Intelligent Design

Is the Royal Society Finally Catching Up with Our Own Upright Biped?

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For some time now Upright Biped has been arguing that information cannot be reduced to chemistry, and last year he started his own website to further his key idea that when information is translated by cellular machinery, it organizes inanimate matter (carbon, hydrogen, nitrogen, etc) into all the living things on earth.  See biosemiosis.org  Essentially, UB says all of life is an artifact created by the manipulation of chemicals according to the information embedded in the cell.

Now comes the March 2016 issue of the Philosophical Transactions of the Royal Society with a special issue on DNA as Information.  The table of contents is here.

We would like to draw special attention to the article What is Information by Marcello Barbieri.  The abstract (but for the English spellings) could have been written by UB:

Molecular biology is based on two great discoveries: the first is that genes carry hereditary information in the form of linear sequences of nucleotides; the second is that in protein synthesis a sequence of nucleotides is translated into a sequence of amino acids, a process that amounts to a transfer of information from genes to proteins. These discoveries have shown that theinformation of genes and proteins is the specific linear order of their sequences. This is a clear definition of information and there is no doubt that it reflects an experimental reality. What is not clear, however, is the ontological status of information, and the result is that today we have two conflicting paradigms in biology. One is the ‘chemical paradigm’, the idea that ‘life is chemistry’, or, more precisely, that ‘life is an extremely complex form of chemistry’. The other is the ‘information paradigm’, the view that chemistry is not enough, that ‘life is chemistry plus information’. This implies that there is an ontological difference between information and chemistry, a difference which is often expressed by saying that information-based processes like heredity and natural selection simply do not exist in the world of chemistry. Against this conclusion, the supporters of the chemical paradigm have argued that the concept of information is only a linguistic metaphor, a word that summarizes the result of countless underlying chemical reactions. The supporters of the information paradigm insist that information is a real and fundamental component of the living world, but have not been able toprove this point. As a result, the chemical view has not been abandoned and the two paradigms both coexist today. Here, it is shown that a solution to the ontological problem of information does exist. It comes from the idea that life is artefact-making, that genes and proteins are molecular artefacts manufactured by molecular machines and that artefacts necessarily require sequences and coding rules in addition to the quantities of physics and chemistry. More precisely, it is shown that the production of artefacts requires new observables that are referred to as nominable entities because they can be described only by naming their components in their natural order. From an ontological point of view, in conclusion, information is a nominable entity, a fundamental but not-computable observable.

 

And then there is The Meaning of Biological Information by Eugene Koonin.  Abstract:

Biological information encoded in genomes is fundamentally different from and effectively orthogonal to Shannon entropy. The biologically relevant concept of information has to do with ‘meaning’, i.e. encoding various biological functions with various degree of evolutionary conservation. Apart from direct experimentation, the meaning, or biological information content, can be extracted and quantified from alignments of homologous nucleotide or amino acid sequences but generally not from a single sequence, using appropriately modified information theoretical formulae. For short, information encoded in genomes is defined vertically but not horizontally. Informally but substantially, biological information density seems to be equivalent to ‘meaning’ of genomic sequences that spans the entire range from sharply defined, universal meaning to effective meaninglessness. Large fractions of genomes, up to 90% in some plants, belong within the domain of fuzzy meaning. The sequences with fuzzy meaning can be recruited for various functions, with the meaning subsequently fixed, and also could perform generic functional roles that do not require sequence conservation. Biological meaning is continuously transferred between the genomes of selfish elements and hosts in the process of their coevolution. Thus, in order to adequately describe genome function and evolution, the concepts of information theory have to be adapted to incorporate the notion of meaning that is central to biology.

17 Replies to “Is the Royal Society Finally Catching Up with Our Own Upright Biped?

  1. 1
    bloodymurderlive says:

    This will come as a shock to code denialists.

  2. 2
    Mapou says:

    Wait till the code denialists begin to claim that this is exactly what they’ve been saying all along. One must never underestimate the deviousness of the enemy. Their lack of honor is legendary and blatant.

  3. 3
    Mapou says:

    It comes from the idea that life is artefact-making

    How did this get past the Darwinist reviewers at the Royal Society? This is clearly admitting intelligent design. Marcello Barbieri found a clever way to fool the fools.

  4. 4
    mike1962 says:

    +1

  5. 5
    smordecai says:

    “The supporters of the information paradigm insist that information is a real and fundamental component of the living world, but have not been able to prove this point. As a result, the chemical view has not been abandoned and the two paradigms both coexist today.”

    Certainly the chemical paradigm has not been proven either but at least the information paradigm offers empirical evidence. All chemistry can offer is “time makes anything possible”

  6. 6
    groovamos says:

    I think that what Koonin is saying is misleading. Shannon purposely skirts the topic of meaning in his classic 1948 paper because it was not necessary for the mathematics and statistics he was presenting – and he effectively says such. This does not mean that Shannon’s work has no philosophical relationship to meaning. Here are a couple of examples. Astronomical instruments spew out data that can be converted into measurements or images. That data is generated not only by the part of the cosmos being probed, but also by the instruments employed, neither of which obviously have human-like concerns of meaning. The data can be processed by human facilities that can result in scientific papers which then have the properties of meaning. Therefore the characteristic of meaning has been added by mind (humans) to the otherwise meaningless data collected.

    Here is another one and I wish I knew if Shannon ever discussed this. The central concern of his work was the corruption of information by noise. In this respect, noise is the antithesis of any properties of meaning, at the very least devoid of meaning. But supposing the mind is interested in the noise source, then the noise source becomes an object of study and a source of information itself. Thus just the addition of mind to the question can convert anti-meaning into meaning. Shannon assumed Gaussian distribution for the noise in his analysis, but there are other properties of noise, such as spectral density and power. The noise can be determined to be largely electrical Johnson noise, which is the low frequency component of black-body radiation, and so the temperature of the noise source can be determined.

    The interesting thing about biology is that if the view of the primacy information takes hold, then it will persuade the view of the advent of life to be dependent on mind at the outset.

  7. 7
    Robert Byers says:

    We are not a bunch of chemicals or water with chemicals.
    We are a organized(information) entity first. Then its elements are water , chemical, etc.
    It was never true , as kids, to be told we were mostly made of water and some chemicals.
    We are mostly information that uses water and chemicals.
    Thats the true equation and if its novel then its a true modern paradigm changing.

  8. 8
    GBDixon says:

    Groovamos@6 +1.

    As I grapple with what physicists mean by ‘information’ and what most scientists mean by ‘Shannon information’ and ‘Shannon entropy’, it has become clear that Koonin, among others, is making the fundamental mistake of confusing the capacity to transfer or hold information (the ‘channel capacity’)with information itself. Shannon’s work applies perfectly to biological information, but one must understand it first.

    Again, Shannon’s underlying assumption was that information was an encoded set of messages that could be decoded and understood by the receiver of the messages. In the cell, the receivers are obviously those molecular machines that carry out commands coded in the DNA messages. The sequences have meaning to the machines and are information to them.

    Somewhere along the way someone got the confused notion that the Shannon capacity is really Shannon information and therefore this information has no meaning and no relevance to ‘real’ information. This mistake so pervasive I don’t think we can hope to correct it, but at least we can point it out when the opportunity is present.

    Regarding noise, if the receiver is interested in the noise and is learning something from it, it is information to her. To the rest of us it is noise. Information is not a neatly tied bundle of something exactly the same for everyone. It is what the receiver of the information says it is, and that differs from receiver to receiver, even with the same dataset.

  9. 9
    bloodymurderlive says:

    Some dude on G+ called “Scientist Sam” thinks this paper is garbage, apparently:

    The first thing that I need to point out is that the author is not a biologist. He is a semiotician (someone who studies symbols and meanings). This will readily explain some of his more idiotic claims. It is also important to note that this is not a scientific research paper. It is a philosophical paper and does not present any new experimental paradigm. On this basis, I was willing to dismiss it out-of-hand on the basis of adding nothing to scientific understanding. But, it also makes crap arguments worthy of analysis.

    He starts his paper with an outline of the paradigm that life, when broken down, is a fundamentally chemical process. He asserts that life is based on information without rigorously defining what that entails. What empirical observations can be predicted from this assertion? What does this mean in terms of the functional aspect of the cell? He continues that the rules of the genetic code cannot be reduced to physical quantities. This is just plain nonsense to anyone who has taken molecular biology. The rules and physical constraints of the genetic code is largely known.

    Later on, the author asserts that life is fundamentally different from inorganic matter. Are we back to 19th century vitalism? Biologists have already had this discussion. Life is a collection of biochemical processes. It isn’t some magical entity. One aspect of this process is the ability to self-replicate and the phenotypic aspects of these self-replicating systems. The author treats these as though they are magical rather than a property of living systems.

    The rest of the article takes a turn towards the weird. I was unaware that the chemical reactions in our cells are not spontaneous in biological conditions. Except that they are and this is the central premise of biochemistry. The author is basically making the arguments that reactions in living matter differ from those in non-living matter. Well, no shit! Part of the definition of life are these types of ordered reactions. This line of argumentation verges on circularity by saying that what makes life different is what makes life different. He’s not adding anything new to this discussion.

    The author curiously concedes that the informational aspect of life is non-quantitative and non-qualitative. I almost want to stop here because, as a scientist, why should I care about it? The author’s reasoning is that it acts as a label that we assign to life. He gives examples from physics to support this idea. The problem is that labels in science are only as good as the experiments they guide. We use precise terminology in order to gain insight about the desired phenomena.

    Not sure if I’m allowed to post links, but I guess that’s enough to Google it. Thoughts, guys?

  10. 10
    mike1962 says:

    bloodymurderlive,

    Yes, links are OK. Please post it.

  11. 11
    bloodymurderlive says:

    Ok, per mike1962’s permission, here is a link to the response I quoted at #9:
    https://plus.google.com/u/0/112151470359988857381/posts/VHk4DfQLGrg

  12. 12

    wow

    What a headline…lol

    Thank you Barry.

    I am quite certain that I am Marcello’s list of the most despised people on the planet.

    I wished it wasn’t that way.

  13. 13
    Me_Think says:

    bloodymurderlive @ 9

    Some dude on G+ called “Scientist Sam” thinks this paper is garbage, apparently

    It is a Philosophy paper. What did you expect?

  14. 14

    For whatever it’s worth, my exchange with “Scientist Sam”:

    – – – – – – – – – – – –

    Scientist Sam

    The first thing that I need to point out is that the author is not a biologist. He is a semiotician (someone who studies symbols and meanings). This will readily explain some of his more idiotic claims…

    UprightBiPed

    The author is not a biologist?

    Marcello Barbieri (1940) is professor of embryology at the University of Ferrara, Italy. Before moving to Ferrara he taught biophysics, molecular embryology and theoretical biology respectively at the Universities of Bologna, Sassari and Turin.

    He has conducted research on embryonic development and ribosome crystallization at the Medical Research Council in Cambridge, UK, the National Institutes of Health in Bethesda, USA, and the Max-Planck-Institut für Molekulare Genetik in Berlin. His research interests include embryology, evolution, theoretical biology and code biology.

    In other words, you don’t know what you are talking about. He just doesn’t have a cool name like Scientist Sam and go on pointless rants.

    Scientist Sam

    Thank you for the correction. From the references that immediately jumped, he seemed to study biosemiotics. That’s very disappointing that he actually has conducted research because he is so wrong-headed in his article.

    Scientist Sam

    With regards to my name, I’m a published biologist. I’m a scientist and my name is Sam.

    UprightBiPed

    Hi Sam. Good to know. Take care.

    UprightBiPed

    By the way, he is entirely correct in his paper, you are just unaware of the issues. It happens.

    Scientist Sam

    No he isn’t. I gave very good reasons. This is far closer to my area of research than his.

    UprightBiPed

    Barbieri states that the code is not reducible to physics. He is correct. Like all code systems ever known to exist, the genetic translation system contains a natural (and necessary) discontinuity between the arrangement of the medium and the determination of its effect within the system. This local discontinuity is what makes it possible for a spatial arrangement of bases in a codon to specify a particular amino acid during synthesis. It is what establishes combinatorial permutations and enables open-ended heredity. I can appreciate the fact that this all sounds foreign to you, but that is only because you are unaware of the data – which has been documented in physics literature starting about half a century ago by physicists such as Howard Pattee and others.

    Scientist Sam

    “Like all code systems ever known to exist, the genetic translation system contains a natural (and necessary) discontinuity between the arrangement of the medium and the determination of its effect within the system.”

    There is no discontinuity. You must’ve never taken molecular biology.

    “This local discontinuity is what makes it possible for a spatial arrangement of bases in a codon to specify a particular amino acid during synthesis.”

    How so? This is just a bald assertion.

    “It is what establishes combinatorial permutations and enables open-ended heredity.”

    Again, bald assertion.

    “I can appreciate the fact that this all sounds foreign to you, but that is only because you are unaware of the data – which has been documented in physics literature starting about half a century ago by physicists such as Howard Pattee and others.”

    How about you stop condescending to someone who wrote his Master’s thesis on the dynamics of the genetic code? Please make an argument rather than bald assertions you supercilious imbecile.

    UprightBiPed

    “There is no discontinuity.”

    Like I said, the local discontinuity is an organizational necessity. The arrangement of bases in a codon does not determine which amino acid is presented for binding. I would think this should be obvious to someone of your training.

    Scientist Sam

    “The arrangement of bases in a codon does not determine which amino acid is presented for binding.”

    Strictly speaking, that is true, but there are a lot of contingencies built into the structure of the code. For example, we have the third base wobble. We also have the fact that more similar amino acids correspond to more similar codons. Thus, there seem to be contingencies built into the code. But, even if I grant you this, where does it get you in an argument?

    UprightBiPed

    “where does it get you in an argument?”

    This is one of the empirical markers a physicist would use to identify the organization of a semiotic code, i.e. the preservation of the discontinuity between the arrangement of the medium and the determination of its effect. The cell accomplishes this by isolating the establishment of the code from the reading of the codons, i.e. the amino acid-to-anticodon association is temporally and spatially isolated from the codon-to-anticodon association. This discontinuity is a physical necessity for translation to occur, and is evident in all instances of semiotic translation.

    But that is just the first marker that a physicist would look for. There are others. For instance, genetic translation employs a reading frame code using combinatorial permutations. This requires the arrangement of the bases in each codon to be independent of the minimum total potential energy state of the medium. In other words, a pheromone (for instance) is an informational medium that is recognized in its system by its three-dimensional structure, and that structure is determined by its minimum total potential energy. But in order to enable combinatorial permutations, the arrangement of the medium must be independent of minimum total potential energy – which both DNA and RNA are. This is what physically enables the system to have the informational capacity it requires to describe itself into memory (i.e. to begin the cell cycle, and heredity). It is also what enables the efficient transcription of that high-content information from one medium to another.

    These are the types of empirical observations that a physicist (like Pattee and others) would be acquainted with, as well as someone like Barbieri. Or John von Neuman. Or Francis Crick.

    You are not acquainted with them, and it’s a sure bet they didn’t appear in your masters thesis on the dynamics of translation. No sweat. I am sure your thesis described other areas of interest in a competent manner. But when you step out and rant on areas of empirical findings that you are uninformed about, you make a mistake. In order to organize the heterogeneous cell, you must first be able to specify a thing and place it under temporal control. This is what protein synthesis does, and the translation of an informational medium is the means to accomplish that effect. But the translation of an informational medium requires one arrangement of matter to serve as a representational medium (codons), and another arrangement of matter to establish what is being represented (aaRS). After all, no object in the material universe inherent specifies any other object in the material universe. Nucleobases do not represent or specify amino acids. They have to be organized in a discontinuous translation system (i.e. semiosis) in order to do so. And that is exactly what is found inside the cell. The material observations that identify the system aren’t even controversial.

    Scientist Sam

    Thanks for the tripe.

    “This discontinuity is a physical necessity for translation to occur, and is evident in all instances of semiotic translation.”

    The discontinuity isn’t a physical necessity. You could easily imagine a scenario where amino acids were necessarily assigned to anticodons by chemical properties of tRNAs. I’m sorry but if you can’t get that right, you’re pretty hopeless, idiotically pedantic, and a navel gazer.

    Goodbye.

    UprightBiPed

    In logic, that is called “special pleading”. Your imagination, frankly, doesn’t mean diddly. It doesn’t provide you with any exemptions.

    The minimum requirement for the origin of the system is established by what is physically necessary to record and translate the amount of information that the system needs to successfully describe itself into memory. On this front, there is very little room. A cell that cannot provide a record of itself cannot begin the cell cycle. A cell that cannot translate a record of itself also cannot begin the cell cycle.

    To accomplish what must be accomplished, several of these individual associations (generous estimates typically run between 12 to 15) will need to occur at the same time and place, while the details of their construction are simultaneously encoded in the very information that they make possible.

    Odd, isn’t it. Nature passed up on the fully determined (comparatively easy) associations lurking in your imagination, and instead (already faced with an almost vertical face to climb) picked an unnecessary system that preserves the discontinuity between the arrangements and their effects. And even odder still, every system of translation that has ever been examined has followed that same pattern.

    Special pleading indeed. Goodbye.

    – – – – – – – – – – – – – – – –

    *crickets*

  15. 15
    bloodymurderlive says:

    UprightBiPed That is one of the most amazing, concise interactions I’ve ever seen. How can I learn to articulate about the DNA code like you? Are there books I can read that will teach me about it from the physics perspective that you took in your interaction with Sam?

  16. 16

    Hello BML,

    Thanks, but be assured I have made a lot of mistakes, particularly being unnecessarily combative.

    I can only suggest that you might spend some time absorbing some of the papers listed on the bibliography at my website Biosemiosis.org. I would also offer encouragement when reading someone like Pattee for the first time. When I first read Pattee I could only understand the words themselves (well, most of them anyway), but over time I have come to understand what is being said. For me, it took a lot of reflection, but eventually it comes into focus. Also, on this board, I would stay close to people such as GPuccio, Eric Anderson, and others.

    As for Scientist Sam, he has probably never questioned a word of what he was taught about DNA. With such a huge subject, it would be easy to do. But if during his instruction there had ever been just one professor that asked Scientist Sam to reflect upon the dynamic implications of codons not establishing their effects, maybe he would have.

    Why is this Important?

  17. 17
    Mapou says:

    Scientific Sam = Yosemite Sam?

    Never mind. Just another clueless evotard.

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