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UB Sets It Out Step-By-Step

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UD Editors:  No one has come close to refuting UB’s thesis after 129 comments.  We are moving this post to the top of the page to give the materialists another chance.

I take the following from an excellent comment UB made in a prior post.  UB lays out his argument step by step, precept by precept.  Then he arrives at a conclusion.  In order for his argument to be valid, the conclusion must follow from the premises.  In order for his argument to be sound, each of the premises must be true.

Now here is the challenge to our Darwinist friends.  If you disagree with UB’s conclusion, please demonstrate how his argument is either invalid (as a matter of logic the conclusion does not follow from the premises) or unsound (one or more of the premises are false).  Good luck (you’re going to need it).

Without further ado, here is UB’s argument:

1.  A representation is an arrangement of matter which evokes an effect within a system (e.g. written text, spoken words, pheromones, animal gestures, codes, sensory input, intracellular messengers, nucleotide sequences, etc, etc).

2.  It is not logically possible to transfer information (the form of a thing; a measured aspect, quality, or preference) in a material universe without using a representation instantiated in matter.

3.  If that is true, and it surely must be, then several other things must logically follow. If there is now an arrangement of matter which contains a representation of form as a consequence of its own material arrangement, then that arrangement must be necessarily arbitrary to the thing it represents. In other words, if one thing is to represent another thing within a system, then it must be separate from the thing it represents. And if it is separate from it, then it cannot be anything but materially arbitrary to it (i.e. they cannot be the same thing).

4.  If that is true, then the presence of that representation must present a material component to the system (which is reducible to physical law), while its arrangement presents an arbitrary component to the system (which is not reducible to physical law).

5.  If that is true, and again it surely must be, then there has to be something else which establishes the otherwise non-existent relationship between the representation and the effect it evokes within the system. In fact, this is the material basis of Francis Crick’s famous ‘adapter hypothesis’ in DNA, which lead to a revolution in the biological sciences. In a material universe, that something else must be a second arrangement of matter; coordinated to the first arrangement as well as to the effect it evokes.

6.  It then also follows that this second arrangement must produce its unambiguous function, not from the mere presence of the representation, but from its arrangement.  It is the arbitrary component of the representation which produces the function.

7.  And if those observations are true, then in order to actually transfer recorded information, two discrete arrangements of matter are inherently required by the process; and both of these objects must necessarily have a quality that extends beyond their mere material make-up. The first is a representation and the second is a protocol (a systematic, operational rule instantiated in matter) and together they function as a formal system. They are the irreducible complex core which is fundamentally required in order to transfer recorded information.

8.  During protein synthesis, a selected portion of DNA is first transcribed into mRNA, then matured and transported to the site of translation within the ribosome. This transcription process facilitates the input of information (the arbitrary component of the DNA sequence) into the system. The input of this arbitrary component functions to constrain the output, producing the polypeptides which demonstrate unambiguous function.

9.  From a causal standpoint, the arbitrary component of DNA is transcribed to mRNA, and those mRNA are then used to order tRNA molecules within the ribosome. Each stage of this transcription process is determined by the physical forces of pair bonding. Yet, which amino acid appears at the peptide binding site is not determined by pair bonding; it is determined  by the aaRS. In other words, which amino acid appears at the binding site is only evoked by the physical structure of the nucleic triplet, but is not determined by it. Instead, it is determined (in spatial and temporal isolation) by the physical structure of the aaRS. This is the point of translation; the point where the arbitrary component of the representation is allowed to evoke a response in a physically determined system – while preserving the arbitrary nature of the representation.

10.  This physical event, translation by a material protocol, as well as the transcription of a material representation, is ubiquitous in the transfer of recorded information.

CONCLUSION:  These two physical objects (the representation and protocol) along with the required preservation of the arbitrary component of the representation, and the production of unambiguous function from that arbitrary component, confirm that the transfer of recorded information in the genome is just like any other form of recorded information. It’s an arbitrary relationship instantiated in matter.

Comments
kf:
But then, if you are committed to design not being seen in something like the cell, you will always be able to make up clever sounding objections.
Not clever sounding objections. Rather, strange, convoluted, incoherent objections.Eric Anderson
August 24, 2012
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Great job Barry and especially Upright Biped. Now we have the septic zonites sounding off with nonsense, special pleading and equivocation- one example:
The codon-amino acid linkage may well be substitutable
That's the special pleading- and now for the equivocation:
– but this is precisely why it can evolve into a ‘code’ from a simple polyX-synthetic ribozyme.
1- Your position can't even get a simple ribozyme 2- ID is OK with the system evolving by designJoe
August 24, 2012
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corrected link:
Origin Of Life - No Realistic Explanations - Charles Thaxton PhD. - video http://www.metacafe.com/watch/5222490/
bornagain77
August 24, 2012
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F/N 2: A cybernetic, control system also clearly embeds communication and signalling protocols in a loop or in a straight feed-forward system. Where such includes a digital signal, that implies a definite comms network. Cf here protein manufacture by translation, transfer, setting up a control tape, successive coded chaining of AA's, and sending to chaperones for folding, or running through the Golgi "post office" -- with address headers of all things, much like HTTP and packet switching.kairosfocus
August 24, 2012
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F/N: Arbitrary is indeed a common usage in technical fields. In communications, the discussion is about a conventional assignment, or a protocol that is explicit or implied by structures, as opposed to direct physical causal connexion that is not dependent on a purposeful arrangement. It may help to look at a basic model of a telecomms system: || TRANSMITTER || --> Channel --> || Receiver || Where TX: source --> Encoder and or modulator --> transmission unit --> And Rx: --> reception unit --> demod and decoder --> Sink The modulation scheme and the coding scheme are dependent on conventions that are expressed in purposeful system structures, such as amplitude modulation and amplitude-shift keying as a fairly simple case. Simplest way to do AM is to modify the amplitude of an oscillator based on an analogue [or step-wide] input signal, which physically instantiates the mathematical operation of multiplying the signals, and gives rise to a carrier with side-bands. This can be boosted in an amplifier and transmitted via an antenna or a cable. The antenna in effect couples electrons running up and down a metal conductor to a surrounding oscillating electro-magnetic field. This propagates away, with various interesting possibilities studied under the head: propagation. At a receiver, a tuned circuit set to the carrier frequency and coupled to an antenna can oscillate in sympathy with the vibrating field that has propagated. This can then be boosted and half-wave rectified with some low pass filtering, to yield the base-band signal. You don't even need an amplifier if the signal is strong enough, that is how a crystal receiver works. Thanks to semiconductors due to oxidation etc, a fence wire could sometimes serve as such. Now, at first, I thought UB missed the side of waves carrying signals, where say an E-M wave is not exactly material, but then when I thought about the comms system, it was clear that he is right, there has to be some embodiment of the scheme in a material entity for it to have effect. I think it would be helpful for us to take a look here on in my always linked notes, to help clarify this area, up to a basic intro to info theory and how it links to the design detection controversy. BTW< the presence of a communications network, especially a digital, coded one is -- based on induction and related analysis -- a strong indicator of purpose, knowledge, skill and artifice at work, i.e. design. But then, if you are committed to design not being seen in something like the cell, you will always be able to make up clever sounding objections. But that does not make the fact of a coded info system in the heart of the living cell go away, nor can it change our experience of what creates such systems, and what it takes to do so. KFkairosfocus
August 24, 2012
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A few notes on the fact that the genetic code could have 'arbitrarily' been very different: First and foremost, as has been clearly pointed out on UD many times before, there are no physical or chemical forces between the nucleotides along the linear axis of DNA (where the information is) that causes the sequences of nucleotides to exist as they do. In fact as far as the foundational laws of the universe are concerned the DNA molecule, the protein molecule, and the mRNA molecule, don't even have to exist at all. In fact it can be firmly argued that the laws of nature are against the spontaneous formation of molecules that have the capacity to carry 'arbitrary' sequences of information in a meaningful 'encoded' way, such as Upright meticulously has laid out. This is one of the primary reasons why the origin of molecular life is, from a materialistic perspective, such a unfathomable mystery with no realistic resolution in sight. Here are a few brief notes along that perspective:
British Geneticist Robert Saunders Leaves a Highly Prejudiced Signature in His Review of “Signature in the Cell” - April 2012 Excerpt: Meyer points out a rather astonishing fact – about which there is no scientific controversy – regarding the arrangements of the nucleobases in DNA. There are absolutely no chemical affinities or preferences for which nucleobases bond with any particular phosphate and sugar molecule. The N-glycosidic bond works equally well with (A), (T), (G), or (C). And secondly, there are also no chemical bonds in the vertical axis between the nucleobases. What this means is that there are no forces of physical/chemical attraction and no chemical or physical law that dictates the order of the nucleobases; they can be arranged in a nearly infinite amount of different sequences. http://www.algemeiner.com/2012/04/04/british-geneticist-robert-saunders-leaves-a-highly-prejudiced-signature-in-his-review-of-signature-in-the-cell/ A Substantial Conundrum Confronting The Chemical Origin Of Life - August 2011 Excerpt: 1. Peptide bond formation is an endothermic reaction. This means that the reaction requires the absorption of energy: It does not take place spontaneously. 2. Peptide bond formation is a condensation reaction. It hence involves the net removal of a water molecule. So not only can this reaction not happen spontaneously in an aqueous medium, but, in fact, the presence of water inhibits the reaction. Salt in water only adds to this thermodynamic problem: ...even at concentrations seven times weaker than in today’s oceans. The ingredients of sea salt are very effective at dismembering membranes and preventing RNA units (monomers) from forming polymers any longer than two links (dimers). Creation Evolution News - Sept. 2002
The following videos have a fairly good overview of the major problems facing any naturalistic Origin Of Life scenario:
On the Origin of Life - The Insurmountable Problems Of Chemistry - Charles Thaxton PhD. - video http://www.youtube.com/watch?v=6Ye3oDDAxeE Stephen Meyer - Proteins by Design - Doing The Math - video http://www.metacafe.com/watch/6332250/
In fact, the DNA code 'could have', arbitrarily, been vastly different than the optimal code we find in life:
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) “The genetic code’s error-minimization properties are far more dramatic than these (one in a million) results indicate. When the researchers calculated the error-minimization capacity of the one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution. Researchers estimate the existence of 10^18 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 means of 10^18 codes few, if any have an error-minimization capacity that approaches the code found universally throughout nature.” Fazale Rana - From page 175; 'The Cell’s Design'
Dr. Rana, points out in this following podcast, at the 22 minute mark, that researchers produced a 'alternative genetic system', thus providing solid evidence that the code 'could have', 'arbitrarily', been vastly different than the optimal one we find in biological life:
Evolution of Synthetic DNA (turns out to support Intelligent Design) - Fazale Rana PhD. - podcast http://www.reasons.org/podcasts/science-news-flash/evolution-of-synthetic-dna
Another point that I would like to make is that the chemical elements found in the universe have a very spooky balance,,, a spooky balance that 'just so happens' to be necessary for complex biological life to be possible. Michael Denton, author of both 'Evolution: A Theory In Crisis' & 'Nature's Destiny', comments on the surprising 'chemicals balanced for life' finding in the following two interviews:
Michael Denton - We Are Stardust - Uncanny Balance Of The Elements - Atheist Fred Hoyle's conversion to a Deist/Theist - video http://www.metacafe.com/watch/4003877 "Dr. Michael Denton on Evidence of Fine-Tuning in the Universe" - August 2012 - podcast http://intelligentdesign.podomatic.com/entry/2012-08-21T14_43_59-07_00
The reason why I wanted to point out that the chemicals of the universe appear to be 'balanced for life' is because of the following fact:
Life Leads the Way to Invention - Feb. 2010 Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale. http://creationsafaris.com/crev201002.htm#20100226a
It seems, to achieve such 'unbelievable' energy efficiency, for such massive information processing in the cell, that the integrated coding between the DNA, RNA and Proteins of the cell apparently seems to be ingeniously programmed along the very stringent guidelines laid out by Landauer’s principle for ‘reversible computation’ in order to achieve such amazing energy efficiency.,,, The amazing energy efficiency possible with ‘reversible computation’ has been known about since Rolf Landauer laid out the principles for such programming decades ago, but as far as I know, due to the extreme level of complexity involved in achieving such ingenious 'reversible coding', has yet to be accomplish in any meaningful way for our computer programs even to this day:
Reversible computing Reversible computing is a model of computing where the computational process to some extent is reversible, i.e., time-invertible.,,, Although achieving this goal presents a significant challenge for the design, manufacturing, and characterization of ultra-precise new physical mechanisms for computing, there is at present no fundamental reason to think that this goal cannot eventually be accomplished, allowing us to someday build computers that generate much less than 1 bit's worth of physical entropy (and dissipate much less than kT ln 2 energy to heat) for each useful logical operation that they carry out internally. http://en.wikipedia.org/wiki/Reversible_computing#The_reversibility_of_physics_and_reversible_computing Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon - Charles H. Bennett Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus, dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,, http://www.hep.princeton.edu/~mcdonald/examples/QM/bennett_shpmp_34_501_03.pdf
Thus it seems, although I haven't seen much detailed research in this area, that the 'chemistry of the universe' itself was designed for eventually achieving programming in bio-chemistry along the very stringent guidelines laid out by Landauer's principle for reversible computation.bornagain77
August 24, 2012
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UB, Thank you for your detailed and precise argument. You are outlining a very important, often misunderstood , point: that in the cell specific knowledge of a completely arbitrary code (the genetic code) is implemented at least at two completely different, and independent, levels: 1) In the DNA protein coding genes, that are written according to the code, so that each gene corresponds to a specific functional sequence of AAs. 2) In the translation apparatus, and specifically in the 20 aminoacyl tRNA synthetases, 20 very complex proteins that are structured so that they can attach the correct aminoacid to the correct tRNA. WIthout those 20 complex proteins, no procedure of translation is possible. Both the DNA protein coding genes and the 20 synthetases are structured according to the same symbolic code, the genetic code. But the relation to the code is completely different: 1) in the DNA genes, the code is the foundation of the correspondence between the DNA sequence and the AA sequence. 2) In the 20 synthetases, the specific structure of each protein is the foundation of the biochemical function that allows each protein to correctly attach the right AA to the right tRNA, according to the genetic code. IF we consider that no translation is possible without the 20 synthetases, and that each synthetase is a very complex protein, translated from its DNA gene, we have a very beautiful case of "chicken and egg" problem: IOWs, a beautiful example of irreducible complexity.gpuccio
August 24, 2012
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Thank you again Maus.Upright BiPed
August 23, 2012
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UB:
I understand, but I don’t see it as being at odds. A spoken word is a material representation instantiated in the variations of local air pressure (sound).
Sure, sure. Delay line memory and like as well.
Quite frankly, I feel the same way about your number 3.
This is what we get for giving an infinite number of monkeys access to typewriters.
Only by the observation of function can we tell a material representation from any other arrangement of matter. Think Rosetta Stone.
True enough, but if that's what you're after then you need to make, in your argument, a clean separation between the system as it is and the system as we have knowledge of it. Especially with regards to 'function' specifically. Heiroglyphics and that Nazca Lines are obviously structured affairs for various reasons, but that observation is quite a bit different than watching the flywheel on a donkey engine spin about, lacking knowledge of the rest of the internals. I say 'need' but really it's just a personal kvetch for clarity. You can keep your own counsel on its accessibility.Maus
August 23, 2012
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Hello Maus,
2. ‘instantiated’ generally appeals to, and is understood by myself, in your argument to be synonynous to ‘stored’. True and correct but at odds with ‘spoken words’ in your definition (1). A great help if you clear up early that you are talking about persistent representations rather than temporal/transient ones.
I understand, but I don’t see it as being at odds. A spoken word is a material representation instantiated in the variations of local air pressure (sound). My definition does not turn on the lifespan of the material representation, whether it be a pattern of sound waves, or a book burned after 20 years time.
3. Terribly wordy and a bit tortured: “The material representation and material object represented are distinct and different.” This ought be a definitional point as with (1); as should it be different then the representation of an object is that object and not a representation. Which is not what was assumed and so absurd. (If you want to get proofy with it.)
Quite frankly, I feel the same way about your number 3. In fact, I can’t make heads or tails of it. :)
4. This is terribly ambiguous or I’m being thick. I assume you mean that the physical storage medium is a physical thing-bob. But that the given notion of the encoding stream or representation ordered upon that medium is a purely arbitrary issue.
No, I mean that “ the presence of that representation must present a material component to the system (which is reducible to physical law), while its arrangement presents an arbitrary component to the system (which is not reducible to physical law).”
5. I assume by this that you mean that for the information to be meaningful there must be an observer/recipient/interactor that can interface with the material storage but to which the arbitrary representation elicits a distinguished response. Loosely. If I have that correct, then no worries.
Close enough.
6. It’s wholly unnecessary for it to be ‘unambiguous’ in the sense that I understand your argument. Within the current context there are multiple codons that can signify a given amino acid. But there are also any manner on context specific decorations, etc, that can be bolted onto things that can change the translation environment. This is aside from any issues of general noise tolerance in the channel, etc. This one needs more work, or a clarification, to be useful.
If we could not see a representation and protocol in action, we could not (with confidence) confirm the transfer of recorded information. Only by the observation of function can we tell a material representation from any other arrangement of matter. Think Rosetta Stone.
I’ll stop here but I assume though that your entire point is to draw on analogous reasoning that DNA/Ribosomes/Proteins are in every manner the same — in the abstract — as a Jacquard loom, Turing machine, or Hard drive/Software/CPU set. If that is what you are after then I certainly don’t disagree with the general conclusion. But the argument itself is rather opaque as presented.
The argument is as I stated it above. Thanks for your input.Upright BiPed
August 23, 2012
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Hello steveh,
In point 1, UB lists examples which at first seem to be “intended” to convey information (codes,languages,etc) but then later (sensory input, etc. etc.) not necessarily so (to a non-ID person of course).
Neither the source of the information nor its intent (or lack of thereof) is germane to the material observations. Also, your #2 seems to be devoid of any relevant observations.
In point 3 he starts off with “if that is true” which is already on shaky grounds, but then goes on to say that “that arrangement must be necessarily arbitrary to the thing it represents”.
So far (in #1) you’ve introduced an issue which is not germane to the observations, and then (in #2) you made some comments about my undermining worldviews, which is irrelevant. And with that you’ve determined that my use of the phrase ’if that is true’ is “already on shaky ground”. And what exactly was I talking about when I said “if that is true”? I was talking about something you’ve already agreed would be impossible to exist any other way. :|
What about the shadow that a pair of would-be robbers...
Seeing a robber’s shadow requires vision. If you see a shadow, it is not then a shadow traveling through your optical nerve. It is a material representation of that image which will be translated into a functional effect by a protocol in your visual cortex. The remainder of your post seems to be somewhat content free in relation to the challenge of showing a flaw in either the material observations or the reasoning. If you'd like to actually challenge the observations, I will be happy to answer.Upright BiPed
August 23, 2012
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Hello Timothya,
You use “arbitrary” as a synonym for “not the same as”. I am unable to find any dictionary definition of “arbitrary” that matches this usage. Since you appear to rely on this word throughout your argument, I presume you attach some importance to your meaning for it.
It’s not really the word I rely upon; it the material observation which has been made. Proteins aren’t constructed from nucleotides. There is no inherent physical property in the pattern of cytosine-thymine-adenine which maps to leucine. That mapping is context specific, not an inexorable law. This has been shown in the lab. Perhaps it’s the Popper in me, but I simply don’t find it necessary to drone on about the number of different ways in which to express that reality, it is only the understanding of the observation that is important. That is why I took the time to explain my usage of the word at the time I used it. So if someone tells me that this thing is “materially arbitrary” to that thing and I have any background knowledge on the topic whatsoever, then perhaps I feel less of a need to run to dictionary in order to understand what it could possibly mean. You are free to call it whatever helps you understand. And if that is, as you say, your “only beef”, then I suspect you don’t intend on showing how the material observations are false, or that the reasoning is flawed. If you come up with something of material substance, then I’ll be happy to re-engage. Thanks.Upright BiPed
August 23, 2012
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UB: Some nits. 2. 'instantiated' generally appeals to, and is understood by myself, in your argument to be synonynous to 'stored'. True and correct but at odds with 'spoken words' in your definition (1). A great help if you clear up early that you are talking about persistent representations rather than temporal/transient ones. 3. Terribly wordy and a bit tortured: "The material representation and material object represented are distinct and different." This ought be a definitional point as with (1); as should it be different then the representation of an object is that object and not a representation. Which is not what was assumed and so absurd. (If you want to get proofy with it.) 4. This is terribly ambiguous or I'm being thick. I assume you mean that the physical storage medium is a physical thing-bob. But that the given notion of the encoding stream or representation ordered upon that medium is a purely arbitrary issue. 5. I assume by this that you mean that for the information to be meaningful there must be an observer/recipient/interactor that can interface with the material storage but to which the arbitrary representation elicits a distinguished response. Loosely. If I have that correct, then no worries. 6. It's wholly unnecessary for it to be 'unambiguous' in the sense that I understand your argument. Within the current context there are multiple codons that can signify a given amino acid. But there are also any manner on context specific decorations, etc, that can be bolted onto things that can change the translation environment. This is aside from any issues of general noise tolerance in the channel, etc. This one needs more work, or a clarification, to be useful. I'll stop here but I assume though that your entire point is to draw on analogous reasoning that DNA/Ribosomes/Proteins are in every manner the same -- in the abstract -- as a Jacquard loom, Turing machine, or Hard drive/Software/CPU set. If that is what you are after then I certainly don't disagree with the general conclusion. But the argument itself is rather opaque as presented.Maus
August 23, 2012
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timothya: The use of "arbitrary" is very common in information theory and mathematics. UB is not making this up. My dictionary includes things like: undetermined; not assigned a particular value; not restricted by law; subject to discretion. Maybe you need a better dictionary. Do you have a substantive concern with UB's argument? ----- BTW, DNA does not reproduce itself. It gets copied through a very detailed and complex and carefully orchestrated process involving a whole suite of coordinated systems.Eric Anderson
August 23, 2012
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timothya- DNA is NOT a replicator. DNA gets replicated when the cell divides. That said the mRNA is a representation of the amino acids it encodes. The mRNA does not become the amino acids, the codons it contains is just a representation of them. That means there is knowledge somewhere- knowledge of what codon represents which amino acid. And if that wasn't enough the ribosome is a genetic compiler and it is not reducible to matter and energy- synthesized ribosomes do not function and if they were reducible to matter and energy they would. All that said the morons over on the septic zone just don't get it and they sure as heck cannot demonstrate necessity and chance can do such a thing- that is account for the ribosome nor transcrition and translation. But I am sure that won't stop them from bloviating away.Joe
August 23, 2012
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Upright Biped said this:
And if it is separate from it, then it cannot be anything but materially arbitrary to it (i.e. they cannot be the same thing).
You use "arbitrary" as a synonym for "not the same as". I am unable to find any dictionary definition of "arbitrary" that matches this usage. Since you appear to rely on this word throughout your argument, I presume you attach some importance to your meaning for it.timothya
August 23, 2012
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Hello Steveh, I am now driving home. I will be happy to return and respond. UD Editors: UD does not condone texting, emailing blogging or otherwise distracting oneself while driving.Upright BiPed
August 23, 2012
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In point 1, UB lists examples which at first seem to be "intended" to convey information (codes,languages,etc) but then later (sensory input, etc. etc.) not necessarily so (to a non-ID person of course). In point 2 he says it's not logically possible to transfer information without ... I believe it is not "physically" possible - but "logically", I'm not so sure. In any case I can't help thinking UB could be undermining various in-tent worldviews in which information starts off, apprently, in some difficult to pin down immaterial "woo" dimension (my paraphrasing) and is conveyed to the here and now distant past by a what appear to me to be absolutely undetectable "magic" (ditto) mechanisms. In point 3 he starts off with "if that is true" which is already on shaky grounds, but then goes on to say that "that arrangement must be necessarily arbitrary to the thing it represents". What about the shadow that a pair of would-be robbers standing behind a rock throw on to the ground next to them? It informs an approaching victim that there are other people present; that one is much bigger than the other and appears to be holding a large club. These are not intended messages that the robbers meant to send but are nevertheless information which could save a life and require many bytes for me to pass on to you here. What if the intended victim went back to the scene the next day with a posse of local policemen (all clutching their beloved signed copies of How to calculate CSI&FSCI/O at a crime scene (Dembski, GEM, et al)) * and find footprints? The footprints represent information about the robbers (one was bare foot, the other wore size 10 shoes and walked with a pronounced limp, they walked west and then there seemed to be some sort of struggle, then there's a sort of grooved channel heading off to some bushes and a large set of single barefoot footprints leading away from that. Loads of information, none designed, none intended, all material, all subject to the laws of physics and certainly not arbitrary. In point 4 he starts off again with "if that is true" which is getting shakier by the minute and the rest is, afaict, a recap of point 3. By point 5 which starts of with "if that is true" again, I think he's lost the argument completely by now. But that's just me. * Above scenarios are imaginary, but this one humorously n-tuply so.steveh
August 23, 2012
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Semi OT: Higher level epigenetic information deals another blow to the 'central dogma' (genetic reductionism: DNA makes RNA makes proteins) of neo-Darwinism:
Histone-modifying proteins, not histones, remain associated with DNA through replication - August 23, 2012 Excerpt: A study of Drosophila embryos,, found that parental methylated histones are not transferred to daughter DNA. Rather, after DNA replication, new nucleosomes are assembled from newly synthesized unmodified histones. "Essentially, all histones are going away during DNA replication and new histones, which are not modified, are coming in,",, "What this paper tells us," he continues, "is that these histone modifying proteins somehow are able to withstand the passage of the DNA replication machinery. They remained seated on their responsive binding sites, and in all likelihood they will re-establish histone modification and finalize the chromatin structure that allows either activation or repression of the target gene." http://phys.org/news/2012-08-histone-modifying-proteins-histones-dna-replication.html
related video:
The Mysterious Epigenome. What lies beyond DNA - Woodward - video http://www.youtube.com/watch?v=RpXs8uShFMo
bornagain77
August 23, 2012
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My only beef would be with the use of the term “arbitrary”. In which sense is the term meant?
You ask "how are you using the term" immediately after reading exactly how I was using the term. Which words in the following paraghraph are you having trouble with:
If there is now an arrangement of matter which contains a representation of form as a consequence of its own material arrangement, then that arrangement must be necessarily arbitrary to the thing it represents. In other words, if one thing is to represent another thing within a system, then it must be separate from the thing it represents. And if it is separate from it, then it cannot be anything but materially arbitrary to it (i.e. they cannot be the same thing).
Upright BiPed
August 23, 2012
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I must be a bit dim. DNA: 1. replicates itself more or less faithfully, except when it mutates at random 2. transcribes protein sequences via RNAs more or less faithfully based on its specific nucelotide sequence The information held in the original DNA sequence is preserved through both processes (though it may be modified in both by either base substitution or mis-transcription, which are both observed). Did we need the airy persiflage to know this? My only beef would be with the use of the term "arbitrary". In which sense is the term meant? 1. Determined by chance, whim, or impulse, and not by necessity, reason, or principle: stopped at the first motel we passed, an arbitrary choice. 2. Based on or subject to individual judgment or preference: The diet imposes overall calorie limits, but daily menus are arbitrary. 3. Established by a court or judge rather than by a specific law or statute: an arbitrary penalty. 4. Not limited by law; despotic: the arbitrary rule of a dictator. (pinched from http://www.thefreedictionary.com/arbitrary) Presumably not 3 or 4. In both cases (replication and transcription), the results are necessary - the results are determined by the physics of DNA chemistry. The only arbitrary component arises when random mutations result in a different replicant, or mis-transciption results in a different protein output.timothya
August 23, 2012
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Excellent step by step breakdown of the 'information problem'. Definitely a keeper. Here is a video to help visualize the process:
Journey Inside The Cell - Stephen Meyer - video http://www.youtube.com/watch?v=1fiJupfbSpg
Related notes:
The DNA Enigma - Where Did The Information Come From? - Stephen C. Meyer - video http://www.metacafe.com/watch/4125886/ DNA Enigma - Chemistry Does Not Create Information - Chris Ashcraft PhD. molecular biology - video http://www.metacafe.com/watch/5542033/ Programming of Life - Protein synthesis (DNA transcription, translation and folding) - May 2011 - video http://www.youtube.com/watch?v=erOP76_qLWA
also of note:
Honors to Researchers Who Probed Atomic Structure of Ribosomes - Robert F. Service Excerpt: "The ribosome’s dance, however, is more like a grand ballet, with dozens of ribosomal proteins and subunits pirouetting with every step while other key biomolecules leap in, carrying other dancers needed to complete the act.” http://www.creationsafaris.com/crev200910.htm#20091015a Yonath on “ingeniously designed” ribosome? Everyone tells us she didn’t mean it … - February 2012 https://uncommondescent.com/intelligent-design/yonath-on-ingeniously-designed-ribosome-everyone-tells-us-she-didnt-mean-it/
Here is the ribosome animation that was done 'based on' the work from Yonath's Nobel winning group:
Ribosome animation http://www.youtube.com/watch?v=X9vIOYlZXjE The Ribosome: Perfectionist Protein-maker Trashes Errors Excerpt: The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist...the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products... To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is "shocking" and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis. http://www.sciencedaily.com/releases/2009/01/090107134529.htm
As well, The Ribosome of the cell is found to process information very similarly to a CPU in a electronic computer:
Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems - 2012 David J D’Onofrio1*, David L Abel2* and Donald E Johnson3 Excerpt: The DNA polynucleotide molecule consists of a linear sequence of nucleotides, each representing a biological placeholder of adenine (A), cytosine (C), thymine (T) and guanine (G). This quaternary system is analogous to the base two binary scheme native to computational systems. As such, the polynucleotide sequence represents the lowest level of coded information expressed as a form of machine code. Since machine code (and/or micro code) is the lowest form of compiled computer programs, it represents the most primitive level of programming language.,,, An operational analysis of the ribosome has revealed that this molecular machine with all of its parts follows an order of operations to produce a protein product. This order of operations has been detailed in a step-by-step process that has been observed to be self-executable. The ribosome operation has been proposed to be algorithmic (Ralgorithm) because it has been shown to contain a step-by-step process flow allowing for decision control, iterative branching and halting capability. The R-algorithm contains logical structures of linear sequencing, branch and conditional control. All of these features at a minimum meet the definition of an algorithm and when combined with the data from the mRNA, satisfy the rule that Algorithm = data + control. Remembering that mere constraints cannot serve as bona fide formal controls, we therefore conclude that the ribosome is a physical instantiation of an algorithm.,,, The correlation between linguistic properties examined and implemented using Automata theory give us a formalistic tool to study the language and grammar of biological systems in a similar manner to how we study computational cybernetic systems. These examples define a dichotomy in the definition of Prescriptive Information. We therefore suggest that the term Prescriptive Information (PI) be subdivided into two categories: 1) Prescriptive data and 2) Prescribed (executing) algorithm. It is interesting to note that the CPU of an electronic computer is an instance of a prescriptive algorithm instantiated into an electronic circuit, whereas the software under execution is read and processed by the CPU to prescribe the program’s desired output. Both hardware and software are prescriptive. http://www.tbiomed.com/content/pdf/1742-4682-9-8.pdf
bornagain77
August 23, 2012
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