Linguistics of biological systems

7 Replies to “Linguistics of biological systems”

1. 1
   johnnyb says:

   June 21, 2014 at 1:25 pm

   You should take a look at the vdj recombination system. It has these sequences called recombination signal sequences which tell the cell where to splice the genome.
2. 2
   Mapou says:

   June 21, 2014 at 2:07 pm

   I like the comparison between language and DNA. I think it’s important to note that all languages are organized hierarchically. What I mean is that, at the bottom level, we find elementary sounds and phonemes, followed by syllables, words, sentences, etc. The use of a hierarchy is a superefficient form of data compression because it enforces the reuse of low level entities by high level entities. This eliminates redundancies. It is highly likely that the genome is also organized hierarchically. It is the only way to pack so much information in such a small package.

   In conclusion, I believe that genomic research would be greatly accelerated if researchers worked to fit their findings within a hierarchical model.
3. 3
   bornagain77 says:

   June 21, 2014 at 2:08 pm

   A like your analogy of ‘multiple languages’ interacting with each other in the cell. It gets the point across much better than merely stating that ‘multiple codes’ are found in biological life.

   A few notes that may be helpful:

   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=wqiXNxyoof8

   Refereed scientific article on DNA argues for irreducible complexity – October 2, 2013
   Excerpt: This paper published online this summer is a true mind-blower showing the irreducible organizational complexity (author’s description) of DNA analog and digital information, that genes are not arbitrarily positioned on the chromosome etc.,,
   ,,,First, the digital information of individual genes (semantics) is dependent on the the intergenic regions (as we know) which is like analog information (syntax). Both types of information are co-dependent and self-referential but you can’t get syntax from semantics. As the authors state, “thus the holistic approach assumes self-referentiality (completeness of the contained information and full consistency of the different codes) as an irreducible organizational complexity of the genetic regulation system of any cell”. In short, the linear DNA sequence contains both types of information. Second, the paper links local DNA structure, to domains, to the overall chromosome configuration as a dynamic system keying off the metabolic signals of the cell. This implies that the position and organization of genes on the chromosome is not arbitrary,,,
   http://www.christianscientific.....omplexity/

   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/re.....133252.htm

   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/break.....e_revealed

   Design In DNA – Alternative Splicing, Duons, and Dual coding genes – video (5:05 minute mark)
   http://www.youtube.com/watch?v=Bm67oXKtH3s#t=305

   At the 10:30 minute mark of the following video, Dr. Trifonov states that the concept of the selfish gene ‘inflicted an immense damage to biological sciences’, for over 30 years:

   Second, third, fourth… genetic codes – One spectacular case of code crowding – Edward N. Trifonov – video
   https://vimeo.com/81930637

   In the preceding video, Trifonov elucidates codes that are, simultaneously, in the same sequence, coding for DNA curvature, Chromatin Code, Amphipathic helices, and NF kappaB. In fact, at the 58:00 minute mark he states, “Reading only one message, one gets three more, practically GRATIS!”. And please note that this was just an introductory lecture in which Trifinov just covered the very basics and left many of the other codes out of the lecture. Codes which code for completely different, yet still biologically important, functions. In fact, at the 7:55 mark of the video, there are 13 codes that are listed on a powerpoint, although the writing was too small for me to read.

   Concluding powerpoint of the lecture (at the 1 hour mark):

   “Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages.”
   Edward N. Trifonov – 2010

   Multiple genetic codes
   Excerpt: Trifonov,, was also the first one to demonstrate[20] that there are multiple codes present in the DNA. He points out that even so called non-coding DNA has a function, i.e. contains codes, although different from the triplet code.
   Trifonov recognizes[19]:5–10 specific codes in the DNA, RNA and proteins:,,

   chromatin code (Trifonov 1980)
   RNA-to-protein translation code (triplet code)
   framing code (Trifonov 1987)
   translation pausing code (Makhoul & Trifonov 2002) protein folding code (Berezovsky, Grosberg & Trifonov 2000)
   fast adaptation codes (Trifonov 1989)
   binary code (Trifonov 2006)
   genome segmentation code (Kolker & Trifonov 1995)

   The codes can overlap[19]:10 each other so that up to 4 different codes can be identified in one DNA sequence (specifically a sequence involved in a nucleosome). According to Trifonov, other codes are yet to be discovered.
   – per wikipedia

   Cracking the bioelectric code: Probing endogenous ionic controls of pattern formation – January 2013
   Excerpt: A recent paper demonstrated that a specific voltage range is necessary for demarcation of eye fields in the frog embryo. Remarkably, artificially setting other somatic cells to the eye-specific voltage range resulted in formation of eyes in aberrant locations, including tissues that are not in the normal anterior ectoderm lineage: eyes could be formed in the gut, on the tail, or in the lateral plate mesoderm. These data challenge the existing models of eye fate restriction and tissue competence maps, and suggest the presence of a bioelectric code-a mapping of physiological properties to anatomical outcomes.
   http://www.ncbi.nlm.nih.gov/pubmed/23802040

   Not in the Genes: Embryonic Electric Fields – Jonathan Wells – December 2011
   Excerpt: although the molecular components of individual sodium-potassium channels may be encoded in DNA sequences, the three-dimensional arrangement of those channels — which determines the form of the endogenous electric field — constitutes an independent source of information in the developing embryo.
   http://www.evolutionnews.org/2.....54071.html
4. 4
   Dionisio says:

   June 21, 2014 at 9:15 pm

   BA77,

   thank you for the comments with the links.

   I liked a funny moment at the beginning of professor Trifonov’s presentation in Prague 2010.

   Second, third, fourth… genetic codes – One spectacular case of code crowding – Edward N. Trifonov – video
   https://vimeo.com/81930637

   Around 6:17 Professor Trifonov said it is obvious there are many codes, and also there’s a pathological amnesia in scientific society, because every time a new code was ‘cracked’ (deciphered) the science media called it ‘second code’ forgetting the previous discoveries. I could hear some laughing in the audience.
5. 5
   Dionisio says:

   June 22, 2014 at 10:56 am

   We’re honored to have Piotr as part of the UD discussions.

   I’m glad to see Piotr back in this “echo chamber” (as he called this UD blog not long ago). Hopefully he will enjoy sharing his vast knowledge with the rest of us here.
6. 6
   Dionisio says:

   June 22, 2014 at 12:25 pm

   A semiotic analysis of the genetic
   information system*
   CHARBEL NINO EL-HANI, JOAO QUEIROZ, and CLAUS EMMECHE

   Semiotica 160–1/4 (2006), 1–68
   0037–1998/06/0160–0001
   DOI 10.1515/SEM.2006.039
   Walter de Gruyter

   http://www.cspeirce.com/menu/l.....enetic.pdf
7. 7
   Dionisio says:

   June 22, 2014 at 1:48 pm

   I foresee an odd alliance between the ID community and the biosemiotic community.

   This paper on biosemiotics is 68-page long. The authors do not seem to be ID proponents, as it can be noticed in the quotes from page 6 below. I may not agree with some of their general statements, but still see their proposition very interesting.

   Here are a few quotes from this paper:

   A semiotic analysis of the genetic information system*
   CHARBEL NINO EL-HANI, JOAO QUEIROZ, and CLAUS EMMECHE

   Terms loaded with informational connotations are often employed to refer to genes and their dynamics. Indeed, genes are usually perceived by biologists as basically ‘the carriers of hereditary information.’ Nevertheless, a number of researchers consider such talk as inadequate and ‘just metaphorical,’ thus expressing a skepticism about the use of the term ‘information’ and its derivatives in biology as a natural science.
   First, because the meaning of that term in biology is not as precise as it is, for instance, in the mathematical theory of communication.
   Second, because it seems to refer to a purported semantic property of genes without theoretically clarifying if any genuinely intrinsic semantics is involved.
   Biosemiotics, a field that attempts to analyze biological systems as semiotic systems, makes it possible to advance in the understanding of the concept of information in biology.

   Semiotica 160–1/4 (2006), 1–68
   0037–1998/06/0160–0001
   DOI 10.1515/SEM.2006.039
   Copyright by Walter de Gruyter

   http://www.cspeirce.com/menu/l.....enetic.pdf

   Page 6

   ‘information’ turned into one of the most important but problematic concepts in biology (see Oyama 2000 [1985]; Stuart 1985; Sarkar 1996; Griffiths 2001; Jablonka 2002). The concept of information in biology has been recently a topic of substantial discussion (see, for example, Maynard Smith 2000a; Godfrey-Smith 2000; Sarkar 2000; Sterelny 2000; Wynnie 2000; Jablonka 2002; Adami 2004).
   Furthermore, the evolution of new kinds of information and information interpretation systems in living beings has received a great deal of attention recently (see, for example, Jablonka 1994; Jablonka and Szathmáry 1995;Maynard Smith and Szathmáry 1995, 1999; Jablonka, Lamb, and Avital 1998).
   The evolution of different ways of storing, transmitting, and interpreting ‘information’ can even be regarded as a major theme in the history of life (Maynard Smith and Szathmáry 1995, 1999; Jablonka 2002).

   Page 8

   The concepts of ‘code,’ ‘information,’ ‘signals,’ ‘message,’ ‘signaling,’ ‘transduction’ and so on can be seen as necessary to understand the organization of relations in living beings in such a way that makes it clear that what happens in such beings is much more than simple chemistry.

   ‘about fifty percent of the genome of a multicellular organism may code for proteins involved in cell signaling, . . . organisms can be viewed as complex information-processing systems, where molecular analysis alone may not be sufficient’

   there’s a need to realize that information may be transmitted in ways that may be lost by studying molecules alone

   ‘it may not be possible or even necessary to explain all cellular phenomena in terms of precise molecular interactions’

   Page 9

   These statements indicate that a reason why we can say that more than just chemistry is taking place in living beings lies in the fact that these systems process ‘information’ in quite complex ways, as Signs are produced, communicated, interpreted, translated, etc. In other words, biological meaningfulness is emerging all the time in such systems.

   It is not surprising, then, that biologists felt the need to talk about ‘information’ as they were delving more and more into the molecular microstructure of living systems.

   even though all cellular processes have physical-chemical properties, more than just physics and chemistry is going on there.

   The concept of information and related notions in biology should not only be taken seriously, but also clarified by employing appropriate conceptual tools.
   now widely accepted idea that there is more to information in living systems than just genes

   ‘genetic information’ is a metaphor in search of a theory.

   we should not simply extrapolate the conclusions taken from an analysis of this peculiar [genetic information] system for all other types of information systems in living beings.

   the genetic system, despite its importance, is highly specific and unusual, and, therefore, should not be taken as a prototype for thinking about information in biology

   Page 10

   a first step in a research program aiming at a general semiotic analysis of information systems in living beings

   3. Information, meaning, and semiosis

   specific meaning processes in biology

   inferential processes in general

   apply […] semiotics to understand the nature of genetic information

   Semiotics as the ‘formal science of signs’

   semiotics is based on a theory of categories, including a list of categories (Firstness, Secondness, Thirdness) which can be logically described as an exhaustive system of hierarchically organized classes of relations (monadic, dyadic, triadic)

   Page 11

   semiosis as an irreducible triadic relation between Sign-Object-Interpretant (S-O-I)

   A Sign is a Cognizable that, on the one hand, is so determined (i.e., specialized, bestimmt) by something other than itself, called its Object, while, on the other hand, it so determines some actual or potential Mind, the determination whereof I term the Interpretant created by the Sign, that that Interpreting Mind is therein determined mediately by the Object.

   ‘Sign’4 or ‘Representamen’ as a ‘First’ which stands in such a genuine triadic relation to a ‘Second,’ called its ‘Object,’ so as to be capable of ‘determining a Third,’ called its ‘Interpretant,’ to assume the same triadic relation to its Object in which it stands itself to the same Object

   ‘semiosis’ […] an action, or influence, which is, or involves, a cooperation of three subjects, such as a sign, its object, and its interpretant, this tri-relative influence not being in any way resolvable into actions between pairs.

   semiosis is dynamic – events, not things, are highlighted. The complex S-O-I is the focal factor of a dynamical process

   Sign processes are relationally extended within the spatiotemporal dimension, so that something physical has to instantiate or realize them. This means that Signs cannot act unless they are spatiotemporally realized

   If a Sign is to have any active mode of being, it must be materially embodied.

   It is also important to avoid losing sight of the distinction between the interpreter, which is the system which interprets the Sign, and the Interpretant. The interpreter is […] a ‘Quasi-mind’, a description which demands, for its proper interpretation, a clear recognition of Peirce’s broad concept of ‘mind’.

   Page 12

   It is far from being the case that only conscious beings can be interpreters… Rather, a transcription machinery synthesizing RNA from a string of DNA or a membrane receptor recognizing a given hormone can be regarded as an interpreter…

   A basic idea in a semiotic understanding of living systems is that these systems are interpreters of Signs; that is, that they are constantly responding to selected signs in their surroundings. The interpreter does not have to be a conscious being, not even an organism, as it may be some part or subsystem within an organism, or a humanly-designed product

   We must distinguish between the Immediate Object — i.e., the Object as represented in the sign — and . . . the Dynamical Object, which, from the nature of things, the Sign cannot express, which it can only indicate and leave the interpreter to find out by collateral experience.

   . . . we have to distinguish the Immediate Object, which is the Object as the Sign itself represents it, and whose Being is thus dependent upon the Representation of it in the Sign, from the Dynamical Object, which is the Reality which by some means contrives to determine the Sign to its Representation.

   The Immediate Interpretant is the immediate pertinent possible effect in its unanalyzed primitive entirety . . . The Dynamical Interpretant is the actual effect produced upon a given interpreter on a given occasion in a given stage of his consideration of the Sign.

   The Immediate Object of a Sign is the Object as it is immediately given to the Sign, the Dynamical Object in its semiotically available form. The Dynamical Object is something in reality that determines the Sign to its representation, and which the Sign can only indicate, something that the interpreter should find out by collateral experience.

   Page 13

   The Dynamical Interpretant is the instantiation of one of the possible e¤ects established in the Immediate Interpretant.