Trying Hard to Be Charitable

_{Barry Arrington

September 27, 2014

Intelligent Design}

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AVS writes concerning the comparison between human codes/languages and the biological translation system:

Do you not see how superficial your comparison is between the biological translation system and human codes and languages?

Yes all these systems have a “code” of some sort that translates into “meaning,” but once you start digging deeper into the biological side of the equation, the differences become quite clear.

I think the problem is that we as humans explain the translational system using letters and words (how else would we do it), which makes it seem like there is huge similarities between this system and actual languages themselves.

My point is that when you get down to it, the biological translational system does not read letters and comprehend them into a meaning in any way like we do.

Barry responds:

Take a sec to watch this video of robots working on cars:

Now, I take it that the robots run on software. I also take it that the robots don’t “read” the software and “comprehend” it into meaning like a human software engineer would. Now assume all trace of technology, civilization and life vanished from this planet except for these robots, which continued working away. If an alien happened along, under your reasoning he would not be entitled to infer the robots or the software operating them was designed. That is obviously wrong. Ergo, your reasoning is wrong.

AVS replies:

At first glance, yes, this alien would be entitled to think both systems were designed. And this is because that first glance at both systems is extremely superficial, just like your semiotics comparison between the two.

As I said, a more detailed look at these two systems would demonstrate the huge differences in their underlying mechanisms, one designed by intelligent minds, the other derived from natural properties and laws.

I am trying very hard to abide by the principle of charity. I have read AVS’s reply several times and attempted to discern even the merest nod toward a logical argument. I have failed to detect any such nod. It seems to me that either AVS’s argument is far too subtle for me to grasp (a possibility I freely admit), or materialists such as AVS believe that mere contradiction is an adequate stand-in for rational argument. I invite our readers to decide.

Comments

Correct, it is very subtle and requires intimate knowledge of the processes of the transcription/translation apparatus. Therefore it makes sense that my argument went over your head.
AVS, you are obviously bluffing and talking nonsense. Either you are purposely being obfuscatory or have no idea what you are talking about. Which is it?Eric Anderson_{September 28, 2014
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Dr. Snoke relates how the new field of systems biology is pretty much leaving neo-Darwinian thinking in the dust:
How the Burgeoning Field of Systems Biology Supports Intelligent Design - July 2014 Excerpt: Snoke lists various features in biology that have been found to function like goal-directed, top-down engineered systems: *"Negative feedback for stable operation." *"Frequency filtering" for extracting a signal from a noisy system. *Control and signaling to induce a response. *"Information storage" where information is stored for later use. In fact, Snoke observes: "This paradigm [of systems biology] is advancing the view that biology is essentially an information science with information operating on multiple hierarchical levels and in complex networks [13]. " *"Timing and synchronization," where organisms maintain clocks to ensure that different processes and events happen in the right order. *"Addressing," where signaling molecules are tagged with an address to help them arrive at their intended target. *"Hierarchies of function," where organisms maintain clocks to ensure that cellular processes and events happen at the right times and in the right order. *"Redundancy," as organisms contain backup systems or "fail-safes" if primary essential systems fail. *"Adaptation," where organisms are pre-engineered to be able to undergo small-scale adaptations to their environments. As Snoke explains, "These systems use randomization controlled by supersystems, just as the immune system uses randomization in a very controlled way," and "Only part of the system is allowed to vary randomly, while the rest is highly conserved.",,, Snoke observes that systems biology assumes that biological features are optimized, meaning, in part, that "just about everything in the cell does indeed have a role, i.e., that there is very little 'junk.'" He explains, "Some systems biologists go further than just assuming that every little thing has a purpose. Some argue that each item is fulfilling its purpose as well as is physically possible," and quotes additional authorities who assume that biological systems are optimized.,,, http://www.evolutionnews.org/2014/07/when_biologists087871.html Systems Biology as a Research Program for Intelligent Design - David Snoke - 2014 http://bio-complexity.org/ojs/index.php/main/article/viewArticle/BIO-C.2014.3 "It has become clear in the past ten years that the concept of design is not merely an add-on meta-description of biological systems, of no scientific consequence, but is in fact a driver of science. A whole cohort of young scientists is being trained to “think like engineers” when looking at biological systems, using terms explicitly related to engineering design concepts: design, purpose, optimal tradeoffs for multiple goals, information, control, decision making, etc. This approach is widely seen as a successful, predictive, quantitative theory of biology." David Snoke*, Systems Biology as a Research Program for Intelligent Design podcast: "David Snoke: Systems Biology and Intelligent Design, pt. 1" http://intelligentdesign.podomatic.com/entry/2014-08-11T17_19_09-07_00 podcast: David Snoke: Systems Biology and Intelligent Design, pt. 2 http://intelligentdesign.podomatic.com/entry/2014-08-13T16_30_01-07_00
bornagain77_{September 28, 2014
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also of note: James Shapiro on “dangerous oversimplifications” about the cell - August 6, 2013 Excerpt: "Depending upon the energy source and other circumstances, these indescribably complex entities can reproduce themselves with great reliability at times as short as 10-20 minutes. Each reproductive cell cycle involves literally hundreds of millions of biochemical and biomechanical events. We must recognize that cells possess a cybernetic capacity beyond our ability to imitate. Therefore, it should not surprise us when we discover extremely dense and interconnected control architectures at all levels. Simplifying assumptions about cell informatics can be more misleading than helpful in understanding the basic principles of biological function. Two dangerous oversimplifications have been (i) to consider the genome as a mere physical carrier of hypothetical units called “genes” that determine particular cell or organismal traits, and (ii) to think of the genome as a digitally encoded Read-Only Turing tape that feeds instructions to the rest of the cell about individual characters [4]." https://uncommondescent.com/news/james-shapiro-on-dangerous-oversimplifications-about-the-cell/bornagain77_{September 28, 2014
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awstar that's what I was afraid you were driving at, and for that particular question I do not have, nor do I think anyone really has, a firm answer. A few notes in that regards,,,
HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE - Stephen L. Talbott - May 2012 Excerpt: “If you think air traffic controllers have a tough job guiding planes into major airports or across a crowded continental airspace, consider the challenge facing a human cell trying to position its proteins”. A given cell, he notes, may make more than 10,000 different proteins, and typically contains more than a billion protein molecules at any one time. “Somehow a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places”. And further: “It’s almost as if every mRNA [an intermediate between a gene and a corresponding protein] coming out of the nucleus knows where it’s going” (Travis 2011),,, Further, the billion protein molecules in a cell are virtually all capable of interacting with each other to one degree or another; they are subject to getting misfolded or “all balled up with one another”; they are critically modified through the attachment or detachment of molecular subunits, often in rapid order and with immediate implications for changing function; they can wind up inside large-capacity “transport vehicles” headed in any number of directions; they can be sidetracked by diverse processes of degradation and recycling... and so on without end. Yet the coherence of the whole is maintained. The question is indeed, then, “How does the organism meaningfully dispose of all its molecules, getting them to the right places and into the right interactions?”,,, And then we hear that all this meaningful activity is, somehow, meaningless or a product of meaninglessness. This, I believe, is the real issue troubling the majority of the American populace when they are asked about their belief in evolution. They see one thing and then are told, more or less directly, that they are really seeing its denial. Yet no one has ever explained to them how you get meaning from meaninglessness — a difficult enough task once you realize that we cannot articulate any knowledge of the world at all except in the language of meaning.,,, http://www.netfuture.org/2012/May1012_184.html#2 With a Startling Candor, Oxford Scientist Admits a Gaping Hole in Evolutionary Theory - November 2011 Excerpt: As of now, we have no good theory of how to read [genetic] networks, how to model them mathematically or how one network meshes with another; worse, we have no obvious experimental lines of investigation for studying these areas. There is a great deal for systems biology to do in order to produce a full explanation of how genotypes generate phenotypes,,, http://www.evolutionnews.org/2011/11/with_a_startling_candor_oxford052821.html Not Junk After All—Conclusion - August 29, 2013 Excerpt: Many scientists have pointed out that the relationship between the genome and the organism — the genotype-phenotype mapping — cannot be reduced to a genetic program encoded in DNA sequences. Atlan and Koppel wrote in 1990 that advances in artificial intelligence showed that cellular operations are not controlled by a linear sequence of instructions in DNA but by a “distributed multilayer network” [150]. According to Denton and his co-workers, protein folding appears to involve formal causes that transcend material mechanisms [151], and according to Sternberg this is even more evident at higher levels of the genotype-phenotype mapping [152]. https://uncommondescent.com/junk-dna/open-mike-cornell-obi-conference-chapter-11-not-junk-after-all-conclusion/ (Dual Coding) RNA Shows Design, Too - February 4, 2014 Excerpt: A paper in Nature describes how information is stored not only in RNA's base sequence, but in its folds. Because RNA has more degrees of freedom, it can take on a wide variety of forms not possible for DNA. "RNA has a dual role as an informational molecule and a direct effector of biological tasks. The latter function is enabled by RNA's ability to adopt complex secondary and tertiary folds and thus has motivated extensive computational and experimental efforts for determining RNA structures," the authors begin (emphasis added). In their conclusion, they say, "We identify hundreds of specific mRNA regions that are highly structured in vivo, and we show for three examples that these structures affect protein expression." In other words, the structure, not just the sequence, carries functional information. "Our studies provide an excellent set of candidate regions, among the truly enormous number of structured regions seen in vitro, for exploring the regulatory role of structured mRNAs.",,, http://www.evolutionnews.org/2014/02/rna_shows_desig081841.html
Here are a couple of short videos highlighting the complexity being dealt with:
The Extreme Complexity Of Genes - Dr. Raymond G. Bohlin - video https://vimeo.com/106012299 Design In DNA – Alternative Splicing, Duons, and Dual coding genes – video (5:05 minute mark) http://www.youtube.com/watch?v=Bm67oXKtH3s#t=305
etc.. etc.. etc..bornagain77_{September 28, 2014
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Thanks for the response, BA. However, I was looking for more explanation on the logistics of making proteins. if the ribosome is reading one codon at a time, how do the various tRNA (delivery vehicles if you will) know they will be called on next to match up with the mRNA? I picture something like an airport runway where mRNA is read one codon at a time and out of the swarm of tRNA circling the runway, only one is called in at a time to deliver it's payload and take off again (presumably to get another payload). So in my imagination, there would need to be some sort of traffic control tower, advising which of the swarming tRNA's will be called on next to deliver its load -- just as real control tower operators let the incoming airplanes know where they are suppose to be in the que to land. That would require some sort of communication and orchestration function. Where would that happen?awstar_{September 28, 2014
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awstar as to your question,
"can anyone here explain (BA77 perhaps) how does process “know” which tRNA is going to be needed next, so that the correct tRNA’s are queued properly and a lot of time isn’t spent on trial and error matching a tRNA codon to the requesting codon on the mRNA?"
There has been some advances in deciphering alternative splicing codes that may shed some light on your question,,,
Researchers Crack ‘Splicing Code,’ Solve a Mystery Underlying Biological Complexity Excerpt: “For example, three neurexin genes can generate over 3,000 genetic messages that help control the wiring of the brain,” says Frey. “Previously, researchers couldn’t predict how the genetic messages would be rearranged, or spliced, within a living cell,” Frey said. “The splicing code that we discovered has been successfully used to predict how thousands of genetic messages are rearranged differently in many different tissues. http://www.sciencedaily.com/releases/2010/05/100505133252.htm Deciphering the splicing code - May 2010 Excerpt: Here we describe the assembly of a ‘splicing code’, which uses combinations of hundreds of RNA features to predict tissue-dependent changes in alternative splicing for thousands of exons. The code determines new classes of splicing patterns, identifies distinct regulatory programs in different tissues, and identifies mutation-verified regulatory sequences.,,, http://www.ecs.umass.edu/~mettu/ece597m/lectures/hts-papers/barash-splicing-code.pdf Breakthrough: Second Genetic Code Revealed - May 2010 Excerpt: The paper is a triumph of information science that sounds reminiscent of the days of the World War II codebreakers. Their methods included algebra, geometry, probability theory, vector calculus, information theory, code optimization, and other advanced methods. One thing they had no need of was evolutionary theory,,, http://crev.info/content/breakthrough_second_genetic_code_revealed Researchers Crack 'Splicing Code,' Solve a Mystery Underlying Biological Complexity - May 2010 Excerpt: "Understanding a complex biological system is like understanding a complex electronic circuit. Our team 'reverse-engineered' the splicing code using large-scale experimental data generated by the group," http://www.sciencedaily.com/releases/2010/05/100505133252.htm
hope that helps a little awstarbornagain77_{September 28, 2014
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AVS claims:
You guys can twist words and make things seem like its similar to computer coding all you want, but the fact remains: they are nothing alike.
Yet Craig Venter states:
Venter: Life Is Robotic Software - July 15, 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.” http://crev.info/2012/07/life-is-robotic-software/
Moreover,,
Every Bit Digital DNA’s Programming Really Bugs Some ID Critics - March 2010 Excerpt: In 2003 renowned biologist Leroy Hood and biotech guru David Galas authored a review article in the world’s leading scientific journal, Nature, titled, “The digital code of DNA.”,,, MIT Professor of Mechanical Engineering Seth Lloyd (no friend of ID) likewise eloquently explains why DNA has a “digital” nature: "It’s been known since the structure of DNA was elucidated that DNA is very digital. There are four possible base pairs per site, two bits per site, three and a half billion sites, seven billion bits of information in the human DNA. There’s a very recognizable digital code of the kind that electrical engineers rediscovered in the 1950s that maps the codes for sequences of DNA onto expressions of proteins." http://www.salvomag.com/new/articles/salvo12/12luskin2.php
Moreover,,
Towards practical, high-capacity, low-maintenance information storage in synthesized DNA - January 2013 Excerpt: Here we describe a scalable method that can reliably store more information than has been handled before. We encoded computer files totalling 739 kilobytes of hard-disk storage and with an estimated Shannon information of 5.2?×?106 bits into a DNA code, synthesized this DNA, sequenced it and reconstructed the original files with 100% accuracy. Theoretical analysis indicates that our DNA-based storage scheme could be scaled far beyond current global information volumes and offers a realistic technology for large-scale, long-term and infrequently accessed digital archiving. In fact, current trends in technological advances are reducing DNA synthesis costs at a pace that should make our scheme cost-effective for sub-50-year archiving within a decade. http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11875.html
Thus, AVS can claim that the earth is flat (i.e. life is non-digital) all he wants, but those not wedded to neo-Darwinian dogmatism, (flat earth view of denying digital information is in life), are already sailing around the digital DNA world. :)bornagain77_{September 28, 2014
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@AVS: Here's the correct link: http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00140/abstract
Also, please keep using the words software and hardware to talk about biology, it’ll make all your friends even more certain these systems are identical.
Nobody thinks they're identical, don't be silly. There are certain similar principles underlying but the biological system is of course much more sophisticated and complex simply because the requirements are vastly different and much more comprehensive than any computer/machine. It's not that this would make the case for neo-darwinian evolution any better, though...
But I wouldn’t expect any of you guys to know that.
People living in glass houses shouldn't throw stones around. They should throw parties with strippers... SebestyenSebestyen_{September 28, 2014
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AVS #9
No, star, they’re really not anything alike. Also, tRNA has an important 3-dimensional shape, and I think you meant to say that the mRNA is read in a one directional linear sequence. You guys can twist words and make things seem like its similar to computer coding all you want, but the fact remains: they are nothing alike.
Thanks, AVS. mRNA is what I was thinking about. Not being a biologist, but a computer programmer is my excuse. But the tRNA also has one side of the interface that needs to be in proper sequence in one direction, much like keying in a PIN to open an app. By the way, can anyone here explain (BA77 perhaps) how does process "know" which tRNA is going to be needed next, so that the correct tRNA's are queued properly and a lot of time isn't spent on trial and error matching a tRNA codon to the requesting codon on the mRNA?awstar_{September 28, 2014
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What They Really Teach Students In A Evolutionary Biology Class - cartoon http://4.bp.blogspot.com/-96cpSHPgIL4/VCftJobtPmI/AAAAAAAALf8/ZVyC7GB9dm0/s1600/Darwinism_See%2BNo.jpgbornagain77_{September 28, 2014
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Dr. Stephen Meyer: Chemistry/RNA World/crystal formation can't explain genetic information - video Excerpt 5:00 minute mark: "If there is no chemical interaction here (in the DNA molecule) you can't invoke chemistry to explain sequencing" http://www.youtube.com/watch?v=yLeWh8Df3k8 John Lennox – Is There Evidence of Something Beyond Nature? (Semiotic Information) – video http://www.youtube.com/watch?v=F6rd4HEdffw Intelligent design: Why can't biological information originate through a materialistic process? - Stephen Meyer - video http://www.youtube.com/watch?v=wqiXNxyoof8bornagain77_{September 28, 2014
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To Whom This May Concern FYI: Here’s what AVS wrote on March 31, 2014:
Not only do we not know exactly how a lot of these things work, but what we do know would fill stacks and stacks of books. In fact they do. ...we don’t know a lot about how things are happening in cells currently, this makes putting together a picture of the evolution of these biological systems extremely difficult.
Here's the link to the quoted comments: https://uncommondescent.com/intelligent-design/jonathan-wells-far-from-being-all-powerful-dna-does-not-wholly-determine-biological-form/#comment-494560Dionisio_{September 28, 2014
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PS: Observe p 5 2nd col here: "Computer Architecture is the assembly language programmer's view of a computer." The implications for linking hard and software at object code level should be clear. So, yes, we can reverse engineer the object code from its physical storage in a prong-height tape medium, and observe the algorithmic pattern of mobilisation and initiation, start, step by step processes, halt and demobilisation of the processing unit.kairosfocus_{September 28, 2014
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AVS: Are you familiar with computer architecture and organisation, and in particular the old definition that the archi of a computer is the assembly language view of the system? With specific computer and network technologies in hardware at that level, e.g. the classic 6800/6500 family for simple example, or maybe microcontrollers or the like at 16, 32, 64, the RISC debate or long instruction word levels? (For, that is the level of register transfer and operations tied to such processes.) I suggest you pause a moment and glance here at the OP, with particular reference to the last three images. You will first see there functionally specific organisation of arranged and coupled components, which embeds prescriptive information. Next, compare the ribosome and the paper tape reader, bearing in mind the FSCO/I as just shown. You will see how algorithmic information can be coded physically in a control tape, threaded into a read head and fed in to control an operation of a numerically controlled unit, step by step. The coded algorithmic info in DNA is object -- machine level -- code. It starts, is incremented step by step, instructs which of 20 options to implement next, and continues to the point where a halting instruction and demobilisation of the unit are carried out. A code is of course a mapping using a system of symbolic representation, and an algorithm is a step by step goal-directed process that initiates, proceeds, and concludes including a halt. In the case of the code tape, there is remote storage, a transcription and editing process, leading to transfer to the active site where ribosomes act. Click-together chaining chemistry is used and AT RIGHT ANGLES TO THE CHAIN, information is coded on a prong-height system similar to the prongs on a classic Yale lock. (BTW, in von Neumann's kinematic self-replicator proposal, a prong height coding scheme was put forward.) The active unit also uses a position-arm end effector unit, or rather 20 of them, the protein-bearing transfer RNAs. These have two ends, one bearing complementary codes to the prong-height three character codons, and at the other there is a standard CCA coupler unit to which in principle any amino acid may be attached. Yes, ANY . . . used in artificial protein units that reprogram some tRNAs. The tRNAs are loaded using loading enzymes that sense conformation of the folded tRNA and attach the right AA to the coupler. In the ribosome, these are chained by the prong-height key-lock attachment and the protein chaining. Proteins of course also have active units on side chains. Proteins and many RNAs have a process of folding to functional configuration post chaining, which is itself a sohphisticated embedding of information and organisation. In the case of proteins, there are thousands of deeply isolated folding clusters in AA sequence space, many with but few members. The search challenge implicit in this case of islands of function is easily shown to be empirically insurmountable by blind chance and mechanical necessity on the gamut of the available atomic and temporal resources of the observable cosmos. Now of course one may plaster "analogy" all over this and dismiss it on grounds that comparisons "prove" nothing, or the like. But such empirical comparisons and recognition of patterns are not deductive demonstrative exercises. They are inductive reasoning, and particularly an application of inference to best explanation. The comparable patterns and processes are real, and in some cases were predicted in advance )the kinematic self-replicator was put up 1948 - 9, DNA was discovered 1953, and its linked processes were drawn out over decades following, a work still in process.) What is interesting is to see the pall cast by injection of a priori materialism in the guise of a "mere" methodological principle, its blinding effect and the associated selective hyperskepticism in defence of ideological power base. Sadly interesting. Please, wake up from your ideologically induced dogmatic slumbers. KFkairosfocus_{September 28, 2014
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AVS:
Early organisms evolved this translating system to carry out more diverse functions with better efficiency.
lol! priceless! thanks UPB!Mung_{September 27, 2014
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Upright BiPed, I think you're being too hard on AVS. AVS is not aware of the "quality control" and "quality assurance" processes in the cell, but he knows they are not anything like quality control and quality assurance as practiced by human engineers. AVS knows all about the abuse and misuse of semiosis in ID thinking, but he's not really sure what the concept really means. AVS admits to the reality of "codes" and "translation" in the cell, but the use of scare quotes somehow makes it all less real. AVS isn't really close-minded about these issues, it's just that it takes time to change from being an intellectual redneck.Mung_{September 27, 2014
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One of the previous conversations... now ignored, as expected.
AVS: The transcription and translation processes are entirely based on chemistry. Can you explain why functional sequence specific DNA cannot be reduced to chemistry?

UB: Because there is a chemical discontinuity between the nucleic medium and the amino acid effect that must be preserved in order for translation to be obtained.

AVS: And what is this chemical discontinuity exactly, Upright?

UB: There is nothing you can do to the nucleic pattern GCA to relate it to Alanine, except translate it. Which is what the cell does.

AVS: It’s related by another nucleic pattern, bound to alanine, that has a specific sequence that associates with that GCA.

UB: The base pairing that enables transcription between nucleotides does not establish a relationship to alanine. That relationship is established by the protein aaRS before the transfer RNA ever enters the ribosome.

UB: AVS, is there an inexorable chemical relationship between pattern GCA and alanine, or is it a contingent relationship?

AVS: But there is a relationship. You just explained it. The amino acid is associated with the aaRS, which associates with tRNA, which associates with mRNA. This relationship is the product of the evolution of these molecules.

UB: Correct. The relationship is established in spatial and temporal isolation by the protein aaRS. So, there is a physical discontinuity between the nucleic pattern and the amino acid, which is contingent on the structure of the protein aaRS. Therefore, there is nothing about the pattern that determines the amino acid, and consequently, chemistry cannot explain the association. It can only explain the operation of the system with the association in place.

AVS: The association of the tRNA with aaRS determines the amino acid as I said. The chemical evolution that occurred would explain the why these molecules associate in our cells now, an ultimately arbitrary decision, driven by chemical interactions that occurred in early cells.

UB: The cells decided huh? cool AVS, there is a chemical discontinuity between the nucleic medium and the amino acid effect, and that discontinuity must be preserved in order for translation to be obtained. Do you know why? (…think about it)

AVS: That chemical discontinuity between nucleotide and protein is bridged by more chemical interactions though, UB, which as I said are the product of evolution. Yes the cells “decided” for lack of a better word. This is one of the problems with you guys, scientists try to put things in the simplest terms an you completely blow these terms out of proportion.

UB: I’m glad you now recognize the discontinuity. My question is: Do you know why it’s there, and why the system must preserve it during translation? (hint: it’s not evolution)

AVS: It is evolution UB. Early organisms evolved this translating system to carry out more diverse functions with better efficiency. The system we see today is the result of the chemical evolution that occurred in these early organisms and has been conserved to this day.

UB: This is not an answer to the question. Do you know why it’s there, and why the system must preserve it during translation? There is an identifiable reason. What is it?

AVS: UB, there obviously needs to be a connection to nucleotide and amino acid that is conserved. The system we have been talking about does this and it does this based on chemical interactions. And the evolution of this system was based on chemical interactions. That’s it. Make your point already.

UB: AVS, I was giving you the benefit of the doubt, hoping you could think for yourself. Why would a physical discontinuity be required in a chemo/mechanical system in order to get a particular amino acid presented at the peptide binding site? Why would such a system need to preserve that discontinuity in order to produce the effect? … The physical effect of having a particular amino acid presented at a binding site at a particular point in time is not something that can be derived from physical law – it’s not some innate property to be drawn from, or activated in, the atomic composition of matter. So a discontinuity will naturally exist in any system that produces such an effect. That discontinuity is required in order to allow the input of formal constraint (information) into the system, where it can produce an effect that operates under physical law, but is not determined by it. In other words, it’s an operational necessity to achieve the result. And the system must preserve that discontinuity for much the same reason. From a purely mechanical standpoint, if the effect were derivable directly from the physical properties of the medium, then it would be so by the forces of inexorable law, and those inexorable forces would limit the system to what can be physically derived from that medium, thus making the input of form (not derived from that medium) impossible to achieve. However, incorporating the discontinuity by preserving it allows the effect to be determined by a second arrangement of matter operating in the system. This second arrangement establishes a local relationship between the medium and its effect (bridging the discontinuity while preserving it). This relationship then becomes an identifiable regularity of the system, allowing the system the capacity to produce lawful effects not determined by physical law.

UB: …by the way. This entire arrangement is a necessary precondition of the genotype-phenotype distinction. It must be in place prior to the onset of Darwinian evolution. To say this system is the product of Darwinian evolution, is to say that a thing that does not yet exist on a pre-biotic earth can cause something to happen. Which is obviously false.

AVS: *crickets*
:|Upright BiPed_{September 27, 2014
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AVS, The physical conditions required the translate the arrangement of the representations into functional physical effects is the same in both systems. We've been over the facets of these conditions in detail. You deny them. Misrepresenting an argument and attacking those who make it is mankind's oldest means of keeping unsupported beliefs alive. Do what you do.Upright BiPed_{September 27, 2014
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AVS:
Yes, again, “code in, code out=welp these two systems must be identical!”
AVS, code in, code out is a pretty significant similarity. It is what happens in computers, robots, machines, etc. The code is all important. Where did the code come from? How did it grow and add new features and new codes, even codes embedded within codes by chance? Maybe you have it all figured out. I'm sure you have lots of experimental evidence to back up your hypothesis as well. Lay it on us dude! We're all about evidence here - real evidence that is!tjguy_{September 27, 2014
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I use the terms hardware and software to describe the cell. Why is that wrong? Is it because hardware and software are always designed by intelligence, but the stuff of the cell isn't in his mind? If he can explain where the code came from, I'd love to hear it. Maybe if we do some experiments, we can get some new code that codes for something new that will evolve? That would be cool! That would be REAL evidence!tjguy_{September 27, 2014
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AVS:
Also, please keep using the words software and hardware to talk about biology, it’ll make all your friends even more certain these systems are identical.
Where in the post @ 6 did Sebestyen speak about biology in terms of hardware and software? You're just making that up.Mung_{September 27, 2014
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Joe:
Yes, again, more imbecilic drooling from AVS.
LOL. I like your style, Joe. Give them no quarters.Mapou_{September 27, 2014
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AVS:
Yes, again, “code in, code out=welp these two systems must be identical!”
Yes, again, more imbecilic drooling from AVS.Joe_{September 27, 2014
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Yes, again, "code in, code out=welp these two systems must be identical!" Talk about jumping to conclusions. Sebestyn your link doesn't work, but that does sound interesting. Also, please keep using the words software and hardware to talk about biology, it'll make all your friends even more certain these systems are identical. YEAH! For the last time, you cannot compare biology to anything else in the way that you guys try to. Maybe at an extremely superficial level it'll work, but when you start getting into the details, nothing can compare. But I wouldn't expect any of you guys to know that. No, star, they're really not anything alike. Also, tRNA has an important 3-dimensional shape, and I think you meant to say that the mRNA is read in a one directional linear sequence. You guys can twist words and make things seem like its similar to computer coding all you want, but the fact remains: they are nothing alike. Barry, I did not say that, there definitely is information in this system, but I disagree with you guys about how the information is interpreted and whether or not it requires a designer. I'm not about to get into an argument about information with you because we all know how you guys can twist and turn your definition of "information" however you want. Thanks for the fun, but I can't promise I'll be back, I have to leave this world you guys live in and return to reality. <3AVS_{September 27, 2014
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AVS, you seem to be saying that it is all simply a chemical reaction, and a corollary to that is that there is no information being processed.Barry Arrington_{September 27, 2014
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This mechanism is nothing like the linearity of computer codes controlling the movements of a robotic arm.
I'm sorry to point out your error AVS, but transfer RNA, a one dimensional string of only four unique "things" processed in a one directional linear sequence to produce a three dimensional object is SOMETHING like the linearity of computer codes controlling the movements of a robotic arm. The only reason you say otherwise is because in our society where grace happens, you can get away with it without suffering any consequences. (Isn't mr. news a she?)awstar_{September 27, 2014
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And mr. news, don’t tell me what I do and do not believe. thanks
One thing is for sure: You know jack shit about IT. You're comparing hardware with software and think you made an argument that "went over someone's head"? Are you serious? And btw...
...often the third base pair can be incorrect, and yet the amino acid will be still be added, whether it is the correct one or not.
It was recently found that the third base pair is used to alter the speed of the translation decoding process within the ribosome and therefore regulates how the protein folds. http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00140/abstract SebestyenSebestyen_{September 27, 2014
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AVS:
This mechanism is nothing like the linearity of computer codes controlling the movements of a robotic arm.
No one is making that claim. The mechanism is like how source codes get compiled to become object codes.Joe_{September 27, 2014
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AVS: Are you out of your mind? The biological translation system works with biochemical molecules, exactly like a computer works with transistors and electricity. There is no difference. The symbolic coupling of codons and AAs is realized by the 20 aminoacyl tRNA synthetases, and depend critically on their complex tertiary structure. Can you deny that the codons in the protein coding gene are correctly translated to the correct aminoacid? (allowing for minor errors which are inherent to the media used)? How do you think that happens? You understand nothing of biology, and still you think you are subtle! What a shame.gpuccio_{September 27, 2014
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"We have always underestimated cells. Undoubtedly we still do today. But at least we are no longer as naïve as we were when I was a graduate student in the 1960s.,,,, Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines." - Bruce Alberts, "The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists," Cell, 92 (February 6, 1998): 291-294 Venter: Life Is Robotic Software - July 15, 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 (Craig) Venter. http://crev.info/2012/07/life-is-robotic-software/ Cells Are Like Robust Computational Systems, - June 2009 Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,"We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail." http://www.sciencedaily.com/releases/2009/06/090616103205.htm Programming of Life – Don Johnson - video https://www.youtube.com/watch?v=00vBqYDBW5s Ben Stein - EXPELLED - The Staggering Complexity Of The Cell – video https://www.youtube.com/watch?v=5wmhiq25MqU
Here is, according to a Darwinist, a ‘horrendously complex’ metabolic pathway chart:
Map Of Major Metabolic Pathways In A Cell - Diagram http://www.sigmaaldrich.com/img/assets/4202/MetabolicPathways_6_17_04_.pdf
Part of the ‘horrendous complexity’ inherent in metabolic pathways is gone over here:
The 10 Step Glycolysis Pathway In ATP Production: An Overview – video http://www.youtube.com/watch?v=8Kn6BVGqKd8
At the 14:00 minute mark of the following video, Chris Ashcraft, PhD – molecular biology, gives us an overview of the Citric Acid Cycle, which is, after the 10 step Glycolysis Pathway, also involved in ATP production:
Evolution vs ATP Synthase – Chris Ashcraft - video - citric acid cycle at 14:00 minute mark https://www.youtube.com/watch?feature=player_detailpage&v=rUV4CSs0HzI#t=746
Moreover, in spite of the fact of finding molecular motors permeating the simplest of bacterial life, there are no detailed Darwinian accounts for the evolution of even one such motor or system. "There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject." James Shapiro, molecular biologist, National Review, Sept. 16, 1996 Dr. James Tour, who, in my honest opinion, currently builds the most sophisticated man-made molecular machines in the world, will buy lunch for anyone who can explain to him exactly how Darwinian evolution works:
“I build molecules for a living, I can’t begin to tell you how difficult that job is. I stand in awe of God because of what he has done through his creation. Only a rookie who knows nothing about science would say science takes away from faith. If you really study science, it will bring you closer to God." James Tour – one of the leading nano-tech engineers in the world - Strobel, Lee (2000), The Case For Faith, p. 111 Top Ten Most Cited Chemist in the World Knows Darwinian Evolution Does Not Work - James Tour, Phd. https://www.youtube.com/watch?v=_Y5-VNg-S0s
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