Central Dogma: Missing, and presumed dead

_{Denyse O'Leary

May 29, 2014

Genomics, News}

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Further to “Proteome ‘more complex than previously thought’”, from Science:

“The prevalent view was that information transfer was from genome to transcriptome to proteome. What these efforts show is that it’s a two-way road—proteomics can be used to annotate the genome. The importance is that, using these datasets, we can improve the annotation of the genome and the algorithms that predict transcription and translation,” said Steen. “The genomics field can now hugely benefit from proteomics data.”

Hey, aren’t these the cement shoes of the Central Dogma? Remember when One gene coded for one protein?

See also: Information killed the Central Dogma too

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Comments

"This remarkable process of cellular computation implies that cellular materials can show a primitive intelligence," the team writes in Nature. - When slime is not so thick

Here we show that this simple organism has the ability to find the minimum-length solution between two points in a labyrinth. - Intelligence: Maze-solving by an amoeboid organism
Mung_{June 2, 2014
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Piotr,
To be continued (sorry, I’m a little busy tonight).
Sure, take a break buddy. Have a good night sleep and get some rest tomorrow. If you want to come back, get ready to discuss, because the discussion is just starting, the subject is very important and not simple at all. This time I want to get to the bottom of this discussion, while trying our best to communicate well. At some points I may have to consult my friends -biology scientists who work in research at universities in North America and Europe- but I will try as much as I can, not to bother them with questions. However, scientists from your university in Poznan are welcome to join our discussion if they want to. Agree? Thanks! Dobranoc! (here they say 'the brown nuts') ;-)Dionisio_{June 2, 2014
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Piotr and Dionisio: I am not really sure that I know exactly what I mean! Probably, only God knows exactly what we mean. :)gpuccio_{June 2, 2014
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Gpuccio:
What does that mean? If we humans can model what happens as a complex flowchart, it’s because the events in the flowchart take place. A flowchart has nodes, which represent decisions made according to logical evaluations.
But the flowchart is something that we draw on a sheet of paper. It's the way we understand and visualise the process, just like family trees are useful diagrams representing relationships, not real objects in the real world. Living things reproduce and population sometimes diverge to the point of speciation. They "form a tree" only in a highly abstract sense, when we model their history. Likewise, physicists speak of "lines of magnetic force" and chemists of "covalent bonds", and they can visualise them as geometrical objects, but of course they realise such "lines" and "bonds" are convenient figures of speech.
Now, I am not saying that there is any “central agent” (where did you take that idea?) who takes the decisions. The flowchart simply represents events that take place. The reasons for those events can even be “dispersed in the chemistry of the cell”, but that does not mean that they do not exist. Even if they are “dispersed”, that is no reason not to try to understand where they are “written”. I believe you are equivocating my term “written”. It means that, if certain different events take place at different times and in different conditions, but according to a repeated pattern, there must be some objective configuration in the genome, or more generally in the cell, that explains that ordered series of events. That’s what I call “written procedures”. They must be there. Chemistry alone can do nothing to decide the transcriptome of a B lymphocite out of the generic genome.
So you use written metaphorically and then accuse me of equivocating on that? OK, I don't think its "written" in the DNA, to begin with. Let's suppose we can synthesise a fully sequenced genome. That's not enough to build anything. It's the whole cellular context that determines how DNA is used (which is why we have different types of cells containing the same genome in a multicellular organism). It doesn't matter that the transcriptome and the proteome are themselves encoded in the DNA sequence. They must be present before anything happens to the DNA. To be continued (sorry, I'm a little busy tonight).Piotr_{June 2, 2014
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Piotr: "If the procedure is written somewhere, we should be able to see it." Why? There are certainly so many things that exist, and that we are not yet able to see.gpuccio_{June 2, 2014
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Piotr,
Only Gpuccio knows exactly what he means, but I believe we are able to communicate.
Your answer to my questions 2, 3 and 4 could be interpreted as "No, I don't know" - is this correct? If you don't know exactly what he meant by 'procedure', 'written', 'intrinsic', 'extrinsic', then how can you write absolute statements about gpuccio's definitions? It doesn't seem like you are able to communicate well with gpuccio, because he has explained several concepts that you don't seem to understand well. Understanding each other doesn't necessarily mean agreeing with each other. But in your case the understanding part seems poor. Or at least that's the perception outside observers might get.Dionisio_{June 2, 2014
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Piotr,
I hope so. If the procedure is written somewhere, we should be able to see it.
You failed to answer correctly the first question, buddy. Your original sentence was not a scientific statement at all. We don't know everything in this field of science, therefore we must watch carefully what we say or write about it. Absolute statements demand absolute knowledge, which you or no one else possesses in this particular case. Even your answer to my first question lacks qualifications to be considered scientific. You seem to know much more than I do, so you should have been able to figure it out yourself, or could have asked someone at the university in Poznan, where you work, maybe they could have helped you to answer my first question. It's pretty obvious. Actually, I'm surprised you answered the way you did. If we have not seen them yet, and we know we are still discovering things as we dig deeper, and we are still answering outstanding questions, while new questions are popping up, and we know we don't understand well many things, then we don't have any rights to imply that gpuccio's procedures don't exist anywhere. That's an absolute statement about something you are not absolutely certain. Hence, that sentence does not qualify as scientific, because it's misleading. In addition, since you're not absolutely certain about the meaning of gpuccio's term 'procedure' then you can't say much about its possible existence. First you must know what the Italian Doctor means by 'procedure' within the discussed context, although he has explained it to certain point in some of his postings, but you can always require additional clarification of the term, if it's not sufficient clear to you. Humility is an important requirement for a scientist to be genuine. However, apparently you're not a scientist, and I'm not a scientist either. Fortunately most true scientists are humble enough to admit their lack of absolute knowledge on certain areas of their endeavors. The rest of us must crave for that virtue too. Rozumiez teraz? Bardzo dobrze!Dionisio_{June 2, 2014
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Oh no, Kepler was a Creationist who understood science as a way to understand God's Creation.Joe_{June 2, 2014
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1. Is that a scientific statement? I hope so. If the procedure is written somewhere, we should be able to see it.
2. Do you know exactly what gpuccio means by ‘procedure’? 3. Do you know exactly what gpuccio means by ‘written’? 4. Do you know exactly what gpuccio means by ‘explicit’ or ‘implicit’ procedures?
Only Gpuccio knows exactly what he means, but I believe we are able to communicate.
5. Do you know the mechanisms that determine the precise timing for the centrosome segregation, so that the spindle apparatus works correctly in the intrinsic asymmetric mitosis, thus leading to the appropriate fate determination, differentiation and migration, for every cell during the initial stages (first few days) of human embryonic development, starting at the zygote? 6. If your answer to question 5 is yes, then can you provide a brief summary of those mechanisms, or provide links to recognized peer-reviewed publications, where those mechanisms are described in detail?
Spindle checkpoints? Why should I even attempt to "summarise briefly" such a complex technical issue in a blog comment box? Of course there are plenty of peer-reviewed publications describing it in much detail in different eukaryotes and different types of cell divisions. I'm sure you can find those publication on you own, or start here and follow the references.
7. When your ‘rodak’ Nicolas Copernicus wrote his heliocentric theory, did he base his conclusions on solid evidences he had observed and worked on, or just on speculations that conformed to his worldview?
A little bit of this and a little bit of that. For example, he was still under the spell of the ancient Eudoxan model with transparent crystal spheres (hence "perfect" circular orbits, corrected with the use of epicycles). There was no observational justification for any such things (not to mention a physical theory to account for them quantitatively) -- just a philosophical tradition going back to ancient Greece. It was Kepler who began to make the heliocentric model mathematically elegant.Piotr_{June 2, 2014
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Piotr at #33: I am rather surprised of your statements here. You say:
There is no procedure written anywhere. What we humans could model as a complex flowchart or an algorithm is actually dispersed in the chemistry of the cell, with no central agent to control its execution.
What does that mean? If we humans can model what happens as a complex flowchart, it's because the events in the flowchart take place. A flowchart has nodes, which represent decisions made according to logical evaluations. Now, I am not saying that there is any "central agent" (where did you take that idea?) who takes the decisions. The flowchart simply represents events that take place. The reasons for those events can even be "dispersed in the chemistry of the cell", but that does not mean that they do not exist. Even if they are "dispersed", that is no reason not to try to understand where they are "written". I believe you are equivocating my term "written". It means that, if certain different events take place at different times and in different conditions, but according to a repeated pattern, there must be some objective configuration in the genome, or more generally in the cell, that explains that ordered series of events. That's what I call "written procedures". They must be there. Chemistry alone can do nothing to decide the transcriptome of a B lymphocite out of the generic genome.
DNA sequence doesn’t do anything by itself. It contains no program or procedure; it’s only data.
Yes, and so? Procedures are data too, until they are executed.
Life is a complex quasi-periodic process which uses DNA as a memory.
That seems really meaningless.
The memory is used to store recipes for structural, catalytic, signalling and regulatory molecules — inherited recipies that have worked in the past.
OK. So, in our genome we have those recipes. For n molecules, some of them structural, other regulatory, and so on. Those recipes are the same in all cells. So, how do those recipes generate 500 different and complex transcriptomes, in definite order and with definite form? If you have a list of 500 ingredients, how do you get 1000 different recipes from it? Do you just shake the list and hope for a good result?
The memory is replicated and passed on from cycle to cycle, making sure that the process is repeated as faithfully as possible.
What do you mean by "cycle"? What governs each individual "cycle"? Please, be specific. Remember, the memory is the same in all cells, and the transcriptomes and proteomes are different in each cell type.
Proteins are chemicals. They don’t think and they don’t carry out commands. They are not intelligent nanorobots moving smoothly along an assembly line. They move about and fluctuate due to Brownian motions. They interact with other molecules in ways determined by physics and chemistry, and not because a sequential algorithm tells them to execute “step number 8453?.
Excuse me, but this is really silly. It's the last version of the famous, and infamous, "it's all chemistry" triteness. OK, you are a linguist and you certainly use words better, but the concept remains silly just the same. Of course "proteins are chemicals". Of course "they don’t think and they don’t carry out commands". Whoever said anything like that? Proteins obey chemical laws. They move about and fluctuate due to Brownian motions. They interact with other molecules in ways determined by physics and chemistry. What a brilliant discovery that is! But, if they "execute “step number 8453?, whatever it is, the reason is that some sequential algorithm (IOWs, some ordered series of events) creates the circumstances that force them, by the laws of chemistry, to execute step number 8453. You know, molecules are not there in the wild executing step number 8453 all the time, just because chemical laws require it. Step number 8453, whatever it is, is a very definite circumstance which happens at a very definite time in a very definite cell. Why? That's the reason why a B lymphocyte is not a fibroblast. Because step 8453 takes place in the B lymphocite, but not in the fibroblast. That step, the fact that makes it happen in the B lymhocite, and all the 8452 steps that preceded it, and the many that will follow it, are what I call "the procedures". And believe me, they are written somewhere.gpuccio_{June 2, 2014
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Piotr @ 33
There is no procedure written anywhere.
1. Is that a scientific statement? 2. Do you know exactly what gpuccio means by 'procedure'? 3. Do you know exactly what gpuccio means by 'written'? 4. Do you know exactly what gpuccio means by 'explicit' or 'implicit' procedures? 5. Do you know the mechanisms that determine the precise timing for the centrosome segregation, so that the spindle apparatus works correctly in the intrinsic asymmetric mitosis, thus leading to the appropriate fate determination, differentiation and migration, for every cell during the initial stages (first few days) of human embryonic development, starting at the zygote? 6. If your answer to question 5 is yes, then can you provide a brief summary of those mechanisms, or provide links to recognized peer-reviewed publications, where those mechanisms are described in detail? 7. When your 'rodak' Nicolas Copernicus wrote his heliocentric theory, did he base his conclusions on solid evidences he had observed and worked on, or just on speculations that conformed to his worldview? No need to rush in order to answer the above questions. You may take all the time you want to. Also, remember that "I don't know" is a valid scientific statement, which demonstrates humility, a virtue that is not abundant in this world. Thank you. Serdecznie pozdrawiam.Dionisio_{June 2, 2014
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Mung: You are conflating different levels of organisation. An ant colony is more than a set of n ants, and a neural network is more than a set of n neurons. Even water is more than a large collection of H20 molecules. Interactions between components are an essential party of any system (without them there is no system in the first place). Now if you claimed that even a single neuron did "computations", I would agree. It's the function of a neuron to do just that -- it is a cell specialised in processing and transmitting signals. But is it "a computer"? I would hesitate to say so, because I don't care for stretched metaphors. If somebody says that any cell is a computer with an operating system, a processor, a library of programs, etc., I can only hope they don't mean it literally. If they explore the metaphor still further for rhetorical effect and say, "A cell is a computer and we know that all computers have to be built and programmed by highly intelligent beings, so it must be true of living cells", they've lost me. Inferences from an analogy are not valid. It's like saying that since stars are thermonuclear reactors, and since the only other thermonuclear reactors we know of are human-made (and small, and very imperfect), an efficient thermonuclear reactor, such aa a star, can only be the work of a superintelligence. Has anyone ever seen a molecular cloud organise itself into something that even the human genius can't imitate? There are also people who claim the the whole Universe is one humongous computer. Fine, but by doing so they dilute the semantic content of the word "computer" homeopathically. If it can mean anything complicated, it means nothing in particular.Piotr_{June 2, 2014
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Basic Concepts for Neural NetworksMung_{June 1, 2014
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Piotr:
Sorry, but the cell is not a neural network either.
Are you sure? What are neural networks composed of and where do neural networks come from, if not from cells? Are you one of those epi-phenomenalists? ;) Take a bunch of cells that have nothing remotely similar to a neural network in them and place them together at just the right time and in just the right place and in just the right relationship to each other using random modifications and natural selection and 'voila', you have a neural network? Seriously? Isn't it more reasonable to believe that there's nothing really new in neural networks, that cells have been doing this on their own for millennia?Mung_{June 1, 2014
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Piotr, you are really on a roll today.
Sorry, but the cell is not a neural network either.
So? Relevance please. I'm not engaging in ad hominem and perhaps you could respond by not engaging in non sequiturs. Fair enough? Why are you being so dismissive? Have I treated you badly somewhere? If so I apologize. Piotr:
Sorry, Gpuccio, those threads have been buried under a heavy layer of sediments. I’ll start commenting here for want of a better place.
So I tried to engage you on the issue of processes in the cell, the topic you address in your post @33. I've raised a number of relevant points which you haven't even bothered to attempt to respond to. Yet you even agree that processes exist!
It’s the biochemical processes taking place in the cell that “read” the data and make use of it, but the analogy between those processes and a computer is a poor one.
So let's try a different approach. In what sense do you say these processes exist? Do they only exist as analogy or metaphor? If so, how is it that they manage to have a predictable physical effect? How is it that they manage to have a repeatable predictable physical effect? Don't you realize that by taking the position that these procedures are not "written down" anywhere that you're appealing to magic? And gpuccio is asking, if they are written down, where are they written? And if not in DNA, then where? And if not in DNA, how are they heritable? You are obviously an intelligent person. You can see the implications. But you should also face them and deal with them. If your current paradigm has problems providing answers, then perhaps there is something wrong with your paradigm. Peace.Mung_{June 1, 2014
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Piotr, the cell is a miniature automated factory.Joe_{June 1, 2014
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Mung:
http://en.wikipedia.org/wiki/Wetware_computer
Sorry, but the cell is not a neural network either.Piotr_{June 1, 2014
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What you are doing, Piotr, is concentrating on the hardware, not the processes. gpuccio is asking about the processes. You claim there are none. I offer the testimony of what ought to be a recognized expert in the field, and you poo-poo it by mistaken analogies. The point here is on computation. The cell is, quite literally, performing computations. Now if perhaps you'd care to say something about the nature of computation and offer something relevant to whether or not cells do or do not carry out computation?
Computation is a process following a well-defined model understood and expressed as, for example, an algorithm, or a protocol.

A computation can be seen as a purely physical phenomenon occurring inside a closed physical system called a computer. Examples of such physical systems include digital computers, mechanical computers, quantum computers, DNA computers, molecular computers, analog computers or wetware computers.
http://en.wikipedia.org/wiki/Computation http://en.wikipedia.org/wiki/Wetware_computer Note the reference section of the second link for a review of Bray's book.Mung_{June 1, 2014
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Mung: #41 Here I part ways with Bray. A computer processor (or one of a battery of parallel processors) performs a sequence of explicit instructions stepwise. A living cell does not do "the same thing" #42 Analogy. Figure it out yourself.Piotr_{June 1, 2014
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Piotr, speaking of trajectories, why the flight away from data and biology into physics?Mung_{June 1, 2014
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Piotr, "There is to begin with, the matter of computation. In a circuit board or microchip, sets of logic elements linked in precise networks perform defined logical processes, repeating the same simple steps over and over again. The same thing happens in a living cell..." - Dennis Bray (p. 27) "The central thesis of the book - that living cells perform computations - arises from contemporary findings in the biological sciences, especially biochemistry and molecular biology. It is a leitmotif of systems biology, although the philosophical ramifications of that new discipline are rarely expressed." (p. xi)Mung_{June 1, 2014
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Information Theory, Evolution, and the Origin of Life - Hubert P. Yockey, 2005 Excerpt: “Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.” http://www.cambridge.org/catalogue/catalogue.asp?isbn=9780521802932&ss=exc A New Design Argument - Charles Thaxton Excerpt: "There is an identity of structure between DNA (and protein) and written linguistic messages. Since we know by experience that intelligence produces written messages, and no other cause is known, the implication, according to the abductive method, is that intelligent cause produced DNA and protein. The significance of this result lies in the security of it, for it is much stronger than if the structures were merely similar. We are not dealing with anything like a superficial resemblance between DNA and a written text. We are not saying DNA is like a message. Rather, DNA is a message. True design thus returns to biology." http://www.arn.org/docs/thaxton/ct_newdesign3198.htm "And at this point, strangely enough, the discovery of DNA, which is so widely thought to prove that life is mere chemistry, provides the missing link for proving the contrary. That the formation of a DNA molecule is embodied in the morphology of the corresponding offspring, assures us of the fact that this morphology is not the product of a chemical equilibration, but is designed by other than chemical forces." Michael Polanyi, “Life Transcending Physics and Chemistry,” Chemical and Engineering News 45 (August 1967): 66, 55-66 Assessing the "Algorithmic Origin of Life" (Paul Davies' Recent Paper) - December 18, 2012 Excerpt: It is the functionality of the expressed RNAs and proteins that is biologically important. Functionality, however, is not a local property of a molecule. It is defined only relationally, in a global context, which includes networks of relations among many sub-elements,, One is therefore left to conclude that the most important features of biological information (i.e. functionality) are decisively nonlocal. Biologically functional information is therefore not an additional quality, like electric charge, painted onto matter and passed on like a token. It is of course instantiated in biochemical structures, but one cannot point to any specific structure in isolation and say "Aha! Biological information is here!",,, ,,,For example, mechanical stresses on a cell may affect gene expression. Mechanotransduction, electrical transduction and chemical signal transduction -- all well-studied biological processes -- constitute examples of what philosophers term "top-down causation", where the system as a whole exerts causal control over a subsystem (e.g. a gene) via a set of time-dependent constraints. http://www.evolutionnews.org/2012/12/assessing_the_a067541.html Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems - 2012 David J D’Onofrio1*, David L Abel2* and Donald E Johnson3 Excerpt: The DNA polynucleotide molecule consists of a linear sequence of nucleotides, each representing a biological placeholder of adenine (A), cytosine (C), thymine (T) and guanine (G). This quaternary system is analogous to the base two binary scheme native to computational systems. As such, the polynucleotide sequence represents the lowest level of coded information expressed as a form of machine code. Since machine code (and/or micro code) is the lowest form of compiled computer programs, it represents the most primitive level of programming language.,,, An operational analysis of the ribosome has revealed that this molecular machine with all of its parts follows an order of operations to produce a protein product. This order of operations has been detailed in a step-by-step process that has been observed to be self-executable. The ribosome operation has been proposed to be algorithmic (Ralgorithm) because it has been shown to contain a step-by-step process flow allowing for decision control, iterative branching and halting capability. The R-algorithm contains logical structures of linear sequencing, branch and conditional control. All of these features at a minimum meet the definition of an algorithm and when combined with the data from the mRNA, satisfy the rule that Algorithm = data + control. Remembering that mere constraints cannot serve as bona fide formal controls, we therefore conclude that the ribosome is a physical instantiation of an algorithm.,,, The correlation between linguistic properties examined and implemented using Automata theory give us a formalistic tool to study the language and grammar of biological systems in a similar manner to how we study computational cybernetic systems. These examples define a dichotomy in the definition of Prescriptive Information. We therefore suggest that the term Prescriptive Information (PI) be subdivided into two categories: 1) Prescriptive data and 2) Prescribed (executing) algorithm. It is interesting to note that the CPU of an electronic computer is an instance of a prescriptive algorithm instantiated into an electronic circuit, whereas the software under execution is read and processed by the CPU to prescribe the program’s desired output. Both hardware and software are prescriptive. http://www.tbiomed.com/content/pdf/1742-4682-9-8.pdfbornagain77_{June 1, 2014
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Unguided evolution cannot be modeled, Piotr. And unguided evolution can't even account for DNA. BTW if a metaphor is inescapable then it most likely isn't a metaphor.Joe_{June 1, 2014
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Piotr: It’s the biochemical processes taking place in the cell that “read” the data and make use of it, but the analogy between those processes and a computer is a poor one. I partly agree with the blurb you linked:
You're basically right. It's not really analogous to a sequential computer. It is more analogous to a CNC machine. No less astounding. http://en.wikipedia.org/wiki/Numerical_controlVishnu_{June 1, 2014
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Piotr: Proteins are chemicals. They don’t think and they don’t carry out commands. They are not intelligent nanorobots moving smoothly along an assembly line. They move about and fluctuate due to Brownian motions. They interact with other molecules in ways determined by physics and chemistry, and not because a sequential algorithm tells them to execute “step number 8453?.
All true. Except only part of the truth. Consider Dawkin's "Weasel" program. Despite a random number generator as the source of variation, the result always ends up as "METHINKS IT IS A WEASEL" within a fairly small number of iterations. Why? Because the randomness is highly constrained. While the proteins are most definitely molecules, they have a highly specific shape that, in relation to other "keyed" proteins, yields highly specific functions when they encounter one another. Proteins may bounce around with a cell with Brownian motion, but they do so with blazingly fast speed, such that proteins encounter their keyed proteins fast enough to allow their specific function to be performed in a timely manner. It's the "software" that makes the difference; that defines the constrains that shapes all the flurry of randomness into extremely specific function. The "software" in this case being the particular codon sequences in the DNA that produce proteins with their specific molecular shapes that constrain the randomness with their particular function. The source of the highly constrained boundaries is the source of controversy between those who "see" intelligence as the source and those who don't- the source of the software. Hand-waving statements that they are "determined by physics and chemistry" is no more pertinent or explanatory than saying computers operate determined by "physics and electronics." True, but hardly a full or useful description of what occurs.Vishnu_{June 1, 2014
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Even if DNA is “only data” it doesn’t follow that it contains no program or procedures, wouldn’t you agree?
It's the biochemical processes taking place in the cell that "read" the data and make use of it, but the analogy between those processes and a computer is a poor one. I partly agree with the blurb you linked:
Dennis Bray taps the findings of the new discipline of systems biology to show that the internal chemistry of living cells is a form of computation.
... as long as it's understood that we are speaking figuratively, and a metaphor is only a metaphor. There is no actual processor and no actual algorithm.Piotr_{June 1, 2014
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Mung: I am not contradicting myself. We can model things, but our models should not be confused with reality. You can model the motion of a canonball mathematically and calculate its trajectory. Where are the equations written? In a handbook of physics, perhaps, but canonballs don't read handbooks and don't solve the differential equations we write for them. The "laws of physics" are generalisations formulated by humans. They reflect our current understanding of reality, which is inherently provisional and incomplete. We update our knowledge, change out models, sometimes have to pull down the whole theoretical edifice and build a new one from sctratch. Cannonballs don't care and nobody informs them of our paradigm shifts anyway.Piotr_{June 1, 2014
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Piotr:
DNA sequence doesn’t do anything by itself. It contains no program or procedure; it’s only data.
Even if DNA is "only data" it doesn't follow that it contains no program or procedures, wouldn't you agree? Your computer hard drive contains "only data," as does your computer's RAM, but that data includes many programs and procedures. And programs and procedures can be distributed, processes can run in parallel, and there doesn't have to be a central agent controlling them all. Agreed?Mung_{June 1, 2014
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Piotr:
There is no procedure written anywhere. What we humans could model as a complex flowchart or an algorithm is actually dispersed in the chemistry of the cell, with no central agent to control its execution.
Again, you seem to claim both that no procedure exists anywhere and that procedures do exist, but they are distributed. Whether there is a 'central agent' to control the execution seem to be irrelevant, wouldn't you agree? Wetware: A Computer in Every Living CellMung_{June 1, 2014
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Piotr, you appear to be contradicting yourself.
There is no procedure written anywhere. What we humans could model as a complex flowchart or an algorithm is actually dispersed in the chemistry of the cell, with no central agent to control its execution.

Life is a complex quasi-periodic process which uses DNA as a memory. The memory is used to store recipes for structural, catalytic, signalling and regulatory molecules — inherited recipes that have worked in the past. The memory is replicated and passed on from cycle to cycle, making sure that the process is repeated as faithfully as possible.
Mung_{June 1, 2014
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