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

_{Barry Arrington

October 19, 2011

Intelligent Design}

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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.

Comments

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.kairosfocus_{October 20, 2011
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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 TKIkairosfocus_{October 20, 2011
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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 TKIkairosfocus_{October 20, 2011
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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.Petrushka_{October 20, 2011
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Oops, my reply at #13 was meant to be a reply to Barry's #12.1NormO_{October 20, 2011
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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.NormO_{October 20, 2011
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“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.Chas D_{October 20, 2011
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OK NormO, and after you've done that and still think the expert is wrong what should you do?Barry Arrington_{October 20, 2011
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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.Charles_{October 20, 2011
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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">Elizabeth Liddle_{October 20, 2011
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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."material.infantacy_{October 20, 2011
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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.material.infantacy_{October 20, 2011
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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.Elizabeth Liddle_{October 20, 2011
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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.Elizabeth Liddle_{October 20, 2011
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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 :)Elizabeth Liddle_{October 20, 2011
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--- "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.Upright BiPed_{October 20, 2011
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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?Elizabeth Liddle_{October 20, 2011
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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.Upright BiPed_{October 20, 2011
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"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.Chas D_{October 20, 2011
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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".NormO_{October 20, 2011
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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.Upright BiPed_{October 20, 2011
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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.Eocene_{October 20, 2011
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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/dictionary/information ( 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"Eocene_{October 20, 2011
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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.DrREC_{October 20, 2011
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"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."Eric Anderson_{October 20, 2011
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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?Upright BiPed_{October 20, 2011
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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!markf_{October 20, 2011
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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.lastyearon_{October 20, 2011
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Yes, on first observation (obviously apart from the word "spontaneous"). Now please give us an example of that being spontaneusly organised.Eugene S_{October 20, 2011
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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.kairosfocus_{October 20, 2011
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