Even Wikipedia Acknowledges the Link Between Semiotics and Biology

Alan Fox:

But regarding the point about definitions, it is common sense...

Well, that's what some philosophers say, anyways.

I can’t be responsible for inadvertently straying into philosophy territory. There must be some aspects that coincide with reality.

Why? Why can't one do philosophy without regard to reality, and why should our definitions coincide with reality? And how do we even know what it is real such that we can say that our definition coincides with reality? Perhaps reality is just what we define it to be! Philosophy. All philosophy. You can't even get science off the ground without it, and "common sense" is itself a philosophical notion. Philosophy is not bunk. You (yes you, Alan) "stray" into philosophy all the time. You can't avoid it. Better to embrace it. Mung

But that would be philosophy, which as you’ve told us, is bunk.

I can't be responsible for inadvertently straying into philosophy territory. There must be some aspects that coincide with reality. Actually, I regret that throw-away remark. I'm quite fond of Vincent Torley and I think I might have upset him. But regarding the point about definitions, it is common sense, as trying to communicate with you clearly illustrates. ;) Alan Fox

Alan Fox:

Which is why I must emphasize again that in any discussion about reality, definition of terms has to precede any meaningful discussion.

But that would be philosophy, which as you've told us, is bunk. Mung

Not to YOUR satisfaction, but that is meaningless. IOW Alan, both have been properly defined and are better defined than anything your position has to offer. So your words are empty.

You know someone said of you somewhere "he's the only guy I know who could start a fight in an empty bar and still lose!" I call you on those empty words. Not just defined, but properly defined, better defined than anything! Well, Joe! Empty words? A quick cut & paste should do it. Have away at it. Whip out those definitions! Alan Fox

How to Play the Gene Evolution Game – Casey Luskin – Feb. 2010 http://www.evolutionnews.org/2010/02/how_to_play_the_gene_evolution032141.html Common Ancestry: Wikipedia vs. the Data - Casey Luskin - October 5, 2012 Excerpt: In fact, the largest category of genes here is eukaryotic (cells with a nucleus) genes that have no homolog among prokaryotes (cells without a nucleus) -- they don't even have any possible candidate ancestors to explain where these genes came from, much less a consistent pattern of similarity pointing to one particular ancestor. All this is the opposite of "a direct correlation with common descent.",,, ,,, if two phylogenetic trees aren't congruent, the problem isn't that common descent is wrong, but rather the conflict is simply evidence of HGT.,,, Syvanen, (in "Evolutionary Implications of Horizontal Gene Transfer," Annual Review of Genetics, Vol. 46:339-356 (2012), invokes widespread HGT (Horizontal Gene Transfer), but he's uncommonly honest about the data and its implications, offering the radical suggestion that "life might indeed have multiple origins.",,, let's now look within eukaryotes.,,, The biochemical organization of the innate immune systems of plants and animals is strikingly similar -- but this is a direct non-correlation with common descent. Thus, evolutionary scientists are forced to call them "unexpectedly similar," postulating that the similarities were "independently derived." This data is not explained by Darwinian evolution and common descent. It is explained by common design. Somehow, something tells me not to expect any corrections over at Wikipedia. http://www.evolutionnews.org/2012/10/common_ancestry_1065001.html An Enzyme’s Phylogeny Reveals a Striking Case of Convergent Evolution – Jonathan M. – February 11, 2013 Excerpt: The authors attempt to account for the incongruity by positing that “the STC gene has been laterally transferred among phylogenetically diverged eukaryotes through an unknown mechanism.” They thus attribute the shared genes to horizontal gene transfer (with no offered mechanism), a proposition that has become a catch-all to explain away severe conflicts between evolutionary phylogenies.,,, “phylogenetic conflict is common, and frequently the norm rather than the exception” (Dávalos et al., 2012). Is it possible that the real reason for such striking and widespread phylogenetic discordance is that evolutionary biologists are looking at biology through the wrong lens? Could the reason that there is so much difficulty in correlating organisms to a tree be that no such tree exists? http://www.evolutionnews.org/2013/02/an_enzymes_phyl068911.html Here’s the Latest Just-So Story: Recurrent Evolution - Cornelius Hunter - April 2012 Excerpt: The first step to explaining something away is to give it a name. And so evolutionists have labeled this awkward evidence as recurrent evolution.,,, If the pattern fits the evolutionary tree, then it is explained as common evolutionary history. If not, then it is explained as common evolutionary forces. Heads I win, tails you lose.,, Common descent has always been an auxiliary hypothesis for the simple reason that evolution’s theoretical core does not mandate common descent, or anything else for that matter, aside from its insistence that the species arose naturally. Beyond that, anything goes.,, Evolutionists insist the species arose naturally, their religion requires it. http://darwins-god.blogspot.com/2012/04/heres-latest-just-so-story-recurrent.html Pattern pluralism and the Tree of Life hypothesis – 2006 Excerpt: Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. http://www.pnas.org/content/104/7/2043.abstract Bernard d'Abrera on Butterfly Mimicry and the Faith of the Evolutionist - October 5, 2011 Excerpt: For it to happen in a single species once through chance, is mathematically highly improbable. But when it occurs so often, in so many species, and we are expected to apply mathematical probability yet again, then either mathematics is a useless tool, or we are being criminally blind.,,, Evolutionism (with its two eldest daughters, phylogenetics and cladistics) is the only systematic synthesis in the history of the universe that proposes an Effect without a Final Cause. It is a great fraud, and cannot be taken seriously because it outrageously attempts to defend the philosophically indefensible. http://www.evolutionnews.org/2011/10/in_this_excerpt_from_the051571.html Here is how neo-Darwinian evolution avoids falsification from the fossil record; Seeing Ghosts in the Bushes (Part 2): How Is Common Descent Tested? – Paul Nelson – Feb. 2010 Excerpt: Fig. 6. Multiple possible ad hoc or auxiliary hypotheses are available to explain lack of congruence between the fossil record and cladistic predictions. These may be employed singly or in combination. Common descent (CD) is thus protected from observational challenge. http://www.evolutionnews.org/2010/02/seeing_ghosts_in_the_bushes_pa031061.html The Case of the Mysterious Hoatzin: Biogeography Fails Neo-Darwinism Again – Casey Luskin – November 5, 2011 Excerpt: If two similar species separated by thousands of kilometers across oceans cannot challenge common descent, what biogeographical data can? The way evolutionists treat it, there is virtually no biogeographical data that can challenge common descent even in principle. If that’s the case, then how can biogeography be said to support common descent in the first place? http://www.evolutionnews.org/2011/11/the_case_of_the_mysterious_hoa052571.html bornagain77

"Of course past results don’t guarantee future performance so you can’t really claim you will always be right on this." Ironically, if IDists practiced science in the deceptive manner Darwinists do, we could guarantee that we will always be right: Science practiced Darwinian style with ‘junk’ DNA - Data Peeking, an Indispensible Implement in the Darwinian Toolbox - Nov. 19, 2012 Excerpt: This is called "Data Peeking," and it is also called "Bad Faith." It works this way: 1. Gather data and/or run an experiment. 2. Determine the results. 3. Think up an explanation (perhaps a just so story, or maybe a worthwhile explanation). 4. Label your explanation a theory. 5. Unveil the data in public, proclaiming, "Just as my theory predicts..." The key (to making this work) is the order of presentation. You offer the results to others after you run the experiments. When discussing, you give the just-so-story first, then the data, and then grandly proclaim that the results are just as you predicted. http://www.evolutionnews.org/2012/11/data_peeking_an066501.html "Moving the Goalpost: How Darwin's Theory Survives" - podcast - January 2013 http://intelligentdesign.podomatic.com/entry/2013-01-16T16_09_48-08_00 Let's not forget another prevalent means in which neo-Darwinism avoids falsification; the blatantly fraudulent practice of literature bluffing; "A Masterful Feat of Courtroom Deception": Immunologist Donald Ewert on Dover Trial - audio http://intelligentdesign.podomatic.com/player/web/2010-12-20T15_01_03-08_00 bornagain77

Alan Fox:

and so far nothing remotely approaching an operational definition has emerged for “semiotic” thingy or FSCO/I.

Not to YOUR satisfaction, but that is meaningless. IOW Alan, both have been properly defined and are better defined than anything your position has to offer. So your words are empty. Joe

No fear. I am right. And the evidence supports me.

Absolutely! You said: "And it has become painfully obvious that nothing wrt ID will ever be defined to your satisfaction." and so far nothing remotely approaching an operational definition has emerged for "semiotic" thingy or FSCO/I. Of course past results don't guarantee future performance so you can't really claim you will always be right on this. Alan Fox

No fear. I am right. And the evidence supports me. Joe

And it has become painfully obvious that nothing wrt ID will ever be defined to your satisfaction.

Like the proverbial stopped clock, Joe, in this case I fear you may be right. :) Alan Fox

And dictionaries are the authority when it comes to the definitions of words. Alan Fox:

Not in my experience.

LoL! Who are you?

Dictionaries respond to usage.

So what? There still needs to be accepted terminology and definitions.

Which is why I must emphasize again that in any discussion about reality, definition of terms has to precede any meaningful discussion.

And it has become painfully obvious that nothing wrt ID will ever be defined to your satisfaction. Joe

And dictionaries are the authority when it comes to the definitions of words.

Not in my experience. Dictionaries respond to usage. The Académie Française has wasted much effort and hot air in trying to restrain the French language from evolving. Despite their best efforts, the language evolves. Which is why I must emphasize again that in any discussion about reality, definition of terms has to precede any meaningful discussion. Alan Fox

KF:

I also suggest you look at a bit of embryology on how body plans are built out from zygotes, as an indicator of what I mean, maybe by looking at what you seem ever so eager not to engage, here on in context.

Thank-you for the link. Following it, I am taken to a Google blog entitled "The Independent Origins Science Education course". Now, who turns out to be the creator of this rather unskillfully crafted blog? Mr GEM of TKI himself! G, I don't think your knowledge of evolutionary developmental biology is reliable enough for me to consider your blog a source of information on Evo-devo? Do you have any experience in the biology lab, any qualifications, any peer-reviewed publications? Alan Fox

AF: I am sorry, but at this point I am forced to read that as finding yet another excuse to avoid facing evidence, very conveniently blaming me for giving and highlighting extensive linked information; elaborating on a summary given to lead up to it. I see no sign of actual engagement with evidence, facts or reasoning, especially the way the CCA coupler works in the system as a UNIVERSAL link, i.e. at this point there is no physical force that makes the particular AA couple to a given tRNA, as can be seen form experiments that reprogrammed tRNAs and led to novel AA chains -- as was highlighted and remarked on. This shows contingency and it further shows that the loading of the enzyme is programmed and informational not deterministic and merely a matter of physico-chemical foirces. I also suggest you look at a bit of embryology on how body plans are built out from zygotes, as an indicator of what I mean, maybe by looking at what you seem ever so eager not to engage, here on in context. KF kairosfocus

Alan, You're being obtuse. Why is it that no other evo has an issue with the transcription and translation process being semiotic? That seeto be your peronal bit of ignorance. Transcription/ translation is semiotic by definition, Alan. And the genetic code is a code by definition. And dictionaries are the authority when it comes to the definitions of words. Joe

G If you can restrain yourself a bit with the volubility, clarity and relevance of your comments, I'll try and engage with you. Your dictionary definition of the word "semiotics" is all fine and dandy. It is very clearly an umbrella word for a diverse field of study. The essential difficulty I have with whether Upright Biped has any kind of coherent scientific (or even logical) argument hinges on whether there is a property, which UB calls "semiotic" that can usefully be assigned to sundry things, processes, whatever. The unavoidable first step in getting anywhere is to propose an operational definition for "semiotic" in the context. A tool to decide which things, processes, whatevers are semiotic and which are not is what we need. Unless this is accomplished, absolutely nothing is accomplished. If this is accomplished then we can discuss the assertion that semiotic things, processes, whatevers are always designed and whether that is a coherent claim for which it is possible to present evedence. Alan Fox

AF: Take this:

se·mi·ot·ics also se·mei·ot·ics (sm-tks, sm-, sm-) n. (used with a sing. verb) The theory and study of signs and symbols, especially as elements of language or other systems of communication, and comprising semantics, syntactics, and pragmatics. semi·o·tician (--tshn) n. The American Heritage® Dictionary of the English Language, Fourth Edition copyright ©2000 by Houghton Mifflin Company. Updated in 2009. Published by Houghton Mifflin Company. All rights reserved.

I would think that ostensive definition by key cases and close family resemblance, multiplied by the issue that what has the features and behaviour of a duck is presumptively just that, tell decisively. Remember -- as has again been pointed out recently -- there is no generally accepted precising definition of life or for that matter any generally accepted operational definition of same. That does not stop us from forming adequate concepts and studying life and even developing related sciences. Going on, there is no good undebatable definition of matter, energy, time or nature either. In short, this looks, walks, and quacks like a rhetorical opening for either selective hyperskepticism or willful obtuseness. The material issue is not what semiotics is [opening the door to rhetorical antics with semantics . . . ], but that mRNA in particular is a quite evident case of a data tape, using prong height differences to code digital info in three-element clusters with 64 states. On a Yale-type key-lock fitting basis, tRNAs in sequence, in the Ribosome, are used to click together amino acids, assembling proteins per known code tables. Furthermore, investigation of the tRNA shows that the AA's are loaded to a universal tool tip, the CCA-tip, joining the carboxylic group end of the AA, leaving its amine end to do the chaining. This means that the tRNS is not forced to hold any given AA at its tip, indeed there has been recent work on loading with novel acids. And there are naturally occurring variants. The tRNA is loaded with what for simplicity I have called a loading enzyme, that senses the folded config of the tRNA and loads up. Notice Wiki -- testifying against known agenda interest -- on tRNA:

Transfer RNA (abbreviated tRNA and archaically referred to as sRNA abbreviating soluble RNA) is an adaptor molecule composed of RNA, typically 73 to 93 nucleotides in length, that serves as the physical link between the nucleotide sequence of nucleic acids (DNA and RNA) and the amino acid sequence of proteins. It does this by carrying an amino acid to the protein synthetic machinery of a cell (ribosome) as directed by a three-nucleotide sequence (codon) in a messenger RNA (mRNA) . . . . The specific nucleotide sequence of a mRNA specifies which amino acids are incorporated into the protein product of the gene from which the mRNA is transcribed, and the role of tRNA is to specify which sequence from the genetic code corresponds to which amino acid.[1] One end of the tRNA matches the genetic code in a three-nucleotide sequence called the anticodon. The anticodon forms three base pairs with a codon in mRNA during protein biosynthesis. The mRNA encodes a protein as a series of contiguous codons, each of which is recognized by a particular tRNA. On the other end of the tRNA is a covalent attachment to the amino acid that corresponds to the anticodon sequence. Each type of tRNA molecule can be attached to only one type of amino acid, so each organism has many types of tRNA (in fact, because the genetic code contains multiple codons that specify the same amino acid, there are many tRNA molecules bearing different anticodons which also carry the same amino acid) . . . . The covalent attachment to the tRNA 3’ end is catalyzed by enzymes called aminoacyl-tRNA synthetases. During protein synthesis, tRNAs with attached amino acids are delivered to the ribosome by proteins called elongation factors (EF-Tu in bacteria, eEF-1 in eukaryotes), which aid in decoding the mRNA codon sequence. If the tRNA's anticodon matches the mRNA, another tRNA already bound to the ribosome transfers the growing polypeptide chain from its 3’ end to the amino acid attached to the 3’ end of the newly-delivered tRNA, a reaction catalyzed by the ribosome . . . . Aminoacylation is the process of adding an aminoacyl group to a compound. It produces tRNA molecules with their CCA 3' ends covalently linked to an amino acid. Each tRNA is aminoacylated (or charged) with a specific amino acid by an aminoacyl tRNA synthetase. There is normally a single aminoacyl tRNA synthetase for each amino acid, despite the fact that there can be more than one tRNA, and more than one anticodon, for an amino acid. Recognition of the appropriate tRNA by the synthetases is not mediated solely by the anticodon, and the acceptor stem often plays a prominent role.[8] Reaction: amino acid + ATP --> aminoacyl-AMP + PPi aminoacyl-AMP + tRNA --> aminoacyl-tRNA + AMP Sometimes[clarification needed], certain organisms can have one or more aminoacyl tRNA synthetases missing. This leads to mischarging of the tRNA by a chemically related amino acid. The correct amino acid is made by enzymes that modify the mischarged amino acid to the correct one. For example, Helicobacter pylori has glutaminyl tRNA synthetase missing. Thus, glutamate tRNA synthetase mischarges tRNA-glutamine(tRNA-Gln) with glutamate. An amidotransferase then converts the acid side chain of the glutamate to the amide, forming the correctly charged gln-tRNA-Gln . . . . Once translation initiation is complete, the first aminoacyl tRNA is located in the P/P site, ready for the elongation cycle described below. During translation elongation, tRNA first binds to the ribosome as part of a complex with elongation factor Tu (EF-Tu) or its eukaryotic (eEF-1) or archaeal counterpart. This initial tRNA binding site is called the A/T site. In the A/T site, the A-site half resides in the small ribosomal subunit where the mRNA decoding site is located. The mRNA decoding site is where the mRNA codon is read out during translation. The T-site half resides mainly on the large ribosomal subunit where EF-Tu or eEF-1 interacts with the ribosome. Once mRNA decoding is complete, the aminoacyl-tRNA is bound in the A/A site and is ready for the next peptide bond to be formed to its attached amino acid. The peptidyl-tRNA, which transfers the growing polypeptide to the aminoacyl-tRNA bound in the A/A site, is bound in the P/P site. Once the peptide bond is formed, the tRNA in the P/P site is deacylated, or has a free 3’ end, and the tRNA in the A/A site carries the growing polypeptide chain. To allow for the next elongation cycle, the tRNAs then move through hybrid A/P and P/E binding sites, before completing the cycle and residing in the P/P and E/E sites. Once the A/A and P/P tRNAs have moved to the P/P and E/E sites, the mRNA has also moved over by one codon and the A/T site is vacant, ready for the next round of mRNA decoding. The tRNA bound in the E/E site then leaves the ribosome . . .

Med biochem page, here (nice pic):

Activation of amino acids is carried out by a two step process catalyzed by aminoacyl-tRNA synthetases. Each tRNA, and the amino acid it carries, are recognized by individual aminoacyl-tRNA synthetases. This means there exists at least 20 different aminoacyl-tRNA synthetases, there are actually at least 21 since the initiator met-tRNA of both prokaryotes and eukaryotes is distinct from non-initiator met-tRNAs. Activation of amino acids requires energy in the form of ATP and occurs in a two step reaction catalyzed by the aminoacyl-tRNA synthetases. First the enzyme attaches the amino acid to the ?-phosphate of ATP with the concomitant release of pyrophosphate. This is termed an aminoacyl-adenylate intermediate. In the second step the enzyme catalyzes transfer of the amino acid to either the 2'– or 3'–OH of the ribose portion of the 3'-terminal adenosine residue of the tRNA generating the activated aminoacyl-tRNA. Although these reaction are freely reversible, the forward reaction is favored by the coupled hydrolysis of PPi. Accurate recognition of the correct amino acid as well as the correct tRNA is different for each aminoacyl-tRNA synthetase. Since the different amino acids have different R groups, the enzyme for each amino acid has a different binding pocket for its specific amino acid. It is not the anticodon that determines the tRNA utilized by the synthetases. Although the exact mechanism is not known for all synthetases, it is likely to be a combination of the presence of specific modified bases and the secondary structure of the tRNA that is correctly recognized by the synthetases. It is absolutely necessary that the discrimination of correct amino acid and correct tRNA be made by a given synthetase prior to release of the aminoacyl-tRNA from the enzyme. Once the product is released there is no further way to proof-read whether a given tRNA is coupled to its corresponding tRNA. Erroneous coupling would lead to the wrong amino acid being incorporated into the polypeptide since the discrimination of amino acid during protein synthesis comes from the recognition of the anticodon of a tRNA by the codon of the mRNA and not by recognition of the amino acid. This was demonstrated by reductive desulfuration of cys-tRNAcys with Raney nickel generating ala-tRNAcys. Alanine was then incorporated into an elongating polypeptide where cysteine should have been.

We are talking major and even notorious results of science here, not dubious obscurities. Coded info is in use and the means of transfer of info from DNA to protein is essentially informational, not simple direct chemistry. Notice a case of engineering the system to code and load a different AA, proving the essentially informational character in what is going on. KF kairosfocus

Has anyone spotted anything in the literature (the papers linked above, for example) about defining "semiotic" in such a way (operationally) that we might be able to decide what is semiotic and what is not and what the implications might be? Alan Fox

F/N: Identity of indiscernibles, SEP. Second, observe the issue of different specific instantiations of an underlying general pattern or type. Where, as has been REPEATEDLY highlighted across the months since UB has put the issue on the table:

code (kd)n. 1. A systematically arranged and comprehensive collection of laws. 2. A systematic collection of regulations and rules of procedure or conduct: a traffic code. 3. a. A system of signals used to represent letters or numbers in transmitting messages. b. A system of symbols, letters, or words given certain arbitrary meanings, used for transmitting messages requiring secrecy or brevity. 4. A system of symbols and rules used to represent instructions to a computer; a computer program. 5. Genetics The genetic code. 6. Slang A patient whose heart has stopped beating, as in cardiac arrest. v. cod·ed, cod·ing, codes v.tr. 1. To systematize and arrange (laws and regulations) into a code. 2. To convert (a message, for example) into code. v.intr. 1. Genetics To specify the genetic code for an amino acid or a polypeptide. 2. Computer Science To write or revise a computer program. 3. Slang To go into cardiac arrest. [Middle English, from Old French, from Latin cdex, book; see codex.] The American Heritage® Dictionary of the English Language, Fourth Edition copyright ©2000 by Houghton Mifflin Company. Updated in 2009. Published by Houghton Mifflin Company. All rights reserved.

A reasonable dictionary will summarise typical usages. It should be quite clear, from what a code is and does, that the genetic code is just that. Those who want to put up heavy clouds of rhetorical flak in objection need to take up an argument with, say, Sir Francis Crick, from as early as 1953:

"Now we believe that the DNA is a code. That is, the order of bases (the letters) makes one gene different from another gene (just as one page of print is different from another)" [March 19, 1953 remarks to his son.]

Indeed, let us note that the notoriously ideological Wikipedia, on this subject, against what seems to be the obvious interest of fending off implications of semiotics, is forced to speak as follows on the genetic code:

Genetic code The genetic code is the set of rules by which information encoded within genetic material (DNA or mRNA sequences) is translated into proteins (amino acid sequences) by living cells. Biological decoding is accomplished by the ribosome, which links amino acids in an order specified by mRNA, using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms, and can be expressed in a simple table with 64 entries. The code defines how sequences of these nucleotide triplets, called codons, specify which amino acid will be added next during protein synthesis. With some exceptions,[1] a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid . . . . Not all genetic information is stored using the genetic code. All organisms' DNA contains regulatory sequences, intergenic segments, chromosomal structural areas, and other non-coding DNA that can contribute greatly to phenotype. Those elements operate under sets of rules that are distinct from the codon-to-amino acid paradigm underlying the genetic code.

In short, there are multiple codes involved in the genetic process that creates the specific body plan of a given organism in a given environment and also supports the associated key life processes. And, on biosemiotics, the same Wikipedia is reduced to saying:

Biosemiotics (from the Greek bios meaning "life" and semeion meaning "sign") is a growing field that studies the production, action, and interpretation of signs and codes[1] in the biological realm. Biosemiotics attempts to integrate the findings of scientific biology and semiotics, proposing a paradigmatic shift in the occidental scientific view of life, demonstrating that semiosis (sign process, including meaning and interpretation) is its immanent and intrinsic feature . . . . To define biosemiotics as “biology interpreted as sign systems study” is to emphasize not only the close relation between biology as we know it (as a scientific field of inquiry) and semiotics (the study of signs), but primarily the profound change of perspective implied when life is considered not just from the perspectives of molecules and chemistry, but as signs conveyed and interpreted by other living signs in a variety of ways, including by means of molecules. In this sense, biosemiotics takes for granted and respects the complexity of living processes as revealed by the existing fields of biology – from molecular biology to brain science and behavioural studies – however, biosemiotics attempts to bring together separate findings of the various disciplines of biology (including evolutionary biology) into a new and more unified perspective on the central phenomena of the living world, including the generation of function and signification in living systems, from the ribosome to the ecosystem and from the beginnings of life to its ultimate meanings. Furthermore, by providing new concepts, theories and case studies from biology, biosemiotics attempts to throw new light on some of the unsolved questions within the general study of sign processes (semiotics), such as the question about the origin of signification in the universe. Here, signification (and sign) is understood in a very general sense, that is, not simply the transfer of information from one place to another, but the generation of the very content and meaning of that information in human as well as non-human sign producers and sign receivers. Sign processes are thus taken as real: They are governed by regularities (habits, or natural rules) that can be discovered and explained. They are intrinsic in living nature, but we can access them, not directly, but indirectly through other sign processes (qualitative distinction methods, for instance) – even though the human representation and understanding of these processes (in the construction of explanations) builds up as a separate scientific sign system distinct from the organisms’ own sign processes. One of the central characteristics of living systems is the highly organized character of their physical and chemical processes, partly based upon informational and molecular properties of what came to be known in the 1960s as the genome. Distinguished biologists, such as Ernst Mayr and Manfred Eigen have seen these informational aspects as one of the emergent features of life as a process that distinguish life from anything else in the physical world, except, perhaps, man-made computers. However, whereas the informational teleology of computer programmes is derived, by being designed by humans to achieve specific goals, the teleology and informational characteristics of organisms are intrinsic to them and evolve naturally. Traditional biology (and philosophy of biology) has seen such processes as being purely physical and, being influenced by a reductionist and mechanistic tradition, has adopted a very restricted notion of the physical as having to do with only efficient causation. Biosemiotics uses concepts from semiotics (in the sense of C.S. Peirce as the broad logical and scientific study of dynamic sign action in humans as well as elsewhere in nature) to answer questions about the biological emergence of meaning, intentionality and a psychical world. These questions are either hard to answer or completely incoherent within a purely mechanist and physicalist framework.

Obviously, Wikipedia is trying to absorb the implications of sign systems in its typical materialistic context, but that does not detract from the force of what it has had to concede. At this point it strikes me that what we are really dealing with is putting up heavy flak to protect a critical vulnerability, through selective hyperskepticism. KF kairosfocus

We need to bone up on the issue of the identity of identicals. As in “if it looks like, walks like and quacks like a duck . . . ” on steroids.

more like the Incredible Duck on steroids M. Holcumbrink

I say Piper's 'rabid arminian worldview' because that is how he himself described it. M. Holcumbrink

I love John Piper’s story how he himself went through a sharp grieving stage when his rabid Arminian worldview crumbled and was replaced by a reformed worldview. He said at one point he put his face into his hands and sobbed. I myself at various points in my life have been forced to dramatically shift my thinking on a number of things, to my great discomfort, and in most of those cases is wasn’t so much a ‘decision’ as it was simply being swept away by an onslaught of data, genuine or contrived. But with that said, the individual that I spoke of is not likely anywhere near that point, as far as I can tell. In fact, the bugging out may just as well have been due to the fact that we had sat there and spent way too much time already discussing ID, and neither one of us had the time to devote to such intense discussion. One of us had to cut it off at some point (with no hope of a segue). Although, I have engaged him twice on the issue, and both times it ended very abruptly soon after he ran out of talking points. But like I said, that very well could be a coincidence. And I struggle mightily with how often to engage someone that I think might exhibit signs of hope in being able to pull them out of a stifling worldview. I heard a preacher say one time that once you plant a seed, you shouldn’t mess with it too much, if at all, because you might kill the tender shoot. But then again, what hope is there when the individual has friends and frequents websites where the seed is so easily snatched away. But then again, it is God that gives the increase, no? And if he deems that one should be persuaded eventually, who can stop it? M. Holcumbrink

F/N 2: Also, we need to see here the inductive argument's power through the design inference in light of causality and the principle of sufficient reason. As in, what is the sufficient and reliably tested reason for something that has the defining features of a code? kairosfocus

F/N: We need to bone up on the issue of the identity of identicals. As in "if it looks like, walks like and quacks like a duck . . . " on steroids. KF kairosfocus

MH: The "bug-out" response, provided that you have managed to maintain a relationship, is actually a good sign. The key thing is to understand that this non-verbal response is actually -- and here comes the semiotics thingy again -- is a highly meaningful sign of an underlying process. What it means is that: you have broken the programmed "case_X --> handy dandy talking point a . . . " pattern and the escape routine has been called up: bug out and call for reinforcements! But, where there is a fundamentally flawed system, the reinforcements cannot answer on the merits. (With the new atheists, the usual next resort is to being obnoxious and polarising. The escape routine is to find a red herring to drag away to a set-up strawman soaked in ad hominems and set alight, to cloud, poison, polarise and confuse the atmosphere, allowing escape to the nearest fever swamp for reinforcement and reinfection. But if (i) there is a relationship basis, that temporary escape won't work so well, and (ii) if you have targetted cracks in the foundation, they cannot be adequately plastered over. However, understand (iii) men often cling to darkness and reject genuine light because the light will expose what they don't want exposed, i.e. this is now more than just a rational issue, it is a life challenge. [And yes, there is a biblical allusion there, a rather sobering one. The response that works, in the end is the 12-step, spiritually-driven type life reconstruction response that breaks the power of destructive addictions, habits and associated lifestyles. Sorry if that is not welcome, it is reality, tested reality.) If there is a sufficient basis for onward friendship and counselling, that challenge can be addressed and a worldview and social support system re-foundation initiated. However, note that there are two dynamics involved: (i) unfreezing-changing-refreezing, and (ii) grief work. Grieving is a pivotal concept, which we can outline in five stages:

1: shock, denial and isolation of oneself in the face of loss --> 2: anger at loss, targetted on some blame object (possibly including oneself, often a designated scapegoat) --> 3: trying to make some sort of bargain with that object (or in other cases, lashing out to punish it for its "crime") --> 4: depression (often triggered by realising impotence in the face of an overwhelming situation, often compounded by guilt, real or imagined [lashing out at innocents and shifting blame to them does not help], where also suicide is a known hazard here . . . especially if depression sets in deeply) --> 5: if you make it that far, acceptance, coming to terms, recovery, finding a new way forward.

In parallel with that, we can look at the Edgar Schein model for "thought reform" (yes, this came out of brainwashing research in the '50's - '60's [cf. here for how it has been tamed down and fitted into a business change process model]) that speaks to how we change worldviews and life systems, in ways ranging from mild to extreme:

1: Frozen in a set of attitudes, relationshisp, roles, expectations, routines etc in a social situation [normality] --> 2: Unfreezing, as one is decanted into an isolation, physical, social, emotional, intellectual, whatever, that triggers a destabilisation in the context of "this is not working" (triggering cognitive dissonance and a sense of survival threat that motivates change [can be dangerous and highly manipulative]) --> 3: Changing, through identifying with new role models and/or discovering a new way in the new situation (NB: very prone to manipulation and deceit, a key sign of the difference between honest and dishonest institutions or bodies) --> 4: Refreezing, through consolidating the new state in a new setting, often reinforced by evident success (or, this is about the best bargain I can get . . . )

The pivotal issue here is the integrity of the grieving and changing process, and so you will need to model that integrity. Hope that helps. KF kairosfocus

I once discused the nature of DNA at its core (which is that it is a bona fide coding system) with a particular colleague of mine at work. It is obvious to me that he has been heavily influenced by the rabid anti-ID railings here and there, because he regurgitates canned responses like “it's a science stopper” and “who designed the designer” type stuff (Alan Fox, your efforts are not in vain). But after being able to disarm such vapid arguments (which requires some level of patience and tenacity), it is possible to engage in fruitful discussion with him. I was able to explain how information (codes, symbols, meaning) can be exchanged in all manner of ways, from holes punched in mylar tape, to radio frequencies, to magnetic discs, to DNA, the only difference between them being the 'channel' through which the signal is conveyed. I also discussed how codon triplets carry meaning in the exact same way that ASCI codes do. For Pete's sake, DNA can even be used to store English text, and can even be optimized to suit whatever uses humans can devise for DNA computing. And if this be the case, how then can DNA not be a code? But he kept repeating that "it is not the same thing as a code”, to which I said “but it is the same thing in every way imaginable”, to which he said “we simply can't call it a code, because to call it a code would mean that it had been written by someone”, and then he got up and left before I had a chance to say “yes, exactly.” But therein lies the difficulty. Some people just can't swallow the implication. It is as bald-faced and stark as anything could ever be, but some people just can't accept it. “He casteth out devils by the prince of the devils” M. Holcumbrink

Kantian, If I designed a cell in a lab, would that mean that I, or a predecessor, was designed by a supernatural source? Collin

Alan Fox:

Do you think Biosemiotics has elements that are compatible with “Intelligent Design” ideas?

Biosemiotics only makes sense in light of Intelligent Design. Joe

AF: The heavy flak concentration effect that has been playing out for months, in light of EA's inductive summary. When people have big difficulties admitting that the genetic code is a code, that should tell us something. KF kairosfocus

F/N: AF, clip no 1:

Dear Colleagues, The simplest and most informative linguistic messages are the kind found in ordinary true narratives. Such valid messages ? laden with pragmatic information ? provide the limiting antithesis of biosemiotic entropy. Generalizing from linguistic to biological systems, and taking account of some of the countless ways any complex arrangement of symbols can be rendered senseless, the thesis to be explored in this special issue is that the corruption of biological messages from genetics upward to epigenetics, proteins, cells, tissues, and the organs of viable organisms ? which can be described as biosemiotic entropy ? is, unsurprisingly, the proximate cause of disorders, diseases, and mortality. We invite contributions ? pro, con, or offering any plausible alternative ? to the idea that corrupted biological messages account for (but, of course, are not limited to) anaphylaxis, preeclampsia, sudden death syndrome, immune disorders, autism, and so forth. Empirical and theoretical articles are invited exploring pathways by which toxins, disease agents, and their interactions, and/or injuries from microwave, electromagnetic, radiological, or other energy sources can be shown to increase biosemiotic entropy. Empirically grounded arguments showing how cascading series of effects lead to certain injuries, diseases, and/or known disorders are preferred. Prof. Dr. John W. Oller, Jr. Guest Editor

Clip no 2:

Biosemiotics is the synthesis of biology and semiotics, and its main purpose is to show that semiosis is a fundamental component of life, i.e., that signs and meaning exist in all living systems. This idea started circulating in the 1960s and was proposed independently from enquires taking place at both ends of the Scala Naturae. At the molecular end it was expressed by Howard Pattee’s analysis of the genetic code, whereas at the human end it took the form of Thomas Sebeok’s investigation into the biological roots of culture . . .

Sounds like supportive stuff to me! KF PS: Pardon, above I should have addressed DK in the main. kairosfocus

Wiki is unable to indulge its known bias on this subject.

I've posted a couple of papers on the subject of biosemiotics. I managed to track them and others down using Wikipedia. I'm interested to know why you think Wikipedia might wish to suppress the subject. Do you think Biosemiotics has elements that are compatible with "Intelligent Design" ideas? Alan Fox

PS: That, too, is a significant sign as any air raid planner will tell you. Heavy flak comes out when you are nearing a sensitive target. kairosfocus

AF: With all due respect, you are missing the point. First, arguments persuade by one or more of three appeals: emotions, authority, fact and reasoning. Emotions may or may not trace to accurate perceptions and sound judgements -- a car is headed your way, JUMP. Authorities are used in 99% of practical argument, starting with the dictionary. No authority is better than the underlying facts, assumptions and reasoning. And of course it is quality of these that gives warrant in the end. In the case of a known biased source, conceding an embarrassing or undesirable fact for that bias, is material. It is to be further evaluated in terms of fact-logic, but it is significant as any judge will tell you. In the case of Wikipedia, I have consistently pointed its biases and where that is likely to make a difference; including recently exposing -- I laid out corrective facts and reasoning -- an outright hatchet job on ID. I have then said that one needs to be better than Wiki on a given topic, and it is wise to know what the no 5 or so web site is saying on a topic. If you will look at the headline above, you will see that BA is arguing that EVEN Wiki is unable to indulge its known bias on this subject. The mods etc could not pull off a hatchet job on this, unlike what happened with the main article on ID. In that context, observe what Wiki concedes:

To define biosemiotics as “biology interpreted as sign systems study” is to emphasize not only the close relation between biology as we know it (as a scientific field of inquiry) and semiotics (the study of signs), but primarily the profound change of perspective implied when life is considered not just from the perspectives of molecules and chemistry, but as signs conveyed and interpreted by other living signs in a variety of ways, including by means of molecules. In this sense, biosemiotics takes for granted and respects the complexity of living processes as revealed by the existing fields of biology – from molecular biology to brain science and behavioural studies – however, biosemiotics attempts to bring together separate findings of the various disciplines of biology (including evolutionary biology) into a new and more unified perspective on the central phenomena of the living world, including the generation of function and signification in living systems, from the ribosome to the ecosystem and from the beginnings of life to its ultimate meanings.

The highlighted obviously in material part speaks to the role of coded, DNA based genetic information in cells. That does not depend on Wiki for its credibility, but so strong is the case that Wiki, even after its hatchet job on ID cannot deny that. That grudging concession is significant. Earlier today, I cited:

David Chandler: >> The concept of the ‘code’ is fundamental in semiotics. Whilst Saussure dealt only with the overall code of language, he did of course stress that signs are not meaningful in isolation, but only when they are interpreted in relation to each other. It was another linguistic structuralist, Roman Jakobson, who emphasized that the production and interpretation of texts depends upon the existence of codes or conventions for communication (Jakobson 1971). Since the meaning of a sign depends on the code within which it is situated, codes provide a framework within which signs make sense. Indeed, we cannot grant something the status of a sign if it does not function within a code. Furthermore, if the relationship between a signifier and its signified is relatively arbitrary, then it is clear that interpreting the conventional meaning of signs requires familiarity with appropriate sets of conventions. Reading a text involves relating it to relevant ‘codes’. Even an indexical and iconic sign such as a photograph involves a translation from three dimensions into two, and anthropologists have often reported the initial difficulties experienced by people in primal tribes in making sense of photographs and films (Deregowski 1980), whilst historians note that even in recent times the first instant snapshots confounded Western viewers because they were not accustomed to arrested images of transient movements and needed to go through a process of cultural habituation or training (Gombrich 1982, 100, 273). As Elizabeth Chaplin puts it, ‘photography introduced a new way of seeing which had to be learned before it was rendered invisible’ (Chaplin 1994, 179) . . . Semioticians argue that, although exposure over time leads ‘visual language’ to seem ‘natural’, we need to learn how to ‘read’ even visual and audio-visual texts (though see Messaris 1982 and 1994 for a critique of this stance). Any Westerners who feel somehow superior to those primal tribesfolk who experience initial difficulties with photography and film should consider what sense they themselves might make of unfamiliar artefacts – such as Oriental lithographs or algebraic equations. The conventions of such forms need to be learned before we can make sense of them. >>

This comes from an intro to semiotics by an academic in the UK. I of course went on to distinguish another use, that traces to e.g. Hippocrates of Cos, where a sign is an observable feature that lets us reliably infer a state of affairs, Hippocrates giving a well known example of a sign of impending death of a patient. Now, and the links between what Chandler has said and what UB has been saying for months is absolutely obvious:

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.

The intensity of resistance to something that should be pretty much uncontroversial in a day and age of layered protocol comms models, is telling. G kairosfocus

Anyone can use Wikipedia sensibly by following the links to the primary sources. Anyone had a look at the papers upthread yet? Alan Fox

Daniel King @6-7: Wikipedia was quoted as a "hostile witness" :) as mentioned in the other post. Wikipedia isn't the only one. There are all kinds of materialistic-minded folks who use design terminology, talk about the design of life in a loose sense, admit that biological systems look designed, etc. They of course go on to proclaim blind faith in the power of matter and energy bumping into each other to produce all life as we know it and argue that the appearance of design is all an illusion. But their design-relevant statements are certainly free game for discussion. Eric Anderson

KN @4: No. Biosemiotics offers good evidence that we are dealing with a semiotic system. We don't need any panpsychism or anything else. It is also certainly false that an argument for intelligent design would need to show that some designer is not living in our sense. Sober also doesn't know what he is talking about with the need for an alleged regress (assuming you have reflected his opinion accurately). Look, this is very simple. We don't need to get into philosophical discussions about some panpsychism, who designed the designer, non-living designers, etc. It is called an inference to the best explanation and it follows a very simple approach: 1. Semiotic systems are regularly seen to arise from intelligent agents. As a corollary, semiotic systems have never been known to arise from purely natural causes. Indeed, in every instance in which we see a semiotic system and know the provenance, it started with an intelligent agent. 2. There is a semiotic system in biology. 3. Therefore, the most likely explanation is that it came from an intelligent agent. Is this deduction? Of course not. But it is a perfectly appropriate form of inductive reasoning and inferring to the best explanation. Eric Anderson

The difference, Daniel, is when we disagree with Wikipedia we make an argument as to why they are wrong. Mung

Sorry, that's "So much for arguments from authority. Daniel King

How convenient to quote Wikipedia. When it agrees with you, it's fine. When it disagrees, it's wrong. So much for arguments for authority. Daniel King

A Short History of Biosemiotics (PDF) @ UB: It mentions Howard Pattee! Alan Fox

Biosemiotics offers good evidence for what's been called "biological panpsychism" (see here, which holds that life and mind are necessarily co-extensive. But to generate an argument for intelligent design, one would need to show that at least some intelligent designers are not necessarily living (in our sense of life, anyway). Indeed, Eliot Sober has taken this one step further and claimed that intelligent design is committed to positing at least one extra-cosmic designer, in order to stop the regress. Kantian Naturalist

Biosemiotic Entropy: Disorder, Disease, and Mortality includes the magic buzz word in its title. It's available as a PDF to anyone with the time to download and read it.I'd be interested in other people's comments. I'll keep my own council for a while so as not to "poison the well". :) Alan Fox

...the profound change of perspective implied...

No wonder they are fearful. Mung

Even they can't deny what's right in front of their eyes. Mapou