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Writing Biosemiosis.org

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In September of 2009 I started a new document on my computer entitled “A System of Symbols”, where I was going to write about the part of design theory that interested me the most – that is, the representations that are required for self-replication (von Neumann, Pattee). My goal was to inventory all the physical conditions necessary for one thing to represent another thing in a material universe. I wrote and rewrote that essay for more than four years — reading, learning, and sharing along the way. As it turns out, writing that essay was my way of coming to understand the issues, and I spent a great deal of that time trying to articulate things I had come to understand conceptually, but could not yet put into words. Eventually I came into contact with the types of scientists and researchers who had substantial experience with these issues, up to and including those who had spent their entire careers on the subject. It was a humbling experience to share my thoughts with people of that caliber, and have them respond by sending me papers of their own that reflected the same concepts.

Then In 2014, I retired that essay and began writing Biosemiosis.org in its place. Since that work is available to any reader, I won’t recapitulate it here, but there are a couple of concepts I’d like to highlight – particularly the discontinuity found in the translation of recorded information. Read More

[I’d like to thank Barry and Uncommon Descent for allowing me to publish this introduction to my two projects]

Comments
peptidyltransferase - the ribosomal enzyme that catalyzes the elongation step in polypeptide synthesis - Oxford Dictionary of Biochemistry and Molecular BiologyMung
November 11, 2015
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I hope I'm not the only one who will miss Alicia Cartelli.Mung
November 9, 2015
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Upright BiPed: I am not sure what response you are wanting from me regarding anticipatory systems. Speaking of which. Anticipatory Systems: Philosophical, Mathematical, and Methodological Foundations But not cheap.Mung
November 9, 2015
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Mohammad,
In this paper, I will focus on anticipation, … Anticipation refers to the establishment and operation of symmetry inducing normative habits of morphological formation. Anticipation is not only related to predictions but to decisions: hyperincursive systems create multiple choices and a decision process selects one choice ... Strong anticipation refers to an anticipation of events generated by the system itself. Weak anticipation refers to an anticipation of events predicted or forecasted from a model of a system’. -- Edwina Taborsky
I am not sure what response you are wanting from me regarding anticipatory systems. The writing I have done on semiosis is specifically limited to the physical process of representation -- i.e. what is necessary for a representation to be a representation. Also, I have no desire at all to pass judgment on the specialized thoughts of semiosis provided by others, but in reading Taborsky’s paper, I am quickly reminded of comments made by Pattee:
While the language of physics is reasonably simple and unambiguous, I discovered quickly that the terminologies of semiotics are so complicated and controversial that I could not hope to find consensus on primitive symbol system terminology. As I stated earlier, linguistic terminology originated at the highest levels with human language and human behavior. Not only that, but in the recent past it was believed that symbolic language was what distinguished humans from lower animals. Consequently, the idea of a symbolic language at the origin of life was simply resisted by many linguists, anthropologists, and philosophers as unreasonable except as a vague metaphor or distant analogy. Evolution does not exhibit sharp and clear distinctions between functional activities like language usages even though we can see enormous differences between genetic symbol systems and the brain’s symbol systems. The important question for biosemiotics is what similarities are fundamental and what differences are irrelevant for their primary survival functions. I define symbol as a material constraint not determined by physical laws that controls specific physical dynamics of a self-replicating system. My usage is consistent with other definitions of a symbol, like Peirce’s triadic symbol–interpreter–referent definition. However, all the detailed refinements of Peirce’s complicated terminologies I find empirically ambiguous and unnecessary at the cellular level. I should add that symbols are arbitrary only to the extent that they are not proximally or structurally determined by laws. However they are non-arbitrary to the extent that they have been naturally or artificially selected to satisfy functional requirements.
p.s. – If a reviewer accused Edwina Taborski of being an intelligent design advocate, they must have not read her paper. She clearly discounts “agency” within the text of the paper.Upright BiPed
November 9, 2015
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@upright biped What about Edwina Taborsky? Biological Organisms as Semiosic Systems: the importance of strong and weak anticipation https://tidsskrift.dk/index.php/signs/article/viewFile/71446/128775 "The semiosic biological system is not a random or mechanical process but an informed, reasoned and self? controlled process." Quite a dated article now. She was "accused" by a reviewer of intelligent design science, which accusation she then rejected saying intelligent design is different. That group of scientists around CASYS conferences, Peter Rowlands, Daniel Dubois, Peter Marcer, Vanessa Hill, Edwina Taborsky, astronaut Edgar Mitchell, Walter Schempp. They are very much more advanced than any intelligent design science in producing theory based on the fact that freedom is real.mohammadnursyamsu
November 9, 2015
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Steve: Glad you quoted Darwin. His comment shows he was totally oblivious to excess reproduction as a designed object. Your claim was that "design deniers" never talk about excess reproduction. That was false. It's been part of the theory of evolution since its inception. Steve: If you had any integrity, you would reply directly to the issue and show evidence of how evolution is the cause of excess reproduciton Evolution by natural selection is due to heredity, fecundity, and differential reproductive potential due to heritable variations. Steve: You could alternately show how one-to-one reproduction was so cheap energy-wise and how in fact there was no barrier to increased reproduction etc etc. The simplest mechanism of fecundity is binary fission.Zachriel
November 9, 2015
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Box, that is not the only sign but it is one. KFkairosfocus
November 9, 2015
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Alicia Cartelli,
AC: It’s been a fun weekend guys, but unless someone has something interesting to say, hopefully I won;t be back.
How does it fail to qualify as "something interesting" when someone points out that your position is self-referentially incoherent? You don't even blink. What does that tell us about you and your position?
AC: Enjoy life on ID island!
Enjoy "your" life in a universe with "no design, no purpose, no evil, no good, nothing but pitiless indifference."Box
November 9, 2015
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F/N: Just for reference, here is Orgel, 1973:
. . . In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity . . . . [HT, Mung, fr. p. 190 & 196:] These vague idea can be made more precise by introducing the idea of information. Roughly speaking, the information content of a structure is the minimum number of instructions needed to specify the structure. [--> this is of course equivalent to the string of yes/no questions required to specify the relevant "wiring diagram" for the set of functional states, T, in the much larger space of possible clumped or scattered configurations, W, as Dembski would go on to define in NFL in 2002, also cf here, here and here (with here on self-moved agents as designing causes).] One can see intuitively that many instructions are needed to specify a complex structure. [--> so if the q's to be answered are Y/N, the chain length is an information measure that indicates complexity in bits . . . ] On the other hand a simple repeating structure can be specified in rather few instructions. [--> do once and repeat over and over in a loop . . . ] Complex but random structures, by definition, need hardly be specified at all . . . . Paley was right to emphasize the need for special explanations of the existence of objects with high information content, for they cannot be formed in nonevolutionary, inorganic processes. [The Origins of Life (John Wiley, 1973), p. 189, p. 190, p. 196.]
. . . and here is Wicken, 1979:
‘Organized’ systems are to be carefully distinguished from ‘ordered’ systems. Neither kind of system is ‘random,’ but whereas ordered systems are generated according to simple algorithms [[i.e. “simple” force laws acting on objects starting from arbitrary and common- place initial conditions] and therefore lack complexity, organized systems must be assembled element by element according to an [[originally . . . ] external ‘wiring diagram’ with a high information content . . . Organization, then, is functional complexity and carries information. It is non-random by design or by selection, rather than by the a priori necessity of crystallographic ‘order.’ [[“The Generation of Complexity in Evolution: A Thermodynamic and Information-Theoretical Discussion,” Journal of Theoretical Biology, 77 (April 1979): p. 353, of pp. 349-65.]
The direct root of the descriptive phrase and its acronym, is obvious. So is its relevance and pivotal importance. Also, its commonplace presence in a world of technology. The truth is, starting with something so simple as a 6500 fishing reel, and going to cases of text, oil refineries etc, we can find direct cases all over the world of life; which, is based on functionally specific, complex organisation and associated (often, CODED) information in the cell and in organisms. Where, at OOL, appeal to incremental blind progressive changes through chance variations and differential reproductive success leading to incremental branching tree evolution is off the table as the vNkSR required has to be accounted for as a case of FSCO/I. The force of vera causa then comes to bear and design sits at the table as of right. Beyond, it then sits at the table and is confronted by a curious fact: there are in fact zero cases of actually observed macro-evolutionary origin of body plans. All is gross extrapolation from micro changes that typically have to do with breaking not creating bio-information (per Behe's first rule). In short, when we observe the locking out of design as a serious contender, we see the imposition of an ideology on origins science, not an objectively grounded scientific inference much less the confident manner assertion of fact, Fact, FACT! So in the above, we see speaking with disregard to truth in hopes of profiting from what is said or suggested being thought to be true. We see doubling down in the face of challenge. We see projection of motivation that is irrelevant and baseless. We see the ideologised, closed mind. We see unwarranted hostility and contempt. We see something so puerile as resort to name twisting and namecaling dismissal. And, underneath is the ideological assumption of having cornered the market on the plausible -- truth having long since been driven out. In that context, UB's discussion, however reasonable, will meet the sort of violent reaction we just saw from an advocate of a priori evolutionary materialist scientism and/or its fellow traveller ideologies. But in the end, such ideologies, the closed minded mentality they inculcate and their domineering agendas will fail. KF PS: Those fixated on the "fact" claim, may find here helpful: http://iose-gen.blogspot.com/2010/06/introduction-and-summary.html#isevofctkairosfocus
November 9, 2015
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AC, a saddening resort to schoolyard level, ill-bred name twisting, namecalling and dodging of an issue as close to hand as that to comment, you had to create text strings dependent for function on specific configuration of ASCII characters: *-*-*- . . . -*. The rhetorical violence of the reaction is a clear indication of the actual unanswered force of the point on the only observed origin -- trillion cases+ in hand -- of functionally specific complex organisation and associated information [FSCO/I] and of the root issue, the sadly obvious fallacy of the ideologised, closed and patently hostile mind. KF PS: The onlooker may wish to look here for a discussion on the significance of the functional form of complex specified information, the form relevant to the world of life as Dembski noted in NFL and as had been highlighted in the 1970's by Orgel and Wicken.kairosfocus
November 9, 2015
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Alicia Cartelli:
When faced with a decision between the “science” behind ID and the field of evolutionary biology, I’m gonna go ahead and stick with the well proven scientific field (hint, it’s not ID).
Evolutionary biology is devoid of details and lacks methodology to test its grand claims. The only thing proven is that genomes change. The concepts of natural selection and drift are irrelevant for medical research. Biology is fine without the "evolutionary" label in front of it. We can study life without the imaginary narrative of universal common descent via NS and drift.Virgil Cain
November 8, 2015
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Daniel Koochy-koo, aka my little pufferfish @ 446- Given the evidence, out of all of the options to explain it, only ID posits testable entailments.Virgil Cain
November 8, 2015
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DK, VC is replying to an appeal to consensus and pointing out that there is significant weight of view the other way. KFkairosfocus
November 8, 2015
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Mung it would appear that your reading comprehension is what is shot. Let's go back to what I originally said @370 when this conversation started: 'Mung, the only thing that “detaches the amino acid from the tRNA so that it can be added to the peptide chain” is the ribosome.' Then @375 you assert that the enzyme is "peptidyl transferase" But the problem is that the only peptidyl transferase "enzyme" that "detaches the amino acid from the tRNA so that it can be added to the peptide chain," is actually a ribozyme and it is called the ribosome. @380 I explain to you how the non-ribosomal peptidyl transferases do not "detach the amino acid from the tRNA so that it can be added to the peptide chain." but instead link R-groups of amino acids within fully formed proteins. And it is at this point that you begin to lose it altogether with enzyme vs. ribozyme and what you were actually looking for. But that's alright, when your background in biology amounts to next to nothing, how could anyone expect better? I'm done with you Mungy, say whatever you want, just know that it's probably wrong. I've hung around here long enough to know that FIASCO is a bust, Kairos. Bye now!Alicia Cartelli
November 8, 2015
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Glad you quoted Darwin. His comment shows he was totally oblivious to excess reproduction as a designed object. He believed excess reproduction was a problem for the biosphere, when actually we can observe that it is excess reproduction which supports and balances life. He saw the glass half-empty, when in fact it was half-full. With reference to this comment by Darwin, we can also see that Zachriel is yet again not willing to grapple with an issue head on, but simply prefers to lean on 'their' rope-a-dope style of argumentation. Yes, I understand Zachriel you will not allow yourselves to get pinned down on any issue as the cost to Neo-Darwinism's reputation would be just too costly. If you had any integrity, you would reply directly to the issue and show evidence of how evolution is the cause of excess reproduciton, and how excess reproduction is a make-shift solution to a random problem faced by early life. You could alternately show how one-to-one reproduction was so cheap energy-wise and how in fact there was no barrier to increased reproduction etc etc. Yet you chose to copy/paste a quote from Darwin that exposes his ignornance of the actual positive effect of excess reproduction on the biosphere. So I guess the next question would be do Zachriel agree with Darwin that excess reproduction was/is a problem for life in general?
Steve: This is a clear barrier to neo-darwinian evolutionary concepts. Zachriel says: Steve: design deniers never talk about excess reproduction Darwin, Origin of Species 1859: Every being, which during its natural lifetime produces several eggs or seeds, must suffer destruction during some period of its life, and during some season or occasional year, otherwise, on the principle of geometrical increase, its numbers would quickly become so inordinately great that no country could support the product. Hence, as more individuals are produced than can possibly survive, there must in every case be a struggle for existence, either one individual with another of the same species, or with the individuals of distinct species, or with the physical conditions of life.
Steve
November 8, 2015
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AC, functionally specific complex organisation and associated information is not "nonsense." The resistance to such a simple description of a reality you have to instantiate even to object speaks volumes. The associated irritation itself speaks volumes. KFkairosfocus
November 8, 2015
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Alicia Cartelli:
For the last time, they are talking about the ribosome when they say “RNA enzyme.”
You claimed it did not exist. You are wrong. You also said you weren't arguing about the name, but about whether or not it existed. It exists. Even you admit that. So now you all of a sudden want to argue about it's name. credibility. shot.Mung
November 8, 2015
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Yup, here we go with the FSCO/I nonsense. Thanks, but no thanks Kairos. When faced with a decision between the “science” behind ID and the field of evolutionary biology, I’m gonna go ahead and stick with the well proven scientific field (hint, it’s not ID). And oh yes, for correct usage of terms we turn to none other than Wikipedia, as if I needed more convincing of your scientific illiteracy. It's been a fun weekend guys, but unless someone has something interesting to say, hopefully I won;t be back. Enjoy life on ID island!Alicia Cartelli
November 8, 2015
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Virgil Joe:
The majority accept some form of ID.
That settles it. It must be correct.Daniel King
November 8, 2015
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Kairosfocus: And, BTW, a priori evolutionary materialism is inherently self-referentially incoherent and self-refuting (...)
KF very good to point this out time and again. Materialists, like Alicia Cartelli, are standing on quicksand.Box
November 8, 2015
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PS: You may wish to adjust your usage of the term enzyme i/l/o recent developments that are reflected in, say, Wiki:
Enzymes /??nza?mz/ are macromolecular biological catalysts. [--> notice, focus on function not composition as AA chain based molecules. That functionality of course is typically a manifestation of FSCO/I] Enzymes accelerate, or catalyze, chemical reactions. The molecules at the beginning of the process are called substrates and the enzyme converts these into different molecules, called products. Almost all metabolic processes in the cell need enzymes in order to occur at rates fast enough to sustain life.[1]:8.1 The set of enzymes made in a cell determines which metabolic pathways occur in that cell. The study of enzymes is called enzymology. Enzymes are known to catalyze more than 5,000 biochemical reaction types.[2] Most enzymes are proteins, although a few are catalytic RNA molecules. Enzymes' specificity comes from their unique three-dimensional structures.
kairosfocus
November 8, 2015
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AC, dismissiveness does not answer to the substantial issue. On a trillion member observational base, the reliable and only actually observed cause of FSCO/I is intelligently directed configuration, which is backed up by the needle in haystack search challenge. From OOL forward, design sits at the explanatory, observationally anchored inductive reasoning table as the only explanation that passes the vera causa test. You are also still unable to acknowledge the difference between a fact and an explanation preferred by an institution-dominating ideology. Your dismissiveness therefore boils down to, you have no answer on the merits but have no wish to actually examine the case on the merits. Sad, but not particularly unexpected on such matters, on long experience. I think it is particularly revealing to observe your insistence on calling an explanatory model that has not met the vera causa test a "fact," and your appeal to in effect ideological dominance, on a matter where cogent correction has been given. That speaks for itself on the true balance on the merits. I suggest to you, it is time for serious re-thinking. KFkairosfocus
November 8, 2015
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Alicia Cartelli:
That’s all fine and dandy, Kairos, but again, no need for the Latin, and no need for you to write a novel just to deny what has already been accepted as scientific fact by the majority of the people on planet earth.
The majority accept some form of ID. Who actually thinks we owe our existence to a long series of accidents, some that worked out and some that didn't? Alicia did you know that without our large moon we wouldn't exist? Couple that fact with the other fact of total solar eclipses along with the perfect timing of intelligent observers who can use them to make scientific discoveries about the universe in which they live. As long as you have your imagination and your denialism you will be alright. Just don't take a long look at the real world, Alicia.Virgil Cain
November 8, 2015
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For the last time, they are talking about the ribosome when they say "RNA enzyme." You are looking for an enzyme that isn't the ribosome (which is technically a ribozyme). I'm done with you; you will not be able to find an enzyme that "detaches the amino acid from the tRNA so that it can be added to the peptide chain," other then the ribosome (which as I said from the beginning is technically a ribozyme, despite incorrect usage of the term "enzyme" even by researchers).Alicia Cartelli
November 8, 2015
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That’s all fine and dandy, Kairos, but again, no need for the Latin, and no need for you to write a novel just to deny what has already been accepted as scientific fact by the majority of the people on planet earth. You’re a dying breed and if those who actually engage in science have even heard of Intelligent Design, what goes on at the DI, or is “published” in your journal, you guys are nothing but the laughing stock. Don’t venture too far from UD, Kairos, you won’t like what you find.Alicia Cartelli
November 8, 2015
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Alicia Cartelli
Still waiting for the name of an ENZYME with peptidyltransferase activity...
The crystallographic structures compellingly confirmed that peptidyl transferase is an RNA enzyme. Alicia Cartelli:
Until you come up with the enzyme or admit that it doesn’t exist, I will not be responding to you.
The general consensus here seems to be that the less you say here the better off we all are.Mung
November 8, 2015
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AC, 433:
you can use all the Latin phrases you want, but it still just amounts to you denying what the majority of the world has already accepted as scientific fact.
First, the phrase comes from Newton. Who, wrote in Latin; then the standard language of scholarship. It stuck around and is a term for an epistemological principle of phil of sci. Namely, to prevent unbridled metaphysical/ideological speculation dressed up in a lab coat, in explaining traces of temporally or spatially remote (so, not directly observable) things causally, it is reasonable to insist that proposed causes be shown capable of producing the effects in the here and now observable. Then, one may reasonably argue to like causes like, especially when a unique factor is identified. The Alinsky-rule attempt to personalise, polarise, trivialise (oh, it's just him putting on airs . . . ) and dismiss fails. Next to that, a scientific, theoretical explanation is not and cannot be a fact, indeed that is one reason such need to be testable and tested. The fact that you have confused a theoretical explanation that has not passed the vera causa test for a fact, in fact inadvertently shows that you have been caught up in ideological bewitchment by lab coat clad evolutionary materialism. Ideology is not fact. Confident manner assertions even when made while dressed in lab coats, are not facts. Question-begging ideological a pioris imposed on scientific investigations and their findings are not facts. In case you forgot, here is Rational Wiki's telling, massively question-begging summary, complete with a shoal of projected strawman caricatures:
"Methodological naturalism is the label for the required assumption of philosophical naturalism when working with the scientific method. Methodological naturalists limit their scientific research to the study of natural causes, because any attempts to define causal relationships with the supernatural are never fruitful, and result in the creation of scientific "dead ends" and God of the gaps-type hypotheses."
They say bluntly what many others put in subtler form. Ideological captivity of science, in a nutshell. Undermining the credibility of science as open-mindedly seeking the truth about our world in light of empirical, observational evidence. And, BTW, a priori evolutionary materialism is inherently self-referentially incoherent and self-refuting; never mind the lab coat and domineering of ideologues over science, education and media institutions etc. Going on, science, logic and warrant are not matters of majority vote or edicts of august bodies whether dressed in lab coats, judicial robes or whatever. Reasoning either provides good grounds or it fails to. In this case FSCO/I is to be explained at OOL and origin of body plans down to our own. It will not escape the notice of the astute observer that if you had the goods, they would have long since been triumphantly trotted out. That's the 800 lb gorilla in the middle of the room that is being studiously ignored. The balance on the merits is as I have described. On a trillion member observation base backed up by the needle in haystack island of function search challenge, FSCO/I has just one empirically reliable observed cause, intelligently directed configuration -- aka design. Thus per inductive inference to best explanation, it is a credible signature of design. This holds for OOL, the root of the tree of life, and that drastically shifts understanding of balance of credibility on origin of FSCO/I rich body plans. Never mind what the lab coat clad magisterium wishes to impose. Or even pretend is "fact." KFkairosfocus
November 8, 2015
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Alicia Cartelli:
Everything in biology points to chemical/biological evolution producing life and eventually the diversity of species we see today.
Nothing in biology points to chemical/biological evolution producing life and eventually the diversity of species we see today. We wouldn't even know how to test such a claim. It would be like saying that physicochemical processes can produce cars and computers.Virgil Cain
November 8, 2015
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Talk about dishonesty or delusion- Alicia Cartelli says there is evidence for a more primitive cell. She conflates a need for evidence. And to the following questions: Do you think physicochemical processes can A) produce your ribozyme B) provide the raw materials to carry on and C) be capable of evolving new functions? she answered yes, yes and yes. Great, Alicia, thank you. Do you have any evidence to support your enthusiasm? Or any way to test to see if your answered are warranted?Virgil Cain
November 8, 2015
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mungy, I've said from the start that the ribosome is a "ribozyme." Still waiting for the name of an ENZYME with peptidyltransferase activity that "detaches the amino acid from the tRNA so that it can be added to the peptide chain." You are a complete waste of time, and to single you out for that says a lot here at UD. Until you come up with the enzyme or admit that it doesn't exist, I will not be responding to you. Toodaloo!Alicia Cartelli
November 8, 2015
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