“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

I'm puzzled by this thread. Requirements are something that come up as part of design. A requirements explosion could be a serious problem for ID proponents. I don't see where it is relevant to questions on the natural origin of life.Neil Rickert_{October 21, 2011
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Could thoughts be physical ??? If "dmullenix's" posts(thoughts) are nothing more than protons bouncing randomly and endlessly inside his skull, I am merely responding to protons spinning endlessly inside "dmullenix's" skull or is there an actual consciousness ??? Is consciousness physical (not talking immortal soul here) ??? Just a freewilled living entity able to intelligently guide and direct the physical. And if that is the case, then how do his random spinning protons bouncing off those thick Skull walls know what I am saying or talking about and how do they know how to properly respond to what I am saying by giving me a specific reply ??? Are those random protons angry at my beliefs and if they are, then are emotions also physical ??? Hmmmmmmmmmm?????????????????????? The problem with a strict materialist accepting an Intelligent Designer is that they are also admitting that there is accountability that naturally comes with recognizing an intelligent designer who has the right to set moral boundaries and that is totally unacceptable. Hence, we get walnut shell gaming. No doubt their only way of retreat on this is to escape into the realm of New Age Star Trekky myths which in themselves were inspired of Buddhist/Hinduist scribes. ----- Joseph: "Software is physical?" ==== It's only physical when an intelligence etches it into material substrate, such as a CD. But as George Gilder explained, that information is still the immaterial property of the mind that created it. Much like the brain power of those collective Microsoft Programmers and Computer Engineers who created "Windows 7" on that plastic CD disk to be downloaded into a computer to make it functional. The information is still immaterial and only appears as material by the intelligent 'wishes'(another immaterial item) by the intelligence that made it so. That's why the definition shell gaming about snowflakes being information or Grand Canyon geology being information or gravity being information don't actually become information until an intelligence comes along, studies them and reveals information to other intelligent minds. Information is only information to another intelligence, otherwise it's nothing more useless patterns for which other patterns are incapable of caring one way or the other. Remember, just blind pointless purposeless indifference. A water molecule or group of water molecules have no encoded information etched into it for the purpose/intent of various pattern formation of a snowflakes or any other H2O anomalie(and there are many). Not like the protein material of DNA where vast amounts of information are etched into it.Eocene_{October 21, 2011
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From SciAm:
"We let it run for 100 hours," Joyce recalls, "during which we saw an overall amplification in the number of replicator molecules by 1023. Pretty soon the original replicator types died out, and the recombinants began to take over the population." None of the recombinants, however, could do something new that is, something that none of its ancestors could perform. That crucial missing ingredient still separates artificial evolution from true Darwinian evolution. "This is not alive," Joyce emphasizes. "In life, novel function can be invented out of whole cloth. We don't have that. Our goal is to make life in the lab, but to get there we need to increase the complexity of the system so that it can start inventing new function, rather than just optimizing the function we've designed into it."
Joseph_{October 21, 2011
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Elizabeth, Joyce said nothing new evolved, I will go with him. Thanks.Joseph_{October 21, 2011
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Letters that Darwin wrote says directed evolution is not DarwinianJoseph_{October 21, 2011
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Darwin spent the first section of "Origin" discussing artificial selection. What makes you think directed evolution isn't "Darwinian"?Petrushka_{October 21, 2011
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dmullenix: "What does ID say the first living thing was?" ==== I doubt they could give any more accurate answer than you, since none of them were present way back when either. ---- dmullenix: "Can I gloat and declare victory if ID can’t give me an answer?" ==== If ID is unable to give an accurate answer for the very same (lack of having a DeLorean Time Machine) reasons you have, perhaps that makes you brothers. You wouldn't want to mistreat your brothers would you ??? ---- dmullenix: "Most magic implies intelligence." ==== Correct!!! Any Laboratory where cheating intelligence is used to concoct Abiogenesis myths and fables and promote these as fact would qualify as "magic". Especially where the black cloak of intelligence was actually used in any and all experiments, but with puff of gray area smoky explanations gives it the appearance of random luck and chance as accomplishing great and wonderous things.Eocene_{October 21, 2011
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Excuse me for saying this and of course I do understand this may get me flamed, but that is an absolute lie.
No, it is not a lie. I don't lie.
We are constantly bombarded by Atheists/Evolutionists who insist we don’t know the definition of just what Evolution is. The official continual pounding we get is that evolution is not about anything to do with origins, it’s about life evolving once it happens. We get condescendingly informed that origins is “Abiogenesis” and has ZERO to do with Molecules Evolving.
Well, that would be incorrect. Anything about evolving molecules is about evolution. Obviously. And anything about the diffential reproduction of heritable variance is about Darwinian evolution, because that's what the Darwinian mechanism is. You can set up Darwinian mechanisms intentionally, as in a GA, or in Joyce's lab, or in selective breeding, or you can watch them happen without human interference. But they are Darwinian either way - at least in the sense I meant it, which is the sense in which it is usually used, and is the sense in which Joyce's results were described as Darwinian: he observed replication with heritable variation in reproductive success (Darwinian mechanism) resulting in a prevalence in the population of variants that outbred the originals (Darwinian evolution). You may have misunderstood my use of the term (though it's absolutely standard) but I did not lie, and AFAIK, what I said is correct.
Of course we also witness the word/term “evolution” being used with reference to the evolution of planets, etc, but hey, let’s not go there.
No, let's not.
In any case, what evolution ultimately means is blind undirected purposeless forces and chemical cocktails accomplishing everything necessary for the conscious extistance we all know and experience now. Gerald Joyce’s magic RNA-World molecule experiment did NOT in any way represent anything which falls under the criteria of blind undirected forces making Darwinian evolution happen in any way or form.
Yes, they did. the "blind undirected" part was the mis-copying of some of the molecules. the "undirected forces" part is simply the self-evident logic that variants that replicate better will replicate more often. Undesigned variants (variants that mutated from the original) eventually emerged that replicated better than the starting population. Ergo blind undirected forces resulted in a better replicator than those designed by the experimenters.Elizabeth Liddle_{October 21, 2011
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dmullenix you state;
All information is physical.
This statement comes from Rolf Landauer's dictum:
'Information is Physical':
And perhaps the belief that all 'information is physical' (merely emergent from a material substrate) can more specifically be traced to this specific paper by Landauer:
The physical nature of information - Rolf Landauer - 1996 Excerpt: Information is inevitably tied to a physical representation and therefore to restrictions and possibilities related to the laws of physics and the parts available in the universe. http://qi.ethz.ch/edu/qisemFS09/papers/64_Landauer_The_physical_nature_of_information.pdf
The discussion behind this particular dictum that 'information is physical' has been quite detailed and extensive; Here is one paper giving a overview:
Maxwell’s Demon and Landauer’s Principle http://www-scf.usc.edu/~justinsc/Papers/2005_11Nov_Maxwells_Demon.pdf
Landauer held that information was 'merely' physical (merely emergent from a material substrate) because he believed that information ALWAYS required energy to erase it from a computer. Yet dmullenix you do not seem to be aware that this 'proof', that Landauer's used, to prove information was merely physical is now shown to be false. i.e. The 'proof' underlying Landauer's dictum is now overturned, thus the dictum 'information is physical' (merely emergent from a material substrate) is now falsified. Here is the work that falsified Landauer's dictum:
Quantum knowledge cools computers: New understanding of entropy – June 2011 Excerpt: No heat, even a cooling effect; In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy. Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.” http://www.sciencedaily.com/releases/2011/06/110601134300.htm
A short synapses is that quantum mechanics has shown that information is its own completely unique entity that is completely independent of any space-time constraints. Moreover this 'transcendent' (and dominate) quantum information was used to show that classical information, such as we find encoded on computers and on DNA (material substrates), was used to show that information IS NOT 'physical' (in the sense that Landauer was using the term 'physical' to imply emergent from material substrate), but that this classical information encoded on computers (and DNA) was indeed a subset of quantum information that is to be regarded with full respect of a independent entity separate from matter and/or energy! further notes:
Falsification Of Neo-Darwinism by Quantum Entanglement/Information https://docs.google.com/document/d/1p8AQgqFqiRQwyaF8t1_CKTPQ9duN8FHU9-pV4oBDOVs/edit?hl=en_US
music and verse:
Theory Of A Deadman - By The Way http://www.youtube.com/watch?v=8Py8nRJGma0 John 1:1-3 In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made.
bornagain77_{October 21, 2011
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In the context of this discussion, it is the lack of informational entropy that should concern us. For example, syntax and semantics are quite clearly present in the genetic code of organisms. > Is entropy a physical reality or an illusion? Entropy is both a physical reality (e.g., the thermodynamic entropy in a system of material objects) and a non-physical reality (e.g., the Shannon entropy in a million-bit sequence of binary numbers). Is a bit physical? A bit (as a unit of information) may map to the state of some physical entity, but it is not that entity.kdonnelly_{October 21, 2011
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You're confusing the medium (the physical substrate that carries the information) with the information itself. They are quite obviously not the same.kdonnelly_{October 21, 2011
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Requirements explosion as a consequence of increased complexity Yesterday I logged a comment about the phenomena of "requirements explosion" during the software development process. I referenced Robert L. Glass's book, Facts and Fallacies of Software Engineering (Addison-Wesley / Pearson Education, 2003). At the time I wrote the comment, I didn't have Glass's book handy, so I had to "wing it" from memory as I wrote. Later I was able to re-read the relevant section of his book. Those of you who have an interest in software engineering, and its possible bearing on the ID debate, might find the following clarifications useful. Glass brings up the topic of requirements explosion in the context of a discussion about complexity. He asserts the following as one of the facts of software engineering: For every 25 percent increase in problem complexity, there is a 100 percent increase in the complexity of the software solution. That's not a condition to try to change (even though reducing complexity is always a desirable thing to do); that's just the way it is. If Glass is correct, the relationship between software solution complexity and problem complexity is obviously super-linear. Solution complexity increases at a much faster rate than problem complexity. According to Glass, this fact (perhaps better called a heuristic) illuminates at least 13 frequently asked questions about phenomena commonly observed during the software development process. Here are three of those questions (again quoting Glass): * Why are people so important [to the successful development of software]? (Because it takes considerable intelligence and skill to overcome complexity.) * Why is estimation so difficult? (Because our solutions are so much more complicated than our problems appear to be.) * Why is there a requirements explosion (as we move from requirements to design, explicit requirements explode into the hugely more numerous implicit requirements necessary to produce a workable design)? (Because we are moving from the 25 percent part of the world to the 100 percent part of the world.) Glass makes the conventional distinction between specification and design. The specification of a software system defines what a system is required to do: given some set of inputs, we expect some set of outputs. Specification answers the questions, "How must the system behave?" On the other hand, design answers the question, "How will we go about building a system that meets the requirements -- that delivers the expected behavior?" In my remarks yesterday, I suggested that the requirements explosion manifests itself when actual implementation of the system begins, i.e. after the formal design phase is presumably complete. But Glass observes the beginning of the explosion at an earlier stage, during the transition from specification to design. As design proceeds, implicit requirements multiply. While it's true that the construction phase may cause even more requirements to surface, Glass is correct to point out that many implicit requirements are discovered during design. I don't claim that the parallels between software development and the OOL problem are perfect, but it seems to me that they are, at a minimum, suggestive.kdonnelly_{October 21, 2011
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And? Length, depth and width are also physical. But it does not stop us from measuring objects' dimensions and reasoning about them. Likewise, information is something that can be objectively measured and reasoned about. A common notion of information theory relates information with entropy (uncertainty associated with the value of a discrete random variable). Is entropy a physical reality or an illusion? We can ovbserve information being communicated and processed across the living cell. I guess you agree that it is an objectively observed process (unless you are a solipsist).Eugene S_{October 21, 2011
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A longer reply. I agree that the first living thing was very different from what we see today - much simpler. I could answer your quesstion about how life arose a lot better if I knew what the first life was. Science has no data so it can only make informed guesses. What does ID say the first living thing was? Can I gloat and declare victory if ID can't give me an answer? Most magic implies intelligence.dmullenix_{October 21, 2011
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That was posted in the wrong place accidentally. I meant it as a response to DMullenix.Eugene S_{October 21, 2011
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So the information that comes out of people's mouths is physical? Software is physical?Joseph_{October 21, 2011
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We have two positions whereby one assumes that: 1. the first living thing was a complex unicellular organism that must be able to have metabolism and relication capabilities. 2. the "no magic" position: the first living thing is inorganic. For the first position, we have something concrete that we can study, i.e. unicellular organisms of today. Furthermore, analysis of what we have today strongly suggests that there are requirements for minimal functionality that the first living organism(s) must satisfy. These requirements lead to serious questions of functional irreducibility, parameter tuning and information processing. No one is saying they must have been as complex as today. But the bad news is that they must have already been incredibly complex. For the second assumption, we have no evidence whatever. What material evidence can you produce to show that such a thing as (inorganic) First Self-Replicator existed outside of your imagination? Elsewhere you attempted to aswer a list of questions. Apparently, you did not even mention that FSR was no more than a hypothesis. Can you the the stretch of imagination? On whose side is this?Eugene S_{October 21, 2011
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All information is physical.dmullenix_{October 21, 2011
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dmullenix: > Would somebody on the ID side of > the argument kindly tell us what > the First Living Thing was like > and how you know it? The first living thing was unlike what scientists normally call "inorganic matter". It exhibited properties and behaviors that are very different from what we observe in non-living things. If I am not mistaken, any biology textbook worth its salt will help you answer your question. I don't intend to be flippant. The really interesting question is not, "What, specifically, was the first living organism like"?, but rather, "How is it, given certain properties and behaviors we observe in all non-living things, that any kind of life could have arisen via purely 'natural' processes?" > it [science] notes that life is 100 percent material Not so. Life bears information; indeed, life is a medium of information. Information is a fundamental entity, on par with matter or energy. Information drives the processes that sustain life, and is absolutely necessary to life. But information is neither matter nor energy. > I honestly think that some of > you [ID adherents] still believe > that life is somehow magical. It's not ID adherents who are waving the magic wand. An appeal to intelligent agency is the polar opposite of an appeal to magic. And it seems to me that, by any truly empirical standard, the OOL just-so stories put forward by molecular evolutionists would appropriately be followed by the exclamation, "Presto change-o!"kdonnelly_{October 21, 2011
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Would somebody on the ID side of the argument kindly tell us what the First Living Thing was like and how you know it? And if nobody on the ID side has an answer, then where do you get the gall to demand that others tell you what it was like and consider it some sort of victory when they can't? So far, the argument looks like this to me: Science: Has no samples of the First Living Thing. However, it notes that life is 100 percent material (physical if you're BA77 - see the definitions of materialist and physicalist) and thinks it's pretty likely that the First Living Thing was also 100 percent material/physical. It also assumes it was very simple because complex things are too unlikely to appear spontaneously in any reasonable amount of time. Most also think that polymers were vital to First Life because they're vital to modern life. ID: I honestly think that some of you still believe that life is somehow magical. Has no samples of the First Living Thing. Since the Intellignet Designer is credited with being able to adjust the universe's constants to make it suitable for life, I assume that you think that He is supernatural too or at least a highly complex being from outside this universe. No surprise in that case that you all seem to think that the First Living Thing was a modern organism. What else would a magical / complex being from outside the universe make? But if you can't tell us what the First Living Thing was, then I'm going to take a page out of your own playbook and declare victory.dmullenix_{October 21, 2011
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Elizabeth Liddle: "In Joyce’s experiment, cross-replicating molecules underwent Darwinian evolution." ===== Excuse me for saying this and of course I do understand this may get me flamed, but that is an absolute lie. We are constantly bombarded by Atheists/Evolutionists who insist we don't know the definition of just what Evolution is. The official continual pounding we get is that evolution is not about anything to do with origins, it's about life evolving once it happens. We get condescendingly informed that origins is "Abiogenesis" and has ZERO to do with Molecules Evolving. Of course we also witness the word/term "evolution" being used with reference to the evolution of planets, etc, but hey, let's not go there. In any case, what evolution ultimately means is blind undirected purposeless forces and chemical cocktails accomplishing everything necessary for the conscious extistance we all know and experience now. Gerald Joyce's magic RNA-World molecule experiment did NOT in any way represent anything which falls under the criteria of blind undirected forces making Darwinian evolution happen in any way or form. ---- Elizabeth Liddle: "The molecules were designed by Joyce’s team, in pairs, and when “fed” with designed RNA “food” molecules “mated” with their opposite number, producing progeny that were not always identical to the originals. In particular, some “mated” with the “wrong” partner, producing novel progeny. Some of these novel progeny also continued to cross-replicate, more successfully than the originals, so that by the end of the experiment, they outnumbered the originals." ===== The above is nothing more than intelligent designing by an intelligent agent who admitted he had intent, purpose and goals with regards his experiment. Seriously, go to the Scripps Research Institute's Gerald Joyce page and read what he admits. You also left out the fact that Gerald Joyce and his intelligent white coated Lab Assistants intelligently designed a device(for which they have a patent for) which confines the molecules in an imaginary perfect environment created from the intelligent mind of Gerald Joyce whose own plans, thoughts and ideas chose just how this ecosystem in early world would be for a success. You also left out that it was run by a specific intelligently designed computer progam which forced along the so-called molecule evolution and also acted as an Intelligent Selection agent with preprogrammed selection criteria fed into the device. That's hardly Darwinian Evolution. The ballsy thing Joyce did was completely fabricate a fable of mindless molecules coming to self-awareness life, competing for food and weeding out lesser molecules in a survival of the fittest game helped along by that computer program, then having sex with each other, having babies, many being given the lable of different species after the computer intelligently selected for them, etc, etc and finally we get this bold lie at the end. "This is evolution at the level of molecules as a fact, not a theory," says the study's senior investigator, Gerald Joyce of the Scripts Research Institute. ---- Here's a further quote from Scripps own site with regards Joyce's experiment: ********** "NEWS and VIEWS online weekly of Scripts Research Institute "Scientists Automate Molecular Evolution" By Renee Twombly "Under the control of a computer at The Scripps Research Institute, a population of billions of genes morphed through 500 cycles of forced adaptation to emerge as molecules that could grow faster and faster on a continually dwindling source of chemical fuel—a feat that researchers describe as an example of "Darwinian evolution on a chip." "The super molecules that resulted, a species of RNA enzyme, were produced in about 70 hours using an automated tool that is about the size of a compact disc, according to the study published in the April issue of PLoS Biology. The Scripps Research investigators who designed the device note that the findings provide an example of the Darwinian principle of selective pressure at work, seen in real time." ************* And finally there appears to be some ignorance by some others here as to just exactly what Gerald Joyce's experiments was all about. Here is a link to Stephen Myers take on what Gerald Joyce actually did. http://www.signatureinthecell.com/responses/response-to-tls.php -------Eocene_{October 21, 2011
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InVivoVeritas, I’m going to attempt to answer your questions. I’m assuming for this quiz that the First Self Replicator is a large polymer that has been encapsulated by a bubble shaped membrane that is porous to the smaller molecules that the polymer is made of and impervious to the larger polymer. 1. I guess we agree – based on authority of Dr. Szostak – and our common sense that a membrane presence is an accepted requirement. Most likely. Since we don’t know what the First Self Replicator was, we can’t say for absolutely sure. A polymer stuck to a wall in a microscopic subterranean passage making copies of itself from small molecules flowing by and releasing those copies into the stream to stick on the walls and start reproducing themselves would not. But since membranes would also do the job and are observed to form naturally and easily, they may very well have been part of the FSR. But again, nobody knows what the First Self Replicator was. It may have been completely unlike anything anybody has thought of. 2. Will this replicator have any in-take of materials? Yes / No Yes. 3. Will this replicator have any output of materials? Yes / No There will probably be some leakage. What can diffuse into a membrane can diffuse out as well. 4. Will this replicator take in ANY type of material? Yes / No Just small molecules. 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 There will almost certainly be selectivity by size of molecule – small ones get through, big ones don’t. 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 Same as number five. Small molecules yes, large molecules 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 See 5 and 6. Also see 1.2.2 8. Will the mass inside the replicator (its membrane) grow indefinitely? Yes / No No. Eventually the bubble membrane will burst, releasing the large molecules that have been building inside it. If pieces of the membrane then close around more than one of the large molecules that have been building up inside the membrane, we have reproduction and hence life. 9. Will the membrane itself have a self-replicating capability ? Yes / No (see: http://www.lapetus.uchile.cl/l.....nglife.pdf). Membrane bubbles made from sheets of small molecules can grow by adding new molecules. Eventually they grow too big and burst. If the pieces of the large bubble close around the polymers growing inside them, they will have reproduced. 10. What would be the source of energy that will ‘animate’ the replicator and its ‘replication’ process ? answer: xxxxx Ordinary thermal energy that keeps molecules jigging and crashing into each other. Brownian motion, basically. 11. Will this replicator must manifest a ‘materials-to-energy’ conversion capability ? Yes / No 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 Faster than the large molecules are broken up, whatever time that is. 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, YYYYY No. Upright BiPed: Every “Darwinian capable self-replicator” in existence is the product of billions of years of evolution. You can only see modern organisms in your microscope, not the organisms of billions of years ago. In that time they have become very complex, efficient and hardy self replicators and consequently probably have very little in common with the First Self Replicator beyond self replication itself. Looking at one of these modern organisms and saying that the First Organism has to have any or all of the modern organism’s properties just gets you to chasing red herrings, oil-soaked or otherwise.dmullenix_{October 21, 2011
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DrRec: Most membrane functions are mediated by specific membrane proteins, receptors, channels, and so on.gpuccio_{October 21, 2011
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DrRec: I like your idea. Could you please suggest one that is of general interest, and pertinent to the debate? I would be happy do discuss it in detail. I have already discussed on detail a very important paper from Szostak in the past, and found it deeply biased. So, please, suggest one of those papers, kindly summarize the points it makes that, in your opinion, are important, and let's discuss.gpuccio_{October 21, 2011
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Definitions of which words? I'm talking about "representions" and "protocols". It is their observed dynamic physicality that matters, not the words. Fine. In which case please define the "observed dynamic physicality" that they refer to.
I suspect this indicates that you do not intend to challenge the evidence of a semiotic state in protein synthesis. Fair enough.
Possibly. I owe about three people replies to substantial posts. I'd like to tackle yours, but substantial posts require substantial thought.Elizabeth Liddle_{October 20, 2011
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The charge of being ill-defined is rather weak against the fact that the argument was restated for you using the definitions of these words (taken directly from Merriam-Webster) in place of the words themselves. In any case, as has been the offer made to you from the very start, you can call these things anything you wish. Be my guest. It is their observed dynamic physicality that matters, not the words. I suspect this indicates that you do not intend to challenge the evidence of a semiotic state in protein synthesis. Fair enough.Upright BiPed_{October 20, 2011
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It's not that the words do not "suit my views" UBP, but that they are ill-defined, abstract words that IMO beg the very question you are asking. However we have already discussed this to death, and I think we'd better leave it at that.Elizabeth Liddle_{October 20, 2011
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In Joyce's experiment, cross-replicating molecules underwent Darwinian evolution. The molecules were designed by Joyce's team, in pairs, and when "fed" with designed RNA "food" molecules "mated" with their opposite number, producing progeny that were not always identical to the originals. In particular, some "mated" with the "wrong" partner, producing novel progeny. Some of these novel progeny also continued to cross-replicate, more successfully than the originals, so that by the end of the experiment, they outnumbered the originals. As for the fact that it has been "pointed out" to me that this is not "self-replication in any meaningful sense", as with many things that are "pointed out" to me on this site, I disagree with the pointer-outer! I think this is self-replication in an extremely meaningful sense, indeed, the crucial sense: the experiment started with a population of N molecules; after a while x*N of those molecules existed; i.e. they replicated themselves (cross-replication, sure, but then, that's what we do too). Even more importantly, by the end of the experiment the most numerous molecule types were not those that matched the originals, but were a novel type that out-bred the originals. Joyce (and I) freely admit that this is not "life" and that the original population was "designed". However, what emerged had evolved by Darwinian processes, was different, in unplanned ways, to the originals, and outperformed them in reproductive success. In other words the two basic conditions for Darwinian evolution were present, and Darwinian evolution occurred.Elizabeth Liddle_{October 20, 2011
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At the risk of incurring your wrath for being tangential, my response to your comment is that there is a huge difference between drawing up a specification for something, and investigating what the minimum specification is. It is possible that the simplest Darwinian-capable self-replicator is the kind of cross-replicating RNA system designed by Joyce et all, which has no membrane at all. However, such a system may have limited capacity to move beyond a fairly meagre optimum. So my list would look very different from yours, and wouldn't contain "solutions" at all, but simply present the conditions necessary for Darwinian evolution not only to occur, but to result in successful adaptation to new environmental niches. 1. The system must be able to replicate itself with sufficient fidelity to ensure that reproductively successful variant pass those traits to their offspring, but sufficient variability to ensure differential reproductive success. 2. It must be capable of generating phenotypic variants with enhanced reproductive success within the current environment. 3. It must be capable of generating a rich enough range of phenotypic variants that to ensure that reproductive success can be enhanced along several dimensions. 4. This range should also include a rich range of neutral variants that may prove beneficial in a changed environment. The first two are the necessary conditions for Darwinian evolution - self-replication with heritable variance in reproductive success. The second two are essential to avoid extinction in the face of environmental change. How these conditions are achieved seems to me to be up for grabs. Which came first (if any)? Self-replicating lipid vesicles? Self-replicating polynucleotides? Self-replicating peptides? All three together? But, as I said, that seems to me to be an empirical question, not one we can answer from first principles.Elizabeth Liddle_{October 20, 2011
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"You can read, can't you?" Well, I'm working on it! :) BTW, nice literature bomb! And also BTW, I did not accuse Szostak of vague statements (other than the "we're halfway there" statement). Rather, I was referring to the comments by abiogenesis supporters on this and other threads. Szostak has done some great work (as I have previously said), and I hope his team keeps it up. Nevertheless, let's take a look. Just taking the first paper you cite, what do we find? We find permeability of many different "nutrients" (pentoses, selected aldohexoses, ketohexoses, and three- to six- carbon alditols) across the membrane. There are different diffusion times across the membranes, but lots of nutrients are allowed in, without any particular regard to usefulness in the nascent cell. Szostak's team concludes that "primitive cells might have had better access to ribose than the other aldopentoses," which seems a reasonable assumption, based on their work. Then come the caveats: - "However, if metabolic processes within the cell converted externally supplied sugars into products such as nucleotides and/or polynucleotides, those transformations could have been limited by the spontaneous permeation of the sugar across the membrane barrier." - "Four-carbon sugars such as threose do enter even more rapidly than ribose, and if abundant, might have led to an advantage for a polymer such as threose nucleic acid." And here is the most interesting statement: "Rate-limiting nutrient uptake apparently occurred frequently during the history of life, hence the evolution of the numerous sugar, amino acid, and ion transporters that now constitute a large fraction of many bacterial genomes." Notice how the authors *assume* evolution came up with sugar, amino acid, and ion transporters to deal with the rate-limiting nutrient uptake issue. So we have a tacit acknowledgement that those transporters are needed currently, but perhaps -- it is proposed, without demonstration -- they weren't needed earlier. Yeah, perhaps. But inquiring minds want to know. We certainly don't see a conclusion that these proto membranes deal with either the rate-limiting uptake, or the type of nutrient updake issues. I know, I know, there are lots more papers in the list. But after wading through some of these (including the other Szostak paper Elizabeth referred to and which we discussed on another thread), I can't help but feeling like we've been served up a literature bluff. Szostak is doing great work. I hope he and his team continue. But let's not get carried away and, based on a priori assumptions about how easy we think abiogenesis should be, make proclamations that aren't actually supported by the work.Eric Anderson_{October 20, 2011
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