Home » Intelligent Design » But, what if the Cambrian robot is self-replicating?

But, what if the Cambrian robot is self-replicating?

Dr Liddle, commenting on the Cambrian Robot thread (itself a takeoff on the Pre- Cambrian Rabbit thread), observes at comment no 5:

the ribosome is part of a completely self-replicating entity.

The others aren’t.

The ribosome didn’t “make itself” alone but the organism that it is a component of was “made” by another almost identical organism, which copied itself in order to produce the one containing the ribosome in question.

It is probably true that the only non-self-replicating machines are those designed by the intelligent designers we call people.

But self-replication with modification, I would argue, is the alternate explanation for what would otherwise look like it was designed by an intelligent agent.

I don’t expect you to agree, but it seems to me it’s a point that at least needs to be considered . . .

The matter is important enough to be promoted to a full post — UD discussion threads can become very important. So, let us now proceed . . .

In fact, the living cell implements a kinematic von Neumann Self Replicator [vNSR], which is integrated into a metabolising automaton:

Fig. A: A kinematic vNSR, generally following Tempesti’s presentation (Source: KF/IOSE)

Why is that important?

First, such a vNSR is a code-based, algorithmic, irreducibly complex object that requires:

(i) an underlying storable code to record the required information to create not only
(a) the primary functional machine [for a "clanking replicator" as illustrated in Fig. A, a Turing-type “universal computer”; in a cell this would be the metabolic entity that transforms environmental materials into required components etc.] but also
(b) the self-replicating facility; and, that
(c) can express step by step finite procedures for using the facility;
(ii) a coded blueprint/tape record of such specifications and (explicit or implicit) instructions, together with
(iii) a tape reader [[called “the constructor” by von Neumann] that reads and interprets the coded specifications and associated instructions; thus controlling:
(iv) position-arm implementing machines with “tool tips” controlled by the tape reader and used to carry out the action-steps for the specified replication (including replication of the constructor itself); backed up by
(v) either:
(1) a pre-existing reservoir of required parts and energy sources, or
(2) associated “metabolic” machines carrying out activities that as a part of their function, can provide required specific materials/parts and forms of energy for the replication facility, by using the generic resources in the surrounding environment. 

Also, parts (ii), (iii) and (iv) are each necessary for and together are jointly sufficient to implement a self-replicating machine with an integral von Neumann universal constructor

That is, we see here an irreducibly complex set of core components that must all be present in a properly organised fashion for a successful self-replicating machine to exist. [Take just one core part out, and self-replicating functionality ceases: the self-replicating machine is irreducibly complex (IC).]

This irreducible complexity is compounded by the requirement (i) for codes, requiring organised symbols and rules to specify both steps to take and formats for storing information, and (v) for appropriate material resources and energy sources.

Immediately, we are looking at islands of organised function for both the machinery and the information in the wider sea of possible (but mostly non-functional) configurations.

In short, outside such functionally specific — thus, isolated — information-rich hot (or, “target”) zones, want of correct components and/or of proper organisation and/or co-ordination will block function from emerging or being sustained across time from generation to generation. So, once the set of possible configurations is large enough and the islands of function are credibly sufficiently specific/isolated, it is unreasonable to expect such function to arise from chance, or from chance circumstances driving blind natural forces under the known laws of nature.

Q: Per our actual direct observation and experience, what is the best explanation for algorithms, codes and associated irreducibly complex clusters of implementing machines?

A: Design as causal process, and thus such entities serve as signs pointing to design and behind design, presumably one or more designers. Indeed, presence of such entities would normally count in our minds as reliable signs of design. And thence, as evidence pointing to designers, the known cause of design.

So, why is this case seen as so different?

Precisely because these cases are in self-replicating entities. That is, the focus is on the chain of descent from one generation to the other, and it is suggested that sufficient variation can be introduced by happenstance and captured across time by  reproductive advantages that one or a few original ancestral cells can give rise to the biodiversity we see ever since the Cambrian era.

But is that really so, especially once we see the scope of involved information in the context of the available resources of the atoms in our solar system or the observed cosmos — the cosmos that can influence us in a world where the speed of light seems to be a speed limit?

William Paley, in Ch II of his Natural Theology (1806) provides a first clue. Of course, some will immediately object to the context, a work of theology. But in fact good science has been done by theologians and good science can appear in works of theology [just as how some very important economics first appeared in what has been called tracts for the times, e.g. Keynes' General Theory], so let us look at the matter on the merits:

Suppose, in the next place, that the person who found the watch should after some time discover that, in addition to all the properties which he had hitherto observed in it, it possessed the unexpected property of producing in the course of its movement another watch like itself – the thing is conceivable; that it contained within it a mechanism, a system of parts — a mold, for instance, or a complex adjustment of lathes, baffles, and other tools — evidently and separately calculated for this purpose . . . .
The first effect would be to increase his admiration of the contrivance, and his conviction of the consummate skill of the contriver. Whether he regarded the object of the contrivance, the distinct apparatus, the intricate, yet in many parts intelligible mechanism by which it was carried on, he would perceive in this new observation nothing but an additional reason for doing what he had already done — for referring the construction of the watch to design and to supreme art . . . .
He would reflect, that though the watch before him were, in some sense, the maker of the watch, which, was fabricated in the course of its movements, yet it was in a very different sense from that in which a carpenter, for instance, is the maker of a chair — the author of its contrivance, the cause of the relation of its parts to their use. [Emphases added.]

So, the proper foci are (i) the issue of self-replication as an ADDITIONAL capacity of a separately functional, organised complex entity, and (ii) the difference between generations 2, 3, 4 . . . and generation no 1. That is, first: once there is a sub-system with the stored information and additional complex organisation and step by step procedures to replicate an existing functional complex organised,  entity then this is an additional case of FSCO/I to be explained.

Hardly less important, the key issue is not the progress from one generation of self-replication to the next, but the origin of such an order of system: “the [original] cause of the relation of its parts to their use.”

Third, we do need to establish that cumulative minor variations and selection on functional and/or reproductive advantages, would surmount the barrier of information generation without intelligent direction, especially where codes and algorithms are involved.

In the case of the Ribosome in the living cell these three levels interact:

 

Fig. B: Protein synthesis and the role of the ribosome as “protein amino acid chain factory” (Source: Wiki, GNU. See also a medically oriented survey here. )

Fig. C: The Ribosome in action, as a digital code-controlled “protein amino acid chain factory.” Notice the role of the tRNA as an amino acid [AA] taxi and as a nano-scale position-arm device with a tool-tip, i.e. a robot-arm. Also, notice the role of mRNA as an incrementally advanced digitally coded step by step assembly control tape.  (Source: Wiki, public domain.)

But — as Dr Liddle suggested –  isn’t this just a matter of templates controlled by the chemistry, much as the pebbles on Chesil beach, UK, grade based on whether a new pebble will fit the gaps in the existing pile of pebbles? And, what is a “code” anyway?

Let us begin from what a code is, courtesy Collins English Dictionary:

code, n
1. (Electronics & Computer Science / Communications & Information) a system of letters or symbols, and rules for their association by means of which information can be represented or communicated for reasons of secrecy, brevity, etc. binary code Morse code See also genetic code
2. (Electronics & Computer Science / Communications & Information) a message in code
3. (Electronics & Computer Science / Communications & Information) a symbol used in a code
4. a conventionalized set of principles, rules, or expectations a code of behaviour
5. (Electronics & Computer Science / Communications & Information) a system of letters or digits used for identification or selection purposes . . .

[Collins English Dictionary – Complete and Unabridged © HarperCollins Publishers 1991, 1994, 1998, 2000, 2003]

Immediately, we see that codes are complex, functionally organised information-related constructs, designed to store or convey (and occasionally to conceal) information. They are classic artifacts of design, and given the conventional assignment of symbols and rules for their association to convey meaning by reference to something other than themselves, we see why: codes embed and express intent or purpose and what philosophers call intentionality.

But at the same time, codes are highly contingent arrangements of elements, so could they conceivably be caused by chance and/or natural affinities of things we find in nature? That is, couldn’t rocks falling off the cliff at the cliff end of Chesil beach spontaneously arrange themselves into a pile saying: “Welcome to Chesil beach?”

This brings up the issues of depth of isolation of islands of function in a space of possible configurations, and it brings up the issue of meaningfulness as a component of function. Also lurking is the question of what we deem logically possible as a prior causal state of affairs.

Of course, any particular arrangement of pebbles is possible, as pebbles are highly contingent. But if we were to see beach pebbles at Chesil (or the fairly similar Palisadoes Jamaica long beach leading out to Port Royal and forming the protecting arm for port Kingston) spelling out the message just given or a similar one, we would suspect design tracing to an intelligence as the most credible cause. This is because the particular sort of meaningful, functional configuration just seen is so deeply isolated in the space of possibilities for tumbling pebbles, that we instinctively distinguish logical possibility from practical observability on chance plus blind natural mechanisms, vs an act of art or design that points to an artist or designer with requisite capacity.

But that is in the everyday world of observables, where we know that such artists are real. In the deep past of origins, some would argue, we have no independent means of knowing that such designers were possible, and it is better to infer to natural factors however improbable.

But in this lurks a cluster of errors. First, ALL of the deep past is unobservable so we are inferring on best explanatio0n from currently observed patterns to a reasonable model of the past.

Second, on infinite monkeys analysis grounds closely related to the foundations of the second law of thermodynamics, we know that such configurations are so exceedingly isolated in vast sets of possibilities that it is utterly implausible on the gamut of the observed cosmos. Such a message is not sufficiently likely to be credibly observable by undirected chance and necessity.  And from experience we know that the sets of symbols and rules making up a code are well beyond the comp0lexity involved in 125 byes of information. That is, 1.07 * 10^301 possibilities, more than ten times the square of the 10^150 or so possibilities for Planck time quantum states of the 10^80 atoms of our observed universe.

Third, there is a lurking begging of the question: in effect the assertion of so-called methodological naturalism would here block the door to the possibility of evidence pointing to the logically possible state of affairs that life is the product of design.  We can see this from a now notorious declaration by Lewontin:

To Sagan, as to all but a few other scientists, it is self-evident that the practices of science provide the surest method of putting us in contact with physical reality, and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test . . . .

It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. 

[From: “Billions and Billions of Demons,” NYRB, January 9, 1997. Bold emphasis added.]

That looks uncommonly like closed-minded question-begging, and — as Johnson pointed out — falls of its own weight, once it is squarely faced. We can safely lay this to one side.

But also, there is a chicken-egg problem. One best pointed out by clipping from a bit further along in the thread at 30 (which clips from Dr Liddle at 26):

the common denominator in the “robots” itemized in the OP, it seems to me, is that they are products of decision-trees in which successful prototypes are repeated,

a: as created by intelligent designers, in a context of coded programs used in their operation

usually with variation, and less successfuly prototypes are abandoned.

b: Again, by intelligently directed choice

In two of the cases, the process is implemented by intelligent human beings, who do the replicating externally, as it were (usually), set the criteria for success/failure, and only implement variants that have a pre-sifted high probability of success.

c: In short, you acknowledge the point, i.e that it is intelligence that is seen empirically as capable of developing a robot (and presumably the arms and legs of Fig A are similar to the position arm device in B).

In the third case (the ribosome) I suggest that the replicating is intrinsic to the “robot” itself,

d: The problem here is the irreducible complexity in getting to function, as outlined again just above.

in that it is a component within a larger self-replicating “robot”;

e: it is a part of both the self-replicating facility and the metabolic mechanism, and uses a position-arm coded entity the tRNA that key lock fits the mRNA tape that is advanced step by step in protein assembly, and has as well a a starting and a halting process.

the criteria for success/failure is simply whether the thing succeeds in replicating,

f: The entity has to succeed at making proteins, which are in turn essential to its operations, i.e this is chicken-egg irreducible complexity. I gather something like up to 75 helper molecules are involved

and the variants are not pre-sifted so that even variants with very little chance of success are produced, and replicate if they can.

g: If the ribosome does not work right the first time, there can be no living cell that can either metabolise or self-replicate.

h: For that to happen, the ribosome has to have functioning examples of the very item it produces — code based, functioning proteins.

i: In turn, the DNA codes for the proteins have to be right, and have to embrace the full required set, another case of irreducible complexity.

j: In short, absent the full core self replicating and metabolic system right from get-go, the system will not work.

But in both scenarios, the result is an increasingly sophisticated, responsive, and effective “robot”.

k: This sort of integrated irreducible complexity embedding massive FSCO/I has only one observed solution and cause: intelligent design.

l: In addition, the degree of complexity involved goes well beyond the search resources of the observed cosmos to credibly come up with a spontaneous initial working config.

m: So, we see here a critical issue for the existence of viable cell based life, and it points to the absence of a root for the darwinian style tree of life.

So, once we rule out a priori materialism, and allow evidence that is an empirically reliable sign of intelligence to speak for itself, design becomes a very plausible explanation for the origin of life.

What about the origin of major body plans?

After all, isn’t this “just” a matter of descent with gradual modification?

The problem here is that this in effect assumes that all of life constitutes a vast connected continent of functional forms joined by fine incremental gradations. What is the directly observed evidence for that? NIL, the fossils — the only direct evidence of former life forms — notoriously are dominated by suddenness of appearance, stasis of form and disappearance or continuation into the modern era. That’s why Gould et al developed punctuated equlibria.

But the problem is deeper than that: we are dealing with code based, algorithmic entities.

Algorithms and codes are riddled with irreducible complexities and so don’t smoothly grade from say a Hello World to a full bore operating system. Nor can we plausibly plead that more sophisticated code modules naturally emerge from the Hello World module through chance variation and trial and error discovery of novel function so that the libraries can then be somehow linked together to form more sophisticated algorithms. Long before we got to that stage the 125 byte threshold would have repeatedly been passed.

In short, origin of major new body plans by embryogenesis is not plausibly explained on chance plus necessity, i.e. we do not have a viable chance plus necessity path to novel body plans.

To my mind, this makes design a very plausible — and arguably the best — causal explanation for the origin of both life and novel body plans.

So, what do you think of this? Why? END

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37 Responses to But, what if the Cambrian robot is self-replicating?

  1. 1
    Elizabeth Liddle

    An interesting and complex essay, kairofocus, and it will take me some time to digest! Unfortunately I am busy for the rest of today, and back to work tomorrow, but I will try to do some sort of justice to your OP within the next few days.

    In the mean time I look forward to reading other responses.

  2. A code (remotely stored) a storage medium, a retrival mechanism, a translation system, a sense and error-correction system (one could go on) all working in concert and all accessible, first, as concept mapped into the code.

    No one should be debating, any longer, if the idea of design is warranted – Dawin was wrong. Only philosophical considerations, or deeply held prejudice would reject the idea…clearly empirical science has little to do with it.

    Is it any wonder we laymen have come to veiw the educated classes (indeed the institution of education itself) with a great deal of skepticism?

    What most call science these days seems little more than materialist philosophy -a philosophy wielding the hammer it calls “science” and using that to enforce its philosophical hegemony.

  3. Thanks, kairosfocus! I read Dr. Liddle’s comment on the other thread and just couldn’t believe it. How does appealing to the added complexity of self-replication help her argument? So, we know it takes humans to create robots with complexity, but with ADDED complexity, robots are probably just naturally occurring???

  4. Darwin believed that the basic components of life were basically primordial “goo” (I remember my old biology textbook; protoplasm, nucleus, cell wall) that in aggregate would somehow generate life due to their innate natural qualities.

    If we could send back in time the 3D animations that faithfully recreate the vast, factory-like operation and nanotechnology that goes on and is present in a single cell, I think Darwin would probably burn his manuscript and make quick for the nearest church.

    It is only after a century and a half of being acclimated to Darwinism and desensitized to the growing, sheer nonsense of it in the face of modern knowledge that keeps it from being outed as nothing more than materialist, victorian-age myth.

    Well, that and the fact that so many reputations and egos would be shattered, and culture would dramatically shift in response.

  5. 5
    Elizabeth Liddle

    @Brent, #3

    I’ll chip in in response here, but I haven’t forgotten the OP!

    Thanks, kairosfocus! I read Dr. Liddle’s comment on the other thread and just couldn’t believe it. How does appealing to the added complexity of self-replication help her argument? So, we know it takes humans to create robots with complexity, but with ADDED complexity, robots are probably just naturally occurring???

    OK, so why does self-replication matter?

    Well, although self-replication can be (and, in the case of modern living things, is) incredibly complex, at it’s simplest, it needn’t be.

    For example, if you look at frost patterns on a window pain, you are looking at a very simple example of self-replication – a pattern begins, possible because of a speck of dust on the window, and that pattern spawns a copy, which spawns a copy, etc until you have a repeating pattern stretching across the glass.

    That means that if a very simple “probiont”, consisting perhaps of no more than lipid bubbles going through cycles of enlargement, driven by, for example nothing more complex than convection currents and osmotic forces, you’ve got something that is potentially, I would argue, a “self-designing system”.

    The reason being, and this was Darwin’s key insight, even though he had very little idea of the mechanics, that when you have self-replicators replication with variance, and where some variants replicate better than others, little by little the best replicators, even though they may have gained their “edge” purely by virtue of stochastic events, well tend to dominate the population.

    And we know that this does in fact work, because it’s exactly how GAs work. You start with a very simple self-replicator, and you let it replicate with random variation for many generations, in an “environment” in which some variants will replicate better than others.

    And the result is often really very effective “critters” that appear to have been “ingeniously” devised. However, the only “ingenuity” involved was setting up the thing in the first place. The writer of the GA is not responsible for the winning “design”.

    So it’s not that I’m “adding” complexity by invoking self-replication (although in the case of human design, making a self-replicating robot would of course be a far greater challenge than making a non-self-replicating robot). What I’m saying is if you start with a population of self-replicators, you will tend to get a self-designing system.

    I will add one important proviso, though – the seed self-replicators, although they can be very simple, must not be “brittle”. In other words, there must be a reasonable number of possible variants that won’t actually break the thing. That’s the other big difference (as I think I pointed out on the other thread) between living things and human-designed robots. Human designs tend to be “brittle”, both metaphorically and actually (and the two things are somewhat related).

    Whereas a bit of DNA can be subjected to repeats or deletions or substitutions and still result in some protein or other, or some signal or other.

    OK, I have to go out for dinner now, but I promise I’ll read the OP more thoroughly in the next couple of days, and try to post a response.

  6. 6
    Elizabeth Liddle

    Meleager: I think you are peddling a myth :)

    Now it may well be that we “Darwinists” are wrong, and eventually the ID argument may prove persuasive.

    But really, we are not the blind egotists you seem to think we are! To us, the story does, actually, make sense!

    Plus, the big incentives in science aren’t to support the status quo but to overturn it. That’s where the Nature papers and the Nobel prizes are.

    Seriously, we neither have horns nor are we stupid!

    But we do disagree with you, that’s for sure. I’m grateful to be given the opportunity to find out just where and why.

    Cheers

    Lizzie

  7. Elizabeth Liddle,

    And the result is often really very effective “critters” that appear to have been “ingeniously” devised. However, the only “ingenuity” involved was setting up the thing in the first place. The writer of the GA is not responsible for the winning “design”.

    But that statement is entirely dependent on the writer’s knowledge, intentions, actions during the program, and otherwise. If the writer (let’s say programmer) set up the environment to spawn particular results, responsibility is added. If the programmer intervened in the program, responsibility is added. If the programmer did not intervene but nevertheless knew just where the program would end up, responsibility is added.

    That’s the other big difference (as I think I pointed out on the other thread) between living things and human-designed robots. Human designs tend to be “brittle”, both metaphorically and actually (and the two things are somewhat related).

    “Tend to be”? What about self-replicating computer programs? You know, like GAs.

    While it’s probably not the point kairos was trying to make, what I’d note here is that your statement depends heavily on current technological limitations of humans. And even there the situation is complex – we’ve been “designing” organisms for a long time with selective breeding.

    Now, that’s not entirely fair, since you’re drawing the distinction between human-designed robots and living organisms – I think GAs and similar software could reasonably fit in there, but I’ll even put that aside. But still, the objection here comes down to “yes, but our technology is inferior”.

    So I have to ask: And what happens if, or even when, our technological capabilities converge more on what’s seem in nature? Would you say that would strengthen a design inference with regards to biology, particularly evolutionary biology?

    Plus, the big incentives in science aren’t to support the status quo but to overturn it. That’s where the Nature papers and the Nobel prizes are.

    I’m pretty sure Nature papers and Nobel prizes are sometimes, even typically, written by and given to scientists who supported the status quo. Not to mention that not every status quo is purely scientific – see Lysenkoism.

    Really – the history of science is not nearly this ideal. There is a reason Max Planck made this quote: “A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it”.

  8. Thanks, kairosfocus.

    This reminds me of a recent debate I had online with a couple of individuals about the origin of life. One of the key tenets of the materialistic origins story is that at some point, by chance, a self-replicating molecule was formed on the early earth. (Once this self-replicating molecule came into existence, proponents imagine that Darwinian mechanisms could then take over and form the diversity and complexity of life that we currently see. Both claims are utterly preposterous, but I like to home in on the first one, and that was the source of the recent discussion I had online.)

    I had read the quote before, but a few months ago I happened to again run across Dawkins’ statement that somehow on the early earth a self-replicating molecule formed. I nearly fell out of my chair laughing. Since then, I’ve had a chance to press this point in discussions, by asking if anyone can point me to a self-replicating molecule, as this is a fundamental requirement of the materialistic origins narrative.

    They cannot. There is no such thing.

    Replication involves significant coordination and restraint parameters. Even at its simplest, the process is indeed irreducibly complex.

  9. Eric A:

    ” . . . by asking if anyone can point me to a self-replicating molecule . . . ”

    Obviously it doesn’t match your criteria but in what ways does DNA fail?

  10. Elizabeth Liddle @5:

    For example, if you look at frost patterns on a window pain, you are looking at a very simple example of self-replication – a pattern begins, possible because of a speck of dust on the window, and that pattern spawns a copy, which spawns a copy, etc until you have a repeating pattern stretching across the glass.

    This is no more self-replication than when iron filings align with magnetic field lines from the poles of a magnet.

    If the water (frost) molecules actually replicated themselves as opposed to merely repeating their orientation, you’d have a point.

    That means that if a very simple “probiont”, consisting perhaps of no more than lipid bubbles going through cycles of enlargement, driven by, for example nothing more complex than convection currents and osmotic forces, you’ve got something that is potentially, I would argue, a “self-designing system”.

    Acretion of inanimate mass is not replication. Similarly crystals “enlarge” their crystaline structure by acretion of molecules that come out of suspension from the surrounding liquid and “crystalize” into patterns dictated by molecular bonds. We say the crystal grows or enlarges but we don’t ascribe it the ability to self-replicate. OTOH, If one lipid bubble formed around a discontinuity and somehow copied itself (without acreting around a discontinuity) and that copy inturn copied itself such that all lipid bubbles were identical copies and each entirely dependant in its formation upon its “parent” and only the first formed around a discontinuity, you’d have a point. But independent instances of growth by acretion each from a discontinuity are not replication.

    Neither repetitive orientation nor independent acretion are examples of organic self-replication.

  11. EL:

    Please attend to the behaviour of the specific type of replication we are discussing: a metabolising automaton that has the added facility of replicating itself based on stored coded representations through a vNSR.

    There are no cell based metabolising life forms that comprise giant molecules that simply replicate by autocatalysis or crystallisation. Dawkins’ replicator just so story is a myth, not an observed fact. (Notice, how viri get replicated: they hijack cells and act as rogue programs.)

    W@e are dealing with a step by step, coded informaiton based process using specially organised nanomachines. Three of these happen to be the ribosome, the tRNA and the mRNA.

    And of course the mRNA in the ribosome acts as a control tape, and the tRNAs are AA taxis and position-arm units that click together the elongating protein.

    This is key to both metabolism and to self replication.

    GEM of TKI

  12. Obviously it doesn’t match your criteria but in what ways does DNA fail?

    What would it take to establish the thesis that DNA is a self-replicating molecule?

    I don’t think it is.

    I think the very idea of self-replication is philosophically nonsensical.

  13. Mung:

    “I don’t think it is.

    I think the very idea of self-replication is philosophically nonsensical.”

    Well, what does the evidence and data say? ALL of the evidence and data.

    In conditions where are the building blocks are available (and I should think you’d have to grant the raw materials being present) DNA seems very good at creating a copy of itself. It makes mistakes sometimes but mostly it does a pretty good job.

    Philosophy should reflect the world. The philosopher must make sure that that is the case ’cause the world isn’t going to change to match him.

  14. Let’s take a scroll back down memory lane:

    (1) What is the only empirically observed source of codes, algorithms, and assembly lines?

    Elizabeth Liddle:

    a) artefacts produced by living things
    b) self-replicating systems

    However, at a stretch I could put them under a single heading:

    Living things.

    That works for me, as long as it is understood to include the process by which populations of self-replicators (i.e. living things) differentially self-replicate.

    So. The answer is. Non living things (artefacts produced by living things), and living things (self-replicators). But for sake of ease, let’s just lump them all together under living things.

    I am really scratching my head on this one.

    Let’s see if we can narrow it down a bit, by process of elimination.

    (1) What is the only empirically observed source of codes, algorithms, and assembly lines?

    Let’s start with a) artefacts made by living things.

    Such as? What are some artefacts, made by living things, which have been observed via empirical means to be the source of:

    1. Codes
    2. Algorithms
    3. Assembly lines.

  15. I think I’ve been a bit strident this evening and I apologise. I am trying to establish a dialog and answer questions but I admit I could be more amicable. Please don’t interpret my tone to imply any judgements on anyone’s character or conviction. Those are not, or ever have been in question as far as I am concerned. I trust you all to be honest, open and truthful. It’s in my nature to do so and it’s the right approach.

    But it is past 11pm here and I need my beauty sleep. A lot.

    See y’all later!

  16. 16
    Elizabeth Liddle

    BTW, whether you are a “Darwinist” or an “IDist”, I really recommend The Music of Life”, by Denis Noble.

    It presents a way of thinking about biological systems that I found extremely refreshing, and is an interesting response (antidote?) to Dawkins’ “Selfish Gene” model.

    http://www.musicoflife.co.uk/

    OK, more tomorrow :)

  17. DNA seems very good at creating a copy of itself.

    DNA is an inert molecule which doesn’t do anything to itself, least of self-replicate.

    It’s similar to having a program which can read the contents from one hard drive and write those contents to another hard drive, where the program itself is read from the hard drive that is being copied.

    Would anyone argue that the hard drive is self-replicating?

  18. Mung:

    “DNA is an inert molecule which doesn’t do anything to itself, least of self-replicate.”

    So, in cell meiosis the DNA molecules do not make (sometimes imperfect) copies of themselves?

    How do humans grow from a single fertilised egg if the DNA is not duplicated? How does a copy of your DNA exist in most cells of your body if it doesn’t replicate? How is all that lovely, multi-layered information disseminated if there isn’t copies of the DNA in each cell which came from the combination of the egg and sperm?

    I’m sure I’m misreading your comment but your statement is pretty nonsensical.

  19. ellazimm: I think what Mung is getting at is that DNA replication requires additional enzymes and other proteins. You can say that the cell replicates its DNA but not that the DNA replicates itself.

  20. I’m sure I’m misreading your comment but your statement is pretty nonsensical.

    I have to work hard to make no sense, so please, credit where credit is due :)

    You can say that the cell replicates its DNA but not that the DNA replicates itself.

    Close enough. That’s the general idea.

    DNA is a storage medium. It’s hard to make a case that it actually does much at all.

    There are however other entities in the cell besides DNA, and those entities makes use of whatever it is that is stored in DNA.

    So what is it, in the DNA itself, that begins the self-replication process? What kicks it off?

    How does the DNA molecule “know” when it’s time to make another copy of itself?

    If you cannot tell me that, I cannot see how you can convince me that the DNA molecule “self-replicates.”

    I’ll try to keep an open mind though.

  21. Think of DNA as being the software (zeros and ones) stored on your Microsoft Windows or Office or Mac OSX CDs or DVDs.

    By itself, the DVD is pretty useless. Perhaps suitable only as a coaster to put your drink on.

    Put in into the right computer however and it, like magic, can perform all sorts of tasks, like accessing the UD website :-)

  22. code, n
    1. (Electronics & Computer Science / Communications & Information) a system of letters or symbols, and rules for their association by means of which information can be represented or communicated for reasons of secrecy, brevity, etc. binary code Morse code See also genetic code

    No wei! It actually says “See also genetic code”?

    By the way, notice the “rules for their association.”

    Notice the presence of teleology:

    …by means of which information can be represented or communicated for reasons of secrecy, brevity, etc.

    Now if we are granting that DNA contains information, and that within the cell there is a system by which the information in DNA can be “represented or communicated,” what better than a code to do so?

  23. 23
    Elizabeth Liddle

    Kairosfocus:

    Dr Liddle, commenting on the Cambrian Robot thread (itself a takeoff on the Pre- Cambrian Rabbit thread), observes at comment no 5:

    the ribosome is part of a completely self-replicating entity.
    The others aren’t.
    The ribosome didn’t “make itself” alone but the organism that it is a component of was “made” by another almost identical organism, which copied itself in order to produce the one containing the ribosome in question.
    It is probably true that the only non-self-replicating machines are those designed by the intelligent designers we call people.
    But self-replication with modification, I would argue, is the alternate explanation for what would otherwise look like it was designed by an intelligent agent.
    I don’t expect you to agree, but it seems to me it’s a point that at least needs to be considered . . .

    The matter is important enough to be promoted to a full post — UD discussion threads can become very important. So, let us now proceed . . .
    In fact, the living cell implements a kinematic von Neumann Self Replicator [vNSR], which is integrated into a metabolising automaton:
    [snip figure]
    Fig. A: A kinematic vNSR, generally following Tempesti’s presentation (Source: KF/IOSE)
    Why is that important?
    First, such a vNSR is a code-based, algorithmic, irreducibly complex object that requires:
    (i) an underlying storable code to record the required information to create not only
    (a) the primary functional machine [for a "clanking replicator" as illustrated in Fig. A, a Turing-type “universal computer”; in a cell this would be the metabolic entity that transforms environmental materials into required components etc.] but also
    (b) the self-replicating facility; and, that
    (c) can express step by step finite procedures for using the facility;
    (ii) a coded blueprint/tape record of such specifications and (explicit or implicit) instructions, together with
    (iii) a tape reader [[called “the constructor” by von Neumann] that reads and interprets the coded specifications and associated instructions; thus controlling:
    (iv) position-arm implementing machines with “tool tips” controlled by the tape reader and used to carry out the action-steps for the specified replication (including replication of the constructor itself); backed up by
    (v) either:
    (1) a pre-existing reservoir of required parts and energy sources, or
    (2) associated “metabolic” machines carrying out activities that as a part of their function, can provide required specific materials/parts and forms of energy for the replication facility, by using the generic resources in the surrounding environment.
    Also, parts (ii), (iii) and (iv) are each necessary for and together are jointly sufficient to implement a self-replicating machine with an integral von Neumann universal constructor.
    That is, we see here an irreducibly complex set of core components that must all be present in a properly organised fashion for a successful self-replicating machine to exist. [Take just one core part out, and self-replicating functionality ceases: the self-replicating machine is irreducibly complex (IC).]
    This irreducible complexity is compounded by the requirement (i) for codes, requiring organised symbols and rules to specify both steps to take and formats for storing information, and (v) for appropriate material resources and energy sources.
    Immediately, we are looking at islands of organised function for both the machinery and the information in the wider sea of possible (but mostly non-functional) configurations.
    In short, outside such functionally specific — thus, isolated — information-rich hot (or, “target”) zones, want of correct components and/or of proper organisation and/or co-ordination will block function from emerging or being sustained across time from generation to generation. So, once the set of possible configurations is large enough and the islands of function are credibly sufficiently specific/isolated, it is unreasonable to expect such function to arise from chance, or from chance circumstances driving blind natural forces under the known laws of nature.

    OK, to take this part of your OP first, as the second hangs on it:
    I would agree that if a vNSR were to be both Irreducibly Complex the simplest possible self-replicator, then it is difficult to see how evolutionary processes could get going without an initial Intelligent Designer (a von Neumann, if you will). If it is only IC, but not the simplest possible self-replicator, then there isn’t necessarily a problem for abiogenesis, because IC structures can and do evolve by Darwinian processes, but there has to be some self-replicating precursor, and evolution can in fact involve simplification. And I am prepared to accept that your vNSR is IC (will break if you remove any one component).
    So the key question for me is: is it the simplest possible self-replicator?
    Here is a specification for a self-replicator that I believe is simpler. It’s a kind of toy macro-chemistry (Duplo Chemistry if you like :))

    Imagine four kinds of object. For convenience I will call them A, B, C and D. A and B are convex, and C and D have a concavity, at the bottom of which is a spike. C’s spike is cylindrical, and D’s spike is square-section. A will fit snugly inside C, because A has a cylindrical hole, but will not fit inside D. B will fit snugly inside D, because B has a square-section hole, but will not fit inside C. And D will not fit inside C, nor will C fit inside D.

    In addition, imagine that each of the four objects has pair of hooks, one on each side.

    Now, put large numbers of them in a box and jiggle them. Now check the box. What will probably have happened is that some of them will have hooked together to form chains. Not only that, but the As will tend to have stuck to Cs and Bs to Ds, so there will be lots of pairs of ACs and BDs in the box. There will also be some chains of AC, BD, CA and DB pairs, especially if we design the objects (yes, I said design :)) so that when the pairs pair up, their hooks align in corresponding orientations.

    Now, imagine that the material from which the objects are made is a kind of plastic that is fairly adhesive when the temperature is high, but becomes much less adhesive when the temperature is low.

    And mount your box of objects on the kind of baggage carousel you find at airports, only make sure the bearings are really bad, and the box is constantly jiggled around.

    Finally, round the back, behind the black flap, keep the temperature low – imagine it’s a cold store of some kind. Keep the temperature warm in front.

    Now, if we’ve got the spec right, what should happen is this:

    Initially, all the objects are loose (imagine you put them in the box one by one at the beginning). However, as the box jiggles, pairs of objects will start to assemble, and so will chains, including chains of pairs. Now, as the conveyor belt goes into the cold store, the pairs will start to come apart, but the chains will tend to stay together. Then as they come back into the warmth, those single chains will start to stick to new paired objects, creating new double chains.

    We now have our self-replicator. If we sample one double chain going in, and note the sequence, e.g.

    ‘C’ ‘A’
    ‘B’ ‘D’
    ‘D’ ‘B’
    ‘B’ ‘D’
    ‘B’ ‘D’
    ‘B’ ‘D’
    ‘D’ ‘B’
    ‘A’ ‘C’
    ‘B’ ‘D’
    ‘D’ ‘B’
    ‘C’ ‘A’

    When we look again, on the next round, we have a sporting chance of finding that the original double chain has split, and that each single chain has acquired a new set of paired objects. So we now have two versions of the chain where we once had only one.
    Now, it may be possible to express my Duplo Chemistry as a vNSR, I need to think this out. But either it is simpler than your vNSR, or your vNSR can be expressed without the word “code”. My Duplo Chemistry can be described as a “code” – my single strands “code” for the sequence in its new partner strand, but there is no code in addition to the fabrication components of the machine, the code is intrinsic to the morphology of the item to be duplicated.

    More to the point, it translates very neatly into basic chemistry – polymers with a specific (if not “specified” :)) , and all we need in addition to the components is a circulatory system and a temperature gradient.

    However, my population will only “evolve” if the duplication does not always produce an entirely faithful copy, and if different variants have different probabilities of copying successfully. But I can build this into my Duplo Chemistry. For instance, I could design the hooks in such a way that the more items there were on the chain, the tighter the bonding. However, I could also make it so that after a certainly length, the chains tended to tie themselves in knots and split less efficiently, and bond to matching objects less easily.

    And what I would expect to find, after setting my system going for a while, is that chains of certain lengths would tend to be the most common in the box. I might also find that a particular sequence dominated the “population” of sequences, simply because one of the first chains to reach optimum length was one with a particular sequence, and that was the one that got propagated. On another run, a completely different sequence might be the “winning” sequence.

    Moreover, sometimes chains will break, and propagate as smaller units, and sometimes chains will join together. So we will also get variation in the sequences propagating through the population.
    But that is to digress – we seem to agree that once we have a minimal self-replicator, Darwinian processes may have a chance of continuing. My argument is that a minimal self-replicator can be much simpler than a vNSR, and, in particular, that it can be described without the word “code” while still in many senses, acting as one.

    So, with regard to the rest of your post, my response is that I have just given an example of a self replicator that, while being IC, requires only simple “chemical” properties and a circulatory temperature gradient, not a highly improbable combination of rare events. The result is what could be described as a “code” that transfers “information” (as embodied in the sequence of objects) into generation after generation. Moreover any happenstance change to the code (let’s say that a few “successful” chains break into two shorter ones and these recombine to produce a longer chain that is particularly successful, that new sequence information will be propagated through subsequent generations.

    So we have an example of simple physical properties in a simple physical environment giving rise to self-propagating “information”, and no inference about an intelligent designer of that information need be postulated. Indeed I could start the thing off, go off for lunch, and have very little idea of what sequences I would find on my return – I’d be a “deist” kind of designer! Responsible for the Duplo, the conveyor belt, the cold store and the box, but not for the information contained inside the box.

    I’m sorry to have made you wait so long for this reply. I’ve actually coded up a virtual version of my Duplo Chemistry in MatLab, so I could post that later, maybe. It would be more fun to do it with coloured plastic though :)

    Anyway, thanks for making me think about this :)

    Cheers

    Lizzie

  24. Anyway, thanks for making me think about this

    No one made you think about this.

    You made a decision to think about this.

    Dare I say you selected this topic to think about:?

  25. 25
    Elizabeth Liddle

    OK, OK, I take full responsibility for my own actions :)

    Yes indeed, I made the decision, but it was prompted by kairosfocus’s interesting reference to von Neumann self-replicators, of which I had heard, but was not familiar.

    So to rephrase:

    Thanks, kairosfocus for bringing this interesting topic to my attention :)

  26. 26
    Elizabeth Liddle

    Erratum: I should have written, in 23,

    More to the point, it translates very neatly into basic chemistry – polymers with a specific (if not “specified” :)) sequence , and all we need in addition to the components is a circulatory system and a temperature gradient.

    I’m not quite sure how the word “sequence” got replaced by a space! Cat on keyboard, probably.

    Also I messed up the close italics tag at one point, but I think the sense is still clear.

  27. Dr Liddle:

    Let us clip from 23:

    I am prepared to accept that your vNSR is IC (will break if you remove any one component).
    So the key question for me is: is it the simplest possible self-replicator? . . . .

    Imagine four kinds of object. For convenience I will call them A, B, C and D. A and B are convex, and C and D have a concavity, at the bottom of which is a spike. C’s spike is cylindrical, and D’s spike is square-section. A will fit snugly inside C, because A has a cylindrical hole, but will not fit inside D. B will fit snugly inside D, because B has a square-section hole, but will not fit inside C. And D will not fit inside C, nor will C fit inside D. . . . .

    Initially, all the objects are loose (imagine you put them in the box one by one at the beginning). However, as the box jiggles, pairs of objects will start to assemble, and so will chains, including chains of pairs. Now, as the conveyor belt goes into the cold store, the pairs will start to come apart, but the chains will tend to stay together. Then as they come back into the warmth, those single chains will start to stick to new paired objects, creating new double chains.

    We now have our self-replicator.

    1 –> I am afraid, you have cut down the problem in a way that converts it into a strawman.

    2 –> The real issue, since Paley, is that you have an object with an EXISTING separate capacity, and the ADDITIONAL requisite of self-replication on stored coded representation. (His self replicating watch would have to have been programmed to carry out steps using cam bars or the equivalent! His “baffles” sound a lot like Coanda effect fluidic logic gates.)

    3 –> Yes, the chemistry in the 4-state DNA/RNA system hinges on the ability to form complementary chains [with a leetle help from some enzymes coded for within the system and assembled based on other entities coded for within the system . . .], but the issue is not chaining and duplication as such —

    though, the biologically relevant monomers are quite endothermic to form, mostly show chirality [which can really mess up geometry when we realise that the thermodynamic tendency is to racemic mixes] and complex, and have to be shepherded in bonding the right way –

    . . . but instead the formation and proper functional organisation of informational bio-molecules that put us, collectively, at an operating point for a very complex system.

    4 –> In turn this points to the origin of process logic, algorithms, codes [thus, language] and storage data structures and the regulatory mechanisms that co-ordinate such.

    5 –> So, to merely say once we have components, we can use complementarity to self replicate by appropriate jiggling, does not answer the material question, but distracts attention from it and indeed caricatures it.

    6 –> In the case of direct relevance, we have a living cell that carries out metabolic functions AND self replicates in a causal cycle where the components for the one are inextricably involved in the process for the other.

    7 –> Moreover, the involvement of digital codes where there is symbolic representation [a particular codon MEANS to add a certain AA to the chain, or to start and add, or to stop, etc] implies the presence of symbols and rules for their combination in light of the requisites of an algorithm, to create and implement an assembly-line process, for protein manufacture.

    8 –> In turn the highly complex and specifically functional, informationally assembled product of this process is intimately involved in the work of the process itself.

    9 –> this kind of cluster of items has but one known source: intelligence.

    10 –> And, that chance driven trial and error could create a simpler process that leads to an RNA world of self-replicators, that then spontaneously take up the business of coding and manufacturing proteins to do the metabolic work and help in the manufacturing, is it self a riddle of utter implausibilities on the implied configuration spaces.

    11 –> That symbolic language would spontaneously emerge from chance driven trial and error is similarly utterly implausible.

    12 –> Such suggested models only succeed because, by a priori imposition, the empirically routinely observed source of codes, algorithms, assembly lines and integrated complex functional, information based systems is ideologically ruled out.

    ___________

    There is another name for that: censorship that artificially suppresses what would otherwise be patently plain and obvious as the best explanation for what we are now seeing. Nor, should we underestimate the power of the dominant ideological view of the relevant institutions to impose such censorship.

    (Remember, to even raise the hint of a shadow of the above, is enough to get one branded as an ignorant, stupid, insane or wicked anti-science religious theocratic zealot and shunned, demoted, subjected to bullying “supervision” or expelled in too many circles. Why else do you think that the Darwinist zealots are thinking that their best response to me is to try to “out” me by name and to heap abuse and slander on me? What do you think is the message being sent to those who are in the system and are all too aware of the dangers involved in saying or hinting at the sort of issues above? talk about showing the torture intruments to intimidate the targets of the thought police!)

    But the very intensity of that sort of response is telling us that the absurdities in the system are becoming ever more evident, and its party-line champions are ever more finding it hard to kick against the pricks.

    GEM of TKI

  28. 28
    Elizabeth Liddle

    @ kairosfocus, #27

    I’m a little confused by most of your response, but I’ll address it point by point inasmuch as I understand what you are saying.

    1 –> I am afraid, you have cut down the problem in a way that converts it into a strawman.

    In that case I haven’t understood the problem.

    2 –> The real issue, since Paley, is that you have an object with an EXISTING separate capacity, and the ADDITIONAL requisite of self-replication on stored coded representation. (His self replicating watch would have to have been programmed to carry out steps using cam bars or the equivalent! His “baffles” sound a lot like Coanda effect fluidic logic gates.)

    I don’t understand how it relates to my scenario. Would you agree that my scenario results in a self-replicator? And, if so, that it is simpler than the von Neumann self-replicator?

    3 –> Yes, the chemistry in the 4-state DNA/RNA system hinges on the ability to form complementary chains [with a leetle help from some enzymes coded for within the system and assembled based on other entities coded for within the system . . .], but the issue is not chaining and duplication as such —

    Well, while my scenario is in some sense analogous to the DNA/RNA system, in many ways it is not (I posited no cell membrane equivalent, for example – mine is simply a series of naked chains, formed by virtue of shape of the bits plus energy in theh form of jiggling. But, having formed, they then duplicate themselves so we have multiple copies of the originally fortuitous sequences. My point was simply that a vNSR is not the simplest self-replicator – there are simpler ones. Therefore we cannot say that the earliest “natural” self-replicators can have been no simpler than a vNSR. There are simpler models, and mine is one.

    though, the biologically relevant monomers are quite endothermic to form, mostly show chirality [which can really mess up geometry when we realise that the thermodynamic tendency is to racemic mixes] and complex, and have to be shepherded in bonding the right way –

    . . . but instead the formation and proper functional organisation of informational bio-molecules that put us, collectively, at an operating point for a very complex system.

    I’m afraid I’m not following you.

    4 –> In turn this points to the origin of process logic, algorithms, codes [thus, language] and storage data structures and the regulatory mechanisms that co-ordinate such.

    Well, I don’t see this. In my example the “code” was intrinsic to the “Duplo Chemistry” which was reduced to two very simple binding rules. Nonetheless, what emerged, without interference from the Duplo manufacture, a series of strings whose physical conformation “coded” for their own duplication. Of course living cells (and even polymers) are much more complicated than my Duplo Chemistry. But what my scenario indicates is that there is nothing intrinsic to a self-replicating “code” that requires intelligent input.

    5 –> So, to merely say once we have components, we can use complementarity to self replicate by appropriate jiggling, does not answer the material question, but distracts attention from it and indeed caricatures it.

    Well, obviously I disagree! I don’t think it solves the problem of abiogenesis, obviously, it was just a toy model. But the fact that such a model can be imagined (and, indeed implemented, as I did using a virtual simulation, but it could be done in plastic) just as von Neumann imagined his, demonstrates that you do not need to separate the “coding” from the corporeal reality of what is coded. As for the “jiggling” – it doesn’t need to be “appropriate” jiggling exactly, it needs to be nothing more than a macro-analogy of heat. Which is abundant in our universe.

    6 –> In the case of direct relevance, we have a living cell that carries out metabolic functions AND self replicates in a causal cycle where the components for the one are inextricably involved in the process for the other.

    Yes indeed. That’s where I think Joe Szostak’s lab are doing interesting work (I linked on another thread to the lab, but here it is again: http://genetics.mgh.harvard.edu/szostakweb/)

    7 –> Moreover, the involvement of digital codes where there is symbolic representation [a particular codon MEANS to add a certain AA to the chain, or to start and add, or to stop, etc] implies the presence of symbols and rules for their combination in light of the requisites of an algorithm, to create and implement an assembly-line process, for protein manufacture.

    Well, I disagree :) One point of my example is that you don’t need “symbols” at all. My A block “codes” for a C block not symbolically, but simply because C is the only blockshape that will “mate” with A. However, the result of that “chemical” rule, coupled with the rule that any block can link to any other block in the orthogonal dimension means that entire double chains embody sequences that “code” for their own duplication (“Duplo” was a fortuitous choice of name for my chemistry :)). There are no symbols involved, yet the thing can be described a “code”, IMO, with no less validity that DNA is described as a “code”.

    8 –> In turn the highly complex and specifically functional, informationally assembled product of this process is intimately involved in the work of the process itself.

    Yes indeed.

    9 –> this kind of cluster of items has but one known source: intelligence.

    Well, no, not in my view :) As I’ve just shown, a much simpler version can be assembled by purely stochastic processes, given a starting “Chemistry”. And this brings me back to the point I was trying to make on the other thread, that once you have self-replication with variance, if you also have (as I did only clumsily in my toy scenario) a scenario where those variants vary in reproductive success, then you have the recipe for increasing complexity as fortuitously modified heritable bits of the organisms turn out to enhance reproductive success. As we both agreed – Darwinian process only kick in if you already have a self-replicating entity. What I’m suggesting is that the very first self-replicators can be sufficiently simple that fortuitous assembly does not require the inference of an intelligent designer (or at least not an intelligent coder). And once you have that first step, then Darwinian processes can be invoked explain subsequent diversification, complexity, and tuning to the environment.

    10 –> And, that chance driven trial and error could create a simpler process that leads to an RNA world of self-replicators, that then spontaneously take up the business of coding and manufacturing proteins to do the metabolic work and help in the manufacturing, is it self a riddle of utter implausibilities on the implied configuration spaces.

    Well, I would have to disagree. I would certainly agree that we don’t have definitive answers, and may never have definitive answers, but we certainly have potential candidate answers, I would suggest.

    11 –> That symbolic language would spontaneously emerge from chance driven trial and error is similarly utterly implausible.

    hmm. Well, firstly, I don’t think the “language” of the cell is symbolic anyway. But I do think that symbolic language has emerged because I am using it right now! And I would attribute it to “chance drive trial and error” only in the Darwinian sense (i.e. with natural selection), and which “selected” our symbol-using capacity for its clear reproductive advantage. But that’s a very long way (maybe 3 billion years!) from abiogenesis!

    12 –> Such suggested models only succeed because, by a priori imposition, the empirically routinely observed source of codes, algorithms, assembly lines and integrated complex functional, information based systems is ideologically ruled out.

    I really disagree here. I think assuming that an a priori ideology “rules out” certain solutions to problems of biological origins is just wrong. I would agree that the assumption that mechanistic processes are worth testing is a key notion, but with justification – such investigations have yielded fruitful findings. But that’s quite different from refusing to follow other lines of investigation for “ideological” reasons. There’s absolutely no reason not to investigate the possibility that an organism was, for example, deliberately bred, nor that an organism was deliberately genetically enginnered, and testable hypotheses can be devised that could yield answers.

    What I do think, though, is that the argument that because a thing is code-like it must have the same kind of origins as man-made codes is logically flawed, and equivalent to the fallacy: All mammals have fur; cats have fur; all mammals are cats (cf: These things are codes; man-made codes are man-made; all codes are man-made). The interesting question to my mind is: can codes arise spontaneously? And my answer is, that in the sense that DNA is a code, yes. And that one condition under which codes can arise spontaneously are those in which self-replicators replicate. And they can elaborate under an additional condition which is: if the self-replicator replicate with variance, and some variants self-replicate more efficently than others. Because under those conditions, the most efficient self-replicators will come to dominate the population, thus hugely multiplying the probability that the efficiency gained, however fortuitously, in a first step will be built on in a second.

  29. Dr Liddle:

    I need to be getting ready for the day, butr will pause.

    The key point above is that the kinematic vNSR has to symbolically represent and store the information for the main facility that carries on the main function. So, it is not merely replicating itself but an object that does something significant in its own right — Paley’s watch or our metabolising cell based organism — has the ADDITIONAL ability to be replicated by being symbolised, thereby instructing component assembly subsystems, and then putting such together in an organised new, functional whole that can carry on to the next generation.

    Autocatalysis is not enough.

    How is the main facility symbolised accurately?

    How is the set of instructions to make parts set up?

    Where do the assembly lines to effect the instructions come from?

    How does the system then organise components into a fresh new whole, through higher level instructions?

    Where does all of this functionally specific complex information and organisation come from ORIGINALLY? (As opposed to, how does it get passed on from one generation to the next)

    And remember, the vNSR has to be referring to something separate form itself that is being symbolised and built.

    GEM of TKI

  30. PS: The genetic code and associated regulatory codes are not code-like, they are codes. The issue is not whether code-like things that mysteriously appear in nature resemble codes, but whether codes — sets of meaningful symbols and rules for their expression and use — can come about without intelligent direction. The hesitation to see that a code is a code, suggests that the force of the point is plain.

  31. 31
    Elizabeth Liddle

    No, the hesitation doesn’t mean that the force of the point is plain! It means that I think that symbolic codes are different from non-symbolic codes, and I am not persuaded that DNA is a symbolic code!

    This seems to be our fundamental difference, though. Perhaps we need to unpack that thoroughly before proceeding.

    But there’s no rush, nor compulsion :)

    Cheers

    Lizzie

  32. Dr Liddle:

    The genetic code, per Wiki in the guise of testifying against known interest:

    The genetic code is the set of rules by which information encoded in genetic material (DNA or mRNA sequences) is translated into proteins (amino acid sequences) by living cells. The code defines a mapping between tri-nucleotide sequences, called codons, and amino acids. With some exceptions,[1] a triplet codon in a nucleic acid sequence specifies a single amino acid. Because the vast majority of genes are encoded with exactly the same code (see the RNA codon table), this particular code is often referred to as the canonical or standard genetic code, or simply the genetic code, though in fact there are many variant codes. For example, protein synthesis in human mitochondria relies on a genetic code that differs from the standard genetic code.

    Not all genetic information is stored using the genetic code. All organisms’ DNA contains regulatory sequences, intergenic segments, chromosomal structural areas, and other non-coding DNA that can contribute greatly to phenotype. Those elements operate under sets of rules that are distinct from the codon-to-amino acid paradigm underlying the genetic code.

    Just for example, with mRNA codons:

    AUG –> methionine (and START)

    GUA –> Elongate with Valine

    GCA –> Elongate with Alanine

    UAG –> STOP (halting is of course a key feature of algorithms)

    And so on across the 64 possibilities for three 4-state digital elements. . .

    I see here symbols and rules for their use, including start and stop elements. Of course, once an AA chain has been assembled, Onward it has to fold (often needing to be chaperoned to fold reliably), may be clustered with other chains, and may need activating additions. There is also often an internal “postage” system, with extra strung on AAs guiding transfer.

    Collins English Dictionary, again:

    code [k??d]
    n
    1. (Electronics & Computer Science / Communications & Information) a system of letters or symbols, and rules for their association by means of which information can be represented or communicated for reasons of secrecy, brevity, etc. binary code Morse code See also genetic code
    2. (Electronics & Computer Science / Communications & Information) a message in code
    3. (Electronics & Computer Science / Communications & Information) a symbol used in a code
    4. a conventionalized set of principles, rules, or expectations a code of behaviour
    5. (Electronics & Computer Science / Communications & Information) a system of letters or digits used for identification or selection purposes
    vb (tr)
    (Electronics & Computer Science / Communications & Information) to translate, transmit, or arrange into a code
    [from French, from Latin c?dex book, codex]

    Collins English Dictionary – Complete and Unabridged © HarperCollins Publishers 1991, 1994, 1998, 2000, 2003

    So far as I can see the matter should be uncontroversial, but perhaps there is something that makes me not see what the objection to this being a code is.

    (To my mind the issue is whether such a code is possible as a spontaneous, undirected process, as well as the algorithms it is used to specify, and the onward functional information being stored through it. I think that as an abstract logical possibility, such could happen by chance, as chance can in principle account for any highly contingent outcome. But I also think that the scope of the config space is so large and the functionality is so specific that clusters of functional configs are a case of the needles in a haystack on steroids problem; i.e the scope of search on teh gamut of the observed cosmos is grossly inadequate to be materially different from no search.. A far superior explanation is the routinely observed source of coded FSCI: design.)

    Perhaps, my view is shaped by the experience that I am used to dealing with modulation and coding systems, both analogue and digital. But, be that as it may, once I see a scheme that symbolises and uses some physical medium to chain symbols, in ways that convey meaning or make a difference to function, I think I have reason to see a code.

    Remember in particular, that in the tRNA, the anticodon that key-lock fits the mRNA codon triplet, is set up so the appropriate AA is on the other end of arm, and uses the CCA standard socket to hook to the -COOH end of the AA: H2N-CHR-COOH. There is thus a standard coupling that is independent of the particular AA. (The tRNA is fitted up by an enzyme that key-lock fits and sticks on the right AA.)

    This is an informational mapping, not a physical-chemical one.

    This is further underscored by the existence of variant codes, which means that there are dialects with variations. The most important is the shift to U from T for RNAs. Similarly, we see that in mitochondria there are variants, and in some organisms there are similar variants.

    All of this variety is typical of a linguistic phenomenon, not of a physically determined one.

    I would like to see why you think not.

    GEM of TKI

  33. 33
    Elizabeth Liddle

    So can I ask you, kairosfocus: if the mapping is informational and not physical, how would you, for example, encrypt it?

    For a linguistic code, encryption is easy – you just reassign signifiers to new signifieds.

    This is because the signifiers are purely symbolic.

    But how would you do this with DNA?

  34. F/N: I will respond on points to clips from the earlier remark:

    ___________

    >>EL: . . . I don’t understand how it relates to my scenario. Would you agree that my scenario results in a self-replicator? And, if so, that it is simpler than the von Neumann self-replicator?

    1: We need not just replication but replication that stores coded representation of the main object, and uses that stored representation to replicate it.

    KF: 3 –> Yes, the chemistry in the 4-state DNA/RNA system hinges on the ability to form complementary chains [with a leetle help from some enzymes coded for within the system and assembled based on other entities coded for within the system . . .], but the issue is not chaining and duplication as such —

    EL: Well, while my scenario is in some sense analogous to the DNA/RNA system, in many ways it is not (I posited no cell membrane equivalent, for example – mine is simply a series of naked chains, formed by virtue of shape of the bits plus energy in theh form of jiggling. But, having formed, they then duplicate themselves so we have multiple copies of the originally fortuitous sequences.

    2: The sequences in DNA are not fortuitous, they are based on coding for separately functional molecules, the proteins

    My point was simply that a vNSR is not the simplest self-replicator – there are simpler ones.

    3: Not in dispute, and irrelevant to the point: the living cell is based on a metabolic entity with a vNSR facility.

    4: That vNSR facility allows for encoded representation and replication, supporting the cells ability to metabolise and to replicate itself

    EL: Therefore we cannot say that the earliest “natural” self-replicators can have been no simpler than a vNSR. There are simpler models, and mine is one.

    5: the object to be addressed is the cell, not a hypothetical replicator molecule that is not coding information for something else that has to also do a job

    KF: though, the biologically relevant monomers are quite endothermic to form, mostly show chirality [which can really mess up geometry when we realise that the thermodynamic tendency is to racemic mixes] and complex, and have to be shepherded in bonding the right way –

    . . . but instead the formation and proper functional organisation of informational bio-molecules that put us, collectively, at an operating point for a very complex system.

    I’m afraid I’m not following you.

    5: Endothermicity means energy has to be added to drive formation, which would also normally trend to disrupt complex molecules

    6: Chirality is handedness, a geometric difference that makes molecules be like left and right hands, which directly affects key-lock fitting, folding etc. AAs are left handed, and RNA and DNA are right handed (seen from the way they rotate the plane of polarised light)

    7: the heat to form the two forms is about the same, and the undirected formation would tend to form a 50-50 mix, called the racemic form. This would mean that the geometry of polymers would be messed up, by overwhelming likelihood: in effect we have for every monomer, an additional bit of information: handedness. (This is usually not worried about in a biological context, precisely because biological systems form molecules of the right handedness under informational control.)

    8: In addition, AAs would naturally tend to form about 50% of peptide bonds if they chain, so being consistently peptide bonds is another bit per monomer. (That is what the shepherding of the molecules with the TRNA’s acting as position arm devices is in part about: the COOH end is grabbed and the NH2 end is made accessible to click to the last COOH end of an AA)

    9: having formed proteins, they have to be sent to the right place at the right time to do their job, and in fact there is an internal postal system that uses the Golgi apparatus. There are even little tractor molecules that move vesicles along the cytoplasmic skeleton — UPS in the cell.

    KF: 4 –> In turn this points to the origin of process logic, algorithms, codes [thus, language] and storage data structures and the regulatory mechanisms that co-ordinate such.

    EL: Well, I don’t see this. In my example the “code” was intrinsic to the “Duplo Chemistry” which was reduced to two very simple binding rules.

    10: Your code was just the complementation across the two strands, the relevant code is in the sequence in the chain of monomers in a given strand, which is then complemented between the DNA strands, giving redundancy that helps with keeping things correct.

    11: Maybe that is the key issue: DNA is a double helix, with a ladder between tie strands. To use the information (coded in the sequence of a given strand), the ladder is unzipped and the mRNA templates off the sequence on one strand.

    EL: Nonetheless, what emerged, without interference from the Duplo manufacture, a series of strings whose physical conformation “coded” for their own duplication.

    12: this is just saying that one string can be complemented by another string, recreating the twisted ladder. that has nothing to do with the functional information coded in the sequence of bases in a given strand.

    Of course living cells (and even polymers) are much more complicated than my Duplo Chemistry. But what my scenario indicates is that there is nothing intrinsic to a self-replicating “code” that requires intelligent input.

    13: the issue is not the chemistry of complementing two strands, but the code in one strand that tells the ribosome to make a given protein.

    KF: 5 –> So, to merely say once we have components, we can use complementarity to self replicate by appropriate jiggling, does not answer the material question, but distracts attention from it and indeed caricatures it.

    EL: Well, obviously I disagree!

    14: You seem to be looking at the complementarity across strands as I talked about, rather than the sequence in the strand that specifies the protein, which in turn targets folding and functioning in the cell.

    I don’t think it solves the problem of abiogenesis, obviously, it was just a toy model. But the fact that such a model can be imagined (and, indeed implemented, as I did using a virtual simulation, but it could be done in plastic) just as von Neumann imagined his, demonstrates that you do not need to separate the “coding” from the corporeal reality of what is coded.

    15: I think you are missing where the code is, and that the code is distinct from the capacity to complement it chemically once you have a pool of the requisite bases to do so.

    EL: As for the “jiggling” – it doesn’t need to be “appropriate” jiggling exactly, it needs to be nothing more than a macro-analogy of heat. Which is abundant in our universe.

    16: heat is available but at this level it is randomness,and is actually a disruptive force. DNA is not the stablest of molecules and the cell devotes considerable resources to keeping it in good repair.

    KF: 6 –> In the case of direct relevance, we have a living cell that carries out metabolic functions AND self replicates in a causal cycle where the components for the one are inextricably involved in the process for the other.

    EL: Yes indeed. That’s where I think Joe Szostak’s lab are doing interesting work (I linked on another thread to the lab, but here it is again: http://genetics.mgh.harvard.edu/szostakweb/)

    KF: 7 –> Moreover, the involvement of digital codes where there is symbolic representation [a particular codon MEANS to add a certain AA to the chain, or to start and add, or to stop, etc] implies the presence of symbols and rules for their combination in light of the requisites of an algorithm, to create and implement an assembly-line process, for protein manufacture.

    EL: Well, I disagree :) One point of my example is that you don’t need “symbols” at all.

    18: Cf above, symbols are used. and in a step by step assembly process that is finite and halts.

    EL: My A block “codes” for a C block not symbolically, but simply because C is the only blockshape that will “mate” with A.

    19: this is complementarity across the strands, which has nothing to do with the coded information in the sequence of the strings. Maybe the description and video here will help

    EL: However, the result of that “chemical” rule, coupled with the rule that any block can link to any other block in the orthogonal dimension means that entire double chains embody sequences that “code” for their own duplication (“Duplo” was a fortuitous choice of name for my chemistry :) ). There are no symbols involved, yet the thing can be described a “code”, IMO, with no less validity that DNA is described as a “code”.

    20: Nope, not at all, I think there is a conflation of what happens across the ladder and what happens along the chain of a given strand. The relevant code is in the chain along the strand. And that is what is coded as ATG etc.

    21: this is the context of my earlier remarks

    KF: 8 –> In turn the highly complex and specifically functional, informationally assembled product of this process is intimately involved in the work of the process itself.

    EL Yes indeed. . . . >>
    ____________

    I curt here as unless we can come to a mutuality up to here, going on further will just be repetition of the problems above.

    GEM of TKI

  35. Dr Liddle:

    It would be in principle possible to reprogram this, indeed Venter has done just that to write in his sign-off. In ENGLISH!

    GEM of TKI

  36. PS: This video will help clarify.

  37. PPS: this one gives a broader context, though the way it shows the Ribosome is defective [top and bottom not front and back!], and I would have preferred to see the tRNAs in the L-arm form not the cloverleaf form, as was also a defect with the previous one.

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