UB Schools Bob O’H

_{Barry Arrington

February 7, 2020

Intelligent Design}

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As is his wont, national treasure Upright Biped took materialist Bob O’H to school:

Bob @ 63,

we can replicate the process without having to resort to adding anything immaterial”

Is that right Bob?

Okay, let us make you the Director of a research team with unlimited personnel, unlimited time, and unlimited funding. And let us say that with this extraordinary intellectual and research power, it is not long before you can control, manipulate, and bind together whatever molecules you wish, and not only can you do that, but you can also successfully predict the results of that manipulation. So, if you need a replacement for the extant ribosome, you got it. If you need a de novo tRNA, you got it. If you need an aaRS to fulfill the box on a diagram of chemical pathways, you got it. Now comes the time to “replicate the process”, so you set your team out to organize a dissipative system where your de novo DNA/RNA is manipulated by your de novo ribosome and whatever array of other helper molecules you need, to the extent that the sequence of your de novo DNA/RNA is used to successfully establish the functional re-construction of the system.

Let me ask you Bob: Will you have to coordinate the descriptions of each the de novo aaRS, with the descriptions of the other molecules in the system? That is to say – will the individual sequences within the portion of your de novo DNA/RNA that describe your de novo aaRS’s have to be simultaneously coordinated so that the remainder of the descriptions result in a successful replication? And would you also say, and agree, that without that simultaneous coordination, your system will not result in a successful replication?

If this is so, Bob, can you then stand before your intricate diagram of the system’s pathways and properties (with the great formulas of physical law at hand, and with your team’s documented intimate knowledge of every facet and dynamic interaction within the system) and point out where exactly you find the source of that coordination?

Comments

@UB Perhaps in has something to do with this?
If this is so, Bob, can you then stand before your intricate diagram of the system’s pathways and properties (with the great formulas of physical law at hand, and with your team’s documented intimate knowledge of every facet and dynamic interaction within the system) and point out where exactly you find the source of that coordination?
First, it's unclear how this observation actually gets to you ID, given that it's impossible to extrapolate observations without first putting them into some kind of explanatory framework to interpret it. What is that explanation? (or, as always, explain how that's possible.) The issue you're referring, which is specific to the current conceptions of physics, is one of the motivations of constructor theory. Any argument based on an inability to "point out where exactly you find the source of that coordination" is parodical, in that it is narrow in scope. From this paper on the Philosophy of Constructor Theory...
Very few such transformations happen spontaneously; that is to say, almost all require a constructor, which I shall define as anything that can cause transformations in physical systems without undergoing any net change in its ability to do so. I shall call those physical systems the constructor’s constructor input state of substrate(s) ------------------> output state of substrate(s) A transformation, regarded as being caused by a constructor, I call a construction. Constructors appear under various names in physics and other fields. For instance, in thermodynamics, a heat engine is a constructor because of the condition that it be capable of ‘operating in a cycle’. IBut they do not currently appear in laws of physics. Indeed, there is no possible role for them in what I shall call the prevailing conception of fundamental physics, which is roughly as follows: everything physical is composed of elementary constituents such as particles, fields and spacetime; there is an initial state of those constituents; and laws of motion determine how the state evolves continuously thereafter. In contrast, a construction (1) is characterised only by its inputs and outputs, and involves subsystems (the constructor and the substrate), playing different roles, and most constructors are themselves composite objects. So, in the prevailing conception, no law of physics could possibly mention them: the whole continuous process of interaction between constructor and substrate is already determined by the universal laws governing their constituents. However, the constructor theory that I shall propose in this paper is not primarily the theory of constructions or constructors, as the prevailing conception would require it to be. It is the theory of which transformations input state of substrates -> output state of substrates can be caused and which cannot, and why.
So, our inability to point to constructors in biology - in the prevailing conception of physics - isn't remotely controversial. Nor is it clear what it has to do with Neo-Darwnism. Rather, it's a reflection of the limits of the prevailing conception of physics. Fortunately, we're not limited to the prevailing conception. IOW, it seems that the theory you're using to interpret the observation (Bob cannot "point out [exactly to] the source of that coordination") that gets you to ID implicitly includes the prevailing conception of physics, it's limitations, and that we cannot make any progress beyond those limits, via constructor theory. However, it seems that you'd still need more than that to get to ID.critical rationalist_{March 1, 2020
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@UB Having gone back and forth several times, I’m still not clear what your objection is or how the coordination you’re referring to implies it. Let’s try again, shall we? The constructor theory of life poses the following question: do biological replicators perform replication at such high fidelity that the design of biological replicators had to be present in the laws of physics? Would you agree that, despite not being directly aimed at ID, the answer to that that question would have profound implications for it?critical rationalist_{March 1, 2020
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Bob O'H Schools UB. It's true.Mung_{February 15, 2020
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, It appears that Bob may have abandoned his argument, and that this thread has run its course. So I will just reiterate that the requirement of coordination discussed in the title post stands, as does the fact that the source of that coordination is not derived from the physical properties of the system. Without simultaneous coordination of the sequences, the system cannot begin to function.Upright BiPed_{February 15, 2020
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Bob
I’m afraid I have no idea what you’re trying to say here.
I'm afraid I agree with you.EugeneS_{February 13, 2020
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Bob O'H:
I don’t need to assume any intelligence at all.
Because you don't have any, at all.ET_{February 13, 2020
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Agents use rules and a communication protocol (if then else statements prescribing what they should do in response to stuff).
You're using teleological language, so it's no surprise that you end up concluding teleology.
The prescriptive context (protocol and rules) should exist before the system starts functioning, otherwise this is just chaos.
Chaos and order aren't absolutes, and systems can evolve from something very simple (look at telecommunications!). So I don't see why this is a necessary conclusion.
However, to argue coherently for a bottom up approach you would need to assume that agents are intelligent enough from the start to work out rules on the fly (as children can do when they play),
No I don't. I don't need to assume any intelligence at all. Feedback plus an advantage to control would, I think, be the main properties that would be needed. I don't see that this needs intelligence (e.g. it seems to have resulted in the stability of natural nuclear reactors, where the 'advantage' is simply continued existence).
The behavior of a living system critically depends on specific constraints achieving rate independence of the system’s description (read/write from/to memory) and semantic closure.
I'm afraid I have no idea what you're trying to say here.Bob O'H_{February 13, 2020
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. Sorry for the delay. So, where are we at? Bob claimed that he could replicate the genetic translation system, and all that was needed was the purely material components of the system. I then remined Bob that he’d need to simultaneously coordinate the all descriptions that the genes contain with the specific descriptions of the interpretive constraints within the system (the aaRS), and that failure to do so would render the system inoperable (it could never start to function). He objected to that, throwing out the fact that “we know” that distributive systems work. Unfortunately for Bob, distributive systems have nothing whatsoever to do with the issue. So, then he threw out the discipline of systems dynamics; stating that there was vast amounts of evidence having some sort of impact on the issue. Again, it has exactly zero impact on the issue, so I asked him to go into this vast array of evidence and produce just one example of researchers deriving the source of critical coordination from the dynamic properties of the system -- which is something he would be clearly unable to do. And thus, as the ID critic dodges back and forth in front of the issue, I am left having to argue (with an otherwise intelligent being) that if you don’t coordinate the descriptions of the system with the descriptions of the coding constraints, the system will not (and cannot) begin to function. Good grief, the extent that ID critics will go to avoid physical evidence is simply dumbfounding, but there it is for all to see. Over and over again. - - - - - - - - - - - - - - - - - Bob, none of the papers you cite demonstrates anyone deriving the required coordination from the dynamic properties of the material components in the system. Such calculations do not exist.Upright BiPed_{February 13, 2020
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Pw Thanks :)EugeneS_{February 12, 2020
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EugeneS @133: Excellent!pw_{February 12, 2020
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Bob @132 Good. Agents use rules and a communication protocol (if then else statements prescribing what they should do in response to stuff). The prescriptive context (protocol and rules) should exist before the system starts functioning, otherwise this is just chaos. Top down, not bottom up. Top down is exactly how these things are implemented in technology. And ID maintains that this is how biological systems came about. But that is not an acceptable answer to you. I understand that. However, to argue coherently for a bottom up approach you would need to assume that agents are intelligent enough from the start to work out rules on the fly (as children can do when they play), which, I suppose, defeats your purpose as I understand it. Either way is awkward for you. The bottom up approach is even harder to defend for somebody who supports evolution. It is just a can of worms Darwin was not aware of. It does not stand up to scrutiny. Another point is constraints vs motion distinction. Pattee, Polanyi and others are complementarianists. They maintain that system dynamics alone is not sufficient to explain how living things function and replicate (even less how they came to be). The behavior of a living system critically depends on specific constraints achieving rate independence of the system's description (read/write from/to memory) and semantic closure.EugeneS_{February 12, 2020
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EugeneS - Yes, I agree with you that control can be distributed across the system. It's not clear that there would be one agency, though. I suspect that would end up as a semantic argument!Bob O'H_{February 12, 2020
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LoL! @ Bob O'H- How do you propose to get enzymatic control without the genetic code and all it requires already in place and operational?ET_{February 12, 2020
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Bob OH Up the thread you said this:
There is no controlling agency that ensures...
I objected saying that there can be cases where controlling agency is distributed across the system. In such scenarios, control is still present even though it is distributed. So decentralized control =/= no control. To which objection you responded as follows:
Right. That might be why I didn’t write that.
It is not clear to me from your later comment if you agree with me or contradict yourself.EugeneS_{February 12, 2020
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UB @ 125 -
How exactly would gene expression take place without the coordination being discussed?
I've no idea.
No Bob, I am not “simply wrong”. But you are, completely. You cannot provide a single document describing how researchers applied the equations of physics to the dynamic properties of the constituents of gene system, and from that, were able to demonstrate a source of the simultaneous coordination required at the origin of the system.
As I mentioned, it has a long history. here's one old paper from 1981. It cites this paper which is exactly about how control can be distributed in an enzymatic system, using standard tricks of the trade of physics. For a review of more recent work, see here.
The paper I cited above is available on Pattee’s Binghamton University website.
Which one? As you point out, there are 50 or 60.Bob O'H_{February 12, 2020
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BO'H, please note the just above. KFkairosfocus_{February 11, 2020
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UB, Patee is fascinating. Let me clip just one thing for the moment:
Pattee H. H. (1978) Biological systems theory: Descriptive and constructive complementarity. In: Klir G. J. (ed.) Applied general systems research. Plenum, New York: 511–520. . . . . The introduction of this complementarity into systems description has profound epistemological and methodological significance. By recognizing that all living systems depend on internal, rate-independent, linguistic descriptions, we are forced to introduce the classical symbol-matter (or subject-object) dualism into the system itself. This is no metaphor or analogy; it is a literal interpretation of what we normally mean by the symbol-matter distinction. The genetic DNA is a linear, discrete set of symbols that is interpreted by the transducing, protein-synthesizing constraints of the cell to construct and control the structure and dynamics of the organism in its environment. This internal description is also responsible for the growth of new degrees of freedom, new parts, and new functions into the systems that are competent to read it. The reading process is relatively rate- independent, but its execution requires rate-dependent control that is accomplished by constructing thousands of enzymes whose dynamical description would each require thousands of degrees of freedom. Of course all these complex dynamical processes could not be described in the cell. The trick of genetic description (Cf. Lofgren [Note 9] ; von Neumann [Note 25] ) is that the description of the constraints that harness the dynamics is relatively simple and abstract (i.e., obey arbitrary syntactic rules), while the dynamics that they constrain are incredibly complex and entirely physical (i.e., obey natural laws).Biologists now know many of the key molecular hardware mechanisms underlying reproduction, development and evolution, although much of the molecular hardware remains to be discovered. The molecular biological descriptions of the gene and its mechanism of expression have been interpreted by some biologists as a total reduction of life to physics, but to others the details of molecular structure have only served to emphasize the basic ambiguity between structure and function. As a consequence, many biologists are now shifting from questions of hardware structure to the questions of the programming and control of the morphologies and activities of organisms. We are finding that useful explanations of living systems’ behavior require a dualistic description that recognizes the linguistic, proscriptive activity of life as complementary to the dynamical hardware activity. Longuet-Higgins [Note 10] has characterized life as “programmed matter” which succinctly focuses on this essential complementarity. The earlier emphasis in biology on the anatomical and molecular structures is being augmented with the concepts of biological languages and programs
LANGUAGE, manifested in coded algorithms and linked data structures [D/RNA is a string]. LANGUAGE, antecedent to humans, and as a key component of the living cell. LANGUAGE. KFkairosfocus_{February 11, 2020
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. Bob, be sure and reciprocate with a paper showing how researchers applied the equations of physics to the dynamic properties of the constituents of the gene system, and from that, were able to demonstrate a source of the simultaneous coordination required at the origin of the systemUpright BiPed_{February 11, 2020
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. Bob, How exactly would gene expression take place without the coordination being discussed? - - - - - - - - - - - The paper I cited above is available on Pattee’s Binghamton University website. https://binghamton.academia.edu/HowardPattee There is an array of 50-60 titles dealing with the physics of symbol systems and semiotic control. You are welcome to take your pick.Upright BiPed_{February 11, 2020
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UB -
You also know that using the laws and equations of physics, this coordination cannot be derived from the dynamic properties of the system.
No, I actually don't know that. Can you provide the references from the scientific literature that show this? I'd like to see more than just an unreferenced citation from one person - there should be some modelling to demonstrate this, to go alongside the modelling of the dynamics of gene expression that has been going on since at least the 70s.Bob O'H_{February 11, 2020
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. Bob, as I suggested earlier, have you ever considered what would be all-that-wrong with just acknowledging the physical reality?Upright BiPed_{February 11, 2020
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. From Wiki: Howard Hunt Pattee (born October 5, 1926) is an American biologist, Professor Emeritus at Binghamton University and Fellow of the American Association for the Advancement of Science. He graduated at Stanford University in 1948 and completed a Ph.D. there in 1953. Professor Pattee's main research interests are theoretical biology with a focus on origin of life, artificial life, biosemiotics, semiotic control of dynamic systems, and the physics of codes and symbols. His many contributions to the "symbol-matter" problem within the cell have had much influence on theoretical biology, biosemiotics, complex systems and artificial life.
Physical laws and semiotic controls require disjoint, complementary modes of conceptualization and description. Laws are global and inexorable. Controls are local and conditional. Life originated with semiotic controls. Semiotic controls require measurement, memory, and selection, none of which are functionally describable by physical laws that, unlike semiotic systems, are based on energy, time, and rates of change. However, they are structurally describable in the language of physics in terms of non-integrable constraints, energy degenerate states, temporal incoherence, and irreversible dissipative events. --H. H. Pattee, Department of Systems Science, Binghamton, NY
Upright BiPed_{February 11, 2020
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.
I’m sorry, but you’re wrong. The reason I wrote ” I’ve no idea what this has to do with whether there’s an immaterial component to the system.” is because I had no idea what this has to do with whether there’s an immaterial component to the system.
No Bob, you’re not sorry and I’m not wrong. You know exactly what is being said to you, and you understand it. You know that there is a critical coordination between multiple discrete sequences in the system that must occur for the system to even begin to function. You also know that using the laws and equations of physics, this coordination cannot be derived from the dynamic properties of the system.
When you write “You also know that using the laws and equations of physics, this coordination cannot be derived from the dynamic properties of the system.”, you’re simply wrong. There is a tonne of work on precisely this – it’s called system dynamics. Basically, because we know how the pieces work we can model how they operate together in coordination.
No Bob, I am not “simply wrong”. But you are, completely. You cannot provide a single document describing how researchers applied the equations of physics to the dynamic properties of the constituents of gene system, and from that, were able to demonstrate a source of the simultaneous coordination required at the origin of the system. As a discipline, even applied to biology, systems dynamics doesn’t begin to address this issue among its proponents, nor is it intended to. I invite anyone reading this to go to the System Dynamics Society and read their proceedings.Upright BiPed_{February 11, 2020
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SA @ 115 -
Again, the decision to put the very same material composition upside down came from an immaterial, rational choice to do it. The very same material components cannot work because of the input of an immaterial, logical, decision-process.
It may have or it may not. The reason the car won't work is because it's upside down, which is a very material property. And this is true regardless of whether it was put upside down because someone tipped it over or if it was blown over in the wind. UB @ 116 - I'm sorry, but you're wrong. The reason I wrote " I’ve no idea what this has to do with whether there’s an immaterial component to the system." is because I had no idea what this has to do with whether there’s an immaterial component to the system. When you write "You also know that using the laws and equations of physics, this coordination cannot be derived from the dynamic properties of the system.", you're simply wrong. There is a tonne of work on precisely this - it's called system dynamics. Basically, because we know how the pieces work we can model how they operate together in coordination. EugeneS @ 117 -
Decentralization of control does not equate ‘no control whatsoever’.
Right. That might be why I didn't write that.Bob O'H_{February 11, 2020
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Bob just keeps doubling down.
Bob: “UB – but we know that distributed systems work. It’s how the free market operates. There is no controlling agency that ensures that fresh papaya gets delivered to the middle of Norway in the Nordic winter. Not, it is the coordinated actions of individuals in the supply network.” EugeneS: This is actually wrong. Decentralization of control does not equate ‘no control whatsoever’. Distributed decision making agents will have to coordinate their activities. A different heuristic is a heuristic nonetheless. You can’t just get away with it unfortunately.
I wouldn’t be so sure about that. Bob can get away with anything he wants because Bob doesn’t care about reason, logic, intellectual honesty or the truth. Point out the fallacies in his reasoning, as I have done @ #73, #75 and #90, he just doubles down on it. As an epistemological subjectivist he just moves the goal posts where ever he wants and when confronted with the facts just doubles down on it. In other words, Bob believes what he believes because he believes it. It’s his ”default” positionjohn_a_designer_{February 11, 2020
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EugeneS @83, @92, @117: Exactly right. Excellent.pw_{February 11, 2020
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Bob O'H @97:
UB – but we know that distributed systems work. It’s how the free market operates. There is no controlling agency that ensures that fresh papaya gets delivered to the middle of Norway in the Nordic winter. Not, it is the coordinated actions of individuals in the supply network.
This is actually wrong. Decentralization of control does not equate 'no control whatsoever'. Distributed decision making agents will have to coordinate their activities. A different heuristic is a heuristic nontheless. You can't just get away with it unfortunately.EugeneS_{February 11, 2020
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.
I’ve no idea what this has to do with whether there’s an immaterial component to the system.
Yes you do, Bob. You know that there is a critical coordination between multiple discrete sequences in the system that must occur for the system to even begin to function. You also know that using the laws and equations of physics, this coordination cannot be derived from the dynamic properties of the system. And thus, you know you must merely assume otherwise. - - - - - - - - - - - - - - - - (psssst Bob ... it has been known for half a century that the genetic translation system requires complimentary physical descriptions; one for its dynamic properties and another for its semantic organization. This is an issue that will not go away, so all the squirming is truly unnecessary. There is, of course, the obvious caveat that you don't actually have to do anything whatsoever, but you could choose to simply acknowledge the documented organizational requirements of the system and walk away with the integrity that comes from not ignoring physical evidence. As a materialist, it simply represents yet another hill that must be climbed in order to establish some empirical legitimacy for your preferred belief system. But it cannot be merely BS'd away as if it doesn't exist in reality. Your head in the sand doesn't really cut it, Bob. As the old adage goes, you don't get your own facts).Upright BiPed_{February 10, 2020
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Bob O'H
Nobody said anything about flipping cars. But if you want to go there, I’d hope it’s obvious that in this case it’s unable to be driven because of the very material fact that it’s the wrong way up, so its tires aren’t touching the ground.
Again, the decision to put the very same material composition upside down came from an immaterial, rational choice to do it. The very same material components cannot work because of the input of an immaterial, logical, decision-process. But you are saying that rational decisions from humans are material objects, and that's where we disagree. You' should be able to show that thoughts are material objects.Silver Asiatic_{February 10, 2020
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Bob O'H
Are you seriously arguing that my argument is invalid because it requires thought?
You seem exasperated or amazed, but I believe your view is that thoughts are material objects. My view is that they are immaterial entities. I believe you need to demonstrate that thoughts are material things, and thus far nobody has been able to do that. With no evidence supporting that point of view, the idea that thoughts are immaterial is the best explanation that we have.Silver Asiatic_{February 10, 2020
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