4
Evolutionists have long argued that the optimal genetic code is universal for all lifeforms, and maintain that that fact is strong evidence for evolution from a universal common anscestor, yet it appears they were wrong once again:
Venter vs. Dawkins on the Tree of Life - and Another Dawkins Whopper - March 2011 Excerpt:,,, But first, let's look at the reason Dawkins gives for why the code must be universal: "The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation...this would spell disaster." (2009, p. 409-10) OK. Keep Dawkins' claim of universality in mind, along with his argument for why the code must be universal, and then go here (linked site listing 23 variants of the genetic code). Simple counting question: does "one or two" equal 23? That's the number of known variant genetic codes compiled by the National Center for Biotechnology Information. By any measure, Dawkins is off by an order of magnitude, times a factor of two. http://www.evolutionnews.org/2011/03/venter_vs_dawkins_on_the_tree_044681.html
As well, besides the optimality found for the DNA code, there is a ‘optimality’ found for the 20 amino acid set used in the 'standard' Genetic code when the set was compared to 1 million randomly generated alternative amino acid sets;
Does Life Use a Non-Random Set of Amino Acids? - Jonathan M. - April 2011 Excerpt: The authors compared the coverage of the standard alphabet of 20 amino acids for size, charge, and hydrophobicity with equivalent values calculated for a sample of 1 million alternative sets (each also comprising 20 members) drawn randomly from the pool of 50 plausible prebiotic candidates. The results? The authors noted that: "…the standard alphabet exhibits better coverage (i.e., greater breadth and greater evenness) than any random set for each of size, charge, and hydrophobicity, and for all combinations thereof." http://www.evolutionnews.org/2011/04/does_life_use_a_non-random_set045661.html
Moreover the first 'optimal' DNA code of life on earth had to be at least as complex as the current DNA code found in life or mathematical impossibilities arise:
Shannon Information - Channel Capacity - Perry Marshall - video http://www.metacafe.com/watch/5457552/ “Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible” Donald E. Johnson – Bioinformatics: The Information in Life DNA - The Genetic Code - Optimal Error Minimization & Parallel Codes - Dr. Fazale Rana - video http://www.metacafe.com/watch/4491422 Nick Lane Takes on the Origin of Life and DNA - Jonathan McLatchie - July 2010 Excerpt: It appears then, that the genetic code has been put together in view of minimizing not just the occurence of amino acid substitution mutations, but also the detrimental effects that would result when amino acid substitution mutations do occur. http://www.evolutionnews.org/2010/07/nick_lane_and_the_ten_great_in036101.html
Though the DNA code is found to be optimal from a error minimization standpoint, it is also now found that the fidelity of the genetic code, of how a specific amino acid is spelled, is far greater than had at first been thought:
Synonymous Codons: Another Gene Expression Regulation Mechanism - September 2010 Excerpt: There are 64 possible triplet codons in the DNA code, but only 20 amino acids they produce. As one can see, some amino acids can be coded by up to six “synonyms” of triplet codons: e.g., the codes AGA, AGG, CGA, CGC, CGG, and CGU will all yield arginine when translated by the ribosome. If the same amino acid results, what difference could the synonymous codons make? The researchers found that alternate spellings might affect the timing of translation in the ribosome tunnel, and slight delays could influence how the polypeptide begins its folding. This, in turn, might affect what chemical tags get put onto the polypeptide in the post-translational process. In the case of actin, the protein that forms transport highways for muscle and other things, the researchers found that synonymous codons produced very different functional roles for the “isoform” proteins that resulted in non-muscle cells,,, In their conclusion, they repeated, “Whatever the exact mechanism, the discovery of Zhang et al. that synonymous codon changes can so profoundly change the role of a protein adds a new level of complexity to how we interpret the genetic code.”,,, http://www.creationsafaris.com/crev201009.htm#20100919a
further notes:
The coding system used for living beings is optimal from an engineering standpoint. Werner Gitt - In The Beginning Was Information - p. 95 Collective evolution and the genetic code - 2006: Excerpt: The genetic code could well be optimized to a greater extent than anything else in biology and yet is generally regarded as the biological element least capable of evolving. http://www.pnas.org/content/103/28/10696.full Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes.... the present findings support the view that protein-coding regions can carry abundant parallel codes. The data compression of some stretches of human DNA is estimated to be up to 12 codes thick (12 different ways of DNA transcription) (Trifonov, 1989). (This is well beyond the complexity of any computer code ever written by man). John Sanford - Genetic Entropy "In the last ten years, at least 20 different natural information codes were discovered in life, each operating to arbitrary conventions (not determined by law or physicality). Examples include protein address codes [Ber08B], acetylation codes [Kni06], RNA codes [Fai07], metabolic codes [Bru07], cytoskeleton codes [Gim08], histone codes [Jen01], and alternative splicing codes [Bar10]. Donald E. Johnson – Programming of Life – pg.51 - 2010 DNA Caught Rock 'N Rollin': On Rare Occasions DNA Dances Itself Into a Different Shape - January 2011 Excerpt: Because critical interactions between DNA and proteins are thought to be directed by both the sequence of bases and the flexing of the molecule, these excited states represent a whole new level of information contained in the genetic code, Ends and Means: More on Meyer and Nelson in BIO-Complexity - September 2011 Excerpt: According to Garrett and Grisham's Biochemistry, the aminoacyl tRNA snythetase is a "second genetic code" because it must discriminate among each of the twenty amino acids and then call out the proper tRNA for that amino acid: "Although the primary genetic code is key to understanding the central dogma of molecular biology on how DNA encodes proteins, the second genetic code is just as crucial to the fidelity of information transfer."
bornagain77
November 2, 2011
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F/N: Cams (and I believe Yale locks), of course are actually ANALOGUE.kairosfocus
November 2, 2011
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Elizabeth Liddle:
Well, perhaps you could set an example and address my questions in 1.2.2.2.2 and by responding to my request for an explanation as to why you regard my position as “asinine”.
Because adenine uracil guanine and cytosine represent the four possible values of a DNA “digit” and those digits may be combined into longer strings of digits, which longer strings (genes) whether encoded or not (on or off) does not transform the four values of adenine uracil guanine and cytosine into two (base-2) values. Canonical order is found in the strings, not in the values of digits. A string of digits clearly has canonical order. Whether adenine has a higher value than quanine is arguable, but irrelevant in the example of DNA because it is more like content-addressable memory than address-accessed memory, i.e. it the pattern in the string of digits that is determinitive, not any expected relative canonical ordering of adenine uracil guanine and cytosine per se.
A "string of digits" is a string. The elements of a string are not digits (though they may be alphanumeric). As you say, it is irrelevant whether "adenine has a higher value than guanine", and also completely meaningless. It's meaningless because unlike in a "base N digital" system, the "digits" have no quantitative or place value at all. Place is irrelevant, in fact - what matters is the sequence. Which is why, if you look at my examples in 1.2.2.2.2 you will see variants in which "place" is a meaningless concept. It is not "positions" that change "state", but sequences that can change by means of insertion, deletion and duplication as well as substitution.
Also, as “dishonest”.
But you knew all that, yet obdurately insist otherwise and failed to engage the accepted definitions of base four systems as repeatedly explained to you, ad nauseum.
Please explain to me the "accepted definitions of base four systems". Here is one from wiki:
In mathematical numeral systems, the base or radix for the simplest case is the number of unique digits, including zero, that a positional numeral system uses to represent numbers. For example, for the decimal system (the most common system in use today) the radix is ten, because it uses the ten digits from 0 through 9.</blockquote DNA is not a positional numeral system. Please let me have a definition for "base 4 digital" that refers to systems other than positional numeral systems, or, alternatively, define "position" for me in the context of a DNA base pair, with reference to the examples I gave in 1.2.2.2.2.
Charles:
If you think your view is correct, then truely you should present it in a paper at a symposium. Perhaps those attendess will explain it to you further in terms you’ll find less rude.
I doubt if any symposium would accept a paper that made the perfectly obvious point that a system based on strings made up of permutations of four discrete units, and varied by deletion, insertion, duplication and substitution, is not a "base 4 digital" system. Especially when it has no bearing on anything other than what appears to be a desire to use computer terminology when talking about living things. Even though computer terminology is perfectly valid for living things, if used in a way that actually makes sense.Elizabeth Liddle
November 2, 2011
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in base N numbering systems you have a set of positions that can take one of N values. This is not the case with DNA.
There are 4 possible values TCAG, therefore N=4. Given a word of length 3, position 1 can contain T, C, A, or G, position 2 can contain T, C, A, or G, position 3 can contain T, C, A, or G. What am I missing here? Do you think because the way the "memory" works is different that that means it's not base 4?Dunsinane
November 2, 2011
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Dr Liddle: Perhaps, it has not been recognised by you that once the alphabet is discrete state, it is perforce digital? You appear to have a fixed confusion about what defines a digital system. I am therefore simply pointing out (again) that it is discrete stateness that defines a digital system, and that the system of alphabetic spelling -- a digital conversion of speech BTW -- is such that words carry the string data structure *-*-*-*- . . ., where the *'s denote valid positions. The symbol *, takes values from the set A, B, C . . . (with extensions) and between any two neighbouring letters such as A and B there is no third valid letter-value. Insistence on such a basic error as though force of will and novel terms like "graphemes," can change the basic definition and why it is made (the key distinction is that we have a fundamental PHYSICAL and conceptual contrast: discrete/continuous . . . ), does your position no good. When we convert one digital thing to another, we can do so without data loss, but for continuous state -- analogue -- systems, we have to accept a certain level of error, throwing away things beyond a certain precision. But once we accept that conversion error, we can then take steps to essentially eliminate further noise, within limits. (Notice how digital TV is usually very good, then beyond a certain limit utterly broken up into horrible distortions?) And, yes, I am entirely correct to speak of "values," as the old RION set of scales reminds us: ratio, interval, ordinal, NOMINAL. This inherent digitalness is why the alphabetic system was so easily represented in the old 5-bit Baudot code, then onward to 7/8-bit ASCII [and EBCDIC etc]and now 16-bit Unicode. Building on this, I have always been struck by the very direct comparison of 8-bit punched paper tape and how mRNA works in the ribosome. Of course the tape used punched holes, vs non punched, but that is of no great consequence. I have similarly highlighted how Braille used a 6-bit raised dot code, and how von Neumann's original description of the self replicator, used bars of differing height to encode information. (For that matter, Yale type keys do much the same and bars of cams are again similar.) DNA, again, uses a 4-state per digit string data structure. Alphabetic writing, uses a 26 state [or extended to 128 or more depending] system. Maybe, the key thing is to note that digital is not to be equated to binary digital, which happens to be a very convenient base to use in technology. GEM of TKIkairosfocus
November 2, 2011
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GinoB:
It’s impossible to recognize conscious design without at least some external knowledge of the designer – its capabilities, the material resources it has available, knowledge of other designs it has done.
That is unsupportable nonsense. All we need is knowledge of cause and effect relationships. All we know about the designers of Stonehenge we got from studying the evidence left behind.
ID makes the unwarranted assumption that all design must be like human design,
No, ID makes no such assumption. And in the end all YOU have to do to refute ANY given design inference is to actually step up and demonstrate that blind, undirected processes can account for it. You sure as heck are not going to refute ID with your whining ignorance.Joseph
November 2, 2011
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arkady967
Seeing design and identifying a designer are two different things – you may effect one event without the other.
No, that is not true. It's impossible to recognize conscious design without at least some external knowledge of the designer - its capabilities, the material resources it has available, knowledge of other designs it has done. ID makes the unwarranted assumption that all design must be like human design, then attempts to match unknown items to known human-produced forms with a subjective superficial examination ("Looks designed to me!). This includes coming up with meaningless metrics for measuring complexity, like dFSCI. Logically there is no difference between "that fluffy cloud looks like a choo-choo train, so it must be designed!" and "that flagella looks like an outboard motor, so it must be designed!"GinoB
November 2, 2011
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Dunsinane:
That’s how the internet works. Consider “www” in binary: 011101110111011101110111 which is, the first letter (a:01100001) plus 22 under your new system ‘w’ would translate to the first letter plus 11 or 01101011 so nothing would work anymore
Well, obviously if you changed the mapping of alphabetical letters to digital code in a computer then "nothing would work any more"! That's not what I said! I said that the order in which we recite the alphabet has no bearing on the referent (a sound) for each letter. But clearly, if a digital mapping is based on alphabetical order it will change the mapping. That makes my point, not yours!!!!Elizabeth Liddle
November 2, 2011
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Elizabeth Liddle:
Well, perhaps you could set an example and address my questions in 1.2.2.2.2 and by responding to my request for an explanation as to why you regard my position as “asinine”.
Because adenine uracil guanine and cytosine represent the four possible values of a DNA "digit" and those digits may be combined into longer strings of digits, which longer strings (genes) whether encoded or not (on or off) does not transform the four values of adenine uracil guanine and cytosine into two (base-2) values. Canonical order is found in the strings, not in the values of digits. A string of digits clearly has canonical order. Whether adenine has a higher value than quanine is arguable, but irrelevant in the example of DNA because it is more like content-addressable memory than address-accessed memory, i.e. it the pattern in the string of digits that is determinitive, not any expected relative canonical ordering of adenine uracil guanine and cytosine per se.
Also, as “dishonest”.
But you knew all that, yet obdurately insist otherwise and failed to engage the accepted definitions of base four systems as repeatedly explained to you, ad nauseum. If you think your view is correct, then truely you should present it in a paper at a symposium. Perhaps those attendess will explain it to you further in terms you'll find less rude.Charles
November 2, 2011
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Elizabeth Liddle I can’t quite follow your argument. Are you suggesting because DNA is grouped into “3 letter words” that that means it’s not base 4? In base 2 code, the 1s and 0s are grouped into 8 bit bytes. Consider for example ASCII which defines how our alphabet is encoded in base 2 using words 8 bits in length.
No, I'm not saying that DNA is not base 4 because it's grouped in "3 letter words". It could be grouped in any-number-of-letter words and it still wouldn't be in base 4 digital, because in base N numbering systems you have a set of positions that can take one of N values. This is not the case with DNA. For a start, within a single organism we hope that none of sequence changes at all (or we may get cancer). But even if we consider DNA variants within a population, the changes are not rung by changing the "state" of "positions" but by changing the sequence in various ways, where it is not the position that matters, but the sequential context. Sometimes the variants actually "SNPs" - substitution of one base-pair by another, and if all variants were of this type, maybe you could call the system "base 4 digital". But all variants are not of this type, and deletions, insertions and duplication are a major feature of DNA variation. Such variants are not "digital" at all, because no entity changes "state"; rather the sequence is rearranged. That's why the system is much more like text than like digits, and why "base 4 digital" is a very misleading description. Which is not an ideological point at all, as I've said - I see no problem in regarding cells as operating a "base 2 digital" system of gene regulation. But it is being touted by kf as an ideological point, and I'm still waiting for him to walk that back, whether he continues to disagree with me on the "base 4 issue" or not.Elizabeth Liddle
November 2, 2011
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Alphabets are only digital when treated as digits
That's how the internet works. Consider "www" in binary: 011101110111011101110111 which is, the first letter (a:01100001) plus 22 under your new system 'w' would translate to the first letter plus 11 or 01101011 so nothing would work anymoreDunsinane
November 2, 2011
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Elizabeth Liddle, regarding your new alphabet, if it was implemented tomorrow the internet would likely stop working.
No, it would not. Dictionaries wouldn't work too well, but most other things would work fine. Alphabetical order is just a convention that has no bearing on the referents signified by each letter. This is not the case with digits, where digits are ordered in ascending numerical value, and any change to their ordering would change their numerical value. Also, see my post at 1.2.2.2.2
As well as every computer that expected ‘a’ to refer to position 1, ‘b’ to refer to position 2 etc.
Yes, alphanumeric systems would be messed up. Which actually makes my point. Alphabets are only digital when treated as digits, as in alphanumeric numbering systems. Treated as graphemes, they are not. DNA base pairs act as grapheme-like units, not digit-like units.Elizabeth Liddle
November 2, 2011
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That would be as in fatuous, inane (extremely silly or stupid); to wit, being informed of yet in obdurate denial of the definitions of base-four numbering systems.
And yet I see no rebuttal.
Simply asserting that it is is not persuasive, and quite rude.
It wasn’t meant to persuade. As for being rude, that would be in the eye of the beholder, now wouldn’t it.
Not really. Most civilised people would regard the description of someone else's position as "a stunningly asinine [person's surname]ism" as rude, especially if posted without any rebuttal.
If you don’t like your intellectually dishonest arguments being called for what they are, you might try persuading with facts instead of unfounded speculation and engaging the questions put to you instead of deflecting them and implying novel meanings to suit your semantics.
Well, perhaps you could set an example and address my questions in 1.2.2.2.2 and by responding to my request for an explanation as to why you regard my position as "asinine". Also, as "dishonest". Put up or shut up.Elizabeth Liddle
November 2, 2011
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Elizabeth Liddle, regarding your new alphabet, if it was implemented tomorrow the internet would likely stop working. As well as every computer that expected 'a' to refer to position 1, 'b' to refer to position 2 etc.Dunsinane
November 2, 2011
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kf, let me requote the statement of yours that I objected to:
So strong is this that we see objectors trying to tell us that the digital information in DNA is not digital information [e.g. I found the reference to its being alphabetic instead particularly astonishingly ill-informed]
Where have I ever said that base pairs were not "discrete"? What I said was that they were analogous to [discrete] letters, not [discrete] digits. You described my "reference to its being alphabetic instead" as "astonishingly ill-informed". So clearly it is not any assertion of mine that base-pairs are not discrete that you can have objected to because alphabetical letters are discrete. Your stated objection was that I considered them alphabetic not digital. So this:
The word digital comes from the same source as the word digit and digitus (the Latin word for finger), as fingers are used for discrete counting. It is most commonly used in computing and electronics, especially where real-world information is converted to a digital format as in digital audio and digital photography.
is irrelevant. Please answer my questions in 1.2.2.2.2Elizabeth Liddle
November 2, 2011
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Elizabeth Liddle:
Perhaps you could explain to me why it is “asinine”.
That would be as in fatuous, inane (extremely silly or stupid); to wit, being informed of yet in obdurate denial of the definitions of base-four numbering systems.
Simply asserting that it is is not persuasive, and quite rude.
It wasn't meant to persuade. As for being rude, that would be in the eye of the beholder, now wouldn't it. If you don't like your intellectually dishonest arguments being called for what they are, you might try persuading with facts instead of unfounded speculation and engaging the questions put to you instead of deflecting them and implying novel meanings to suit your semantics.Charles
November 2, 2011
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Elizabeth Liddle I can't quite follow your argument. Are you suggesting because DNA is grouped into "3 letter words" that that means it's not base 4? In base 2 code, the 1s and 0s are grouped into 8 bit bytes. Consider for example ASCII which defines how our alphabet is encoded in base 2 using words 8 bits in length.Dunsinane
November 2, 2011
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it would make not the slightest different to the referent signified by any letter, and not a single text written in roman letters would change in meaning. On the other hand if it was agreed that the order of digits would become: 8906245173 it would be tantamount to changing the referent (a value) of every digit, and rendering vast numbers of arithmetical statement false. This is because a letter is a very different thing to a digit. DNA and RNA base pairs are not like digits. They are like letters. They have no "place value" or canonical order that makes any difference to their referents.Elizabeth Liddle
November 2, 2011
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I should also point out, kf, that your error is made explicit in your question: letters do not have "values", they have referents, and the fact that we traditionally recite them in a sequence has no bearing on what those referents are. If it was agreed tomorrow that from henceforth alphabetical order would become: THEQUICKBROWNFXJMPSVLAZYDGElizabeth Liddle
November 2, 2011
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Dr Liddle: Just as a reminder, let me clip Wikipedia on the reason why I ask this:
A digital system[1] is a data technology that uses discrete (discontinuous) values. By contrast, analog (non-digital) systems use a continuous range of values to represent information. Although digital representations are discrete, they can be used to carry either discrete information, such as numbers, letters or other individual symbols, or approximations of continuous information, such as sounds, images, and other measurements of continuous systems. The word digital comes from the same source as the word digit and digitus (the Latin word for finger), as fingers are used for discrete counting. It is most commonly used in computing and electronics, especially where real-world information is converted to a digital format as in digital audio and digital photography.
(And, as someone who has routinely taught digital systems, I cite this not as proof but as a way to try to communicate.) GEM of TKIkairosfocus
November 2, 2011
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Dr Liddle: Again, do tell me what valid alphabetic value lies between A and B? GEM of TKI
None, of course, kf. As I have made perfectly clear, I am happy to consider DNA (and RNA) an alphabetic system with a discrete set of "letters". What I dispute is that these "letters" can usefully be called "digits" of a "base 4" digital code. As you will see if you attempt to answer the questions I pose to you in 1.2.2.2.2Elizabeth Liddle
November 2, 2011
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Perhaps you could explain to me why it is "asinine". Simply asserting that it is is not persuasive, and quite rude.Elizabeth Liddle
November 2, 2011
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Elizabeth Liddle:
This is why DNA cannot be usefully described as a “base 4 digital” system – it has nothing in common with a “base 4 digital” system, although it has plenty in common with a 4 letter alphabetic system in which sequences of “letters” have “meaning”. It could also be usefully described as a “base 2 digital system” because genes can be in one of two states: Off, and On, and indeed switching one gene Off can turn another one Off or On in a logical cascade in which certain inputs result in certain outputs. But Base 4 digital it ain’t.
Yet another stunningly asinine Liddleism for the record books. You should present your analysis at a symposium.Charles
November 2, 2011
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Dr Liddle: Again, do tell me what valid alphabetic value lies between A and B? GEM of TKIkairosfocus
November 2, 2011
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1 9 10 11 12

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