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Software Engineer’s Off the Cuff Requirements List for Simple Cell

InVivoVeritas writes:

Here is the quote from the Jack W. Szostak interview:

We think that a primitive cell has to have two parts. First, it has to have a cell membrane that can be a boundary between itself and the rest of the earth. And then there has to be some genetic material, which has to perform some function that’s useful for the cell and get replicated to be inherited. The part we’ve come to understand reasonably well is the membrane part. The genetic material is the harder problem; the chemistry is just more complicated. The puzzle has been understanding how a molecule like RNA can get replicated before there were enzymes and all this fancy biological stuff, protein machinery, that we have now in our cells.

I am a software engineer with tens of years of experience of implementing
software systems.

A sane software engineer when given a new project, it has a well defined
approach for taking the project from a starting idea to the final, working
product.

One of the first steps of this professional approach is to write a
“Requirement Specification” to clearly, neatly and accurately specify
each and every demand that need to be fulfilled by the final product.

I thought that it would be very instructive to only START sketching
such a “Minimum Requirements Specification for a Most-Primitive Life Form”
and after a first sketch to compare notes with Mr. Jack W. Szostak
statements in his interview.

Below you can find the first iteration of such requirement specification,
and detailed (somewhat, but not too much) only for the first of the eight
major requirements. Please do not forget, that this is the first write up,
produced with not too much thought – where I am sure I may have missed many
other major requirements.

Some conventions:

– we will call this “most primitive” form of life a “cell” – for convenience
– we will call the needed boundary of this ‘cell’ a ‘membrane’

Here is the Initial Requirement List:

1. The cell must have a physical boundary around its volume to clearly
delimit the inside of the cell from outside of the cell. Let’s call
this boundary “membrane”

List of minimum requirements for the membrane of the cell

1.1. Must provide reliable isolation of the cell content from the
outside world

1.2. Must be “permeable” to specific materials or sources of energy
that “feeds” the cell

1.3. Must have ‘substance recognition’ capabilities in order to
allow or prohibit admission inside the cell of the good respective
bad ‘materials’ (sensory capability).

1.4. Must have ‘open gate through membrane’ and ‘close gate through
membrane’ reactions and mechanisms to open ‘pores’ (openings)
in the membrane when good versus bad ‘materials’ are recognized
outside or inside the membrane (reactive capability).

1.5. INFORMATIONAL SUPPORT PERSPECTIVE:

1.5.1. The membrane must exhibit a capacity to store and process
information locally about the nature/identity of the good
materials as well as about bad materials. Logically
that is equivalent with a ‘registry’ of good/bad
materials.

1.5.2. Pattern recognition: the membrane must have pattern
recognition informational capabilities to accurately
recognize any ‘material’ (or ‘material pattern’) that
is available in its own ‘registry’ memory and to
send appropriate signals to the control agents in the
membrane when such materials are detected in its
external or internal environment.

1.5.3. The membrane must have a set of control mechanisms
on how to react to an ‘inventory’ of stored information
of good and bad materials, in particular on what
membrane ‘pores’ to open or to close when particular
materials are identified.

1.5.4. Most probable the membrane should have ability to
‘communicate’ information/signals to the inside the
cell when material ‘signatures’ are detected.
(information communication and signaling)

2. The cell must have mechanisms to feed itself from outside world with
specific substances that provide food/sources of energy for the
(metabolism) processes that animate the cell.

3. The cell must have mechanisms to replicate itself into one or more
similar descendent cells that exhibit the same behaviors and capabilities
as the mother cell.

4. The cell should/may have mobility in order to leave a world environment
that it detects as unfavorable and move toward other areas of the
environment that are more favorable to its continued existence and
proliferation.

5. The cell should/may have mechanism to ‘sense’ its environment and to
‘react’ accordingly. To ‘recognize’ ‘favorable’ conditions/elements in its
environment as well as ‘recognize’ unfavorable conditions/elements
in its environment.

6. The cell must have ability to transform the raw materials/energy
received from environment through its membrane and transform them
into different type of materials that are proper for its own internal
‘construction’ projects.

7. The cell should/may have capability of identifying ‘refuse’ materials
resulting from its material transformation and conversion processes
and forcing these ‘refuse’ out of the cell through the membrane to
outside world.

8. The cell should/may have time measuring / time signaling capabilities
in order to control its own material input, material transformation,
material output and cell replication processes on specific timelines
and coordinated schedules.

I develop to the next level of detail only the ‘membrane requirements’ for this
‘most primitive’ form of life.

I guess that some serious thought on these major requirements will distil
into somewhat unexpected – but logically defensible – lower level
requirements that involve information processing, material transportation,
information communication inside the cells – that, together will construct
an objective picture of the REAL COMPLEXITY that would be required for
such a MOST PRIMITIVE FORM OF LIFE.

What is not immediately apparent for anyone is that the living world and all
its members manifest – it’s true, in a varied degree – the “autonomy”
characteristic which is another name for ‘viability’ ‘survivability’.

This autonomy capability is extremely complex, demanding and multi-faceted
and is also “extremely expensive” to “implement” by a designer,
by evolution or by any entity.

Let’s do not forget that humankind in its most advanced state of
technological progress, was not ever capable of dreaming to construct
any artifact to an approaching level of autonomy – as it is routinely
end richly encountered among the members of the living world.

In conclusion, Mr. Jack W. Szostak – the Nobel laureate – seems to be
extremely naive and ‘uneducated’ about the complexity of the task
he started on about 25 years ago: to figure out the origin of life.

 

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150 Responses to Software Engineer’s Off the Cuff Requirements List for Simple Cell

  1. Szostak: “The part we’ve come to understand reasonably well is the membrane part.”

    Well, this may be true if he is just talking about a basic understanding what is needed for a functional membrane, but if his statement is meant to give the impression — which it appears to be — that getting a functional membrane through naturalistic processes is understood reasonably well, then he is pushing nonsense. Based on his paper we were discussing and his work I think his interest lies primarily with the RNA replication, so perhaps it is somewhat understandable that he glosses over the membrane part, although he should know better. Further, beyond a relatively detailed list of basic requirements for a membrane, we aren’t even close to being able to build one. If you don’t know what is required to build one, then you don’t really understand it.

    InVivoVeritas puts together a fantastic initial list of minimum requirements. I’ve tried putting together a list of minimum requirements myself a while back and it got pretty long. This is why it is critical to have an engineering eye look at these things. Too many true believers gloss over the details and proclaim they are close to a solution when an engineering analysis reveals the proposed pathway or proposed mechanism being offered is simply not workable in the real world or is so general and vague as to be useless for anything other than a just-so story.

  2. No, Barry, that’s the requirement for quite a complex cell.

    Szostak is talking about a simple cell.

    And he has already met some of those requirements.

  3. But why kill the dream of dreamers?

    Ok we know it’s impossible to achieve this machinery by natural processes (if we consider Intellect not very natural process).

    But when one tries to build perpetuma mobile, there is allways chances he will stumble upon nice good construction of convinient engine. So… even if guys never will achieve their dream, it is very likely that during their research they will gather couple of Nobel prises anyway by discovering/inventing stuff which is usefull by itself.

  4. Elizabeth:

    “No, Barry, that’s the requirement for quite a complex cell.
    Szostak is talking about a simple cell.”

    Elizabeth, would you be so kind to try to enumerate (using the numbering in the original post) which of the listed requirements are those for a complex cell, i.e. NOT needed for the simplest cell?

    I anticipated that some of the listed requirements may not be needed by the Simplest cell by using the “should/may” formulation rather than “must” formulation. However, even some requirements listed with the ”should/may” formulation could be moved in the “must” category after some debate/analysis.

  5. Which requirements would you remove for a simple cell?

  6. Actually the question should be,

    “What information would you remove for a cell?”

    If I remember properly, scientists in a cell repair mechanism experiment destroyed or removed from the cell pieces or portions of DNA and watched it repair itself time and again. They eventually went to far in the amount removed and the cell activated it’s own “Kill Switch”.

  7. Well, try reading Szostak’s work.

    The important question is “what is needed for the simplest possible Darwinian-capable self-replicator”, which, Szostak suggests, is a membrane vesicle that encloses self-replicating polymers, where the confirguration of the polymers affects the probability of the whole self-replication.

    In other words something a little bit like the basics of a cell: a lipid vesicle containing genetic material that is passed on to the “progeny” when the vesicle divides.

  8. No, the question is: what could you add to the simplest possible self-replicator to produce a modern cell?

    Trying to do it backwards is silly.

  9. No, we don’t know this.

    That’s the Whole Point of the research.

  10. You mean, what would blind undirected unguided forces without biased purposed goal driven thoughts of a scientists mind, don’t you ???

    Unfortunately these intelligent minds have no clue as to what the simplest cell would even look like. Although they continue using their collective intelligences in experimenting as to just what a Creator would or wouldn’t do. Sorry, I meant blind undirected forces , not Creator.

  11. No, the whole point of the research is proving “NO INTELLIGENCE ALLOWED” and thus far they continue to fail.

    Lying , cheating and stealing I.D. concepts and attaching evolutionary signage/baggage to them doesn’t exactly go along way in proving the worldview which is really what all of this is about anyway.

  12. Well, those are serious allegations, Eocene.

    Please support them.

  13. You mean, what would blind undirected unguided forces without biased purposed goal driven thoughts of a scientists mind, don’t you ???

    Well that bears no resemblance to what I meant, and actually doesn’t appear to mean anything at all!

    Perhaps you mistyped?

  14. Elizabeth:

    No, the question is: what could you add to the simplest possible self-replicator to produce a modern cell? Trying to do it backwards is silly.

    What seems silly is to discuus adding to something that does not exist. If we had the imaginary “simple” self-replicator, then we could discuss, and experiment, about adding to it.

    But that “simple” self replicator is nowhere to be seen, except in the wishful thinking of darwinists. So, all rules of empiricism are inverted, to defend a theory that does not work.

  15. Elizabeth:

    The allegations are serious, but essentially correct.

    The cognitive bias in biological reserach today, and especially in the interpretation of data, is terrifying. All the essential rules of good reasoning and empiricism are violated.

  16. Well, I would not understate the “metabolism” aspect of the first reproductors. We must remember that complex molecules are built at the expense of outer energy, and that uusally that energy comes from other complex molecules, or from light through other complex molecules in phtosynthesis.

    As the electric discharge in a primitive pond is obviously a ridiculous myth (I suppose all agree on that now), I think we should really ask ourselves how the supposed “simple” replicator obtained and controlled the energy necessary for its life.

  17. Finally, a simple question: if that first replicator was really so simple, why hasn’t anyone produced some example of it in the lab?

    Then we could reason with something observable, and try to describe some model of evolution of that “simple” replicator to a prokaryote.

    Just as a reminder, let’s reflect that we cannot produce in the lab even a prokaryiote, even having all the single parts already available.

    Oh, but I was forgetting that electricity in a pond can certainly perform miracles…

  18. gpuccio

    “Simple” is not the same as “easy to create” or “easy to determine what it is”. For example, a superconductor is not complicated but it is really hard to make one and 100 years ago it would have been almost impossible to guess how to make one.

  19. This post has a premise that a cell is responding to a set of requirements. It makes no sense to talk about requirements unless you can say whose requirements or requirements to do something. I guess the ID community is going to steer clear of whose requirements – so maybe someone can say what the requirements are for?

  20. I fully concur with IVV.

    To be a viable cell, there must be:

    1: First and foremost, controlled energy and materials flow through, to provide the requirements for doing work to operate life, and to exhaust waste materials and energy. (This is actually rooted in thermodynamics and is a very rigorous requirement.)

    2: This requires a controlled membrane with energy and/or materials ports for input and output.

    3: Assuming aqueous medium and a single cell, waste heat can be informally got rid of by thermal conduction. Waste materials are another story.

    4: Energy inflow — most life-relevant reactions to build up components and to build up macromolecules are highly endothermic — will be a major challenge, given the issue of the complexity of photosynthesis and the challenge that poisons basically work by interfering with reaction chains. (Energy can come in in the form of chemicals.) Note, too the role of ATP and ATP Synthase in OBSERVED life.

    5: Within the cell we have a need for anabolic and catabolic processes to build up tear down and then get rid of waste products. Controlled metabolism.

    6: Then, the cell indeed has to sense and respond to its environment, moving to better locations and away from worse ones. Sensing, processing, responding, motility.

    7: Self-replication then caps off, even if we do not require the full observed von Neumann self replicator. Dr Liddle and others think this is the sole minimal requirement, but just think about what is required to maintain an internal environment in which a cell can carry out replication. That will bring us back to controlled i/o ports for energy and materials, and controlled metabolic pathways.

    8: Maybe, the membrane is not needed? Then, you have open access by interfering chemicals, whether on clay beds or in warm little ponds or volcanic vents etc.

    _________

    The “simple” cell ain’t. Simple.

    The cell manifests both Wicken wiring diagram functionally specific complex organisation and evident irreducible complexity in several ways.

    The only known way to meet complex functionally specific organisation and information requirements like this? Design.

    If you object to this conclusion, then the onus is on you to show, analytically and preferably empirically, that something simpler will do and would emerge in a realistic prebiotic environment.

    The absence of the celebratory Nobel Prize for this achievement should tell us that there is a huge gap in the heart of this field, and of course that means the Darwinian tree of life has no tap-root so no basis, as was pointed out at UD recently.

    GEM of TKI

  21. Actually, Dr Liddle, the support is here, in the UD current post where we await your response on the 14 points of concern.

    Remember, it is not just Lewontin but the majority of the elites, including those who intervened in Kansas — US NAS, NSTA issued a joint letter of threat, the NCSE orchestrating a media slander campaign through its local arm, the media who enthusiastically came along for the ride, and many more . . . — and those who stood by and let it happen.

    The silence in the face of a priori materialist censorship, manipulation of the very definition of science in the teeth of relevant phil and history and improperly holding the children of that state hostage was deafening. What we heard loud and clear was a media lynching of those who dared to speak up.

    We await your response to the 14 points of concern. Perhaps that will set our minds at ease.

    GEM of TKI

  22. prezactly

  23. MF:

    The requirements at the top of this thread lay out requisites for self-sustaining self-replicating molecule based cellular life. They are constrained by the requisites of metabolic, self-replicating, encapsulated entities that have specific molecular reactions, many of which are endothermic.

    Let’s just say, there is a reason why the cells we actually observe have such a carefully co-ordinated structure to keep things going.

    GEM of TKI

  24. If we had the imaginary “simple” self-replicator, then we could discuss, and experiment, about adding to it.

    Which is exactly what Szostak’s lab is working on!

  25. The cognitive bias in biological reserach today, and especially in the interpretation of data, is terrifying. All the essential rules of good reasoning and empiricism are violated.

    I disagree, which was why I asked for support for the allegation!

    Can you support it?

  26. Well, do read Szostak’s work. He actually does deal with these issues.

  27. markf:

    > I guess the ID community is going
    > to steer clear of whose requirements…

    I would say the requirements are nature’s requirements — those things that the laws of physics demand that a cell must be, and must do, for viability and reproducibility. But that, of course, begs the question: Why is nature so law-bound and orderly? Nature’s orderliness is what makes life possible. To exploit that orderliness, and to be a viable organism, the cell must adhere, within fairly strict bounds, to nature’s “house rules”. Where did nature’s law-boundedness and orderliness originate? You can only evade the elephant in the room (intelligence) for so long.

    Kent
    Omaha, Nebraska, USA

  28. No, they don’t, kf. They lay out requisites for a modern-type cell.

    They are not a set of requirements for “self-sustaining, self-replicating molecule based cellular life”.

    Or at least, we do not know that they are. The OOL researchers’case is that they are not: that the minimal requirements are much simpler.

  29. Elizabeth:

    No, the question is: what could you add to the simplest possible self-replicator to produce a modern cell?

    Everything a modern cell has, including software.

  30. They are not a set of requirements for “self-sustaining, self-replicating molecule based cellular life”.

    You don’t know what the requirements for “self-sustaining, self-replicating molecule based cellular life”

    And of course OoL researchers say the first cells were more simpl,e- they HAVE to say that.

  31. Eo:

    Pardon, but while the underlying issues you raise are well warranted, some of your language is intemperate.

    Please moderate tone, words and implications of widespread conscious dishonesty.

    Yes, there is censorship, there is unjust career busting, there is a twisting of definitions and the structure of science in agenda-serving ways, but most — the vast majority — of those doing things that in the cold light of days to come will be seen as inexcusable, are caught up in the spirit of our age and are blind to the cold import of what is going on.

    It SEEMS to those caught up that those Bible-thumping fundies are the real threat and we must take all steps necessary to block those destructive theocrats, and it seems that those dumb and dishonest Creationists — including the ones hiding in cheap tuxedos — are trying to seize control of Science and pushing “pseudoscience” in by the back door.

    So, freedom must be defended from the theocrats — how dare they insist that marriage can only be between a man and a woman! and the nerve of having coffee shops in Blackpool with TVs showing scripture readings . . . it’s hate speech; let’s call the police under the Public Order Act. (This is an actual recent incident.)

    Likewise, how dare those ignorant, stupid, insane or wicked creationists demand that we replace the proper definition of science:

    KS, 2001:“Science is the human activity of seeking natural explanations of the world around us.”

    . . . with something so obviously loaded with Creationist rubbish and hidden agendas:

    KS, 2005:“Science is a systematic method of continuing investigation, that uses observation, hypothesis testing, measurement, experimentation, logical argument and theory building, to lead to more adequate explanations of natural phenomena.

    (This, again is an actual incident. The 2005 definition is more or less the traditional school level definition that — complete with issues on provisionality and progress — traces back to Newton in Query 31, Opticks. The 2001 definition preloads science with naturalism, i.e. evolutionary materialism, thus begging major questions and breaking down the integrity of science as an objective search for the truth about our cosmos based on empirical evidence, analysis and reasoned discussion.)

    of course in a day not many years hence, all of that will be seen for what it is: the blinding hysteria of our day, wherein judgements have been warped by reckless — and in some few cases willfully malicious — talking points and manipulative arguments.

    But, when one is caught up in the party-spiritedness of an age, it is hard indeed to see the wrongs being done. (Think about why it took 50 years of hard campaigning and one final slave rebellion that exposed the temper of those who suppressed it when they burned down dissenter chapels and tried to hang dissenter missionaries to break the stranglehold of slavery. And yet, to our eyes, such race based chattel slavery seems obviously wrong. Never mind that we have a lot of implicit debt servitude in our day . . . )

    GEM of TKI

  32. Sadly, his minimal requirements as are being highlighted just now duck this vital issue.

  33. InVivoVeritas:

    Thanks for an interesting post.

    As you’re probably aware, there is a well-known phenomenon in software development called the “requirements explosion”. It’s documented, for example, in Robert Glass’s book, Facts and Fallacies of Software Engineering. Even after a specification is complete, and especially as concrete implementation of the specification gets underway (i.e. development of the actual software begins), a plethora of other requirements come out of the woodwork. Several things might account for this, including (1) the requirements were probably incomplete to begin with; (2) not all the implications of the requirements were thought through in advance; (3) the stakeholders don’t like what the “incarnation” of their specifications in functional software actually looks like, or behaves like; etc.

    I observe a similar phenomena in the ongoing naturalistic-macroevolution vs. ID debate. The analogy is imperfect, but it seems to me that scientists (ironically, primarily evolutionists) are presiding over an exponential “requirements explosion” of their own creation. The more they drill down into the nitty-gritty details of life, the more strictly bounded and detailed the specifications for viable life become. And, on purely naturalistic grounds, scientists seem less and less able to account for life’s successful implementation(s) of those increasingly complex and demanding specifications.

    Kent
    Omaha, Nebraska, USA

  34. It would be interesting to me to see requirements specifications (and interface specifcations) for every organ in the human body.

  35. Dr Liddle:

    I must seriously disagree.

    Once you have encapsulation, to protect an environment for required reactions, all else follows on the energetics and related considerations. Where, if you do not have encapsulation, you have breakdown of a process that requires protection and controlled energy and material inflows and outflows to work.

    That’s a dilemma for those who pose the idea of spontaneous origin of life, but that does not mean the dilemma is not real.

    Why not break the dilemma if you can, addressing the underlying thermodynamic and hostile external environment concerns that drive it.

    Remember, the key reactions to build up the sort of complex molecules involved, are going to as a rule be endothermic and subject to interference by cross reactions, many of which would break down the processes. Indeed by the very fact of endothermicity, the breakdown reactions tend to be more energetically favourable, i.e release energy and simplify composition. (Notice how dried organic materials burn? They release energy on oxidation and breakdown into simpler components.)

    What may stabilise is high activation energies [metastability protected by a high energy barrier to break down], but then that puts in high energy walls to be surmounted to build the complex molecules. And enzymes in many cases are there precisely to get around high energy of activation hills.

    Enzymes being very complex proteins.

    GEM of TKI

  36. Not yet known in details but plainly HUGELY complex. Think about what is required to make a heart or liver transplant work.

  37. “Then, the cell indeed has to sense and respond to its environment, moving to better locations and away from worse ones. Sensing, processing, responding, motility.”

    That is a feature not even all modern cells have!

    We could reduce this list to: membrane (semi-permeable by its own properties), genome (or a set of self or mutually replicating polymers), energy.

  38. What about metabolism instead of just vague energy requirement? I.e. something that regulates energy intake, processing and discharge? It is a horrendously complex task.

  39. IOW, the strike anywhere matches and rats scenario. Rats spontaneously cause the matches to set the forest on fire. No human intervention apart from the matches…

  40. The hypothesise it, Joseph, and conduct experiments to find out just how simple the first Darwinian-capable self-replicator might have been.

  41. Yes the energetics are important, kf.

    That’s why the people conducting this research are chemists.

  42. But, when one is caught up in the party-spiritedness of an age, it is hard indeed to see the wrongs being done.

    Yes, indeed, kf.

    And I do think there is irrational paranoia on both sides. I think it’s a major part of the problem.

  43. We await your response to the 14 points of concern. Perhaps that will set our minds at ease.

    Probably not, but I do have a draft!

  44. Well we already know Joyce’s experiment didn’t do that- produce a self-replicator capable of darwinian evolution.

    My bet is we don’t get that until we have bonafied living organisms.

  45. Well, that’s fair enough, Joseph. But I think I’ll put my money on a simple spontaneously self-replicating and evolving system in my life-time :)

    That would be awesome.

  46. 3.1.1.2.1

    As per irrationality on both sides, while I agree in principle, my personal estimation of percentage thereof is I am afraid not in favour of “naturalists”, for want of a better word, advocating against “the Divine foot in the door”. It is not a fair pitch. Just my personal feel.

  47. I’m a software engineer too. And a sometime biochemist. I think the problem has been over-specified – we aren’t looking for ‘big-bang’, but phased implementation! I’d argue the minimal Day 1 requirement is a source of energy. Life is fundamentally based upon tapping the free energy from electrons as they ‘fall’ from electron donors to electron acceptors, whether excited by sunlight or simply existing in a donor. The energy released can do work – chemical or mechanical. Without that ability to do work, the Second Law of Thermodynamics bites us in the backside and degrades any putative replicator (I hope no-one is going to suggest that the Second Law precludes Life???).

    This isn’t Life, of course, or anything like it. But if there is a tappable source of ‘free energy’ (and I don’t mean that it costs nothing!), then that can do work against the tendency to entropy. I am obviously not about to supply details of the leap from energy to self-replicating molecules – that would be a Nobel-winning piece of work! – but I would point out the deep biochemical connection between ‘informational’ molecules – nucleic acids – and ‘energetic’ ones – ATP, NAD, FAD. Every single one of these has an adenine-ribose-phosphate moiety. In RNA/DNA, it is simply one of the four ‘base’ subunits, the “A” of the genetic code, but the energy of its polymerisation derives from exactly the same reaction – phosphate cleavage – as is involved cell-wide in almost every reaction requiring energy input.

    Modern cells make most of their ATP at membranes, which forms an interesting little loop, if membranes are indeed necessary to charge it from scratch. Energy at membranes is generated by pumped storage of protons across the membrane, creating a tappable gradient. This gives an interesting potential – and I’m only saying potential – for a very simple 2-part system: membranes and replicating molecules, the latter ‘feeding’ upon the free energy generated across the first, charging energetic, stackable triphosphates. Nothing else in the list is strictly necessary as a first requirement.

  48. It would be awesome- it would also be awesome if my 9 year old could slam-dunk a basketball- or throw a 99 mph fastball, but that ain’t happenin’ either…

  49. “I hope no-one is going to suggest that the Second Law precludes Life???”

    True, local perturbations may occur that make possible negative entropy differences at the cost of entropy growing overall. An example is the chemical clock or crystallisation. However, as you say, there is an explanatory gap we need to close, of going from self-ordering like this to genuine self-organisation in the sense of spontaneous formation of information systems. No examples are known today of anything like the latter. The onus is therefore on those who claim it is plausible to present a relevant proof.

  50. Well, time will tell.

    Now, are you going to tell me how you put information on/in a molecule without changing it?

  51. Dr Liddle:

    Right now the evidence is that the irrationality in power is a priori materialism. And, the careers being busted and the people whose children are being held hostage, are those who dare question the new materialist magisterium in the holy lab coat.

    So, sorry, trying to spread blame “equally” is not responding to the spirit of the age challenge.

    There is a power that needs truth spoken to it, so let us move away from the tactics of blaming the victim.

    GEM of TKI

  52. Well, let’s have that operational definition of “self-organisation”. The onus is on you to provide that :)

  53. Well it seems all you have are promissory notes.

    That said when a RAM gets information it does not change the component. When information is put on a piece of paper the molecular structure of the paper does not change.

  54. And, the energetics point straight to the complexities as highlighted.

  55. F/N: TMLO is a good place to begin looking at those issues. (No prizes for guessing why it is the first technical design theory book.)

  56. Elizabeth, I have cited a paper by David Abel. There is an attempt to give that definition there, you might want to read it first.

  57. Self-organisation is an alleged spontaneous formation of such a system. Is that a good enough definition? Or do you also want to have a definition of an information system?

  58. If something that reflects Wicken wiring diagram organisation [as opposed to crystal-like order] was not built by external forces, it had to self-assemble, spontaneously. Self-organisation is a descriptive term, not a mystery that needs major definition. (Cf Orgel and Wicken here for basic information from the 1970′s.)

  59. In addition to 8.1.1.1-2

    See http://en.wikipedia.org/wiki/Information_processor for a definition of a system processing system. The onus is on those who claim that systems such as those can/could emerge by themselves (by fluke or necessity), to provide at least one demonstrable example.

  60. I have read it, Eugene (several times in fact). I can find no definition, despite the fact that Abel repeatedly says how important it is to have one, and castigates others for not defining it properly.

    Yes, I think we need a definition of an information system, though I am happy to use Merriam-Webster’s 2b definition of information.

    So we would have something like:

    “The spontaneous formation of a system in which the attributes inherent in and communicated by one of two or more alternative sequences or arrangements of something produce specific effects.”

    Would that do?

  61. Pardon, but it looks very much like you are redefining away the difficulties by pushing them back behind the molecules you introduce to do the work. Once you define a membrane, you are looking at ports and discriminaiton on what is to come in/go out. Once you look at highly endothremic reactions inside the membrane, you are looking at organised energy sources. And to get the relevant molecules you are looking at metabolism, or else an environment that is so implausible that its only credible location is in vitro in a lab. Remember, you have to get to your startup molecules from a plausible pre-life environment.

  62. Yes, on first observation (obviously apart from the word “spontaneous”). Now please give us an example of that being spontaneusly organised.

  63. Joseph…

    My bet is we don’t get [a self-replicator capable of darwinian evolution] until we have bonafied living organisms.”

    It’s the other way around. We don’t get bonafide living organisms until we have darwinian evolution.

  64. Joseph

    That said when a RAM gets information it does not change the component. When information is put on a piece of paper the molecular structure of the paper does not change.

    I think you will find that when RAM gets data or a programme that it is physically altered and that when paper is written on the paper is altered. Otherwise there would be no way to tell if the data/programme/writing were there!

  65. 65

    Dr Liddle, on the previous thread leading up to this conversation, you were making the point that the computer analogy (of information running on an information processing system) has no place in the molecular world. You made the comment “What you have are molecules that obey the laws of physics and chemistry. To which I added “…and which exhibit properties beyond physics and chemistry”.

    Of course, you would know that I was referring to material objects taking on the additional properties of being physical representations and protocols within a system. Indeed you responded that ”Yes indeed. The properties of a system can be, and usually are, different from the properties of its parts.”

    I am interested in trying to clarify that remark. You see, the comparison (as I see it) isn’t between the physical properties of individual objects versus the physical properties of a system; it is a comparison between the physical properties of the objects, versus any additional non-physical properties which they take on by being a part of a system. (By the term “non-physical” here, I mean any properties that are not intrinsic to the physical make-up of the object itself).

    As an example, the nucleic codon CTA is a discrete physical representation (to the genetic system) which results in the binding of leucine to a forming polypeptide. That physical representation is actualized by its specific tRNA and the appropriate aminoacyl synthetase. That particular codon results in the binding of leucine without it ever interacting with leucine (or with the synthetase which actualizes the result). In other words, it only represents that effect within that system, and nowhere else. What the (material make-up of) the codon represents is therefore not intrinsic to the material codon itself – it is an acquired property by virtue of being in the system.

    In comparison, a water molecule may very well become part of a temporal weather system (for instance) but at no point in playing a role in that system does it ever take on any property other than being a compound of oxygen and hydrogen.

    Having said all this, I would like to take some time and study up on the systems you were referring to in your comment above. Can you please offer me a couple of examples of such natural systems where the objects within the system take on properties beyond their physicality?

  66. “A lipid vesicle containing genetic material . . .” Oooo, that’s helpful. My 10-year old could come up with that much detail. What a joke. Where does the additional nucleotide material come from? How does it get into the vesicle? How does the vesicle prevent interfering materials from entering the vesicle? Does the vesicle “divide” in any kind of controlled manner, or does it just get bigger (Szostak) until eventually it is unstable?

    I will quote myself from the first comment above: “This is why it is critical to have an engineering eye look at these things. Too many true believers gloss over the details . . . the proposed pathway or proposed mechanism being offered is simply not workable in the real world or is so general and vague as to be useless for anything other than a just-so story.”

  67. Eric,

    “My 10-year old could come up with that much detail”

    It is pretty easy to conclude there is a lack of detail when you take a snippet of an interview, and ignore the scientific literature behind it.

  68. Elizabeth Liddle:

    Yes, I think we need a definition of an information system, though I am happy to use Merriam-Webster’s 2b definition of information.

    So we would have something like:

    “The spontaneous formation of a system in which the attributes inherent in and communicated by one of two or more alternative sequences or arrangements of something produce specific effects.”
    =====

    Interesting. I used this same definition ( 2b ) from Merriam-Webster over at Cornelius’ blog and got flamed for doing so.

    On another interesting note, you’ve left out the most important and best part of that definition you quoted where it compares DNA sequences as being indentical to the way informational systems run in a computer. Here it is below in it’s un-edited un-quote-mined entirety:

    http://www.merriam-webster.com.....nformation

    ( 2b )
    “the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something (as nucleotides in DNA or binary digits in a computer program) that produce specific effects”

  69. Upright BiPed:

    “Dr Liddle, on the previous thread leading up to this conversation, you were making the point that the computer analogy (of information running on an information processing system) has no place in the molecular world.”
    ====

    Well, now we all know why in that Merriam-Webster definition she gave, she left out the most important part:

    “(((( (as nucleotides in DNA or binary digits in a computer program) )))))”

    But now as I look at it, she has also added more to the definition than was on the link I found for Merriam Webster. See if YOU ALL can pick it out:

    ” (((( “The spontaneous formation of a system in which . ” ))))”

    So apparently some things were deleted and other things added to the Merriam-Webster definition ??? I’ve seriously tried to find if it came from another link or online dictionary and it’s not there. “SPONTANEOUS FORMATION OF A SYSTEM” is clearly not there or anywhere that I can find. Unless she’s tailoring it for HER own definition of what she thinks it should be, since this may be the case as we are discussing the FAITH of life just spontaneously arising.

  70. Hello Eocene, I applaud your effeorts.

    The definiton you give above is only sufficient to a point. I would draw your attention to the word “communicate”. All forms of information are transferred by the use of representations and protocols within a system. If you do not work this function into the definiton, that definition will allow physical reactions to be considered information transfer which are not information transfer. As an example, Dr Liddle has previously used the scenario of a footprint being left on the ground as an example of “information”. She was corrected that a footprint on the ground is no more than the state of the ground after being walked on. In other words, the ground is not in-formed by the foot.

    On the other hand, the state of the ground may in-form an observer to the presence of a foot, but it only does so by virtue of being as representation to the observer, and only then if the observer has the correct protocol to interpret that representation.

  71. When presented with complex research by an expert in a field that is unfamiliar to you, if your first thought is “He/she is doing it all wrong!”, your next thought should be, “perhaps I don’t really understand the problem sufficiently and need to study it further”.

  72. “Pardon, but it looks very much like you are redefining away the difficulties by pushing them back behind the molecules you introduce to do the work.”

    I’m not redefining anything. I am simply pointing out some biochemical fundamentals.

    “Once you define a membrane, you are looking at ports and discriminaton on what is to come in/go out.”

    No. I’m not ‘defining’ a membrane; I’m just illustrating one of their fundamental properties: energy generation through their ability to create a barrier which can be used to sustain a very simple energy source: a proton gradient (it could not actually be much simpler!). Modern membranes perform a host of modern activities, and you are insisting that ancient membranes must perform all of them too. So you chuck the burden of proof over the wall: unless I can build a system with a minimal specification, you will not accept that there is a possible specification below the modern one. Which you can do if you like, but I’ll just chuck it back. I see no reason to reject the hypothesis that a lesser specification is possible. That a lesser specification is not possible is also an undemonstrated hypothesis.

    “Once you look at highly endothremic reactions inside the membrane, you are looking at organised energy sources. And to get the relevant molecules you are looking at metabolism, or else an environment that is so implausible that its only credible location is in vitro in a lab. Remember, you have to get to your startup molecules from a plausible pre-life environment.”

    I am not trying to explain the whole molecules-to-life scenario, but simply to point out that replication and energetic metabolism are far more closely coupled than is realised – and it’s not just the transfer of energy, but the molecules themselves that bridge that gap – specifically, energetic nucleoside phosphates, and their coupling to proton gradients.

  73. Hello Eocene,

    I think she may have simply added the “spontaneous” part because your conversation began with the topic of self-organizing systems. On the other hand, it was in her best interest to leave of the DNA part. Against all evidence to the contrary, she still gets queasie about recognizing DNA is a base-four digital encoding system. The phrase “DNA or the binary digits in a computer system” does not serve her purpose.

  74. Yes Eocene,that’s why I thought it an appropriate definition, because Merriam Webster specifically applies it to the DNA case.

    But note that an example is not “part of a definition” – it merely gives the context in which that definition is used.

    So there was no skullduggerous editing on my part. In fact it’s not the only “edit”, if you read carefully. I simply took the Merriam-Webster definition, and fitted it to yours.

    So it was not “quote-mined” – it wasn’t even a quote!

    This is the kind of antagonistic inference, Eocene, that makes so many conversations with ID proponents difficult – the default assumption that your interlocutor is lying to you, or trying to slip something by you.

    I gave the source, so that you could look it up; I selected it, out of several M-W definitions because it was given as specifically applying to DNA code; and I inserted the actual definition (as opposed to the example) into your own phrase.

    Please do me the justice of making the default assumption that I am posting in good faith. I do it to others; I do not see why the courtesy cannot be returned.

    So, are you happy to accept the operational definition I devised, or not?

  75. “I see no reason to reject the hypothesis that a lesser specification is possible.”

    Do you see any need to support that hypothesis prior to it becoming embedded as an assumption?

    “That a lesser specification is not possible is also an undemonstrated hypothesis”

    So in the face of an ussupported assumption, you ask that others should prove a negative.

    Nice.

  76. I’m still dying to know, with regard to an actual molecule, e.g. DNA, how you put software on it or in it without making changes to the molecule.

    Joseph, I have a feeling you goofed here :)

  77. And, the energetics point straight to the complexities as highlighted.

    Well, they mean that it’s a chemical problem. As I said, that’s why the guys working on this are chemists.

  78. What “laws of physics demand” that a cell “must be, and do” thse things for “viability and reproducibility”?

    The precise question at issue is: what are the minimum requirements for an entity that self-replicates with hereditary variance in reproductive success.

    I know of no “law of physics” that tells us what these requirements are.

  79. 79
    material.infantacy

    Change the molecule into what?

    How do you put information onto a hard disk without changing it?

    In other words, SO WHAT if it’s being changed. Please explain why this amounts to anything.

  80. 80
    material.infantacy

    There’s no “law of physics” that tells us what the requirements for a grandfather clock are either.

    However if you want to build one, you’ll be constrained by those laws, so they most certainly have something to say about the matter, and you won’t be able to violate those rules.

    You’re nitpicking. Constraints exist, and one of those constraints is the “laws of physics.”

  81. Try reading the papers, Eric.

    I was simply giving the principle.

    Where does the additional nucleotide material come from?

    Well, it might not have been nucleotides at first. But (I thought I’d said this?) if the lipid membrane is permeable to monomers but not polymers (as Sosztak seems to have shown) then the “additional material” comes from monomers that can enter, bond with others to form polymers, then be unable to escape.

    How does it get into the vesicle?

    Monomers can get in; polymers can’t get out.

    How does the vesicle prevent interfering materials from entering the vesicle?

    It probably doesn’t at first. What “interfering materials” did you have in mind?” I don’t expect reproductive fidelity in the early stages was very high.

    Does the vesicle “divide” in any kind of controlled manner, or does it just get bigger (Szostak) until eventually it is unstable?

    “Controlled” in what sense? IIRC, Szostak says that bigger ones tend to “eat” smaller ones, and elongate to form tubes, which are then broken up mechanically into smaller ones by mechanical forces without spilling contents (think link sausages).

    Another possibility is circulation currents with a temperature gradient. I don’t know the details of the current hypotheses, but they are available in the Szostak lab papers.

    I will quote myself from the first comment above: “This is why it is critical to have an engineering eye look at these things. Too many true believers gloss over the details . . . the proposed pathway or proposed mechanism being offered is simply not workable in the real world or is so general and vague as to be useless for anything other than a just-so story.”

    Are you saying that the members of Szostak’s lab do not have the required expertise to conduct their studies? That they are just naive “true believers” without any relevant knowledge of organic chemistry?

    tbh, this “we engineers can see at a glance that Darwinism makes no sense” gets a bit old!

    Nano-engineers, maybe, but we tend to call them “chemists”>

  82. Elizabeth Liddle notes above:

    No, the question is: what could you add to the simplest possible self-replicator to produce a modern cell?

    Which is exactly what [a “simple” self-replicator] Szostak’s lab is working on!

    But she seemingly has forgotten her unacknowledged solution to Szostak’s problem:
    Elizabeth LiddleMay 30, 2011 at 12:10 pm

    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”.

    Elizabeth, you should notify Szostak that you have already identified the very simple self-replicators he seeks. Perhaps you’ll share a Nobel with him.

  83. 83

    OK NormO, and after you’ve done that and still think the expert is wrong what should you do?

  84. “I see no reason to reject the hypothesis that a lesser specification is possible.”

    Do you see any need to support that hypothesis prior to it becoming embedded as an assumption?

    I’m not sure of the semantic nicety you are getting at here – I see no reason to reject it, and good reason to support it. I would consider it misguided to insist that the simplest modern cell is the simplest possible cell.

    “That a lesser specification is not possible is also an undemonstrated hypothesis”

    So in the face of an ussupported assumption, you ask that others should prove a negative.

    Nice.

    Ho ho. I am simply arguing for an open mind on the matter. I realise I may have come to the wrong place.

  85. Anything you like Barry! But if anyone thinks that being an expert in one field somehow gives them inherent credibility in a completely different field, they are very mistaken. You can’t simply reformulate a problem from a very specific and technical field in terms of your own skill set. You have to do the hard work of understanding the other field. There are no shortcuts.

  86. Oops, my reply at #13 was meant to be a reply to Barry’s #12.1

  87. I would take a deep breath and consider the possibility that I could be wrong and the expert could be right.

    But it depends on whether the expert is discussing within his area of expertise. There’s a fairly long list of Nobel winners’ silly opinions outside their field of specialty.

  88. CD:

    Pardon, but the problems start a bit deeper than debating barrier potentials at boundaries of one form or another and postulating about modern vs hypothetical ancient membranes and the like.

    The basic challenge is that the OOL researchers need to move from reasonable pre-life conditions and form, without excessive dependence on investigator manipulation of the circumstances — i.e. injection of intelligence — the required membranes and self-replicating contents.

    But, the point of a membrane is to differentiate internal and external environments, which then brings in the issue of ports and controls, metabolism and mass and energy flows to feed required reaction paths and not cross-interfering paths.

    Instead of elaborating overmuch, let me simply cite Orgel [genes first] and Shapiro [metabolism first] from their recent exchange of mutual ruin (noting that no great breakthrough has happened in the past few years to materially change the picture — or this would have been all over the headlines like the Moon landings were):

    ____________

    SHAPIRO: >> RNA’s building blocks, nucleotides, are complex substances as organic molecules go. They each 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. Many alternative ways exist for making those connections, yielding thousands of plausible nucleotides that could readily join in place of the standard ones but that are not represented in RNA. That number is itself dwarfed by the hundreds of thousands to millions of stable organic molecules of similar size that are not nucleotides . . . .

    The RNA nucleotides are familiar to chemists because of their abundance in life and their resulting commercial availability. In a form of molecular vitalism, some scientists have presumed that nature has an innate tendency to produce life’s building blocks preferentially, rather than the hordes of other molecules that can also be derived from the rules of organic chemistry. This idea drew inspiration from . . . Stanley Miller. He applied a spark discharge to a mixture of simple gases that were then thought to represent the atmosphere of the early Earth. ["My" NB: Subsequent research has sharply undercut this idea, a point that is unfortunately not accurately reflected in Sci Am's caption on a picture of the Miller-Urey apparatus, which in part misleadingly reads, over six years after Jonathan Wells' Icons of Evolution was published: The famous Miller-Urey experiment showed how inanimate nature could have produced amino acids in Earth's primordial atmosphere . . .] Two amino acids of the set of 20 used to construct proteins were formed in significant quantities, with others from that set present in small amounts . . . more than 80 different amino acids . . . have been identified as components of the Murchison meteorite, which fell in Australia in 1969 . . . By extrapolation of these results, some 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 . . . I have observed a similar pattern in the results of many spark discharge experiments . . . . no nucleotides of any kind have been reported as products of spark discharge experiments or in studies of meteorites, nor have the smaller units (nucleosides) that contain a sugar and base but lack the phosphate.

    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 . . . .

    The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck. >>

    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 . . . Could a nonenzymatic “metabolic cycle” have made such compounds available in sufficient purity to facilitate the appearance of a replicating informational polymer?

    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. Each proposed metabolic cycle, therefore, must be evaluated in terms of the efficiencies and specificities that would be required of its hypothetical catalysts in order for the cycle to persist. Then arguments based on experimental evidence or chemical plausibility can be used to assess the likelihood that a family of catalysts that is adequate for maintaining the cycle could have existed on the primitive Earth . . . .

    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]? The lack of a supporting background in chemistry is even more evident in proposals that metabolic cycles can evolve to “life-like” complexity. The most serious challenge to proponents of metabolic cycle theories—the problems presented by the lack of specificity of most nonenzymatic catalysts—has, in general, not been appreciated. If it has, it has been ignored. 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. >>
    ______________

    So, pardon my mere physicist’s perpetuum mobile type demand: show us first, please. (And I think ES will join me in this requirement.)

    Demonstration first, then explanation.

    In the meanwhile, we will stick to the known case that observed cell based life implicates metabolism, genetic, coded mechanisms, a von Neumann self replicator and a ported membrane barrier that intelligently controls the internal environment so that the specific controlled reactions of life will not be overwhelmed by the otherwise likely to be dominant reaction paths.

    We will also stick to the dilemma that if there is no membrane, then the uncontrolled environment will plausibly be ruinous through interfering cross-reactions. But if there is a membrane then it has to have a porting mechanism by which required input energy and materials flow in and wastes out, in a controlled fashion. The only empirically known means for that is quite complex and functionally specific.

    The cell looks irreducibly complex in many ways.

    That he cell is also using codes, algorithms and executing machines points strongly to its source: the known source of digital codes, algorithms and executing machinery. Intelligence.

    Shapiro looks like he has hit a serious point, one that hits far and wide beyond :

    The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck.

    GEM of TKI

  89. Norm:

    Please see the Shapiro-Orgel exchange above, as a start point for what top rank experts have had to say after a lifetime of work in the field, over the past few years. Nor have things got better since or that would have been in headlines not paralleled since the Moon landings.

    And BTW, in and around UD and indeed in this thread, are design suportive people qualified to discuss thermodynamics, chemistry, and systems.

    GEM of TKI

  90. Please see just above. Note, the thermodynamics and systems requisites issues are going to be accessible to a fairly broad range of people from diverse technical fields. Chemists, Physicists, Engineers, and the like not just biochemists.

  91. P

    No expert is better than his facts, logic and underlying assumptions, which is one reason why the a priori materialism of Lewontin et al is so corrosive. That context is also an extra reason why appeals to modesty in the face of claimed authority are less than impressive.

    Newton and Einstein triumphed because they showed an explanation that worked and which predicted the unexpected accurately. So, the first requisite is to demonstrate. Then discuss how this may have happened in the remote past in a plausible prelife environment.

    Until that is done, we have speculation driven by a priori materialism, pushed in the back door by so called methodological naturalism.

    In this particular area, the only definitive answer from the chem evo side is going to be an actual demonstration.

    And, given the issues like the ones raised by not only IVV but field leaders like Orgel and Shapiro, that is going to be hard to do indeed.

    Remember, you have to show the rise of self-replicating cell based life from reasonable chemicals in a reasonable environment without undue interference.

    It is no accident that the closest we have yet come is an exercise in genetic engineering by Venter which is proof of concept that cell based life can be engineered.

    GEM of TKI

  92. Actually, I must say I do not agree with the wiki on the example given of the information processing systems. To be honest, I gave it a full read after I posted ;( While the definition given is correct, the interpretation is not. E.g. they consider a rock orbiting the earth and the earth itself an information processing system, which is bizarre to me because without an observer it does not make a lot of sense. However in the interpretation part they do say “it can be argued”.

  93. F/N: Oddly, the very first technical design theory book was by a Chemist, a Polymer specialist and a Geologist, looking at the origin of life from the ground up. Norm, can you tell us what fundamentally is wrong with the thermodynamics and environmental consideration issues here, as a baseline?

  94. KF,

    “The cell looks irreducibly complex in many ways.”

    Absolutely no doubt about it.

  95. oh, for goodness’ sake, guys! I left out the DNA part simply because I was using the definition, not the example they gave of usage!

    Sheesh, I chose the definition because it’s the one that applies to DNA!!!!!

    And I’d actually quoted it in full here!!!!

    This conversation started on the Ink and Hardware thread, where I gave the M-W definition in full, in a response to Eugene, which he responded to, so I assume he read it. So what on earth makes either of you think I wanted to hide it????!

    Look, Eugene gave a definition of “self-organisation” as:

    “Self-organisation is an alleged spontaneous formation of [an information] system. Is that a good enough definition? ” then asked “Or do you also want to have a definition of an information system?”

    So I substituted for “information system” a definition of an information system based on the M-W definition, giving:

    “The spontaneous formation of a system in which the attributes inherent in and communicated by one of two or more alternative sequences or arrangements of something produce specific effects.”

    It wasn’t supposed to be a quote (let alone a “quote-mine”) from the M-W but a description of an information system based on the M-W definition of information.

    As for “gets queasie about recognising DNA is a base-four digital encoding system”, I don’t get “queasie” at all. I just think it’s a really really bad analog. The base is only a switching unit at the level of the population for a start, not at the level of the organism (and not really base four even then, more alphabetic). At the level of the organism, the switching unit is the gene not the base.

    But you know this UBP, because I’ve explained it several times. Feel free to disagree, but I’d be grateful if you did not ascribe queasieness where no queasieness is.

    Also, I think you both owe me an apology, for jumping to the inference that I was attempting to hide the full M-W definition when I’d actually given it myself at the start of the whole conversation!

    Yet again, I repeat my request: please do me the courtesy of assuming I am posting in good faith, because I am. It is an assumption I make about virtually everyone else, and the people I don’t assume it of, I only drop the assumption based on copious evidence. And that applies to no-one here.

  96. KF, you’ve linked to a 228 page book. Obviously I’d have read it first to have an opinion on it … give me 10 minutes and I’ll get back to you ;-) But seriously I would have to read it and then probably many additional references before formulating even a partly informed (hopefully) opinion because as I said, there are no shortcuts. In the meantime I’ll spare you what would be my otherwise ignorant opinion.

  97. 97

    Dr Liddle, you once again, just in the past 48 hours restated that DNA is not properly decribed as a digital system. A couple of months ago KF and I spent several posts trying to get you to understand the idea that DNA is base-four digital. Yet, you instead keep returning to the errant idea that the base has something to do with what the coding system is describing (phenotypic, etc), as oppossed to being the number of individual characters within the encoding system that can occupy any position in the code).

    “A remarkable feature of the structure is that DNA can accommodate almost any sequence of base pairs—any combination of the bases adenine (A), cytosine (C), guanine (G) and thymine (T)—and, hence any digital message or information.” -Biologist, Leroy Hood and David Galas PhD: “The Digital Code of DNA”

  98. 98

    Now, can you please offer me a couple of the systems you were describing earlier (see me post at 11), I would really like to study there physical characteristics.

    Thanks.

  99. A couple of months ago KF and I spent several posts trying to get you to understand the idea that DNA is base-four digital. Yet, you instead keep returning to the errant idea that the base has something to do with what the coding system is describing (phenotypic, etc), as oppossed to being the number of individual characters within the encoding system that can occupy any position in the code).

    And isn’t it just maddening when you keep explaining something to somebody, and they just don’t get it? ;)

    UBP: Look, there is no right or wrong answer as to whether DNA is “base 4 digital” or not. It’s a metaphor, and whether it is a useful one depends on what you are using it for.

    At the level of the organism it isn’t “base 4 digital” in any sense except, possibly the sense of being a static string with four characters, which is not what I would describe as “base 4 digital”. There is no switching, unlike a “base N digital” system, in which the operation of the system involves switching each unit between N states.

    The only switching of the DNA letters occurs between generations, i.e. at the level of the population, not at the level of the organism, and even that isn’t exactly a “base 4 digital” system. Single nucleotide changes do occur, but just as common are deletions and insertions and of course duplications. In other words regarding a DNA base as a “switch” really doesn’t work as a metaphor. Mutations do “switch” DNA bases, but that is a very small part of what they do. Much more interesting are changes like recombination or repeats.

    What works much better is to regard it as a four letter alphabet that “spells” what proteins can be made. Or, some of it does. Better still is to regard it as a digital system in base 2, where the unit is the gene, and where the genes can be switched on and off. This is a really useful analogy, because the switching contingencies can be extremely deep – gene A switches off, stopping it blocking gene B which then switches on Gene C etc – and responsive to incoming signals from outside the cell. So far from being “queasie” about the idea of DNA representing a digital system, I’m quite happy to regard it as such, only not in Base 4!! At Base 4 it is utterly boring, and scarcely (if at all) worthy of the name. At Base 2 it is awesome.

  100. oops. Everything after the first para is me – the first para is UBP.

  101. Sorry, UBP, I don’t understand your request. Can you please link to where I described the systems you are interested in?

  102. 102

    oh for pity’s sake

  103. If you want an answer, you will have to show me where I was apparently describing some systems you were interested in.

    All I have to go on is your quotation of my words:

    “What you have are molecules that obey the laws of physics and chemistry”.

    Please link to the context.

    Thanks.

  104. 104
    material.infantacy

    EL, the physical state of a charged, byte-sized transistor set, is what it is. We impose the binary “metaphor” onto it for the purposes of digital function within an integrated system. The “metaphor” becomes necessarily inherent to the system in which it operates.

    Please explain to the audience how that differs crucially from the quaternary “metaphor” imposed on the DNA molecule, which functions as digital storage, and why you believe that the quaternary code is imposed externally, instead of its being intrinsic to the system in which it’s integrated.

    Additionally, this mock confusion of yours about representations and protocols is becoming tiring in its banality.

    I can represent each distinct atom in the universe with a string of 52 amino acids. Proceeding in lexicographical order, I can define that each permutation represents a discrete atom. That’s a representation. But simply proclaiming that the first permutation represents the first atom is not enough. Something is missing. You really shouldn’t need to be told this; I believe you already know.

    What’s missing from the above specification in order to make it useful in any way?

    Your previous denials aren’t likely confusion nor misunderstanding. A confession on your part would equal a concession it seems, and perhaps a drastic one for your worldview. If the representations and protocols constituting meaningful information must be imposed externally, and are not an emergent property of material interactions, then you can’t win this game.

  105. 105
    material.infantacy

    Correction to my 11.1.2.2.4.

    The phrase “and why you believe that the quaternary code is imposed externally, instead of its being intrinsic to the system in which it’s integrated.

    Should be “and why you believe that the quaternary code is merely metaphorical, instead of its being intrinsic to the system in which it’s integrated.”

  106. DrRec, I apologize. My comment was snide and was directed at Elizabeth’s general statement, not Szostak’s work. I am not ignoring the literature, I hope. We have looked at Szostak’s general approach in basic detail on another thread, and I’m afraid many of us found it to be quite vague as well. But, as I have said before, Szostak is doing great work and I hope his team keeps at it.

  107. The book lays out the baseline to address many of the issues that still surface, sometimes in a slightly updated form. And, in particular, if you cannot directly read chs 7 – 9 on thermo-d issues and implications, pardon directness, but you are in no position to dismiss the pointed questions being asked by those of us who have worked through those issues and related issues in the context of OOL etc. (e.g. cf my always linked through my handle, App 1 which starts from exactly TMLO chs 7 – 9, and Clausius.)

  108. Elizabeth: “Are you saying that the members of Szostak’s lab do not have the required expertise to conduct their studies? That they are just naive “true believers” without any relevant knowledge of organic chemistry?”

    I have not said anything of the kind. I have said, and repeat again, that they are doing great work. When I read their papers I find that they tend to be careful in their statements, and a close reading shows *many* caveats, assumptions and the like. That is as it should be. They are proceeding as best they can in this difficult area.

    What I do object to is folks who make vague general statements, whether in isolation, or coupled with “it’s all in the literature; go read it”. Time and again we go back to the literature and, lo and behold, the claim is actually not supported by the literature. Those are the true believers.

    InVivoVeritas has come up with a decent first list of what we should at least consider might be required for a simple cell. The tenor of the response? “We don’t need no stinkin’ engineering constraints; it’s way easier and much simpler than that, man! Go read the literature!”

  109. Well, if someone tries to explain what is in the papers, and someone else says “not enough detail” then it seems to me fair enough to refer that someone to the papers!

    So what claim have you found here that is not supported by the literature?

    InVivoVeritas has come up with a decent first list of what we should at least consider might be required for a simple cell. The tenor of the response? “We don’t need no stinkin’ engineering constraints; it’s way easier and much simpler than that, man! Go read the literature!”

    What some of us said was: that list of requirements seems to be based on a modern cell. We aren’t talking about a modern cell, we are talking about the simplest possible Darwinian-capable self-replicator.

    Anyway, I have responded in some detail to InVivoVeritas on one of the many threads on this topic, I have given up trying to track where the conversation venue currently is!

  110. I see no apology yet forthcoming, Eugene and UBP, for the insinuation that I was trying to “hide” part of the M-W definition of information, an insinuation clearly refuted by the fact that I had myself earlier quoted the entire definition in a response to Eugene himself, and to which he had responded – indeed it marked the start of this very conversation.

    You goofed guys.

    Kneel please.

  111. Dr Liddle

    You astound me.

    In D/RNA, bases in the string data structure take one of four discrete states. That makes them four state digital, much as our usual numbering system is 10-state digital and binary is 2-state digital.

    That is about as simple a fact as anything else in this area.

    In mRNA, three letter words, called codons, carry out coding for AA’s, to assemble proteins according to the commonly encountered genetic code. Some codons also carry out signaling functions, AUG being start as well as Meth, and there are three stop codons.

    The codon chains are coded, symbolic prescriptive information that functions in the Ribosome to say start with meth, add AA, add AA, . . . STOP. The AA chain is folded and put to work.

    The coupler to the AA in the tRNA that has a matching 3- letter anticodon, at the COOH end of the AA is standard [CCA iirc], i.e. we could misload ant tRNA by forcing it. The loading enzyme recognises the config of the particular tRNA taxi-tool arm molecule and loads it.

    This is digital tape control of an assembly process using a tool-tipped assembly arm system. Just what a kinematic vNSR calls for.

    It is noteworthy that von neumann, in conceptualising the kinematic self replicator a few years before DNA was characterised then decoded, proposed a braille-like raised rods system to code digital information.

    The point is that you may dismiss this set of facts and explanations as you like, but astute onlookers will see the price of reductio ad absurdum needed to cling to the attempt to dismiss the presence of digital, coded prescriptive info in the workings of the cell.

    They will be curious to know what is so threatening about acknowledging that digital code is in the cell. They will spot the quantity of the info, 100,000+ – billions of 4-state bases, and will see that we are well beyond the FSCI threshold. They will see in addition, there is but one known, plausible source for codes, languages, algorithms for step by step execution of solutions, and one observed source for executing machinery to execute such codes. Intelligent designers.

    The light bulb will go on, and they will see that there is therefore excellent reason to infer on what we know to design of key components of the living cell.

    So, they will see why so many of us refuse to accept the question-begging Lewontin a priori materialism and go with the evidence: the living cell is credibly designed.

    And, more and more, they will agree with us.

    GEM of TKI

  112. The self replicating facility especially.

  113. 113

    As far as Eugene, you might want to check who you are calling out. As for myself, I never said that you were “hiding” anything. I said it was in your best interest to leave off the example given by MW, and more importantly, that you were queasy about the idea of DNA being a base four digital encoding scheme. This is an issue with some history behind it were you are concerned. Your subsequent response certainly removed any doubt about that.

    When are you going to get past these games and attack the positive physical evidence of a semiotic state in protein synthesis?

  114. F/n: Machine code is often hard-burned into an embedded system, and is manifested in a static hardware configuration in read only memory. DNA functions like that sort of ROM.

  115. In D/RNA, bases in the string data structure take one of four discrete states. That makes them four state digital, much as our usual numbering system is 10-state digital and binary is 2-state digital.

    No, it does not, kf. The bases do not “take one of four discrete states”. A nucleotide is not a “state”, and the even it you were to call it one, that “state” never changes (well, it shouldn’t) in the lifetime of the organism.

    And mutations do not cause a nucleotide to “change state”. Mutations do cause alterations to the sequence of nucleotides but these are not “state changes”. You might refer to a SNP as a “state change” of that position in a sequence, but a SNP is only one kind of polymorphism. A deletion or an insertion cannot be described as a “state change” of anything.

    And in any case your example is of what happens within the organism itself. Within the organism the nucleotides cannot “take one of four states”. They are stuck in the state they came into existence in. You cannot say that a base pair can “take one of four states” if it never does!

    As I said, there are plenty of senses in which DNA is code, and even a sense in which it is binary code, but there is no sensible sense in which it is in “base 4 digital”.

    The base pairs are not “states”. They are base pairs, and they don’t change during the lifetime of the organism, even when replicated, unless something goes wrong, and when the the sequence changes between generations, it isn’t usually the basepairs “changing state”, except in one very narrow sense (SNPs).

  116. They will be curious to know what is so threatening about acknowledging that digital code is in the cell.

    Speaking for myself: let me repeat that there is so little “threatening about acknowledging that digital code is in the cell” that I freely acknowledge it, as would most people in the field of developmental biology. Read Sean Carroll if you want to know about the “digital code in the cell”. Or any text on gene expression. The working of your brain depends on that digital code.

    It’s just not in “base 4″!

  117. Your previous denials aren’t likely confusion nor misunderstanding. A confession on your part would equal a concession it seems, and perhaps a drastic one for your worldview.

    Please stop doing this. This has absolutely nothing to do “with my worldview” whatever that means, as my position on gene expression should make perfectly clear.

    Sheesh. The number of nasturtiums being cast on the integrity of us evos is enough to make any of us think you guys were worried or something!

    Desist.

    It’s an interesting topic and good people can disagree.

  118. I never said that you were “hiding” anything. I said it was in your best interest to leave off the example given by MW

    heh. I did not have sexual relations with that woman.

    Sure I didn’t hide it, I just had a vested interest in not typing it, eh?

    Come on!

    I quoted the thing in full right at the beginning of the conversation!!!!

    And the only reason it wasn’t there in my attempted operational definition of “self-organisation” for Eugene was because I was trying to substitute a definition of “information system” into his!

    Andy, as I have said repeatedly, there is nothing “queasy” about my objection to the notion of Base 4 digital. It’s just my inner geek gets really annoyed by it. Base 2, fine. Digital, fine. Code, if you insist, fine.

    Base 4, no way. It’s not in base 4 in any meaningful sense, as I have just explained above.

    And when it comes to games UBP, I’d like you to consider stopping with this “game” you seem to be playing of trying to insinuate a dishonest motive to me at every possible opportunity.

    It’s very tiresome.

  119. But you are correct about Eugene. Apologies to him, and to Eocene for mistaking him for Eugene, who had of course read my post. My eyesight is not as good as it should be.

    However, the record is perfectly clear, and I hope you are both prepared to retract your insinuation that I attempted to hide some unwanted part of the M-W definition of information.

  120. Eugene said:

    Actually, I must say I do not agree with the wiki on the example given of the information processing systems. To be honest, I gave it a full read after I posted ;( While the definition given is correct, the interpretation is not. E.g. they consider a rock orbiting the earth and the earth itself an information processing system, which is bizarre to me because without an observer it does not make a lot of sense. However in the interpretation part they do say “it can be argued”.

    You are on the verge of a profound insight into the nature of information. Above, UprightBiped is encouraging your toward a — what to call it? — a “Werner Gitt” model of information, an anthropocentric view of information, and that seems to be the paradigm you are coming from, but the wiki article is a good example of where that paradigm fails; as you say, without an observer, how can that be an information system?

    Why, because the observer (in an anthropocentric sense, all interacting elements of nature are “observers” in a physics sense) is not intrinsic to information. Observers certainly use and process information, and humans make use of information that is highly abstracted and contextualized for language (like the concepts we are discussing in this thread), but information is physical. Or more precisely, physical is information. You can’t have physical without information, or vice versa. (Calling Dr. Landauer…)

    “Software” and “digital” are metaphors that humans use to conceptualize discrete systems. Developers and software geeks like me get so “into it” that we are blinded to the fact that that is only analogous thinking; we confuse the map for the territory. “Digital” is just a way to conceptually abstract physical configurations and physical dynamics. It’s all just atoms and particles and physical law when you get beyond the metaphor.

    Anyway, I suggest that the interpretation you are having a hard time with is the key to a major insight into how information works as a conceptual AND a physical model.

    Think about it: if the footprint was there, and no one ever saw it, was it still information? No observer, no information? That’s a model that doesn’t cohere. The information is implicit in the physical configuration. If a human, or a bear, comes by and can “make sense” of that particular pattern of physical stuff in a way that triggers other physical events (the thought “hey, there was a human here”), then you have an additional kind of processing happening as well.

    But the footprint is information no matter who observes or does not observe the footprint later on.

  121. 121
    material.infantacy

    I’m not sorry for expressing my suspicions, and your indignation doesn’t do much to assuage them. The nature/style of your interactions warranted comment, and I made a few.

    Even your response, “whatever that means,” betrays a certain aloofness. Surely you aren’t suggesting that your worldview contributes nothing to how you evaluate evidence. You seem a little too intelligent, and I would hope too wise, for such nonsense.

    However I’ll withhold further commentary on your possible motives, at least for the time being. I recognize that you’re having discussions on multiple fronts, which is certainly a challenge. But I note that you invite this, as you seem to have some stream-of-consciousness comment to make regarding just about every subject here at UD.

  122. The reason it should be absolutely obvious that my objection to the “DNA is digital base 4″ had nothing to do with my “worldview” is because I have nothing against “DNA is digital base 2″. And I can envisage no worldview that would balk at base 4 but not at base 2. On the other hand I can think of other perfectly good reasons, and I’ve given them.

    The reason I added “whatever that means” is that I never know what “worldview” means. I don’t have a set “worldview” although obviously I have a Point of View, which, I hope, changes as I come across new evidence and persuasive arguments.

    But sure, no-one is free of bias, and I don’t claim to be.

    But I note that you invite this, as you seem to have some stream-of-consciousness comment to make regarding just about every subject here at UD.

    Yes, I should shut up, really.

  123. We will also stick to the dilemma that if there is no membrane, then the uncontrolled environment will plausibly be ruinous through interfering cross-reactions.

    I’m afraid you’ll have to be more specific. If we don’t know the chemistry, we don’t know what interfering cross-reactions we have to worry about.

    But if there is a membrane then it has to have a porting mechanism by which required input energy and materials flow in and wastes out, in a controlled fashion.

    Well, in the scenario I am suggesting, the membrane itself is simply a plane across which a free energy gradient can become established. This is not a living cell; it has no materials or waste products. I am suggesting that such a source of potential energy is an essential preresquisite for a plausible replicator (ie, metabolism first, but only just). And I point again to the striking reappearance of that adenine-sugar-phosphate group in both informational and (in 3 different molecules) in absolutely fundamental energetic roles. Whether by accident or design, this multiple role is, I think, central to the whole shebang.

    The only empirically known means for that is quite complex and functionally specific.

    I cannot resist pointing out that the only empirically known designers (as opposed to inferred ones) are so far incapable of getting within a mile of synthesising a cell from scratch. So far, we don’t know if a cell can be intelligently designed, even though we have numerous examples to base it on.

    Materials and methods would be nice – just how did that first complex mix become animated?

    Demonstration first, then explanation! :0)

  124. 124
    material.infantacy

    The reason it should be absolutely obvious that my objection to the “DNA is digital base 4? had nothing to do with my “worldview” is because I have nothing against “DNA is digital base 2?.

    Note that I suggested the worldview issue had a bearing on your understanding of information, and rounded out the comment with the suggestion of it driving your foregone conclusion that matter gives rise to information. I did not tie it to your insistence that DNA code is a base 4 numbering system.

    Yes, I should shut up, really.

    Maybe you should just slow down, you’re apparently extremely frustrated at any perceived provocation. I didn’t suggest you shut up, not even a little. I noted that you comment prodigiously. Not exactly the same thing.

  125. Note that I suggested the worldview issue had a bearing on your understanding of information, and rounded out the comment with the suggestion of it driving your foregone conclusion that matter gives rise to information. I did not tie it to your insistence that DNA code is a base 4 numbering system.

    OK, fair enough.

    Maybe you should just slow down, you’re apparently extremely frustrated at any perceived provocation. I didn’t suggest you shut up, not even a little. I noted that you comment prodigiously. Not exactly the same thing.

    Well, I do get riled at being accused of dishonesty or subterfuge, and I do get hot under the collar at Christians who try to defend the indefensible!

    And yes, I note that you did not tell me to shut up. I told myself that.

    It was good advice. I should take it and get off to bed :)

    Cheers

    Lizzie

  126. 126
    material.infantacy

    Cheers Elizabeth. I think I’ll take a break myself and cool off a little.

  127. ES, pardon if I add above that you hold a PhD in Physics, as well as your current vocation.

  128. Upright BiPed:

    “Hello Eocene,

    I think she may have simply added the “spontaneous” part because your conversation began with the topic of self-organizing systems. On the other hand, it was in her best interest to leave of the DNA part. Against all evidence to the contrary, she still gets queasie about recognizing DNA is a base-four digital encoding system. The phrase “DNA or the binary digits in a computer system” does not serve her purpose.”
    =====

    Well, let’s be perfectly honest as to why there is this constant definition shell game of what information is and is not. Now we all know what the definition of information is. We know it and they know it. Certainly Merriam-Webster knows it and gave the common sense universal understood definition when they made the comparisons. The comparison for which Merriam-Webster THEMSELVES made between a computer communications system and the even more sophisticated complex communication system of DNA being omitted from her personally architectured version of Merriam-Webster’s definition had more to do with ideology and worldview. Personally I don’t care why it was done, but it was. It would have been easier and more honest just to relate what her personal feeling of information was, but unfortunately it doesn’t hold up to a universally accepted understanding.

    They simply cannot allow for an “Intelligent Agent/Designer” as being responsible for DNA’s origins.(remember the foot in the door quote???) That is the motivation behind all these scientific bickerings, for both sides(one is for, the other against). In making the comparison that both DNA (and let’s be further honest, we do not know the origin of for no other reason than none of of were actually there) and computer codes (which we do know the origin of because it is well documented and many have first hand experience in handling) both fit the Merriam-Webster definition identically. The scientific inference is that once again, all codes that we KNOW the origin of come from an intelligent mind, therefore it is reasonable that we have 100% inference that DNA had it’s origins from an intelligent mind, even though none of us were actually present in the beginning observing it happen before our very eyes.

    The problem is that such a scientific inference infuriates the other side and they try their best to stop such scientific investigation by fuzzying up the very definition of just what the word/term “information” or even “Code” really means. I mean I’ve heard every kind of crackpot definition from ‘stars in galaxies are information’ – ‘rocks in a landslide are information’ – ‘patterns in snowflakes are information’ – ‘gravity is information’ and the insane list forced fed to us by self-promoting intellects who should know better is endless.

    Somehwere out there in the Universe, there must exist some unexplainable un-designed codes that none of us are aware of. Unfortunately for their side the burden of proof is on them to produce and show us these mystery codes. It’s easy for us to show proof of code origins because the evidence is all around us in our modern world. Thus far they have failed miserably to provide a Miller/Urey type experiment where blind undirected purposeless forces of physics magically by means of luck just happen to rearrange a toxic chemcial cocktails into intelligent purpose driven informational codes. As a result of this failure and motivated by a constant hatred of just what consequences would mean to admit that DNA quite possibly had an intelligent designer, we instead get time wasting arguments meant to go nowhere.

    Of course there is a historical precedent for this type of argument. I mean it’s hardly anything new or under the sun as Solomon wrote it. It’s called “What Is Truth?”

  129. Absolutely.

  130. Elizabeth,

    I don’t remember posting any insinuations in your regard. I just agreed to the form of definition you proposed without the word “spontaneous”. In fact I did not look into M-W until it was noticed by somebody else that the definition you gave had in fact been changed. I believe, I have posted nothing that I need to apologise for. Please explain yourself more clearly, what it was that I said which offended you.

  131. 11.1.2.3.3

    Elizabeth, Noted. We have posted ##3 and 4 almost simultaneously.

  132. KF, no problem.

  133. ES, ever so gracious as always.

  134. Eo: spot on.

  135. “Somehwere out there in the Universe, there must exist some unexplainable un-designed codes that none of us are aware of. Unfortunately for their side the burden of proof is on them to produce and show us these mystery codes.”

    Wow…..the goalposts have REALLY shifted this time.

    LOL. What a joke. Explore the universe, produce unexplainable “mystery codes” we are unware of.

    And you know what? If I came back with them, I’ll still be unable to prove they weren’t designed. Because that’s impossible! Time and time again, ID is presented with new enzymes, de novo genes, etc, and you just shout designed! Its all ID is, a predetermination.

    Spot on EO. Spot on.

  136. Well, let’s be perfectly honest as to why there is this constant definition shell game of what information is and is not.

    Excellent! I’ll pull up a chair.

    [...]

    Oh … not quite what I was hoping for.

    [...]As a result of this failure and motivated by a constant hatred of just what consequences would mean to admit that DNA quite possibly had an intelligent designer, we instead get time wasting arguments meant to go nowhere.

    Consequences? Consequences? You say there are consequences in changing one’s position on a scientific issue? Whatever can you mean?

  137. Thanks Barry for beginning the discussion.

    Re: “1.1. Must provide reliable isolation of the cell content from the outside world”
    As I understand it, the membrane must provide an anaerobic interior for numerous cell processes. Consequently, oxygen transfer must be controlled.

    Re: “1.2. Must be “permeable” to specific materials or sources of energy that “feeds” the cell”
    These are two very different requirements:

    1.2A The cell wall must be permeable to each of the materials it requires for it:
    1.2A.1 To reproduce itself.
    1.2A.2 To sustain itself.
    1.2A.3 To process function specific components.

    1.2B The cell wall must be permeable to the energy it requires:
    1.2B.1 To reproduce itself.
    1.2B.2 To sustain itself.
    1.2B.3 To process function specific components.

    For its energy requirements, the cell must:
    1) pass photons and convert them to biochemically useful energetic molecules, (photosynthesis) and/or
    2) pass biochemically useful chemicals.

    (Are there examples of cells using electrons for energy?)

  138. Just to stack my software designer and biochemist hats rather uncomfortably one atop the other, I find myself dissatisfied with the hand-dusting that goes on once people have pursued this particular “IC” argument through. Let us suppose that the specification is as complex as you wish to adduce; that it is as irreducible as you may like to think; that it is based on as code-like a piece of ‘information technology’ as you think appropriate.

    How do those of a mechanistic turn of mind imagine that the project was implemented? One may be wholly unsympathetic to the notion of blind undirected forces arranging molecules just so, such that complexity can arise from simplicity in a stepwise manner. But suppose one has to implement the designed system, and not just sit on the sidelines catcalling. One has all the ingredients in separately labelled glass jars. One knows precisely how they need to be organised. So let’s start organising them. I build a membrane just here; I stitch together a genome; I place these molecules here, and those there, and make these building blocks available in the environment … but I can’t stop them reacting. I can’t just place a couple of molecules next to each other and say ” … staaay … wait for it …” while I get on with building the next bit. And then, when everything is in place, I somehow have to cause the whole set of interacting molecules and systems to kick into action, functioning for all the world like a cell that was replicated from another, all biochemical pathways primed, all transcription factors bound appropriately for the chosen initial phase of the cell cycle and all epigenetic factors in place.

    I dare say the OOL picture assuming complexity arising from simplicity may be a tough one to swallow for many here, but the single-stage assembly one seems to me to have a lot less going for it. One may be happy with the design inference, but to me, designed or not, the most logical route to modern complexity is from ancestral simplicity. Which places the two positions much closer together than this OP, or many commenters, seem prepared to allow. You are aware, I’m sure, how human complexity is established? So why not, taking the idea down a level, cellular complexity?

  139. I place these molecules here, and those there, and make these building blocks available in the environment … but I can’t stop them reacting.

    This problem (of preserving the placement of arranged elements of a system during construction, but before kick-starting the system) cuts both ways. Evolutionists often assert that complex subsystems within an organism develop over many generations. So, during the construction process, I can’t just place a couple of elements next to each other and say, ”Staaay…hold your positions for a thousand generations while the hundred other elements I need for a functional subsystem come into being, and are put into place. There is no selective pressure to help you maintain your positions, since the subsystem is not yet functional and can therefore provide no selective advantage to your host organism. Furthermore, entropic forces are working against you, but don’t let that deter you either.” The problem, in my mind, seems especially acute for molecular evolution.

    It is commonplace to see intelligence overcome obstacles like this. But we have never, to the best of my knowledge, observed random natural processes overcome similar problems. Perhaps, in fact, natural processes have, but the point here is that we have not actually witnessed the event. So, from a purely empirical standpoint, we do not know if natural processes are capable of abiogenesis, or even if they’re capable of modest incremental changes in the real complexity of extant organisms. From a theoretical standpoint, the ability of nature to create life, or to significantly increase the complexity of existing life, is highly suspect — unless you make certain religious assumptions that have no basis in empirical science.

  140. It is commonplace to see intelligence overcome obstacles like this.

    It is commonplace for intelligence to construct complexity from materials, collections of molecules that retain their integrity while you get them all into place – to build a jumbo jet, say. It is also commonplace for intelligence to construct software systems that do not need to function in an integrated way until one turns on the power, and presses “start”. The program’s statements don’t start executing while you are still writing the code. In both of these scenarios, the parts of our construction stay put until we want them to operate, then we can animate them. But this does not hold in the molecular world, and it is NOT commonplace for the kind of complexity observed in a cell to be built by intelligence ab initio.

    But we have never, to the best of my knowledge, observed random natural processes overcome similar problems. Perhaps, in fact, natural processes have, but the point here is that we have not actually witnessed the event.

    We have never observed intelligence achieving the kind of suspension of physical laws that would be necessary to create a complex molecular system in one step, so spare me the “you-weren’t-there” rhetoric. This one does not cut both ways – you are not merely appealing to one of two equally unobserved events, but invoking completely unknown physics.

    So, from a purely empirical standpoint, we do not know if natural processes are capable of abiogenesis, or even if they’re capable of modest incremental changes in the real complexity of extant organisms.

    From a purely empirical standpoint, we do not know if intelligence is capable of abiogenesis. And I think, in this “big bang” scenario, that it is impossible with known physics. Invoke unknown physics if you wish, but don’t attempt to suggest that this is simply an argument that “cuts both ways”.

    From a theoretical standpoint, the ability of nature to create life, or to significantly increase the complexity of existing life, is highly suspect — unless you make certain religious assumptions that have no basis in empirical science.

    From a theoretical standpoint, the ability of intelligence to create life (in one step) is highly suspect — unless you make certain religious assumptions that have no basis in empirical science.

  141. (Are there examples of cells using electrons for energy?)

    All cells use electrons for energy! Electrons are the fundamental unit of energy currency. Cell energetics is all about them moving from molecules with greater affinity for them to those with lesser (redox, or oxidation-reduction pairs), equivalent to rolling a ball down a hill. In photosynthesis, photons merely excite them ‘uphill’, and then they are ‘rolled’ down chains of serially greater electron affinity, the energy being used to do work.

    Some cells rely on importing molecules in which the electrons are still ‘uphill’ with respect to the redox gradient. Ours, for example – we get them courtesy of plants.

  142. Evolutionists often assert that complex subsystems within an organism develop over many generations. So, during the construction process, I can’t just place a couple of elements next to each other and say, ”Staaay…hold your positions for a thousand generations while the hundred other elements I need for a functional subsystem come into being

    Just to note also that this is a fundamentally different issue to that being discussed – abiogenesis. The interactors you refer to here are not interacting through molecular mechanisms, but through larger-scale physical ones. It is a problem of a completely different type to determine the ways in which IC systems in organisms may be achieved, versus the molecular problem of constructing a first cell, by whatever means we happen – religiously or not – to incline towards.

  143. …this [incremental development of a complex subsystem over multiple generations] is a fundamentally different issue to that being discussed – abiogenesis.

    Yes, molecular evolution is different in that it obviously cannot build something over multiple generations, since no replication mechanism is in place. Incremental advances in the process of molecular evolution are more like one-shot propositions: for each molecular step towards life, all the necessary components for chemical “viability” have to be put into place virtually simultaneously. (Not all steps simultaneously, but for each step, all the necessary components simultaneously.)

    However, there is a similarity between the Darwinian problem and the molecular problem. There is the temptation to assume, in the case of molecular evolution, that some molecular sub-component — one that’s necessary but not sufficient for the next evolutionary step forward — having been produced by random processes, will now be somehow preserved until the balance of the required sub-components are introduced. Forces at the molecular level (e.g. entropy, competing chemical attractions, etc) will almost always guarantee that preservation will not occur. If this novel molecular arrangement were stable, it would itself be the next step forward. But it’s not stable, and is therefore highly unlikely to be preserved.

    Assuming that preservation does occur greatly increases the statistical probability that the next step will be reached. But the assumption is wrong, resulting in a vast underestimation of the statistical probability of abiogenesis by naturalistic mechanisms. It’s Dawkins’ METHINKSITISLIKEAWEASEL fallacy at the level of molecular evolution.

  144. It’s Dawkins’ METHINKSITISLIKEAWEASEL fallacy at the level of molecular evolution.

    Mayhap, but I’m not talking about evolution! The topic is abiogenesis – the plausibility of rival proposed mechanisms for creating one, or several, replicating cells. I recognise a connection in the mind between apparent ‘irreducible complexity’ issues in the two systems, and prejudice against incremental arguments, but they really rely upon a wholly different explanatory framework.

    The “first cell problem”, from a design perspective, requires one to prevent molecular interactions from taking place until one is good and ready for them to take place. The “complex specified structure problem”, from a design perspective, relates to means by which the parts can find themselves together in a functioning cell. It is comparatively trivial to engineer multiple elements and place them in a single functional genome. It is not trivial to take multiple molecules and prevent them from following their energetic gradients until you decide it is time.

  145. Cell energetics is all about them moving from molecules with greater affinity for them to those with lesser

    D’oh! Feel free to point out the glaring error in that statement! They move both ways, of course, but you need to put energy in – roll the ball uphill – to make ‘em move the way I’d placed them.

  146. I am using the phrase molecular evolution to refer to the theoretical process by which abiogenesis occurred, i.e. the presumably incremental sequence of natural events by which the first life arose from inorganic systems. Molecular evolution apparently covers much more ground than my definition allows, so I am probably misusing the phrase, or at least using it in a confusing way. I am far from an expert in biology, and I apologize for the confusion. Is there some other term or phrase that would better express my meaning?

    (Abiogenesis, by itself, does not quite capture my intended meaning. I want to emphasize process, and successive stepwise increases in complexity. But the term abiogenesis, unqualified, allows for the possibility of the instantaneous appearance of life, a possibility I wish to exclude for present purposes.)

    I’m not talking about evolution!

    I understand that you’re not talking about evolution in the Darwinian sense; Darwinian evolution could only begin after the first life was on the scene. But if abiogenesis was an incremental process, as opposed to an instantaneous event, wouldn’t the process qualify as a kind of evolution?

    I recognise a connection in the mind between apparent ‘irreducible complexity’ issues in the two systems, and prejudice against incremental arguments…

    I hope that I’ve not written anything that would suggest that I have a prejudice, or even a bias, against the possibility that life was constructed (intelligently or not) by increments. I have no such bias. I see no inherent contradiction in positing intelligent agency while simultaneously allowing for incremental advances in complexity. “Incremental development by intelligent agency” is not a contradiction in terms.

    It is comparatively trivial to engineer multiple elements and place them in a single functional genome. It is not trivial to take multiple molecules and prevent them from following their energetic gradients until you decide it is time.

    I think I agree with everything you assert in your last paragraph, provided that the necessary emphasis is placed upon the comparatively in “comparatively trivial”.

  147. You seem to understand me to be promoting some sort of a “big bang” theory of intelligent intervention into natural processes — large-scale supernatural “fiddling” with nature at one or more points in the process (or perhaps the single instantaneous event) of abiogenesis. I have not consciously promoted any such thing.

    At most, I have intended to assert merely that natural processes, as understood by empirical science, seem incapable of producing life. I suggested that intelligent agency provides a reasonable explanation for the existence of life. I’ve not speculated on how or when intelligent agency may have impinged upon natural processes. Assuming intelligence, or products of intelligence, were injected into the universe, did it happen only at the moment of the cosmic big bang? (If so, why wouldn’t we see obvious evidence that inorganic systems, conforming to the laws of physics, tend towards life, rather than away from life?) Was information injected in one or more massive chunks at points in time well after the big bang? Was it injected in small bits and pieces over millions and millions of years? I don’t know, nor do I care to speculate, for present purposes.

    As I wrote in a previous post, I have no bias against incremental development. But I freely confess that I do believe that ultimately, life arose as a consequence of divine decree. And I recognize that to be a metaphysical belief on my part — a belief that, in my opinion, is fully consistent with science, properly defined.

    From a purely empirical standpoint, we do not know if intelligence is capable of abiogenesis.

    Certainly, intelligence alone is incapable of abiogenesis. But then, intelligence alone is also incapable of building a jumbo jet, or even of writing a letter. To produce a physical effect, an intelligent agent must have the ability to interact with the physical world — to manipulate material entities to his (or her) means and ends. A physically impotent intelligent agent simply will not do. This much seems obvious.

    It also seems obvious that empirical science can say nothing directly about OOL, because the beginnings of life are probably forever beyond our ability to observe. Empirical science can neither confirm nor deny materialistic abiogenesis. Likewise, empirical science can neither confirm nor deny special creation, say, by an omniscient and omnipotent deity. (As an aside, the oxymoron “theistic abiogenesis” is highly suggestive.)

    Empirical science does have a proper place in the OOL discussion, though. We have observed the ability of intelligent agents to swim against the current, so to speak, of thermodynamic entropy. Human beings create physical systems every day — systems that are highly improbable (I would say impossible) apart from intelligence. That makes intelligent agency a reasonable (but not a necessary) inference for OOL purposes. Materialistic abiogenesis has no comparable support from empirical science.

    Your statement raises another, perhaps less obvious, philosophical question in my mind: Does a physical effect that intelligence is incapable of producing fall under the purview of science, given science’s own view of itself?

    Suppose that intelligence is incapable of abiogenesis — that even a supremely intelligent agent, with limitless power, is unable to create life from non-life. Would that not implicitly exclude abiogenesis from the purview of science altogether? (Here I mean science in general, not just empirical science.)

    My thoughts along this line are half-baked, and the question may prove to be vacuous in the end. But I’m out of time to develop my thoughts further.

    From a theoretical standpoint, the ability of intelligence to create life (in one step) is highly suspect — unless you make certain religious assumptions that have no basis in empirical science.

    As I wrote earlier, I have no particular commitment to a one-step beginning for life. As for metaphysical and/or religious assumptions, I’m willing to be explicit and open about them in the workplace, in the classroom, and in the courtroom. Are materialistic abiogenists or macroevolutionists willing to do likewise?

    Thanks for a thought-provoking post, Chas D.

  148. ChasD:

    “Consequences? Consequences? You say there are consequences in changing one’s position on a scientific issue? Whatever can you mean?”
    ====

    Mean ??? Consequences of bastardized science ruining our planet with irresponsible technologies like GMOs because in their minds they know it all. As David Suzuki said, “We don’t know enough about DNA to predict how that organism is going to behave.”

    Don’t tell an evolutionist they don’t know something.

  149. Molecular evolution apparently covers much more ground than my definition allows, so I am probably misusing the phrase, or at least using it in a confusing way. I am far from an expert in biology, and I apologize for the confusion. Is there some other term or phrase that would better express my meaning?

    Not really! It’s fair enough. There is a legitimate term, “chemical evolution”, referring to the progressive sticking together of nuclei inside stars (interestingly, down an energy gradient, with iron at the bottom). Changes in simple molecular systems are probably legitimately so described also.

    But it does cause confusion, and many evo-skeptic commentators have an apparent major difficulty in disentangling the two ideas of “Life-from-non-life” on the one hand and “Modification of that life” in the other. I would put it at the head of the list of “stock misconceptions”, analogous to UD’s list of “arguments we have heard before and don’t want to hear again”!

    I think the problem is that critics of the biological consensus are not always as au fait with the material as they might be. It’s not even common knowledge amongst biologists, to be honest. Very little evolutionary theory was taught in my grad course in biochemistry. I have tried to redress the balance, by buying myself textbooks and trying to get to grips with them – because it is interesting. But of course, if one is hostile to the very idea, one would not spend very long in understanding what can be a densely mathematical topic. Nonetheless, biological evolution is specifically change in populations once you have replication, not anything that might occur before you do.

    So, in short, there is a very sharp mechanistic discontinuity between incremental processes leading towards the first replicator, and those leading from it, which is why I critique the “project design” approach of the OP. If one thinks in terms of a large number of things that have to interact before a functioning replicator can emerge, one finds oneself with a problem either way (if mechanistic considerations actually matter!). If one’s background is in IT, or engineering, one may think it perfectly conceivable that the bits and pieces can be manoeuvred into place. Even skeptical chemists seem to have little problem with this, which surprises me. But I think that this demands more than mere intelligence, but unknown physics as well – unless an incremental approach is considered.

  150. Thanks for a thought-provoking post, Chas D.

    Missed this – thanks for the thanks! Sorry if I misread you.

    A metaphor struck me – hardly original, since we have the “Spark of Life”, but the idea of a flame seems pertinent. You have to have energy. Almost literally, we burn – albeit rather slowly. We roll electrons down gradients of free energy, having been shoved ‘uphill’ by sunlight or raw chemistry. I do think that is the #1 constraint, and must predate everything else, including replication. I think that the presence of that same adenine-ribose-phosphate group in RNA (for ‘information’) and ATP (central energetic unit) and NAD and FAD (central to respiration and to photosynthesis and other more exotic electron transport chains) is deeply fundamental. It does a completely different job in each case, and yet that same molecular group pops up again and again. These molecules are vital, in the deepest sense.

    The essence is igniting the spark of replication. Whether an intelligence spent ages flicking its metaphorical lighter trying to ignite the bare tinder, I don’t know. But once the flame had caught, an endless supply of replicators could keep themselves going like the olympic torch, a wildfire of replicating replicators, spreading outwards to clothe the world. Or that, in my more poetic moments, is how I might express it! :0)

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