Functionally Specified Complex Information & Organization ID Foundations Origin Of Life

ID Foundations, 15: Mignea’s “simplest” self-replicator, the vNSR and a designed origin of cell-based life

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The recent Engineering and ID conference was obviously fruitful. I find it — HT: JohnnyB — helpful to compose Mignea’s schematic for self-replication, and discuss it a bit in the context of the origin of self-replicating entities given von Neumann’s requisites of a successful kinematic self-replicator. [Henceforth, vNSR.]

Let me extract from the just updated discussion in the IOSE course, Unit 2:

_________

>>John von Neumann’s self-replicator (1948 – 49) is a good focal case to study. Ralph Merkle gives a good motivating context:

[[T]he costs involved in the exploration of the galaxy using self replicating probes would be almost exclusively the design and initial manufacturing costs. Subsequent manufacturing costs would then drop dramatically . . . . A device able to make copies of itself but unable to make anything else would not be very valuable. Von Neumann’s proposals centered around the combination of a Universal Constructor, which could make anything it was directed to make, and a Universal Computer, which could compute anything it was directed to compute. This combination provides immense value, for it can be re- programmed to make any one of a wide range of things . . . [[Self Replicating Systems and Molecular Manufacturing, Xerox PARC, 1992. (Emphases added.)]

 

Fig. G.2: A schematic, 3-D/“kinematic” von Neumann-style self-replicating machine. [[NB: von Neumann viewed self-replication as a special case of universal construction; “mak[[ing] anything” under programmed control.] (Adapted, Tempesti. NASA’s illustration may be viewed here. and the Cairns-Smith model here.)

Fig. G.2 (b): Mignea’s schematic of the requisites of kinematic self-replication, showing duplication and arrangement then separation into daughter automata. This requires stored algorithmic procedures, descriptions sufficient to construct components, means to execute instructions, materials handling, controlled energy flows, wastes disposal and more. (Source: Mignea, 2012, slide show; fair use. Presentation speech is here.)

Von Neumann’s thought on a kinematic — physically acting (not a mere computer simulation) — self replicator that has the key property of additionality [[i.e it is capable of doing something of interest, AND is able to replicate itself on a stored, code description and an implementing facility] may be summarised in brief, as De Freitas and Merkle quite nicely do for us:

 Von Neumann [[3] concluded that the following characteristics and capabilities were sufficient for machines to replicate without degeneracy of complexity:

o Logical universality – the ability to function as a general-purpose computing machine able to simulate a universal Turing machine (an abstract representation of a computing device, which itself is able to simulate any other Turing machine) [[310, 311]. This was deemed necessary because a replicating machine must be able to read instructions to carry out complex computations.

o Construction capability – to self-replicate, a machine must be capable of manipulating information, energy, and materials of the same sort of which it itself is composed.

o Constructional universality – In parallel to logical universality, constructional universality implies the ability to manufacture any of the finitely sized machines which can be formed from specific kinds of parts, given a finite number of different kinds of parts but an indefinitely large supply of parts of each kind.

Self-replication follows immediately from the above, since the universal constructor* must be constructible from the set of manufacturable parts. If the original machine is made of these parts, and it is a constructible machine, and the universal constructor is given a description of itself, it ought to be able to make more copies of itself . . . .

Von Neumann thus hit upon a deceptively simple architecture for machine replication [[3]. The machine would have four parts – (1) a constructor “A” that can build a machine “X” when fed explicit blueprints of that machine; (2) a blueprint copier “B”; (3) a controller “C” that controls the actions of the constructor and the copier, actuating them alternately; and finally (4) a set of blueprints f(A + B + C) explicitly describing how to build a constructor, a controller, and a copier. The entire replicator may therefore be described as (A + B + C) + f(A + B + C) . . . .

Von Neumann [[3] also pointed out that if we let X = (A + B + C + D) where D is any arbitrary automaton, then (A + B + C) + f(A + B + C + D) produces (A + B + C + D) + f(A + B + C + D), and “our constructing automaton is now of such a nature that in its normal operation it produces another object D as well as making a copy of itself.” In other words, it can create useful non-self products in addition to replicating itself and has become a productive general-purpose manufacturing system. Alternatively, it has the potential to evolve by incorporating new features into itself.

. . . . Now therefore, following von Neumann generally, such a machine capable of doing something of interest with an additional self-replicating facility uses . . .

 
(i) an underlying storable code to record the required information to create not only (a) the primary functional machine [[here, a Turing-type “universal computer”] 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.>>

________

As we multiply these requisites by the Mignea steps, and implied irreducibly complex, quite specific functional relationships we easily see why it is utterly implausible for such a system to arise and work based on chance collocations of detritus in our proverbial warm little Darwinian pond, on the gamut of the observed cosmos.  The above will run past 1,000 bits of FSCO/I so fast that that barrier is a triviality. Indeed, we also begin to see that the 100,000 – 1 mn bits of stored information in the simplest genomes is a significant underestimate of the information at work. Much of the relevant information is going to be in how the components are organised and communicate.

Moreover, symbolic digital codes, algorithmic processes and execution units already point to purpose, planning and linguistic/logical processing of information.

Before cell based life on earth with such a self-replicating facility existed and as an integral part of the possibility of its existence.

Furthermore, while DeFreitas and Merkle briefly say that the vNSR “has the potential to evolve by incorporating new features into itself,” that is not so simple. For complex new function has to be integrated with the above, and requires 10 – 100 million bits of fresh information dozens of times over for the world of life’s new body plans , that too requires complex functionally integrated information and organisation that can be assembled from a zygote or the equivalent by replication, specialisation and higher level functional organisation.

Those who imagine that this can be had on the cheap incremental accident by accident that then is fixed by differential reproductive success, should be required to empirically show this in a realistic case before going further. Otherwise, this is simply the spinning of just so stories in absence of empirical accountability.

On top of all of that, the above shows that the much derided Paley had a point when, in his Natural Theology, Ch 2, he argued by way of the thought exercise of a self-replicating, time-keeping watch:

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.

In short, at the root of the Darwinian Tree of Life, we find a structure and system that point strongly to design. Design is not only in the door, but sitting at the table as a serious alternative from the outset. And that sharply changes our estimation of the credibility of design as candidate best explanation at higher levels in the tree.

Perhaps, then —pace Dawkins, Lewontin, Coyne, US NAS & NSTA et al —  we should be willing to reflect on whether the reason biological systems, from molecular scale to that of the whole organism have so strong an appearance of being designed is because that is just what they are. Designed. END

23 Replies to “ID Foundations, 15: Mignea’s “simplest” self-replicator, the vNSR and a designed origin of cell-based life

  1. 1
    Jerad says:

    It would be interesting to see this work interpreted in a biological context. I don’t keep up on OoL research but I would think someone would be working on the minimum size of a self replicator, one that only reproduces itself, nothing more. Many viruses have less then 10,000 base pairs in their genomes.

  2. 2

    Kairosfocus,

    Your evolving IOSE course is always a very good reading and source of inspiration.

    The point which I would like to discuss in connection with the Simplest Self Replicator presentation and your comments focusses on the following fragment in your text:
    (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.

    I think it comes rather straightforward that the design and realization of a Self Replicator (SR) that conforms to alternative (2) above rather than (1) above may be much more challenging. This implies that the SR has the capability of generating its own energy and all its construction materials and elementary parts from “raw materials and raw parts” available in the SR environment and accepted at SR input gateways. For the alternative (1) above, the SR can be considered a “universal self-assembler” – although a sophisticated one. However there are good reasons to think of a universal self-assembler as being (at least) one class of complexity below that of a genuine universal self-constructor that conforms to alternative (2).

    And to make the point of difference between the two:

    1. The Lego self-assembly robot (already demonstrated) may be considered a genuine self replicator for the alternative (1) since it uses externally provided energy and a pool of Lego parts from which it can assemble a replica of itself. In my personal opinion, the Lego self-assembly robot is a “fake” self-replicator.

    2. To illustrate alternative (2) if the machine that needs to be replicated contains a contemporary computer (let’s say something of the kind of an Apple IPad/tablet) then the computer parts: microprocessor, ASICs, memories, printed circuit boards, will not be picked from a bin but rather need to be fabricated from scratch from genuine raw materials (silicon, chemicals, copper, etc) (using some “metabolic” machinery – to use your metaphor).

    Now, someone can argue with certain legitimacy that there may not be a clear demarcation between the case (1) and (2) above, but rather a continuum of particular cases. However, the energy generation and “good material extraction” from “raw materials” and “raw parts” entering the SR enclosure gateways is one of the highest of the challenges that needs to be solved by an artificial SR.

    One of the reasons that separate (1) from (2) is that (2) assumes a set of additional capabilities (functions) in the SR which may not be needed for alternative (1):

    • Material and raw parts identification function (which may be very difficult to implement in an artificial SR. Reasons: methods/processes to identify materials: chromatography, weight/density analysis, X-ray analysis, spectrographic analysis, visual analysis, etc); raw materials and raw parts tagging (using something like bar codes or RFID’s);

    • Potential need of handling and transporting non-solid raw materials/parts – with related complications: manufacturing/usage of special containers, significant added difficulty in handling, transportation, cleaning, recycling

    • Material Extraction function: extracting through possible non-trivial material processing processes, good fabrication materials from raw materials.

    • Parts Fabrication function is needed to fabricate higher level components/parts/assemblies from simpler parts not necessary through assemblage operation but rather through complex fabrication processes. Example: semiconductor fabrication from raw silicon. This is not an assemblage procedure.

    In conclusion I wonder if the alternatives (1) and (2) as defined in your text do not define two different classes of Self Replicators?

  3. 3

    Jerad,

    The presentation revolved around a kind of “thought experiment”: a fictitious multi-disciplinary engineering team was asked to design and implement an artificial machinery (object) that has the ability to self-reproduce (a Simplest Self Replicator =SSR). The team completed preliminary research and produced this presentation in which:

    • A list of functional modules that must exist and operate within the SSR was identified.

    • The reason each functional module is necessary was briefly explained

    • Some of the interactions between this functional modules was described

    • The key for achieving self-replication success was also presented: since the SSR must be completely autonomous, its achievement must be based on two ingredients:

    o Full descriptive and operational information stored and accessible within SSR

    o SSR is made of fully automated, computerized modules that exploit stored information to use input of raw materials to produce energy and the growth of itself into a mother SSR and a daughter SSR.

    • The presentation identified the elements of maximum difficulty that will be encountered if the design will transform into a real project

    • The presentation stated that no concrete self-replicator object was created by humans so far while nature has an estimated 10 million types of different self replicators and their numbers being on the order of 10 power 30 (1 followed by 30 zeroes).

    • The presentation compared the intrinsic complexity of the artificial SSR with several high technology artifacts as a mean of evaluating SSR complexity.

    Now I am trying to answer your specific question.

    I believe today our scientists, microbiologists, biochemists, biotechnologists, are lacking the tools to create artificial biological organisms from scratch.

    Craig Venter and his team of scientists, created a synthetic bacterial cell, but this success can be described of transplanting the genome from a microorganism to another one. This is a remarkable achievement but is far from being considered a creation ex nihilo of an artificial organism.

    Below I am expressing some personal opinions that may be considered controversial, but here they are.

    The single way today engineers and scientists may approach the task of creating an artificial self-replicator is at somewhat higher dimensional scale than that of micro-organisms – because of lack of instruments, techniques and abilities to operate at the nano scales encountered in the living world. A more realistic approach would be to use classical engineering methods applied at the minimum geometrical scales for which there is good enough laboratory, manufacturing, manipulation and control technology available. Even so, a realistic evaluation of difficulties that need solution in order to successfully create an artificial self-replicator object, the environment in which it “lives autonomously” may lead to certain skepticism that such an accomplishment might be possible with today technology.

    Certain simplifying assumptions like those listed below may increase significantly the chances of success in creating an artificial SSR with today technology:

    • Energy is supplied from outside SSR instead of being generated by SSR itself

    • Certain parts hard to fabricate by SSR may be supplied from outside

    Another way to answer your comment is how to interpret the SSR design insights identified in the presentation in a biological context. Here are some answers.

    The presentation affirms that multi-faceted, descriptive and operational information must be present inside SSR. The DNA is known to represent detailed protein manufacturing information as well as control information for activating the manufacturing of these proteins. There are some other known information stores in the cell but we speculate that additional repositories of information will be discovered in the future.

    The presentation affirms the presence of a (distributed) information communication and notification function. There are known ways in the cell that the information is communicated (tRNA, etc.), but there are good reasons to believe that additional information communication mechanisms will be discovered.

  4. 4
    kairosfocus says:

    Folks:

    Some notes:

    1] Jerad: Many viruses have less then 10,000 base pairs in their genomes

    Viruses, of course, are not self-replicating. They hijack the machinery of a living cell, and act as rogue programs. (The use of the term computer virus was in part inspired by that.)

    That is, viruses are parasitic on already living, successful cell-based life. They are well below the threshold for self-replication. As, indeed, are the living cells that are about 100,000 base pairs. Those, depend on other cells for key components, i.e. they are parasites. Mitochondria are symbionts, I would say, providing key services to the wider cell. No ATP, no life.

    2] Jerad: I would think someone would be working on the minimum size of a self replicator, one that only reproduces itself, nothing more

    That is exactly what a viable living cell cannot do. There is an inherent need for metabolism, to process materials and energy.

    What Mignea has done is to outline the implications of self-replication in terms of required functionality, once the flows of materials and energy are factored in.

    Thence, we see the need for the code base for self replication to represent the additional capacities to carry out materials flows and energy flows, as well as of course information flows.

    That is where there is an irreducible complexity.

    And, the above working through of the controls logic involved is thus immediately directly relevant to the origin of life, the root of the tree of life.

    The evidence therefore becomes highly relevant to the root of the tree of life and to everything that follows.

    3] IVV: IOSE course

    Thanks for the kind thoughts.

    I have long believed that we need to take up the task of education on origins science into our own hands, and so the IOSE is a first step to demonstrate that we can do it.

    4] IVV: (v) either . . .

    The context of course, is that alternatives 1 and 2 come from the NASA studies. 2 is indeed far more challenging than 1, but 1 may be relevant to cases where pools of existing parts are available or can be manufactured separately. Indeed, it may be advantageous to have in effect a mini economy where the constructor builds work cells that make parts for itself (and other units that harvest energy and convert it into useful form and use this to set up in effect a power utility), then reaches into the pool of parts to make copies.

    In this case, the replicator is setting up an environment or an ecology or an economy, and then exploiting it. To be wholly autonomous, dependent only on generic environmental resources is quite complex.

    Notice, in the world of life we have plants as primary producers, which are responsible for even maintaining the atmosphere with its high concentration of O2, as well as the base of the food chain. Animals depend on that for their existence.

    I take that as a big hint as to what is most likely to be feasible.

    The solar system and galactic explorer long term project looks to be a colony effort in short, not just a one shot single unit that does it all deal. I favour the Bussard fusion reactor and drive for investigation for exploration — 74 days to Titan, from suggestions in the presentations of Bussard.

    (And, yes, the design view is pointing towards solar system colonisation and onward if possible, the grand project for this century if we can survive our folly. As a first step to both solar system colonisation and surviving our folly, I have been tracking Jakubowski’s Global Village Construction Set, industrial civ 2.0 open source tech civilisation on a village or small town scale — notice their 50 technologies idea, think: that is a good glance at the ecosystem of techs we need. This gets my genuinely sustainable development juices flowing. Those who imagine or say that the design view is a science stopper and antiscience and/or antiprogress don’t know what they are talking about. And I am thinking: here is how small island developing states and regions can move to an appropriate technology base.)

    5] IVV: there are good reasons to think of a universal self-assembler as being (at least) one class of complexity below that of a genuine universal self-constructor that conforms to alternative (2)

    I fully agree, noting that on (1) a colony ship could head for an asteroid belt, with its own initial onboard store of key parts and maybe auxiliary machines for mining etc. Then, task 1 is to set up the ecosystem. Settlement and development then replication and onward propagation.

    Create the base then move on to the next prospect.

    Of course, we have a fair amount of time to get out beyond our solar system before the sun exits main sequence.

    What would be dandy is if we could have found a way to fold or scrunch down space and move through a distance-shortening dimension. If the superluminal neutrinos had panned out, that would have been dandy. Ah, well, maybe something else will come along.

    Now, think about the reduction of these tasks to nano-tech, molecular scale, using C-chemistry, aqueous medium technology.

    Do you begin to see the scope of the challenge surmounted at OOL? And why OOL issues and the evident solutions scream “sophisticated design”?

    6] IVV: Lego self-assembly robot . . .

    I find this discussion interesting, and a step towards genuine self-replication. This one, points to the creation of a robot swarm economy modelled on social insects.

    I’d love a link to where full self replication per Lego has been shown. I have no doubt that it is possible, just if you have a demo out there that would be great. Nothing like the real deal!

    (I know, there has been a limited demo using a sort of 3-d printer.)

    7] IVV: the energy generation and “good material extraction” from “raw materials” and “raw parts” entering the SR enclosure gateways is one of the highest of the challenges that needs to be solved by an artificial SR

    Correct.

    That is why the C-chemistry, aqueous medium solution (with chlorophyll and mitochondria as breakthrough energy techs) is so elegant. And, remember, those point straight to the heart of the physics of the cosmos and its fine tuning.

    I find it utterly fascinating that the first four elements per the way resonances worked out, are H, He, O & C. As in, H — stars. He — stars and building a periodic table of ingredients. C & O — organic chemistry and aqueous medium. Then add N and you are at proteins, where N is I think 5th for our galaxy and close to that for the cosmos.

    That looks utterly elegant to me.

    Our cosmos is set up for the architecture of life on a technology that escapes having to go the high temperature, high energy intensity route that our large scale technologies use. But, which then enables intelligent life to do wonderful things with that extended chemistry.

    Cue . . . Privileged Planet.

    8] IVV: (2) assumes a set of additional capabilities (functions) in the SR . . .

    Correct, in all essential details. I suggest parts recognition, handling, dealing with liquids, wastes etc are common to both, but that is not the heart of the matter. 2 is indeed more than 1.

    That is why even the natural ecosystems separate duties, with cells handling self replication, specialisation to create diversity, and then ecosystem integration.

    9] IVV: I wonder if the alternatives (1) and (2) as defined in your text do not define two different classes of Self Replicators

    They do.

    And it is an open question which is better, for what purposes.

    In short, an invitation to exploration, with all sorts of side possibilities for transforming our civilisation’s tech base to a more robust, more sustainable frame.

    KF

  5. 5
    kairosfocus says:

    F/N: It is worth citing Denton’s elegant description of the nanotech world of the cell, from Evo, a Th in Crisis, 1986:

    ___________

    >> To grasp the reality of life as it has been revealed by molecular biology, we must magnify a cell a thousand million times until it is twenty kilometers in diameter [[so each atom in it would be “the size of a tennis ball”] and resembles a giant airship large enough to cover a great city like London or New York. What we would then see would be an object of unparalleled complexity and adaptive design. On the surface of the cell we would see millions of openings, like the port holes of a vast space ship, opening and closing to allow a continual stream of materials to flow in and out. If we were to enter one of these openings we would find ourselves in a world of supreme technology and bewildering complexity. We would see endless highly organized corridors and conduits branching in every direction away from the perimeter of the cell, some leading to the central memory bank in the nucleus and others to assembly plants and processing units. The nucleus itself would be a vast spherical chamber more than a kilometer in diameter, resembling a geodesic dome inside of which we would see, all neatly stacked together in ordered arrays, the miles of coiled chains of the DNA molecules. A huge range of products and raw materials would shuttle along all the manifold conduits in a highly ordered fashion to and from all the various assembly plants in the outer regions of the cell.

    We would wonder at the level of control implicit in the movement of so many objects down so many seemingly endless conduits, all in perfect unison. We would see all around us, in every direction we looked, all sorts of robot-like machines . . . . We would see that nearly every feature of our own advanced machines had its analogue in the cell: artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of components, error fail-safe and proof-reading devices used for quality control, assembly processes involving the principle of prefabrication and modular construction . . . . However, it would be a factory which would have one capacity not equaled in any of our own most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours . . . .

    Unlike our own pseudo-automated assembly plants, where external controls are being continually applied, the cell’s manufacturing capability is entirely self-regulated . . . .

    [[Denton, Michael, Evolution: A Theory in Crisis, Adler, 1986, pp. 327 – 331.] >>
    ____________

    That, folks, is what we are facing, a world of vastly superior nanotech to what we have. And, what the OP above has put back on the table, is the key point that the constructor-replicator facility involved is a massive technological challenge that we have to face.

    KF

  6. 6
    Maus says:

    “(I know, there has been a limited demo using a sort of 3-d printer.)”

    Rep Rap. Not a bad go of it, and not meant to be completely self-replicating. But the history of the project is reasonably illuminating for some of the design issues that crop up.

  7. 7
    Jerad says:

    IVV,

    Thanks for your comments. I shall reread and consider them more deeply later.

  8. 8
    kuartus says:

    Kairosfocus, I have heard some suggestions that self replications can be as simple as salt crystals growing or replicating or lipid bubbles growing by incorporating lipid molecules and after a certain size is attained being divided. Supposedly these scenarios count as primitive types of self replication. I dont buy it, but what is your assesment of these? Are they cases of self replication?

  9. 9
    kairosfocus says:

    Kuartus:

    Observe the contrast of growing crystals etc per forces of necessity leading to the unit structure and repetition (thus, low information: specific but not complex), to the known, symbolic information based duplication, separation and enclosure of daughters through the interaction of metabolic and vNSR subsystems in the living cell.

    The attempted counters are little more than strawmen, and the key differences were marked out by Orgel and Wicken in the 1970’s in foundational writings that helped spark the later birth of ID as a scientific movement:

    WICKEN, 1979:‘Organized’ systems are to be carefully distinguished from ‘ordered’ systems. Neither kind of system is ‘random,’ but whereas ordered systems are generated according to simple algorithms [[i.e. “simple” force laws acting on objects starting from arbitrary and common- place initial conditions] and therefore lack complexity, organized systems must be assembled element by element according to an [[originally . . . ] external ‘wiring diagram’ with a high information content . . . Organization, then, is functional complexity and carries information. It is non-random by design or by selection, rather than by the a priori necessity of crystallographic ‘order.’ [[“The Generation of Complexity in Evolution: A Thermodynamic and Information-Theoretical Discussion,” Journal of Theoretical Biology, 77 (April 1979): p. 353, of pp. 349-65. (Emphases and notes added. Nb: “originally” is added to highlight that for self-replicating systems, the blue print can be built-in.)]

    ORGEL, 1973: . . . In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity. [[The Origins of Life (John Wiley, 1973), p. 189.]

    Those who raise such strawmannish counters know or should know better.

    As for lipid sacs etc, this was addressed in the survey of various scenarios then on the table for OOL in Thaxton et al, TMLO, ch 9 in 1984.

    In none of these cases is the self-replication of encapsulated metabolic automata with integrated vNSR, thus symbolic code and algorithm based duplication of components taken seriously.

    Not to mention, that we are here looking at the ORIGIN of the vNSR facility and its associated codes and symbols representing itself and the metabolic automaton, so appeals to differential success of reproducing populations are off the table.

    Utterly revealing.

    KF

  10. 10
    kairosfocus says:

    Maus: Thanks, I had forgotten the name. KF

  11. 11
    kairosfocus says:

    Onlookers: Notice the silence on the material issues, coming from the evo mat objectors to the design inference. KF

  12. 12
    bloodymurderlive says:

    I know this is an old discussion, but the simplest self-replicator is monumentally important, and I’m hoping that somebody is being notified of new comments. Stephen Meyer’s argument against the “chance” hypothesis is based on a minimum length for a functional protein at 150-amino-acids, equaling 1 chance in 10^164 – well-outside the universe’s probabilistic resources.

    However, there are other sources that suggest far smaller self-replicators:

    This site suggests a “theorized self-replicating peptide is only 32 amino acids long,” which puts it within the universe’s probabilistic resources:
    http://evolutionfaq.com/articles/probability-life

    This site notes several self-replicating molecules, including: 1) Ghandiri’s self-replicating peptide, 2) the hexanucleotide self-replicator, 3) the SunY self-replicator, and 4) Eckland’s RNA polymerase. That first one is just 32 amino acids long – far more probable than Meyer’s 150-amino-acid protein.
    http://www.talkorigins.org/faq.....oprob.html

    This site notes that Carl Sagan was hypothesizing about 100-amino-acid proteins back in the 70’s, so on what basis does Meyer assume that 150 amino acids is the minimum? Especially when, as noted above, there are far shorter, demonstrably self-replicating molecules?
    http://infidels.org/library/mo.....endaB.html

    Did Meyer make a huge blunder in his argument against the chance hypothesis?

  13. 13
    kairosfocus says:

    BML, I am about to head off on a busy day but saw your comment. The issue is not self-replication in a convenient and implausible envt in the abstract, or something akin to crystallisation or polymerisation. We are talking about self replication of an encapsulated automaton with metabolising capability an an integral co-ordinated von Neuman kinematic, molecular nanotech self replicator that uses coded algorithmic information in a context of execution machinery that effects daughter cells with the same capability. That is what needs to be faced, and self replication of a molecule or the like per se is only one step to that. Cf. Op and then onward considerations. Gotta run, KF

  14. 14
    bloodymurderlive says:

    Thanks KF… What I’m having a hard time understanding, and thus articulating, is why the enormously complex automaton you described must be the starting point for OOL? And why it couldn’t be these simpler polypeptides? At one of the links I provided, it lists several intermediary steps prior to the first bacteria. On what grounds are all these intermediary steps precluded from consideration in OOL?

    I’m also specifically interested in whether Meyer’s argument, which assumes a minimum 150-amino-acid functional protein (but really, assumes a much more complex system), is sustainable…

  15. 15
    kairosfocus says:

    BML,

    pausing.

    What I described is in summary what is in the living cell, the unit of observed biological life. Until you have cell based life you do not have the forms of life we observe.

    There is no good evidence of other architectures of molecule based life, just the cell and things dependent on them (such as viruses).

    Origin of life is therefore about the origin of the FSCO/I rich, sophisticated entity known as the living cell, and like it or lump it, what I said above in very brief outline is how cells work. Encapsulation, metabolism [the basic metabolic rxn set is astonishingly complex by sa comparison with an oil refinery’s processes], co-ordinated replication using a von Neumann kinematic self replicator keyed tot he organisation and function of the encapsulated metabolic automaton. Which implicates codes so language, algorithms so step by step goal directed procedures expressed using codes, and executing machinery that effects same. Thus also implied communication systems and networks, control systems and networks and much more.

    That is what the evidence shows.

    And BTW, 150 AAs is shortish for a protein, 300 AAs is a more typical “average” length, and the basic cell has hundreds and hundreds of them. Protein size is shaped by fold-stability-function requisites in a context that is often based on key-lock fitting of components. That leads to unavoidable complexity and as noted 150 is shortish for a typical length.

    Suggested models are besides the point, until they show reality on the ground functioning in ways that show the core phenomena of life and bridge to the cell.

    Just as a sampler, here is the current form of Wiki on Life (noting the insertion of a lot of assumptions on the powers and centrality of evolutionary mechanisms . . . ):

    The smallest contiguous unit of life is called an organism. Organisms are composed of one, or more, cells, undergo metabolism, maintain homeostasis, can grow, respond to stimuli, reproduce (either sexually or asexually) and, through evolution, adapt to their environment in successive generations.[1] . . . .

    Since there is no unequivocal definition of life, the current understanding is descriptive. Life is considered a characteristic of something that exhibits all or most of the following traits:[43][46][47]

    Homeostasis: Regulation of the internal environment to maintain a constant state; for example, electrolyte concentration or sweating to reduce temperature.

    Organization: Being structurally composed of one or more cells — the basic units of life.

    Metabolism: Transformation of energy by converting chemicals and energy into cellular components (anabolism) and decomposing organic matter (catabolism). Living things require energy to maintain internal organization (homeostasis) and to produce the other phenomena associated with life.[43]

    Growth: Maintenance of a higher rate of anabolism than catabolism. A growing organism increases in size in all of its parts, rather than simply accumulating matter.

    Adaptation: The ability to change over time in response to the environment. This ability is fundamental to the process of evolution and is determined by the organism’s heredity, diet, and external factors.

    Response to stimuli: A response can take many forms, from the contraction of a unicellular organism to external chemicals, to complex reactions involving all the senses of multicellular organisms. A response is often expressed by motion; for example, the leaves of a plant turning toward the sun (phototropism), and chemotaxis.

    Reproduction: The ability to produce new individual organisms, either asexually from a single parent organism, or sexually from two parent organisms.[48][49] or “with an error rate below the sustainability threshold.”[49]

    These complex processes, called physiological functions, have underlying physical and chemical bases, as well as signaling and control mechanisms that are essential to maintaining life.

    In fact, here is a clip of the final exchange between Orgel and Shapiro that showed up the magnitude of the challenge, in the context of what is really on the table:

    [[Shapiro:] RNA’s building blocks, nucleotides contain a sugar, a phosphate and one of four nitrogen-containing bases as sub-subunits. Thus, each RNA nucleotide contains 9 or 10 carbon atoms, numerous nitrogen and oxygen atoms and the phosphate group, all connected in a precise three-dimensional pattern . . . . [[S]ome writers have presumed that all of life’s building could be formed with ease in Miller-type experiments and were present in meteorites and other extraterrestrial bodies. This is not the case.

    A careful examination of the results of the analysis of several meteorites led the scientists who conducted the work to a different conclusion: inanimate nature has a bias toward the formation of molecules made of fewer rather than greater numbers of carbon atoms, and thus shows no partiality in favor of creating the building blocks of our kind of life . . . .

    To rescue the RNA-first concept from this otherwise lethal defect, its advocates have created a discipline called prebiotic synthesis. They have attempted to show that RNA and its components can be prepared in their laboratories in a sequence of carefully controlled reactions, normally carried out in water at temperatures observed on Earth . . . .

    Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA . . .

    [[Orgel:] If complex cycles analogous to metabolic cycles could have operated on the primitive Earth, before the appearance of enzymes or other informational polymers, many of the obstacles to the construction of a plausible scenario for the origin of life would disappear . . . .

    It must be recognized that assessment of the feasibility of any particular proposed prebiotic cycle must depend on arguments about chemical plausibility, rather than on a decision about logical possibility . . . few would believe that any assembly of minerals on the primitive Earth is likely to have promoted these syntheses in significant yield . . . . Why should one believe that an ensemble of minerals that are capable of catalyzing each of the many steps of [[for instance] the reverse citric acid cycle was present anywhere on the primitive Earth [[8], or that the cycle mysteriously organized itself topographically on a metal sulfide surface [[6]? . . . Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own . . . .

    The prebiotic syntheses that have been investigated experimentally almost always lead to the formation of complex mixtures. Proposed polymer replication schemes are unlikely to succeed except with reasonably pure input monomers. No solution of the origin-of-life problem will be possible until the gap between the two kinds of chemistry is closed. Simplification of product mixtures through the self-organization of organic reaction sequences, whether cyclic or not, would help enormously, as would the discovery of very simple replicating polymers. However, solutions offered by supporters of geneticist or metabolist scenarios that are dependent on “if pigs could fly” hypothetical chemistry are unlikely to help.

    KF

  16. 16
    Box says:

    Atheists take a look at this powerpoint slide show and weep.

    Arminius Mignea:

    Any OOL credible explanation should provide answers to the following questions:

    How the self describing information (of so many varieties) residing in the SSR originated?
    How the energy generation and transport function originated?
    How the material identification function and the material extraction function originated?
    How the fabrication function originated
    How the transport and manipulation functions originated?
    How the coordinated control of various functions originated?
    How the whole sophisticated design of the SSR originated?
    Is it reasonable to believe/accept that the SSR resulted through random/natural processes when the 21st century scientists are only beginning to understand only SOME OF THE INTERNALS of a cell?
    Is it reasonable to believe/accept that the SSR resulted through random/natural processes when the 21st century scientists and engineers are still not able to design and create an artificial SSR?

    No evolutionary just-so-stories to turn to. How did all this originate by blind chance? How?

    How did it originate defiantly the second law which steers anything into disorder. And how did it continue to exist despite of the second law?

  17. 17
    Zachriel says:

    Box: How did it originate defiantly the second law which steers anything into disorder.

    Please put down the 2nd law of thermodynamics before you hurt yourself. There are many cases in nature of spontaneous order, everything from gemstones to hurricanes.

  18. 18
    Box says:

    Zachriel:
    Tell me, what does the second law do to an organism once it is dead – whatever “dead” means under materialism? IOW why doesn’t the second law do that to an organism while it is “alive”?

    However, you have avoided my main question: How did all this originate? How?
    Did you take a look at the slide show?

  19. 19
    Zachriel says:

    Box: Tell me, what does the second law do to an organism once it is dead

    KING CLAUDIUS: Now, Hamlet, where’s Polonius?

    HAMLET: At supper.

    KING CLAUDIUS: At supper! where?

    HAMLET: Not where he eats, but where he is eaten: a certain
    convocation of politic worms are e’en at him. Your
    worm is your only emperor for diet: we fat all
    creatures else to fat us, and we fat ourselves for
    maggots: your fat king and your lean beggar is but
    variable service, two dishes, but to one table:
    that’s the end.

    KING CLAUDIUS: Alas, alas!

    HAMLET: A man may fish with the worm that hath eat of a
    king, and cat of the fish that hath fed of that worm.

    KING CLAUDIUS: What dost you mean by this?

    HAMLET: Nothing but to show you how a king may go a
    progress through the guts of a beggar.

    http://www.rhymezone.com/r/gwi.....+certain#w

    Box: why doesn’t the second law do that to an organism while it is “alive”?

    An external source of energy.

    Box: However, you have avoided my main question: How did all this originate?

    You had said the 2nd law steers everything to disorder; however, there are many cases in nature of spontaneous order. You might want to correct your previous claim.

    Concerning the origin of life, while there are some tantalizing clues, no one really knows.

  20. 20
    Zachriel says:

    Box: Did you take a look at the slide show?

    Sure. It’s complicated!!!!!!!!!!!!!!!!!! Therefore Master Designer!

    The idea of evolution is that the process started simply, then complexity developed over time. How the process started no one knows, but the power of evolution to increase complexity is well-established, as is common descent from more primitive ancestors. Szostak proposes testable hypotheses, while posting pictures of human-built machines is just rhetoric.

  21. 21
    Box says:

    Zachriel: Sure. It’s complicated!!!!!!!!!!!!!!!!!! Therefore Master Designer!

    Nope, it’s far beyond “complicated”. It’s impossible given a finite universe. Therefor the only way out is invoking a multiverse – see Koonin

  22. 22
    Joe says:

    Zachriel is a willfully ignorant equivocator who doesn’t want to understand what is actually being debated.

  23. 23
    Zachriel says:

    Box: It’s impossible given a finite universe.

    You might try to address our comment rather than making declarations.

    Z: The idea of evolution is that the process started simply, then complexity developed over time. How the process started no one knows, but the power of evolution to increase complexity is well-established, as is common descent from more primitive ancestors. Szostak proposes testable hypotheses, while posting pictures of human-built machines is just rhetoric.

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