“Requirements Explosion”

_{Barry Arrington

October 20, 2011

Intelligent Design}

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In Response to InVivoVeritas, another commenter writes:

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

I find Kent’s post very interesting, because DrRec and Dr. Liddle keep suggesting that it is all really a lot more simple than all that in defense of the un-guided OOL school. Well, DrRec and Dr Liddle, experince suggests that, if anything, we are probably underestimating the problem for un-guided OOL.

Comments

Elizabeth: "including the RNA cross-replicating molecules of Joyce et all, which proved to be a Darwinian-capable system." Elizabeth, would you please describe in (basic) detail how you understand Joyce's experiment to have worked? You keep referring to it. I have read it, and it doesn't demonstrate self-replication in any meaningful sense as you keep claiming, which has been pointed out to you many times. Rather than just referencing it over and over, please describe briefly how you think the experiment took place and what the result was.Eric Anderson_{October 20, 2011
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Dr. Liddle, I appreciate you taking the time to answer item by item my questions. I would focus on this statement you made: ? “My own position is that the key OOL question is not “how could something as complex as a modern cell not have been designed?” but “how simple could a self-replicator be and still be capable of Darwinian evolution?” I am ready to change the TITLE of my original Requirements List into: “The Requirement List for a self-replicator capable of Darwinian evolution”. The next reasonable question would be how the original list may change if we changed the title. Let me try to put on paper my core questions that will lead logically to a list of (possibly adjusted / simplified) requirements. 1. I guess we agree – based on authority of Dr. Szostak – and our common sense that a membrane presence is an accepted requirement. 2. Will this replicator have any in-take of materials? Yes / No 3. Will this replicator have any output of materials? Yes / No 4. Will this replicator take in ANY type of material? Yes / No 5. Will it be any SELECTIVITY – exercised by the membrane or by what is INSIDE the replicator - for what type of materials are taken in ? Yes / No 6. Will it be any SELECTIVITY – exercised by the membrane or by what is INSIDE the replicator - for what type of materials are pushed out ? Yes / No 7. What would be the key / mechanism /rule / affinity by which certain type of materials are accepted in (assuming – as above – some selectivity is manifested) ? answer: xxxx 8. Will the mass inside the replicator (its membrane) grow indefinitely? Yes / No 9. Will the membrane itself have a self-replicating capability ? Yes / No (see: http://www.lapetus.uchile.cl/lapetus/archivos/1208817083Synthesizinglife.pdf). 10. What would be the source of energy that will ‘animate’ the replicator and its ‘replication’ process ? answer: xxxxx 11. Will this replicator must manifest a ‘materials-to-energy’ conversion capability ? Yes / No 12. What shall we consider a reasonable time scale for a “replication cycle” produced by the replcator? I.e. the length in time of a period in which replicator generates a full replica of itself. Is it in the milliseconds, seconds, minutes, hours, days time range ? Answer: XXXX 13. Are there any ABSOLUTELY NECESSARY “support functions” exhibited by the replicator besides the Replication Capability proper?. For example, some cell internal support structure construction (not for the sake of complicating the things, but there is a chance that by logical inference we may conclude that this minimalist replicator cannot operate in a ‘vaccum’). Dor another example, how the supposedly ‘good’ materials are transported from the membrane to ‘place of replication’? Is there any ‘manufacturing capability’ another support function of the replicator? This question naturally arise from wondering if the input materials will be used by the replicator ‘as is’ or they might need to be transformed into something else – another kind of material needed for the replication? Anwsers: XXXXX, YYYYYInVivoVeritas_{October 20, 2011
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Dr Liddle, I am sorry if the words used do not suit your views, but they suit the physical evidence to a tee. I have restated my argument using the definitons of these words (taken from Merriam-Webster) in place of the words themselves. I have also asked the question: “If in one instance we have a thing that actually is a symbolic representation, and in another we have something that just acts like a symbolic representation – then someone can surely look at the physical evidence and point to the distinction between the two." I have yet to have anyone take up that challenge. I have made my argument here. You have said that you might like to attack it. I await the opportunity to discuss the evidence. Alternately, we are not required to respond to each other, if that would suit you better.Upright BiPed_{October 20, 2011
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"No, monomers can get in but polymers can’t get out. So if the monomers form polymers within the vesicle, they stay inside, if they don’t, they can escape. So polymers build up inside the vesicle." If monomers can pass freely the membrane, is the same that polarization occur without the membrane, as the monomers will be in equilibrium with the outside. If not, wich is the permeability for the monomers? for nucleotides or nucleosides?Blas_{October 20, 2011
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Every “Darwinian capable self-replicator” in existence uses physical representations actualized by physical protocols in order to tranfer information from parent to daughter cell.
As far as we know, every Darwinian-capable self-replicator uses DNA and a translation-transcription system. That doesn't mean that no simpler Darwinian-capable self-replicator must have such a system, but it suggests that it is a very efficient one, which, if it once evolved, would tend to outcompete simpler systems. But there is already some evidence for much simpler Darwinian-capable systems, including the RNA cross-replicating molecules of Joyce et all, which proved to be a Darwinian-capable system. Re "physical representations actualized by physical protocols": I know you really like this phrase, but I find it extremely unhelpful. The terms "representations" and "protocols" are far too abstract to serve as diagnostic criteria.Elizabeth Liddle_{October 20, 2011
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Is everything that is let in also let out, or is there some control?
No, monomers can get in but polymers can't get out. So if the monomers form polymers within the vesicle, they stay inside, if they don't, they can escape. So polymers build up inside the vesicle. But as DrREC says, the findings are in Szostak's papers, There is plenty of detail. One particularly interesting paper is about transition from simple lipid layer to phospholipid layer.Elizabeth Liddle_{October 20, 2011
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Dr. Liddle, It appears very clear to me that you employ an unprofessional tactic in the way you debated this topic:
It does, does it? Well, I guess you don't mince your words. I have to say I wasn't particularly aiming to be "professional", whatever that means, but if you mean that my "tactic" lacks integrity, then I beg to differ.
- a very specific list of requirements for a ‘most-primitive life form’ (totally equivalent to what you call: ‘the first, simplest, Darwinian capable self replicator’) was proposed. - You ‘decreed’ that this list of requirements is not for the simplest life form.
Well, it isn't. Or at least you haven't shown it to be - you just "decreed" that it was.
- I asked you to specify exactly which of the requirements in the list should be eliminated.
I don't know which should be eliminated. That's why people are doing research on the topic - to find out what the minimal requirements actually are.
- You did not answered my invitation. Instead you declared that definitely this is not a simplest “replicator”.
Well, it doesn't look like it to me. But I should probably have said "this doesn't look like the simplest replicator to me".
- You avoid pursuing a specific, engineering/scientific – like approach to a particular topic and you respond with generalities, changes in direction and focus, changing the terms or direction of the debate.
Well, I have to confess, I wasn't regarding this as a formal debate, merely comments on a blog! I certainly haven't deliberately attempted to "change the terms or direction of the debate". I do think though that the kinds of question people ask is often itself subject to challenge. My own position is that the key OOL question is not "how could something as complex as a modern cell not have been designed?" but "how simple could a self-replicator be and still be capable of Darwinian evolution?"
- There is a strong suspicion that you are missing arguments and your debate tactic is to “float” ABOVE and BESIDES any specific discussion point and make unsupported statements.
Well, it depends where you are standing I guess. From over here it frequently looks like other people are missing arguments! But rather than generalise about my failings as a debater, why not ask for specific clarifications? I am more than happy to provide them.
- Definitely you will not feel comfortable discussing specific points and trying to consider the proposed empirical approach to the topic in question.
What? Look, we've only just met - I don't think you are qualified to say what I will "definitely" feel about anything! I'm pretty comfortable discussing just about anything. It's why I like discussion boards!
- Please prove that I am wrong and respond to Barry Arrington’s invitation (and mine) to stay on topic and indicate which items on the original list of requirements does not make sense for the “simplest replicator”.
As I said, I don't know. That's what the OOL research is about. My point is simply that your list seems to be derived from the observed properties of modern cells, and I see no reason to think it is correct. I think it's an empirical question, not one you can work out from first principles. That's why Szostak's lab consists of chemists.Elizabeth Liddle_{October 20, 2011
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You can read, can't you? http://scholar.google.com/scholar?q=Szostak+JW+membrane+permeable&hl=en&as_sdt=0&as_vis=1&oi=scholart These publications are not "vague statements"DrREC_{October 20, 2011
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DrRec, we are not confused about semi-permeability. We're looking for details, not vague generalizations. What kind of semi-premeability are we talking about? What molecules are let in, which are kept out? Is there anything that regulates this flow, or is it just a chemical soup that happens to flow in and out of a vesicle? If there is regulation of flow, how is it accomplished? Is everything that is let in also let out, or is there some control? Does the vesicle prevent chemical constituents from entering that would cause interfering cross reactions with the nascent nucleotide sequences? Is there a way to get rid of unneeded constituents? The modern cell membrane has an incredible ability to handle all of these issues and more. There is no evidence (other than a vague statement that 'simpler will do') that you can get a functional cell without taking, at least some of, these things into account.Eric Anderson_{October 20, 2011
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"None of the commenters seem to understand membranes have inherent semi-permeability either." Not the semi-permeability for life.Blas_{October 20, 2011
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Dr. Liddle, It appears very clear to me that you employ an unprofessional tactic in the way you debated this topic: - a very specific list of requirements for a ‘most-primitive life form’ (totally equivalent to what you call: ‘the first, simplest, Darwinian capable self replicator’) was proposed. - You ‘decreed’ that this list of requirements is not for the simplest life form. - I asked you to specify exactly which of the requirements in the list should be eliminated. - You did not answered my invitation. Instead you declared that definitely this is not a simplest “replicator”. - You avoid pursuing a specific, engineering/scientific – like approach to a particular topic and you respond with generalities, changes in direction and focus, changing the terms or direction of the debate. - There is a strong suspicion that you are missing arguments and your debate tactic is to “float” ABOVE and BESIDES any specific discussion point and make unsupported statements. - Definitely you will not feel comfortable discussing specific points and trying to consider the proposed empirical approach to the topic in question. - Please prove that I am wrong and respond to Barry Arrington’s invitation (and mine) to stay on topic and indicate which items on the original list of requirements does not make sense for the “simplest replicator”.InVivoVeritas_{October 20, 2011
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The point of this OP is that it is probably more complex.
The reasonable position would be that we don't know, but that the speculations of Szostak are probably better informed than the speculations of most other people. That's the way I would bet. Self-replicating molecules were made by Spiegelman 50 years ago. Were are just now returning to that line of research. Spiegelman's "monster" evolved into a replicator having just a few dozen base pairs. This is chemistry, not biology. But very interesting.Petrushka_{October 20, 2011
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"I just don’t understand the difficulty there seems to be in differentiating between the problem of how the first, simplest, Darwinian capable self-replicator might have emerged from non-replicators, and the problem of how modern cells might have evolved from simpler proto-cells."
Yes these are two enormous problems that exist in completely separate domains. So separate in fact, that it's hard to understand why it's taken for granted that one has anything to do with the other. However you seem to be having the issue differentiating the two:
"If we can solve the first, we have made a good start on the second. But saying that because a modern cell is to complex to have emerged directly from non-life, therefore it can’t have natural origins is, well, fallacious."
The fallacy is assuming that such is possible, absent any empirical evidence. To say that Szostak is "working on it" is not evidence, it's speculation about a cause that has not been shown to be in effect. It's cognitive dissonance to fault the doubting of a cause which may very well NOT EXIST. And it's more than curious that you fault others for not differentiating something that you cannot seem to differentiate.material.infantacy_{October 20, 2011
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"saying that because a modern cell is to complex to have emerged directly from non-life, therefore it can’t have natural origins is, well, fallacious." "Strawman" is another fallacy with which you might be familiar. I count at least two in your short comment. First, you attack the OP because it fails to differentiate between the OOL problem and the issue of how evolution happens after the OOL problem is solved. You glide right past the fact that the OP does not purport to address the latter issue. So you attack the OP for addressing an issue you don’t want to talk about (because you, like all other un-guided OOL proponents are literally speechless when it comes to explaining how that might have happened) and not addressing an issue you do want to talk about. OK; but the criticism is hardly germane. Secondly, the argument you attack in the quoted portion above is not the argument that anyone (so far as I know) has ever made. You keep stamping your feet and saying that proto-cells are really much more simple than the minimum list of requirements that have been suggested. The point of this OP is that it is probably more complex. Your huff in response is hardly an argument. You are the one advancing the proposition that the proto-cell does not need all of those pieces. Kindly take InVivoVeritis’ list and tell us which ones you think a proto-cell can do without and why.Barry Arrington_{October 20, 2011
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Dr Liddle, Every "Darwinian capable self-replicator" in existence uses physical representations actualized by physical protocols in order to tranfer information from parent to daughter cell. By OBSERVATION this requires an arrangement of matter to serve as a representation within a system, it requires an arrangement of matter to physically establish an immaterial relationship between two discrete objects within that system, it requires an effect to be driven by the input of the representations, and it requires that all these physical things remain discrete. To say that you "can solve" this is to say anything at all. You are staring directly at empirical evidence that a semiotic state exist in replication and you simply refuse to acknowledge it. Are you an empiricist or not?Upright BiPed_{October 20, 2011
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^this. I just don't understand the difficulty there seems to be in differentiating between the problem of how the first, simplest, Darwinian capable self-replicator might have emerged from non-replicators, and the problem of how modern cells might have evolved from simpler proto-cells. These are two separate problems. If we can solve the first, we have made a good start on the second. But saying that because a modern cell is to complex to have emerged directly from non-life, therefore it can't have natural origins is, well, fallacious.Elizabeth Liddle_{October 20, 2011
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"because DrRec and Dr. Liddle keep suggesting that it is all really a lot more simple than all that" Well, a number of the proposed requirements for proto/first life aren't even requirements for modern life (not all living things exhibit them), yeah, I'd say it is simpler than InVivoVeritas makes it out to be. None of the commenters seem to understand membranes have inherent semi-permeability either. There are 70 free full text articles by JW Szostak in Pubmed. Maybe the next post on this topic should be discussion of his research, not one quote, by lawyers and software engineers concluding a Nobel Laureate is "extremely naive and ‘uneducated’" without having read a single publication of his.DrREC_{October 20, 2011
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