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Information killed the Central Dogma too

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Springer Handbook of Bio-/Neuro-Informatics Further to “‘Junk proteins’ hit the antiques road show” (in 2013 functions were identified for many of these “intrinsically disordered proteins” (IDPs), as they are sometimes called): A new book from Springer features a chapter by molecular geneticist Alberto Riva, “Information Processing at the Cellular Level: Beyond the Dogma”:

Abstract: The classical view of information flow within a cell, encoded by the famous central dogma of molecular biology, states that the instructions for producing amino acid chains are read from specific segments of DNA, just as computer instructions are read from a tape, transcribed to informationally equivalent RNA molecules, and finally executed by the cellular machinery responsible for synthesizing proteins. While this has always been an oversimplified model that did not account for a multitude of other processes occurring inside the cell, its limitations are today more dramatically apparent than ever. Ironically, in the same years in which researchers accomplished the unprecedented feat of decoding the complete genomes of higher-level organisms, it has become clear that the information stored in DNA is only a small portion of the total, and that the overall picture is much more complex than the one outlined by the dogma.

Springer Handbook of Bio-/Neuroinformatics

The cell is, at its core, an information processing machine based on molecular technology, but the variety of types of information it handles, the ways in which they are represented, and the mechanisms that operate on them go far beyond the simple model provided by the dogma. In this chapter we provide an overview of the most important aspects of information processing that can be found in a cell, describing their specific characteristics, their role, and their interconnections. Our goal is to outline, in an intuitive and nontechnical way, several different views of the cell using the language of information theory.

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20 Replies to “Information killed the Central Dogma too

  1. 1
    Mung says:

    Nice find News!

    The cell is, at its core, an information processing machine based on molecular technology, but the variety of types of information it handles, the ways in which they are represented, and the mechanisms that operate on them go far beyond the simple model provided by the dogma.

    Why is it that within the cell, types of information require ways of representation but outside the cell it’s just “information everywhere”?

    By what means does one get from homogenous information (if that term can even be meaningful) to information that requires representation?

    Why would such a transition even be necessary?

  2. 2
    Upright BiPed says:

    Why is it that within the cell, types of information require ways of representation but outside the cell it’s just “information everywhere”?

    check

  3. 3
    Mung says:

    Assuming “the Dembski model of information” (aka it could have been otherwise, therefore it’s information) “Dembski information” must exist within the cell as well.

    Given the presence of what must be massive amounts of “Dembski information” within the cell, what precipitated the move to representation of information?

    It must be the case that the representation of information must be a case of “Dembski information,” for a representation is itself one of a set of possible alternatives, is it not?

  4. 4
    Upright BiPed says:

    representation, protocol, discontinuity, function.

    write that down 😉

  5. 5
    Dionisio says:

    In the abstract of Dr. Riva’s chapter we read:

    …but the variety of types of information it handles, the ways in which they are represented, and the mechanisms that operate on them…

    Copied this comment from another thread:

    Interesting topic for exciting discussions.

    In software development for engineering systems, the main engineers directing the projects usually see the future product in their minds long before the first beta version comes out for testing.

    An important part of the process of developing such systems is the accurate and efficient passing of complete information describing the final product and the steps to develop, test, deliver and implement it in a timely fashion.

    All that information must be well documented using established protocols and conventions, so that all the participants in the project can understand what is to be done and how.
    The information given to the analysts is not exactly the same as the information passed down to the programmers or to the testing group or to the implementation team or to the sales and delivery personnel.
    The programmers also follow an established convention (a.k.a. programming language), in order to pass the information they receive from the analyst down to the computer that will process user-provided information in order to produce user-requested results.
    In a way or another all this has to do with information that still relates to the original image of the product that existed in the mind of the persons who came up with the idea to begin with.

    Now, can we relate this to what we observe in the biological systems? Yes, no, maybe?

  6. 6
    Dionisio says:

    gpuccio, can you write to me at my email address?
    I have some questions for you.
    Thank you.

  7. 7
  8. 8
    gpuccio says:

    Dionisio:

    Yes, but how do I get your email address?

  9. 9
    gpuccio says:

    Andre:

    A very good summary, thank you! 🙂

    Now, darwinists will always be there with their just so stories to explain how all that evolved by RV and NS, but at least they will need to generate a lot of very long just so stories, so that will keep them busy, I hope, while real scientists do their work 🙂

  10. 10
    Dionisio says:

    gpuccio, sorry, I thought you had access and could see it in my UD profile info. Here it is: dshared@ymail.com
    Mile grazie !

  11. 11
    Dionisio says:

    gpuccio @ 9

    Now, darwinists will always be there with their just so stories to explain how all that evolved by RV and NS, but at least they will need to generate a lot of very long just so stories, so that will keep them busy, I hope, while real scientists do their work 🙂

    Well stated! thank you.

  12. 12
    Dionisio says:

    Dionisio @ 5

    Regarding Dr. Riva’s quote and the software development example given as illustration, can one distinguish (point to, identify):
    a) types of information,
    b) ways in which they are represented,
    c) mechanisms that operate on them?

  13. 13
    Dionisio says:

    Dionisio @ 5

    Regarding Dr. Riva’s quote and the software development example given as illustration, can one distinguish (point to, identify):
    a) types of information,
    b) ways in which they are represented,
    c) mechanisms that operate on them?

  14. 14
    Dionisio says:

    Sorry. No idea why comment 12 got posted twice. Most probably I messed up something. Oh, well, not my first time.

  15. 15
    bornagain77 says:

    Dionisio, since it is behind a paywall, I don’t know exactly what she is talking about in regards to ‘types of information’, but I do know that Dr Shapiro has listed several ways, contrary to the central dogma which undergirds neo-Darwinism, that epigenetic information flows in the cell in this paper on page 22:

    Revisiting the Central Dogma in the 21st Century – James A. Shapiro – 2009
    Excerpt: Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112).
    http://shapiro.bsd.uchicago.ed.....0Dogma.pdf

    Shapiro also has this fairly recent paper out:

    How life changes itself: the Read-Write (RW) genome. – 2013
    Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.
    http://www.ncbi.nlm.nih.gov/pubmed/23876611

    Denis Nobel, President of the International Union of Physiological Sciences, outlines a short history of the modern synthesis (central dogma) of neo-Darwinism here:

    Modern Synthesis Of Neo-Darwinism Is False – Denis Nobel – video
    http://www.metacafe.com/w/10395212

    ,, In the preceding video, Dr Nobel states that around 1900 there was the integration of Mendelian (discrete) inheritance with evolutionary theory, and about the same time Weismann established what was called the Weismann barrier, which is the idea that germ cells and their genetic materials are not in anyway influenced by the organism itself or by the environment. And then about 40 years later, circa 1940, a variety of people, Julian Huxley, R.A. Fisher, J.B.S. Haldane, and Sewell Wright, put things together to call it ‘The Modern Synthesis’. So what exactly is the ‘The Modern Synthesis’? It is sometimes called neo-Darwinism, and it was popularized in the book by Richard Dawkins, ‘The Selfish Gene’ in 1976. It’s main assumptions are, first of all, is that it is a gene centered view of natural selection. The process of evolution can therefore be characterized entirely by what is happening to the genome. It would be a process in which there would be accumulation of random mutations, followed by selection. (Now an important point to make here is that if that process is genuinely random, then there is nothing that physiology, or physiologists, can say about that process. That is a very important point.) The second aspect of neo-Darwinism was the impossibility of acquired characteristics (mis-called “Larmarckism”). And there is a very important distinction in Dawkins’ book ‘The Selfish Gene’ between the replicator, that is the genes, and the vehicle that carries the replicator, that is the organism or phenotype. And of course that idea was not only buttressed and supported by the Weissman barrier idea, but later on by the ‘Central Dogma’ of molecular biology. Then Dr. Nobel pauses to emphasize his point and states “All these rules have been broken!”.
    Professor Denis Noble is President of the International Union of Physiological Sciences.

    Here is a paper by Dr. Nobel

    Physiology is rocking the foundations of evolutionary biology – Denis Noble – 17 MAY 2013
    Excerpt: The ‘Modern Synthesis’ (Neo-Darwinism) is a mid-20th century gene-centric view of evolution, based on random mutations accumulating to produce gradual change through natural selection.,,, We now know that genetic change is far from random and often not gradual.,,,
    http://onlinelibrary.wiley.com.....4/abstract

    “The genome is an ‘organ of the cell’, not its dictator”
    – Denis Nobel – President of the International Union of Physiological Sciences

    Also of note:

    Die, selfish gene, die – The selfish gene is one of the most successful science metaphors ever invented. Unfortunately, it’s wrong – Dec. 2013
    Excerpt: But 15 years after Hamilton and Williams kited [introduced] this idea, it was embraced and polished into gleaming form by one of the best communicators science has ever produced: the biologist Richard Dawkins. In his magnificent book The Selfish Gene (1976), Dawkins gathered all the threads of the modern synthesis — Mendel, Fisher, Haldane, Wright, Watson, Crick, Hamilton, and Williams — into a single shimmering magic carpet (called the selfish gene).
    Unfortunately, say Wray, West-Eberhard and others, it’s wrong.
    http://www.uncommondescent.com.....-heard-of/

    At the 10:30 minute mark of the following video, Dr. Trifonov, who is IMHO a par excellence biochemist, 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

    Supplemental note:

    The Fate of Darwinism: Evolution After the Modern Synthesis – David J. Depew and Bruce H. Weber – 2011
    Excerpt: We trace the history of the Modern Evolutionary Synthesis, and of genetic Darwinism generally, with a view to showing why, even in its current versions, it can no longer serve as a general framework for evolutionary theory. The main reason is empirical. Genetical Darwinism cannot accommodate the role of development (and of genes in development) in many evolutionary processes.,,,
    http://www.springerlink.com/co.....03g3t7002/

    Science Review Article: “Nothing in Evolution Makes Sense Except in the Light of Biology” – Casey Luskin – March 12, 2014
    Excerpt: One of those now-overturned assumptions, which underlies virtually all of modern population genetics, “molecular clock” studies, as well as the highly criticized methods often used to infer natural selection in genes, is that mutations are random and occur at a constant, gradual rate:,,,
    “Mutations are also nonrandom in genomic space — for example, forming hot spots at DNA double-strand breaks, as demonstrated in bacteria and suggested by local clusters of mutations in cancer genomes.”,,,
    Their conclusion, however, is telling:
    “The evolutionary biologist Theodosius Dobzhansky famously noted that “nothing in biology makes sense except in the light of evolution,” but perhaps, too, “nothing in evolution makes sense except in the light of biology.””,,,
    ,,, In fact, it seems that a lot of evolutionary claims no longer makes sense in the light of biology.
    http://www.evolutionnews.org/2.....83101.html

    Verse and Music:

    John 1:1-4
    In the beginning was the Word, and the Word was with God, and the Word was God.
    The same was in the beginning with God.
    All things were made by Him, and without Him was not anything made that was made.
    In Him was life, and that life was the Light of men.

    Shake – MercyMe
    https://www.youtube.com/watch?v=YJFA5Bitv7w

  16. 16
    Mung says:

    Upright BiPed:

    representation, protocol, discontinuity, function.

    write that down

    rpdf – I can’t pronounce that

    We need an acronym here!

  17. 17
    Dionisio says:

    Mung @ 16

    We need an acronym here!

    ReProDiFun?

  18. 18
    Dionisio says:

    Mung @ 16

    We need an acronym here!

    Here’s another overloaded acronym for CSI:
    COSPOFI
    Complex Specified Purpose-Oriented Functional Information

    😉

  19. 19
    Dionisio says:

    bornagain77 @ 15

    Thank you for the information. Have a good weekend.

  20. 20
    Mung says:

    …the information content of the noncoding portion of the genome, although at present difficult to quantify, is certainly very significant. In fact, the flow of information within the cell is much more complex than the simple conversion of a series of triplets into a chain of amino acids.

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