Intelligent Design

“Requirements Explosion”

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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.

107 Replies to ““Requirements Explosion”

  1. 1
    DrREC says:

    “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.

  2. 2

    ^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.

  3. 3
    Upright BiPed says:

    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?

  4. 4
    Barry Arrington says:

    “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.

  5. 5
    material.infantacy says:

    “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.

  6. 6
    Petrushka says:

    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.

  7. 7
    InVivoVeritas says:

    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”.

  8. 8
    Blas says:

    “None of the commenters seem to understand membranes have inherent semi-permeability either.”

    Not the semi-permeability for life.

  9. 9

    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.

  10. 10
    DrREC says:

    You can read, can’t you?

    http://scholar.google.com/scho.....i=scholart

    These publications are not “vague statements”

  11. 11

    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.

  12. 12

    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.

  13. 13

    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.

  14. 14
    Blas says:

    “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?

  15. 15
    Upright BiPed says:

    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.

  16. 16
    InVivoVeritas says:

    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/l.....nglife.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, YYYYY

  17. 17

    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.

  18. 18

    “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.

  19. 19

    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.

  20. 20

    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.

  21. 21

    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.

  22. 22
    Upright BiPed says:

    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.

  23. 23

    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.

  24. 24
    gpuccio says:

    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.

  25. 25
    gpuccio says:

    DrRec:

    Most membrane functions are mediated by specific membrane proteins, receptors, channels, and so on.

  26. 26
    dmullenix says:

    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.

  27. 27
    Eocene says:

    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......to-tls.php

    ——-

  28. 28
    dmullenix says:

    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.

  29. 29
    kdonnelly says:

    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!”

  30. 30
    dmullenix says:

    All information is physical.

  31. 31
    Eugene S says:

    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?

  32. 32
    Joseph says:

    So the information that comes out of people’s mouths is physical?

    Software is physical?

  33. 33
    Eugene S says:

    That was posted in the wrong place accidentally. I meant it as a response to DMullenix.

  34. 34
    dmullenix says:

    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.

  35. 35
    Eugene S says:

    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).

  36. 36
    kdonnelly says:

    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.

  37. 37
    kdonnelly says:

    You’re confusing the medium (the physical substrate that carries the information) with the information itself. They are quite obviously not the same.

  38. 38
    kdonnelly says:

    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.

  39. 39
    bornagain77 says:

    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/qisemFS0.....mation.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/~justin....._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/re.....134300.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.

  40. 40

    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.

  41. 41
    Eocene says:

    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.

  42. 42
    Petrushka says:

    Darwin spent the first section of “Origin” discussing artificial selection. What makes you think directed evolution isn’t “Darwinian”?

  43. 43
    Joseph says:

    Letters that Darwin wrote says directed evolution is not Darwinian

  44. 44
    Joseph says:

    Elizabeth,

    Joyce said nothing new evolved, I will go with him. Thanks.

  45. 45
    Joseph says:

    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.”

  46. 46
    Eocene says:

    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.

  47. 47
    Neil Rickert says:

    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.

  48. 48
    Upright BiPed says:

    Info is physical?

    Then go get a three and show it to me. Bring me a green too.

  49. 49
    Eocene says:

    Neil Rickert:

    “I’m puzzled by this thread. Requirements are something that come up as part of design.”

    “I don’t see where it is relevant to questions on the natural origin of life.”
    ====

    Why would Natural ONLY origins of life have need of requirements ??? Or even care ???
    Remember, blind pointless purposeless indifference without intent as espoused by one of your own holy men ???

    Requirements ??? Evolution doesn’t need requirements. It just does things despite it’s lack of goal driven ambitions/emotions !!!

  50. 50
    Eugene S says:

    My point was that our abstractions are capable of reflecting physical reality. So information is a very useful notion of something that goes on in reality. Shortcuts such as “rock containing information” are meaningless out of context. I agree with your other post down below, where you say that the major problem in misconceptions like these is the confusion between information and the medium.

  51. 51
    Petrushka says:

    Software is just the current configuration of hardware. There would be less confusion on this is people would think back to the early computers, which were programmed with patch cords and switches. Disk drives and memory chips are just a faster and more convenient set of switches.

    I believe at least one ID poster on this site refers to DNA as configurable switches. I have no problem with that metaphor.

  52. 52
    Joseph says:

    Petrushka:

    Software is just the current configuration of hardware.

    No, it isn’t.

    That was easy…

  53. 53
    kdonnelly says:

    Neil:

    > Requirements are something that come up as part of design.

    More properly, design, whether purposeful or not, follows requirements.

    Requirements are relevant to OOL because requirements are imposed implicitly and unavoidably on abiogenesis by the laws of physics. Inorganic matter behaves in a lawful, consistent way. Living organisms are arranged in ways that run counter to the normal arrangements we would expect from inorganic matter as it moves towards thermodynamic equilibrium. Abiogenesis requires a reversal of entropy — the imposition of a seemingly unnatural order on matter to overcome the effects of the second law. Intelligent causation is routinely observed to overcome this obstacle. Abiogenesis has never been observed, nor does it seem even minutely likely on theoretical grounds, given our present state of empirical knowledge — unless certain assumptions are smuggled in on religious grounds to make materialistic abiogenesis feasible.

    (The openness or closed-ness of a pre-biotic system to energy is irrelevant. The injection of raw, randomly directed energy does not seem sufficient in itself to overcome the entropy problem.)

  54. 54
    eigenstate says:

    bornagain77,

    Your sources do not say what you think say. Your link to the ScienceDaily article does not argue against the Landauer principle at all, but rather relates further questions about WHEN the thermodynamic irreversibility is realized, when the Landauer principle actually kicks in, in other words.

    Your “synapses” is not a synopsis of the article, if that’s what you were going for in that paragraph; while we continue to push the limits of reversibility, there is still an energy cost for irreversible information loss, when that happens.

    UprightBiped,

    Info is physical?

    Then go get a three and show it to me. Bring me a green too.

    Here’s a fairly recent link that covers some of the ground on this since Landauer, including objections by Norton and a couple others, and counters to those objections regarding “Information is physical”:

    http://philsci-archive.pitt.ed.....lity(rev2).pdf

    A concept like ‘green’ has a physical context (brain-state in your head, or mine), just as much as footprint in the sand. We are without exceptions to the implications of Landauer’s insight. We have no “immaterial information”; no matter how abstract or virtual we get in our thinking, our thinking is physical, bringing all those ideas about universals etc. right back to the physical domain.

  55. 55
    bornagain77 says:

    eigenstate, I was not contesting ‘reversible computation’ (Landauer’s principle), I merely showed that the paper shows that the ‘information is physical’ dictum is false!!! Clearly they erased ‘classical information’ that was physically encoded into a computer without consuming energy by using quantum information! That in of of itself falsifies the contention ‘information is physical’!!! I wasn’t even challenging reversible computation!!!

    notes:

    Falsification Of Neo-Darwinism by Quantum Entanglement/Information

    Neo-Darwinian evolution purports to explain all the wondrously amazing complexity of life on earth by reference solely to chance and necessity processes acting on energy and matter (i.e. purely material processes). In fact neo-Darwinian evolution makes the grand materialistic claim that the staggering levels of unmatched complex functional information we find in life, and even the ‘essence of life’ itself, simply ‘emerged’ from purely material processes. And even though this basic scientific point, of the ability of purely material processes to generate even trivial levels of complex functional information, has spectacularly failed to be established, we now have a much greater proof, than this stunning failure for validation, that ‘put the lie’ to the grand claims of neo-Darwinian evolution. This proof comes from the fact that it is now shown from quantum mechanics that ‘information’ is its own unique ‘physical’ entity. A physical entity that is shown to be completely independent of any energy-matter space-time constraints, i.e. it does not ‘emerge’ from a material basis. Moreover this ‘transcendent information’ is shown to be dominant of energy-matter in that this ‘information’ is shown to be the entity that is in fact constraining the energy-matter processes of the cell to be so far out of thermodynamic equilibrium.

    First, Here is the falsification of local realism (reductive materialism).
    Here is a clip of a talk in which Alain Aspect talks about the failure of ‘local realism’, or the failure of reductive materialism, to explain reality:

    The Failure Of Local Realism – Reductive Materialism – Alain Aspect – video
    http://www.metacafe.com/w/4744145

    The falsification for local realism (reductive materialism) was recently greatly strengthened:

    ‘Quantum Magic’ Without Any ‘Spooky Action at a Distance’ – June 2011
    Excerpt: A team of researchers led by Anton Zeilinger at the University of Vienna and the Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences used a system which does not allow for entanglement, and still found results which cannot be interpreted classically.
    http://www.sciencedaily.com/re.....111942.htm

    Physicists close two loopholes while violating local realism – November 2010
    Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview.
    http://www.physorg.com/news/20.....alism.html

    Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009
    Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables.
    http://www.sciencedaily.com/re.....142824.htm

    of note: hidden variables were postulated to remove the need for ‘spooky’ forces, as Einstein termed them — forces that act instantaneously at great distances, thereby breaking the most cherished rule of relativity theory, that nothing can travel faster than the speed of light. This following video illustrates just how ‘spooky’, to use Einstein’s infamous word, this quantum action truly is:

    Light and Quantum Entanglement Reflect Some Characteristics Of God – video
    http://www.metacafe.com/watch/4102182/

    And yet, this ‘spooky’ quantum entanglement, which rigorously falsified local realism (reductive materialism) as the ‘true’ description of reality, is now found in molecular biology on a massive scale!

    Quantum Information/Entanglement In DNA & Protein Folding – short video
    http://www.metacafe.com/watch/5936605/

    Quantum entanglement holds together life’s blueprint – 2010
    Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours (arxiv.org/abs/1006.4053v1). “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford.
    http://neshealthblog.wordpress.....blueprint/

    The relevance of continuous variable entanglement in DNA – July 2010
    Excerpt: We consider a chain of harmonic oscillators with dipole-dipole interaction between nearest neighbours resulting in a van der Waals type bonding. The binding energies between entangled and classically correlated states are compared. We apply our model to DNA. By comparing our model with numerical simulations we conclude that entanglement may play a crucial role in explaining the stability of the DNA double helix.
    http://arxiv.org/abs/1006.4053v1

    Quantum Entanglement/Information is confirmed in DNA by direct observation here;

    DNA Can Discern Between Two Quantum States, Research Shows – June 2011
    Excerpt: — DNA — can discern between quantum states known as spin. – The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team’s results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property.
    http://www.sciencedaily.com/re.....104014.htm

  56. 56
    bornagain77 says:

    The necessity of ‘transcendent’ information, to ‘constrain’ a cell, against thermodynamic effects is noted here:

    Information and entropy – top-down or bottom-up development in living systems? A.C. McINTOSH
    Excerpt: This paper highlights the distinctive and non-material nature of information and its relationship with matter, energy and natural forces. It is proposed in conclusion that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate.
    http://journals.witpress.com/paperinfo.asp?pid=420

    i.e. It is very interesting to note, to put it mildly, that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale, for how can the quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy space/time) ’cause’ when the quantum entanglement ‘effect’ falsified material particles as its own ‘causation’ in the first place? (A. Aspect) Appealing to the probability of various configurations of material particles, as neo-Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the energy/matter particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, you cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘specified’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place!
    ,,,To refute this falsification of neo-Darwinism, one must overturn Alain Aspect, and company’s, falsification of local realism (reductive materialism) !

    =================

    Alain Aspect and Anton Zeilinger by Richard Conn Henry – Physics Professor – John Hopkins University
    Excerpt: Why do people cling with such ferocity to belief in a mind-independent reality? It is surely because if there is no such reality, then ultimately (as far as we can know) mind alone exists. And if mind is not a product of real matter, but rather is the creator of the “illusion” of material reality (which has, in fact, despite the materialists, been known to be the case, since the discovery of quantum mechanics in 1925), then a theistic view of our existence becomes the only rational alternative to solipsism (solipsism is the philosophical idea that only one’s own mind is sure to exist). (Dr. Henry’s referenced experiment and paper – “An experimental test of non-local realism” by S. Gröblacher et. al., Nature 446, 871, April 2007 – “To be or not to be local” by Alain Aspect, Nature 446, 866, April 2007

    =================

    And to dovetail into Dembski and Marks’s previous work on Conservation of Information;,,,

    LIFE’S CONSERVATION LAW: Why Darwinian Evolution Cannot Create Biological Information
    William A. Dembski and Robert J. Marks II
    http://evoinfo.org/publication.....ation-law/

    ,,,Encoded ‘classical’ information such as what Dembski and Marks demonstrated the conservation of, and such as what we find encoded in computer programs, and yes, as we find encoded in DNA, is found to be a subset of ‘transcendent’ (beyond space and time) quantum entanglement/information by the following method:,,,

    ,,,This following research provides solid falsification for the late Rolf Landauer’s decades old contention that the information encoded in a computer is merely physical (merely ‘emergent’ from a material basis) since he believed it always required energy to erase it;

    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/re.....134300.htm

    ,,,And to dot the i’s, and cross the t’s, here is the empirical confirmation that quantum information is in fact ‘conserved’;,,,

    Quantum no-hiding theorem experimentally confirmed for first time
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment.
    http://www.physorg.com/news/20.....tally.html

    Further note:

    Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors
    Excerpt: Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC (Functional Sequence Complexity). FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,,
    Testable hypotheses about FSC
    What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses:

    Null hypothesis #1
    Stochastic ensembles of physical units cannot program algorithmic/cybernetic function.

    Null hypothesis #2
    Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function.

    Null hypothesis #3
    Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function.

    Null hypothesis #4
    Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time.

    We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified.
    http://www.tbiomed.com/content/2/1/29

    The following describes how quantum entanglement is related to functional information:

    Quantum Entanglement and Information
    Excerpt: A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems.
    http://plato.stanford.edu/entries/qt-entangle/

    Anton Zeilinger, a leading researcher in Quantum mechanics, relates how quantum entanglement is related to quantum teleportation in this following video;

    Quantum Entanglement and Teleportation – Anton Zeilinger – video
    http://www.metacafe.com/watch/5705317/

    A bit more detail on how teleportation is actually achieved, by extension of quantum entanglement principles, is here:

    Quantum Teleportation
    Excerpt: To perform the teleportation, Alice and Bob must have a classical communication channel and must also share quantum entanglement — in the protocol we employ*, each possesses one half of a two-particle entangled state.
    http://www.cco.caltech.edu/~qoptics/teleport.html

  57. 57
    bornagain77 says:

    And quantum teleporation has now shown that atoms, which are suppose to be the basis from which ALL functional information ‘emerges’ in the atheistic neo-Darwinian view of life, are now shown to be, in fact, reducible to the transcendent functional quantum information that the atoms were suppose to be the basis of in the first place!

    Ions have been teleported successfully for the first time by two independent research groups
    Excerpt: In fact, copying isn’t quite the right word for it. In order to reproduce the quantum state of one atom in a second atom, the original has to be destroyed. This is unavoidable – it is enforced by the laws of quantum mechanics, which stipulate that you can’t ‘clone’ a quantum state. In principle, however, the ‘copy’ can be indistinguishable from the original (that was destroyed),,,
    http://www.rsc.org/chemistrywo.....ammeup.asp

    Atom takes a quantum leap – 2009
    Excerpt: Ytterbium ions have been ‘teleported’ over a distance of a metre.,,,
    “What you’re moving is information, not the actual atoms,” says Chris Monroe, from the Joint Quantum Institute at the University of Maryland in College Park and an author of the paper. But as two particles of the same type differ only in their quantum states, the transfer of quantum information is equivalent to moving the first particle to the location of the second.
    http://www.freerepublic.com/fo.....1769/posts

    Thus the burning question, that is usually completely ignored by the neo-Darwinists that I’ve asked in the past, is, “How can quantum information/entanglement possibly ‘emerge’ from any material basis of atoms in DNA, or any other atoms, when entire atoms are now shown to reduce to transcendent quantum information in the first place in these teleportation experiments??? i.e. It is simply COMPLETELY IMPOSSIBLE for the ’cause’ of transcendent functional quantum information, such as we find on a massive scale in DNA and proteins, to reside within, or ever ‘emerge’ from, any material basis of particles!!! Despite the virtual wall of silence I’ve seen from neo-Darwinists thus far, this is not a trivial matter in the least as far as developments in science have gone!!

    Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff – video (notes in description)
    http://vimeo.com/29895068

    non-local ‘epigenetic’ information is also implicated in controlling the 3-D spatial organization of body plans;
    https://docs.google.com/document/d/1iNy78O6ZpU8wpFIgkILi85TvhC9mSqzUSE_jzbksoHY/edit?hl=en_US

    verses and music:

    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.

    1 Corinthians 2:14
    The natural person does not accept the things of the Spirit of God, for they are folly to him, and he is not able to understand them because they are spiritually discerned.

    Todd Agnew – This Fragile Breath
    http://www.youtube.com/watch?v=hoGPG4JOcXs

    Brooke Fraser – Lord of Lords(Legendado Português) –
    http://www.youtube.com/watch?v=rkF3iVjOZ1I

  58. 58
    bornagain77 says:

    eigenstate; it might also interest you to know that ‘reversible computation’, which you should know is a extremely difficult, if not seemingly impossible, task to accomplish in programming a computer, is accomplished to a stunning degree within cells:

    Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon – Charles H. Bennett
    Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus, dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,,
    http://www.hep.princeton.edu/~.....501_03.pdf

    And indeed, The energy efficiency achieved in the cell, by such techniques as reversible computation, is something engineers can only drool over;

    Life Leads the Way to Invention – Feb. 2010
    Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “ In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale.
    http://creationsafaris.com/cre.....#20100226a

  59. 59
    eigenstate says:

    bornagain77,

    eigenstate, I was not contesting ‘reversible computation’ (Landauer’s principle), I merely showed that the paper shows that the ‘information is physical’ dictum is false!!! Clearly they erased ‘classical information’ that was physically encoded into a computer without consuming energy by using quantum information! That in of of itself falsifies the contention ‘information is physical’!!! I wasn’t even challenging reversible computation!!!

    The paper doesn’t address that, or show that by implication, though, which is the point I was raising in my previous post. Did you see the “section title” called “Landauer’s principle is given a quantum twist”? del Rio has found a means of employing entanglement to establish “negative conditional entropy”. But that doesn’t change 2LoT or Landauer’s thermodynamic insight one bit. Entropy for the system ratchets up, inexorably, just as always, because the usable energy that must be invested to establish the entanglements that create the negative entropy is greater than that gained on return. Thus it ever is in thermodynamics.

    If anything, this is just a more extreme validation of the principle — information is physical. It’s a cool trick to be able to coordinate entanglement such that (in theory) you can provide a cooling effect, but you still gotta invest energy to do it, and crucially here, information is empirically bound to its physical context. To destroy information, irreversibly, you must abide by 2LoT.

  60. 60
    bornagain77 says:

    Eigenstate, it is really not that hard to understand, they erased information without consuming energy! PERIOD!!! I doesn’t matter one iota what you think it implies!!! The FACT is that the evidence itself clearly, without any ambiguity, shows information was erased without consuming energy!!! Thus proving conclusively that ‘classical’ information is merely a subset of quantum information. It would be hard to find a more direct confirmation of a principle in science!!!

  61. 61
    eigenstate says:

    bornagain77, Landauer’s insight was always grounded in quantum theory — that’s why “irreversible” is the key term here. All information is quantum information, just abstracted to one level or another (abstracted so humans can think and talk about it, the world itself doesn’t care, it is what is). Decoherence is the crucial issue, and the point where information dynamics are unified with physical law: they are inseparable.

    If you understand what is being related in the article you linked (I suspect you are not tracking with the concepts they are covering), you will understand that while the changes from entanglement are not energy consuming in a direct, local sense, that entanglement itself is very much an energy sink, meaning that your claim that “understand, they erased information without consuming energy! PERIOD!!!” is incorrect. You can push the energy investment back, and consume energy in establishing the entanglements themselves, but then your claim is bogus. The “PERIOD!!!!” doesn’t apply. Energy is consumed, just one step up the chain, rather than in the non-entangled erasure step which consumed it directly in Landauer’s examples.

    Nothing to see here, I’m afraid. 2LoT pwns. What you think you can do now — erase information without energy consumption, irreversibly, cannot be done, according to everything we know, including the article you mistakenly linked to in pursuing your point.

  62. 62
    bornagain77 says:

    eigenstate, all I care about is this:

    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.

    Classical Information is shown to be a subset of quantum information by this paper. i.e. they erased information from a computer without consuming energy directly as a result of quantum entanglement. This is about as good as it gets for empirical science. For you to continue to squabble over the second law after entanglement has already ‘left the house’ with the jewels of information is to completely miss the importance of what they have established. Shoot they even admit that ‘“We’re working on the edge of the second law. If you go any further, you will break it.”,,, Perhaps I pushed when I said ‘PERIOD’, but none-the-less, for purposes of directly tying ‘transcendent quantum information to encoded classical information, this proof rocks the house,,, PERIOD!!! 🙂

  63. 63
    Neil Rickert says:

    Requirements are relevant to OOL because requirements are imposed implicitly and unavoidably on abiogenesis by the laws of physics.

    If the laws of physics are a requirement, then is a requirements explosion a sudden increase in the complexity of the laws of physics?

    Sorry, it still does not make sense.

    The problem of requirements and the risk of a requirements explosion come from designing for a specific goal. If there is no design and no goal, then it isn’t clear where the requirements explosion would fit in.

  64. 64
    dmullenix says:

    kdonelly 7.1.2.1 “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.”

    The bit is the arrangement of some physical entity. Information can be in the form of the timing of electrical pulses, the physical arrangement of atoms in a CD, the arrangement of electrons in a memory chip, currents in a microprocessor, density variations in air, swarms of pulses in a brain or countless other arrangements of physical entities. But there ALWAYS has to be some physical entity present to be arranged. No physical entities, no information. If you don’t agree, just try to find an exception to that.

  65. 65
    eigenstate says:

    Classical information is not a subset of quantum information. Classical information (discrete states like {0|1} ) are conceptual devices humans use to think in tidy ways (literally , binary thinking, here with {1|0}).

    Nature is not digital. Anywhere. “Digital” is just a useful human-thinking way to categorize and “quantize” analog, real world information. So when referring to “quantum information” it’s important not to get the “map” confused with the “territory”. Humans have a conceptual models in their heads about quantum information (some of them, anyway), but that is the “map”. The “territory”, the extramental world, is comprised of quantum information. That information is physical; it doesn’t care what you or I think about it, or our attempts to quantize it or simplify it. It is what it is, and from our now rich history of experimenting with it, we have some decent models that are good “maps” to this “territory”.

    Part of the utility in human use of classic information theory is that it allows us to forget out physical representation. It’s not a physical model, it’s a conceptual model. But that’s the rub here, and the reason I take time to point the difference out: REAL information, quantum information, is real because it is physical. Or perhaps its better to say that the physical is real because it is information.

    So when you post an article like this, it augurs the other direction that you hope and suppose it does. It’s trivial to detach classical information theory from physical representations, and thus thermodynamical constraints; the model was never built to incorporate physical representation as an intrinsic. Quantum information, though, is not information at all without physical context. It cannot be divorced from representation, because the representation IS the information.

  66. 66
    bornagain77 says:

    As to: No physical entities, no information. If you don’t agree, just try to find an exception to that.

    notes:

    It is important to note that the following experiment actually proved that information can be encoded into a photon while it is in its quantum wave state, thus destroying the notion, that was/is held by many, that the wave function was not ‘physically real’ but was merely ‘abstract’. i.e. How can information possibly be encoded into a entity that is not physically real but is merely abstract? It simply would not be possible!

    Ultra-Dense Optical Storage – on One Photon
    Excerpt: Researchers at the University of Rochester have made an optics breakthrough that allows them to encode an entire image’s worth of data into a photon, slow the image down for storage, and then retrieve the image intact.
    http://www.physorg.com/news88439430.html

    further notes:

    Wave function
    Excerpt “wave functions form an abstract vector space”,,, This vector space is infinite-dimensional, because there is no finite set of functions which can be added together in various combinations to create every possible function.
    http://en.wikipedia.org/wiki/W.....ctor_space

    Explaining Information Transfer in Quantum Teleportation: Armond Duwell †‡ University of Pittsburgh
    Excerpt: In contrast to a classical bit, the description of a (photon) qubit requires an infinite amount of information. The amount of information is infinite because two real numbers are required in the expansion of the state vector of a two state quantum system (Jozsa 1997, 1)
    http://www.cas.umt.edu/phil/fa.....lPSA2K.pdf

    Quantum Computing – Stanford Encyclopedia
    Excerpt: Theoretically, a single qubit can store an infinite amount of information, yet when measured (and thus collapsing the Quantum Wave state) it yields only the classical result (0 or 1),,,
    http://plato.stanford.edu/entr.....tcomp/#2.1

    Single photons to soak up data:
    Excerpt: the orbital angular momentum of a photon can take on an infinite number of values. Since a photon can also exist in a superposition of these states, it could – in principle – be encoded with an infinite amount of information.
    http://physicsworld.com/cws/article/news/7201

    Now, I find the preceding to be absolutely fascinating! A photon, in its quantum wave state, is found to be mathematically defined as a ‘infinite-dimensional’ state, which ‘requires an infinite amount of information’ to describe it properly, and this ‘infinite dimensional’ photon can be encoded with information while it is in its ‘abstract’ infinite dimensional state, and is also found to collapse, instantaneously, and thus ‘non-locally’, to just a ’1 or 0? state, out of a potential infinite number of possibilities that the photon could have collapsed to instead! Now my question to materialistic atheists is this, “Exactly what ’cause’ has been postulated throughout history to be completely independent of any space-time constraints, as well as possessing infinite knowledge, so as to be the ‘sufficient cause’ to explain what we see in the quantum wave collapse of a photon???

    John 1:1-5
    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. In him was life, and that life was the light of all mankind. The light shines in the darkness, and the darkness has not overcome it.

    Jeremy Camp – The Way (Official Music Video)
    http://www.youtube.com/watch?v=9q6o4sbndVE

  67. 67
    Mung says:

    Dr. Liddle,

    It appears very clear to me that you employ an unprofessional tactic in the way you debated this topic:

    – 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.

    Some people have gone so far as to accuse her of intellectual dishonesty.

    How’s that refutation of ID coming along Dr. Liddle?

  68. 68
    bornagain77 says:

    Eigenstate, I disagree, but I’m done debating you.

  69. 69
    dmullenix says:

    BA77, you seem to have some sort of private version of quantum physics that is shared by few others.

    I keep following your links and finding articles about local realism and other standard quantum physics that are generally considered to be a part of physical reality. Overall, I get the impression that you believe that if there’s not a bright shiny sphere at the center of every elementary particle, then God.

    I disagree. The quantum universe seems bizarre to us macro organisms because we don’t deal with it in our ordinary lives so our brains and minds have never had to develop an intuitive understanding of quantum physics like we’ve had to develop of “ordinary” physics. Nevertheless, the quantum world seems to be “real” in the sense that it follows laws and eventually seems to resolve to “regular” or “macro” physics.

    Biology operates in the macro world. If you want to change the information in DNA, you rearrange atoms. If you want to change the information in RNA, you rearrange atoms. If you want to change the information in tRNA, you rearrange the atoms. If you want to change the information in a protein, you rearrange the atoms. If you want to change a memory or a thought in your own mind, you will eventually have to rearrange some atoms or at least some electrons to do it.

    If you’re dealing with information in the macro world, you will eventually have to rearrange some material part of that macro world. If anybody disagrees, please show us an example.

  70. 70
    dmullenix says:

    “Three” and “green” are concepts in your mind and they are ultimately formed by atoms and pulses in your brain. To ‘give you’ a three or a green, I’ll have to activate those concepts in your mind. To do that, I’ll have to arrange something in threes, whether the something is apples, oranges, RF pulses, xenon atoms, electrons in memory chips or what have you.

    Your brain has circuitry, made ultimately of atoms, to help you read the printed letters “three” or hear the word “three” and trigger that concept in your mind. French speakers have similar circuitry for “trois”.

    For green, I’ll have to arrange some matter so it emits electromagnetic radiation with a wavelength of roughly 520 to 570 nanometers. Atoms in your eye and brain will arrange themselves so as to provide the sensation of green in your mind. Your mind also contains circuitry, also encoded eventually by atoms, which will let you see printed letters on a page and activate the concept of green in your mind. French speakers have circuitry that does the same thing for “vert”.

    In both cases, I’ll have to do something to activate a pre-existing concept in your mind. These concepts will have a material base – atoms and impulses in your brain. If someone doesn’t have those concepts, they’re either very young and haven’t formed them yet or they have a serious problem.

    This is all fairly standard physics, philosophy, psychology and physiology.

  71. 71
    bornagain77 says:

    Well dm, you asked for an example you got it. You don’t like the implications because they don’t fit your illusory materialistic view of reality? Oh well, that’s not my problem!

  72. 72
    bornagain77 says:

    as to: If you’re dealing with information in the macro world, you will eventually have to rearrange some material part of that macro world. If anybody disagrees, please show us an example.

    http://www.uncommondescent.com.....ent-405105

  73. 73
    butifnot says:

    Until there is a demonstrated understanding of ‘brain states’, which could be evidenced by say building your own working brain, proclamations are premature.

  74. 74
    butifnot says:

    I’m trying to reason through a purely physical accounting of events – a concept in brain 1 > innervate muscles > sound waves produced > pressure variations strike ear of another > electric/chemical input to brain 2 > concept (not identicaly equivalent though) in brain 2 ??

    Or a concept in brain 1 > innervate muscles > writing produced > light waves strike eyes of another > electric/chemical input to brain 2 > concept (not identicaly equivalent though) in brain 2 ??

  75. 75
    butifnot says:

    It’s trivial to detach classical information theory from physical representations

    This sounds like the map/territory thing – information could be real and non physical. Maps may well be wrong, reality remains unfazed.

    Intelligence assigns meaning to anything it wants – one if by sea, two if by land.

  76. 76
    butifnot says:

    That a particle or object can ‘contain’ ‘knowledge’ of or reference to something apart or outside of itself, this is why its called ‘quantum information’ ?

    I think it is certain we are not done and we are not without error, quantum effects will be explained in a more complete theory. Probably a non-spooky regular type interaction I think.

    Maybe this – there is an aether, it is the sea of neutrinos, light speed is like the ripple on the water compared to the speed of sound in the water.

  77. 77
    kdonnelly says:

    If the laws of physics are a requirement, then is a requirements explosion a sudden increase in the complexity of the laws of physics?

    I did not intend to imply that the laws of physics are a requirement, in and of themselves. I’ll try to clarify my thoughts.

    There obviously are many unwritten requirements (perhaps a better word would be “constraints”) imposed on life by the physical universe. In our software development analogy, the first organism is the software system: the program, so to speak, which is as yet potential, not actual. The inorganic universe is the platform on and within which two systems must “run”: abiogenesis itself, and the product of abiogenesis — the first life-form.

    On materialistic grounds, any pre-existing systems or processes that have a role in the genesis of life must play by the rules; they must adhere to the laws of physics. And the first life-form must play according to the same rules that governed the systems that created it.

    The working assumption of most biologists is materialistic: life is 100% material (i.e. it has no immaterial component), both in its origins and in its actualized forms. How is it, then, that life’s genesis seems to be an obvious violation of the second law of thermodynamics? The onus is on the molecular evolutionists to answer that question.

    However a scientist defines life, at a minimum (at least for Darwinian purposes), the definition must include viability and replicability. Physics places severe constraints on how matter can be arranged to satisfy the viability requirement. For example, if random material processes dysteleologically converge on an arrangement of amino acids as a basis for a life-form, the amino acids must be homochiral. To me, that seems to be a physical constraint. Violation of that constraint, given our current state of knowledge, results in a failure to satisfy the viability requirement, since a mixed-chiral set of amino acids can’t be used to construct a functional life-form.

    Caveat emptor: I am a neophyte in the subject of biology, so my viability example might not be a very good one, and my understanding of chirality in organisms might actually be incorrect. An expert could probably come up with better examples — probably very many of them.

    The analogy that I drew between “requirements explosion” in software development and a similar phenomena I observe in biology is imperfect, as I admitted in my initial post on the subject. But I think it’s fair to say that many constraints are placed on the design of a life-form by the physical universe within which it (at least in its material components) must function. Functionality (viability) is an explicit requirement of life. Since physical constraints have unavoidable implications for satisfying the viability requirement, it seems appropriate in a loose or informal sense to label those constraints as “requirements”. But I’m OK with “constraints” if it helps to avoid ambiguity. There can be no doubt that there has been a “constraints explosion” in biology in the last 60 years or so. Do you agree?

  78. 78
    Neil Rickert says:

    There obviously are many unwritten requirements (perhaps a better word would be “constraints”) imposed on life by the physical universe.

    That’s not obvious to me. I think you are imposing those requirements yourself because your thinking is based on the idea of design.

    For OOL studies, there are requirements, because the goal is to explain the origin of the kind of life that we see. It is not certain that we can achieve those goals.

    For life itself, I see no requirements because there is no goal. It is not a requirement that life should have developed in a way that used DNA. That people speculate about the possibility of silicon based life suggests wide recognition that it is not even a requirement that life be based on carbon chemistry.

  79. 79

    We do understand quite a lot about brain states, and can measure them in various ways.

  80. 80

    Oh boy.

    I am neither morally nor intellectually dishonest, Mung.

    As I think you probably know.

    The accusation gets extremely tiresome.

  81. 81
    kdonnelly says:

    I think you are imposing those requirements yourself because your thinking is based on the idea of design.

    If by “design” you think I am referring to purposeful arrangement, you misunderstand me. Whether life is intelligently arranged or randomly (dysteleologically) arranged is irrelevant to my argument. Life has specific configurations; actual organisms are physically structured in certain ways; living things have the “appearance of [purposeful] design”, as Dawkins and many other materialistic evolutionists assert. Those arrangements, those configurations, those structures, those designs (in a dysteleological sense) are not what one would expect to arise from inorganic matter that’s obeying the second law of thermodynamics.

    Scientists have empirically investigated countless inorganic systems as they proceed towards thermodynamic equilibrium. Life is unexpected (“improbable”, per Dawkins) precisely because it is profoundly unlike anything we’ve actually observed an entropic inorganic system to produce. Furthermore, based on a reasonable extrapolation of our observations, life’s designs don’t look anything like what any entropic inorganic system would or could produce, even given eons of time, and massive injections of undirected energy into the system.

    For OOL studies, there are requirements, because the goal is to explain the origin of the kind of life that we see. It is not certain that we can achieve those goals.

    Agreed. The kind of life that we see is considered life because it satisfies a set of requirements; it qualifies, by our definition of life, as life. And yes, it is not certain that we can achieve the goals of scientifically explaining the origins of life as we see it. I would add that over time, it is becoming less and less likely, based on the empirical evidence, that those goals can be achieved on materialistic assumptions.

    You use the phrase “kind of life”, which implies that there might be other things that would be considered life, if certain characteristics were exhibited — i.e. if some set of specific requirements were satisfied that justified categorizing them as living things. As you rightly point out, it is not certain that life must be DNA-based or even carbon-based. Our definition of life is broad enough to encompass kinds of life which we have not yet observed, but which might potentially exist. But in whatever form a thing might come, it must certainly be viable in the biological sense, and (for Darwinism to succeed) the thing must be replicable, if it is to qualify as life.

    Now if viability is a requirement of life, and the laws of physics constrain what potential designs will be viable, it follows that as the number of known constraints increases, the greater will be the expected difficulty of successfully “designing” life. This is true whether the design process is random and purposeless, or intelligent and purposefully directed.

    There has indeed been something like a “requirements explosion”, or if you prefer, a “constraints explosion”, in biology during the past several decades. Abiogenesis is a harder nut to crack than science anticipated. The more we learn, the more difficult it becomes.

    And the more we learn, the more necessary it becomes for materialists to smuggle in certain religious assumptions to make the abiogenesis problem tractable.

  82. 82
    Eugene S says:

    Are we any wiser now that we can, Elizabeth?

  83. 83

    Yes, I think we are, Eugene. I think we are much more understanding about what is going on when minds don’t work very well, and also better able to help them work better

  84. 84
    dmullenix says:

    InVivoVeritas 1.1.3: “- 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.”

    “- 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”.”

    “- 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”.”

    I responded to your list and haven’t heard a word back from you.

    “- Definitely you will not feel comfortable discussing specific points and trying to consider the proposed empirical approach to the topic in question.”

    It’s hard to be empirical when we don’t know what the first living thing was. Science doesn’t know. It’s trying to find out. We’ve been making plenty of guesses for you to consider.

    ID doesn’t know either. As far as I can tell you’re not making any effort whatsoever to find out. You’re not even telling us what you THINK it might have been like.

    That’s pretty underwhelming.

  85. 85
    Upright BiPed says:

    Hello dmullenix and eigenstate,

    I was not online over the weekend and did not notice your replies before I left on Friday. But I have now read them with interest, and I appreciate your comments. From my immediate perspective, you both seem to want to come at the issue on the same front (its physicality) and in doing so you are both making my point for me (the ‘issue’, for me, being how does information and information transfer relate to the semiotic argument for design).

    Dmullenix wants me to consider the atoms in my brain, and eigenstate posts an article on thermodynamics within a local system – which is more appropriately targeted at someone whose methodologies operate under the assumption that everything contains information. In large part, this is the assumption of theoretical and statistical physics, in which the state of matter becomes computable under certain methodologies. But it represents a modern re-purposing of an almost organically-understood concept; one which has a tremendous history of being so understood. The reason it has such a foundational standing is because it faithfully explains observed phenomena – we see the transfer of information in nature, we know the dynamics involved in the process, and we know those observations are not supervened upon by a re-purposed definition of the word. In other words, we see the heavens crossing the sky and we eventually conclude our planet is rotating in relation to the sun; the addition of neither relativity nor quanta will change the validity of that observation. Moreover, if we accepted for the purposes of argument that everything contains information, that fact itself would not change the validity of the observations already made. We say that an atom of carbon contains a certain number of subatomic particles, and we record their numbers on a piece of paper. We now have two distinct realities; one being that a carbon atom has these particular things, and another being that their numbers have been recorded (in abstract) as a physical object separate from the atom of carbon itself. The question raised by the linked paper (of whether or not a logically irreversible transformation can be implemented thermodynamically reversible) offers no explanation of those two observed realities.

    It is therefore an inter-disciplinary mistake to suggest that observations using the genuine definition of “information” (derived from the Latin root infomare; ‘to give form to’) which highlight a very unique physical dynamic observed in material reality, could be explained by a re-purposed definition of the word (which specifically reduces that phenomena to being entirely ubiquitous among matter). I was interested to see this being referred to by eigenstate as an “anthropocentric view of information.” As a valid model of physical dynamics, the semiotic argument for design needn’t make any reference to mind; it is only about the dynamic entailments of recorded information transfer, and is in no way (specifically or even primarily) tied to human-bound information. The physical observations of information transfer are just as valid in examining transfer among organisms throughout the living kingdom, as well as among non-living machinery. Quite frankly, there could be nothing more anthropocentric than to claim there is “information” (a specific term with foundational meaning) in everything, in order that physical states (and changes to them) become statistically computable to human investigators. And please don’t misunderstand me, I am not suggesting even for a moment that the work of those who have re-purposed the definiton of information have invalid work in any sense, I am saying that it is a disciplinary mistake to conflate the two.

    Information transfer is the transfer of a physical representation to cause an effect. To re-describe the term (to be the transfer of pure physicality instead) doesn’t change the fact that the transfer of abstract representations are still an observed physical phenomena. This is evidenced by the fact that when I see a bird flying above me and write “bird” on a piece of paper, I don’t accomplish that by having a bird in my head. I have an abstract representation operating within a system, which has a relationship to the sight of the bird, and is actualized by the protocol(s) in my brain. The sight of a bird and the letters b-i-r-d do not have an intrinsic physical relationship – it is a relationship that comes about only by being in a system capable of creating it.

    In the end, you both want to highlight the fact that “three” and “green” are a physical states in my brain. Well, they most certainly are. That is an observation, not an explanation. The simple fact remains that they are real; 510nm wavelength on the electromagnetic spectrum is green, one Planck length is 10^-43 seconds, there is only one moon orbiting this planet. The physical protocol that establishes an immaterial relationship between a bee’s dance and the effect it has among the other bee’s in flight, physically exist in the bee – no doubt. They are physical things and they operate in an observable way (which you both pointed out) with observable physical dynamics (which you both ignored).

    In any case, implicit in your objection is that you see this capacity in living things (of creating and assigning representational values to physical objects and patterns) as something that appears (particularly in humans) after billions of years of advancement in living organisms. But that is not what the observable evidence indicates; it documents that the opposite is true.

    Look…this conversation (at this level) has rattled on so many times here at UD that they can’t be counted. People far more studied than I have argued it on both sides of the argument. I have little desire to continue that argument (beyond understanding it to the best of my abilities). However, if you are going to confirm the existence of information transfer as it is actually observed to exist throughout the living kingdom, then it will involve a discrete arrangement of matter acting as a physical representation, it will have a discrete arrangement of matter to physically establish the effect that representation is mapped to within a system, it will have a discrete effect caused by that representation, and each of these will remain physically separate. That is the way recorded information transfer is found. If you’d like to offer your comments on these observations, then I’d be happy to hear them.

  86. 86
    dmullenix says:

    Upright BiPed: “In any case, implicit in your objection is that you see this capacity in living things (of creating and assigning representational values to physical objects and patterns) as something that appears (particularly in humans) after billions of years of advancement in living organisms. But that is not what the observable evidence indicates; it documents that the opposite is true.”

    What is this observable evidence?

  87. 87
    dmullenix says:

    Last I heard, photons were part of the material world.

  88. 88
    bornagain77 says:

    So the transcendent, uncollapsed, ‘infinite dimensional’ quantum wave state of a photon is now considered to be ‘material’ instead of abstract, and thus real in your worldview??? Thanks for admitting that God is ‘materially’ real!!!

  89. 89
    Upright BiPed says:

    Hello dmullenix, I provided a link.

  90. 90

    UBP: as usual, your argument entirely relies on your assumption that you are not equivocating with the word “representation”. In my view you are.

    “Creating and assigning representational values to physical objects and patterns” is indeed something that humans do.

    I simply do not accept that what humans do when they assign a signifier to a referent has any more than a superficial resemblance to the process by which a DNA sequence “represents” a particular protein.

    The huge, elephant-in-the-room-sized difference is that the DNA sequence can only function as a “representation” of a protein in one medium – a sequence of nucleotides. This nucleotides has physical properties that are required for the “translation” of “representation” to “object” to take place. Moreover, the outcome of this “translation” process is not the shared understanding of some referent (as when I write “dog” and you understand “dog”) but a physical object.

    So, on the one hand, we have a molecule (“representation”) that forms a template for a second molecule, that reacts with a third, that reacts with a fourth (the “referent”), thus mapping the first molecule to the fourth.

    On the other hand we have a human with a brain who makes a symbol (“representation”) which can be rendered in any one of a vast number of media, because what matters is the pattern not the substrate, which is then interpreted by another human with a brain, who then understands that the first human wanted to convey the concept “dog”, because they have previously agreed that that symbol means “dog”.

    These two things are not the same. Making an argument on the assumption that they are is therefore fallacious.

  91. 91
    dmullenix says:

    You worship a photon? Whatever happened to that Jesus fellow?

  92. 92
    dmullenix says:

    What she said. Your opinion is not “observable evidence”. Write when you get some.

  93. 93
    bornagain77 says:

    dmullenix you ask:

    Whatever happened to that Jesus fellow?

    He rose from the dead and is now seated at the right hand of God the Father, whose ‘realm’ is the highest ‘infinite dimensional’ realm from which the photon of light ‘collapsed’.

  94. 94
    dmullenix says:

    I’ve heard that theory, but frankly I think it’s a lot more likely that he was killed about 2000 years ago. The Romans were pretty good at that sort of thing and seldom botched an execution. I think the rumors of his resurrection are greatly exaggerated.

  95. 95
    Upright BiPed says:

    Dr Liddle,

    “As usual”, Dr Liddle? I’ll take that as a compliment that I’ve expressed the argument sufficiently, and needn’t alter my position in order to keep you stumbling for a coherent reply. You’ve launched these objections before, and they are as meaningless now as they were then. The reasons have been explained at the physical level. Simply restating your objections does not change the validity of the rebuttal. If it’s empiricism you aspire to, which you say is the case, then emphatically announcing what you “simply do not accept” is not a coherent argument. That’s not going to cut it when there is concrete physical evidence that you’re wrong. You want to force an equivocation upon the use of certain words, yet it’s the physical dynamics which are at issue. I have now told you four times that you may use whatever terms you wish; the fact remains that the observed physical dynamics are what must be accounted for.

    The elephant in the room, Dr Liddle, is that you keep playing off two losing positions. The first is this completely impotent ‘equivocation in terms’ thing, which has been dealt with conclusively (ie: the observations have been lucidly restated using the definitions of these terms [taken directly from a standard dictionary] in place of the terms themselves). These restated definitions are entirely faithful with respect to the dynamics being described. Your objection has therefore been refuted. Fully refuted. That refutation has been further bolstered by asking the simple question: “If in one instance we have an object that is genuinely a representation, and in another we have an object that just acts like a representation, then surely you can look at the dynamic evidence and point to the distinction”. You have thus far failed to describe this distinction – this equivocation. It seems to be invisible among the things clearly seen, yet you insist it’s there. When you decide to describe it, I will respond to your objection with a sense of urgency, because only then will it be meaningful to the discussion. In other words, quite frankly, put up or shut up. 😉

    “the DNA sequence can only function as a “representation” of a protein in one medium – a sequence of nucleotides. These nucleotides have physical properties that are required for the “translation” of “representation” to “object” to take place.”

    Taking this first sentence at face value: ‘a sequence of nucleotides can only be a representation in one medium – a sequence of nucleotides’. Okay.

    Your objection seems to suggest that because nucleotide sequences operate within a system dedicated to specific effect (the production of proteins, among others) then these sequences cannot be considered actual representations. But if we follow that thinking, then we can say that a music box cylinder doesn’t contain representations either, because it can only make a melody when used in a music box. Or we can say that the punch cards from an old fabric loom don’t really represent the final effect in the fabric, because all they can do is make fabric. How is it exactly that you could come to the conclusion that because a system is dedicated to an effect, the information driving the system is not what it is?

    These nucleotides have physical properties that are required for the “translation” of “representation” to “object” to take place.

    Exactly, and again, this has no bearing on the issue. Everything that acts as a representation must have appropriate physical properties (in order to accomplish the task). If I take a stick and spell “Dr Liddle” in the sand, then the sand was appropriate to use as a substrate to accomplish the effect. But what if I take the same stick and follow the same motion in a tub of water? What then? Apparently, a tub of water doesn’t have the properties required to contain the representations I intended to convey. Similarly, wood makes a poor conductor of electrical pulses. Felt makes a poor recording tape on which to arrange lines of iron oxide. This is a
    thoughtless objection, Dr Liddle. Not only is it beneath the intellect of someone with your training, it speaks nothing whatsoever to the dynamics being discussed. Why won’t you attack those dynamics themselves? Why not leave these hapless arguments for the greener grass of actually refuting the evidence as we find it.

    Moreover, the outcome of this “translation” process is not the shared understanding of some referent (as when I write “dog” and you understand “dog”) but a physical object.

    But Dr Liddle, you are deliberately confusing what is at issue. The output of a fabric loom being driven by holes punched into paper cards is “a physical object” as well – an object created by representations operating in a system capable of creating fabric. The nucleotides in DNA don’t know what leucine is, any more than the hole-punched cards of a fabric loom know what “blue thread” is. Or, any more than a music box cylinder knows what the key of “c” is. Observing the critical dynamics does not require any reference to a mind in any way whatsoever, yet you are repeatedly trying (as hard as possible) to inject a mind into the observations so that you can then turn around and claim that its all about a mind. In case you have not yet noticed, you have failed at this position every time you’ve tried it, and you will continue to do so. The reason for this is simple; the observations are correct and you are wrong.

    So, on the one hand, we have a molecule (“representation”) that forms a template for a second molecule, that reacts with a third, that reacts with a fourth (the “referent”), thus mapping the first molecule to the fourth.

    One can imagine you typing out that passage, then swiping your hands together and clapping, as if your task is done. Nothing could be further from the truth. You have deliberately ignored the critical dynamic method in which the immaterial rule “this maps to that” comes to be actualized within the system. I will repeat it here for your benefit:

    BIPED: These same entailments are is found in the transfer of information from a nucleic sequence. During protein synthesis a selected sequence of nucleotides are copied, and the representations contained within that copy are fed into a ribosome. The output of that ribosome is a chain of amino acids which will then become the protein being prescribed by the input sequence. The input of information is therefore driving the output production. But the input and the output are physically discrete, as evidenced by the fact that the don’t directly interact, and that the material output is not assembled from the material input.

    The exchange of information (from input to output) is facilitated by a set of special physical objects – the protocols – tRNA and its entourage of aminoacyl synthetase. Acting together they make it possible for the input to alter the output, and they do so by allowing them to remain separate. The tRNA physically bridges the gap between the input and the output, acting as a passive carrier of the physical protocol. It accomplishes this by being charged with the correct amino acid by the synthetases (the only molecules in biology which actually hold the rules to the genetic code). The synthetases accomplish their tasks by being able to physically recognize both the tRNAs and the amino acids. They charge the tRNAs with their correct amino acids before they ever enter the ribosome. The actions of the synthetases are therefore completely isolated from both the input and output. In other words, the only molecules in biology that can set the rule that “this maps to that” are physically isolated from both the input and output, while the input and output remain isolated themselves.

    So you see Dr Liddle, you’ve left the observable dynamics out of your simplistic “the RNA molecule reacts with a tRNA molecule which reacts with an amino acid” model. If you are expecting me to relinquish on that observed dynamic, I can assure you that I have no intentions of doing so. If you want to defeat the observations, you will first have to attack them with contrary evidence and valid reasoning. Thus far you have failed to do so.

    On the other hand we have a human with a brain who makes a symbol (“representation”) which can be rendered in any one of a vast number of media, because what matters is the pattern not the substrate, which is then interpreted by another human with a brain, who then understands that the first human wanted to convey the concept “dog”, because they have previously agreed that that symbol means “dog”.

    Here we go again with the ‘let talk about minds’ line of defense. Okay, I will throw you a bone and say something about a mind. You’ll have plenty of fodder.

    I concur that a human mind can make symbols out of just about anything, but only as long as its another human mind (or perhaps a wonderful domestic animal) doing the translation. A substrate of pebbles arranged in the shape of a happy face is not too much of an accomplishment for natural symbol-makers like ourselves. Of course, if it’s not another mind doing the translation, then the choices of substrates begin to close up rather quickly, don’t they? Indeed, if a human wanted to record information in order for it to result in a specific effect, even in something as simple as a music box, then the choice of substrates closes up fairly quickly. In fact, as you type your responses in the UK and they appear on my monitor on the other side of the planet, those choices of substrates close up so quickly that it takes hundreds or thousands of generations of discovery just to understand how to synthesis the non-naturally-occurring materials required to get the job done. Is that not correct? So when you say “its the pattern not the substrate” you might want to keep in mind that the spareness of means (a human mind needs to interact with another human mind) is not all that interesting. In other words, these kinds of observations often have a kind of arrow attached to them. It’s really more about the stunning results that can come from information if you master the substrates themselves. (Just a thought).

    And in a beautifully profound irony, you say ‘its the information (pattern) that really matters, not the substrate’ because in the instance of a mind-to-mind interaction, that is perfectly true. And you really need something perfectly true to say. Yet how odd then, in order to defend your remaining views, you believe that (in the end) it was the substrate that created the information in the first place. The details of that be damned, even against observable evidence to the contrary. And its not just any information that the substrate created, its the most incredible display of information processing to ever be seen – so much so that calling it “complex” is an insult to the fact.

    Mycoplasma genitalium is one of the least complex freely living organisms on Earth and it has 450+ genes consisting of 582,000 base pairs. How much of that required function do you think you can get to without a representation-translation-effect system in place; in other words, in the absence of the genuine recorded information processing we find in mycoplasma? And it really doesn’t matter where you put the mark Elizabeth, wherever it is, you’ll need the very simplest of chemical organizations to organically produce the immaterial representations and protocols you must have to get any further. And since we won’t be dealing with any evidence to the contrary, let us open our hymnals to 1859 … Dr Liddle will be leading.

    hit it sister 🙂

  96. 96
    Upright BiPed says:

    Dr Liddle has left UD? Well that’s too bad. Thanks for the conversations.

    All the best.

  97. 97

    Will still log in and lurk, to try to clear up loose ends, but I think you guys need a break from me, and I should probably take a break from you 🙂

    Thanks for your lengthy response UBP. I will post a response at The Skeptical Zone, to which I warmly invite you, if only to drop by, and counter-respond as you wish.

  98. 98

    Elizabeth,

    Taking a break is one thing, leaving altogether is another. What a relief to know that you’re staying around. Thanks for the update. I take breaks from UD from time to time as well – sometimes for months at a time.

  99. 99
    dmullenix says:

    Any organism alive today is the product of billions of years of evolution and contains many features, such as DNA replication, ATP, enzymes to speed up chemical reactions, etc. that the first living thing didn’t have. It has also been optimized for efficiency in order to successfully compete with other evolved organisms. We can’t get any idea of the complexity of the first living thing by looking at modern organisms.

    You’re right that WE have no evidence whatsoever of what the first living thing was like. That is, neither science nor ID has any data on the first organism whatsoever. And so far as I know, ID isn’t even looking for evidence. Yet various ID theorists seem to think it’s a great victory when they demand to know what the first critter was like and science can’t answer.

  100. 100
    Joseph says:

    dmullenix:

    Any organism alive today is the product of billions of years of evolution and contains many features, such as DNA replication, ATP, enzymes to speed up chemical reactions, etc. that the first living thing didn’t have.

    You don’t know that- IOW all of that is just a bald assertion.

  101. 101
    Eocene says:

    Joseph:

    “You don’t know that- IOW all of that is just a bald assertion.”
    =====

    Actually it’s called religious faith!

  102. 102
    Joseph says:

    It’s sad, actually- just plain ole sad.

  103. 103
    dmullenix says:

    Oh, excuse me. I meant to say 6000 years of creation. Since 4004 BC.

    NOT

  104. 104
    dmullenix says:

    Of course, if you have any evidence that first life was like modern life, that would be different. What is your evidence for your claim?

  105. 105
    Joseph says:

    If YOU have ANY evidence that first life was different than modern life, that would be different. What is the evidence for YOUR claim?

  106. 106
    Upright BiPed says:

    Dr Liddle,

    You asked me to respond to a post you made elsewhere. This is that response, but I make it here where you left our last conversation. Your counter-argument is based on a major false premise and several instances of a failure in conceptualization. These permeate your comments. I’ll deal with that false premise, but first a couple of observations about your response.

    So UBP’s starting point seems to be that the “information” we say a genome contains is not different from “information” in other senses.

    Different information systems are different by virtue of their implementation into different substrates, and also in the types of effects that result, but the physical objects involved in the transfer share the same dynamic relationships.

    A musical box is an interesting example, because unlike some other information transfer systems, like the pixels on your screen you are viewing right now and from which you are receiving information about the contents of Upright Biped’s post on UD, the sequence of pins on a music box cylinder are actually instrumental in making something else, in this case a melody, and thus bears a closer homology to the sequence of base pairs on a DNA molecule which, by a series of physical operations, results in the making of a protein.

    The pixels on your screen are “making something else” as well. This is evidenced by the simple fact you know the contents of my post. The substrates change, the effects change, but the dynamics of the transfer stay the same.

    UPB claims the music box represents “recorded information”, which implies that the information started elsewhere and was “recorded” on to the music box. However, I think he is making the point that without a mechanism to get the “recorded” music box back into the form of music again, the information isn’t truly recorded, which seems fair enough. After all, if I translated my post into unbreakable code, it wouldn’t really be recorded information because there would be no way of getting the information back out again. So in the music box example, the music box is a way of “recording” a piece of music composed by someone, and getting that piece of music back out again, at a different time. A phonograph recording (the old wax cylinder kind) would be an even better example.

    If you took the cylinder out of a music box and then lost the box, the representations would still be “truly recorded” even if the box was lost. If you never found the music box, or a replacement, then that would simply be a melody you’ll never hear. That doesn’t change the representation in the cylinder.

    Translating your post into an unbreakable code poses some problems. An unbreakable code, as a matter of principle (practicality may differ) is a code without rules, and a code without rules isn’t a code at all. Moreover, translating your post into a code with no rules has nothing to do with the word “translate”. How would you accomplish it? To say that “it wouldn’t really be recorded information because there would be no way of getting the information back out again” is to make an observation about non-existent entities that have nothing to do with the topic (recorded information transfer). It’s fluff.

    In my last post to you I made the point that you repeatedly try to smuggle a mind into the conversation. The reason for this is obvious; it primes the pump that the observations are anthropocentric, and therefore flawed. But it doesn’t work. The fact that humans are symbol makers is not a question; of course we are. But even if we weren’t, the dynamics of information transfer among humans (as in non-human transfer) wouldn’t change one iota. The anthropocentric flaw is not being able to remove yourself from the sample.

    No, I don’t think that works. For a start, “Lizzie has seen an apple” is not a recording of Lizzie’s thought, it is an inference about what Lizzie was thinking. Lizzie’s hearer has indeed received information from Lizzie, but not exactly the information that Lizzie sent. So it seems to me that language is a very different kind of information transfer system from a phonograph, or a musical box, or, indeed a reproducing organism.

    Lizzie is a symbol-maker saying “I’d like an apple” to another symbol-maker. That fact doesn’t change the dynamics of the transfer in any way; it only changes the effect of that information in the hands of the a free-agent receiver. What you describe as a “very different kind of information transfer” is only a very different kind of effect, coming as the result of a free agent being the receiver. But, the dynamics of the transfer haven’t changed. Like I said, you have to remove yourself from the sample.

    In these three examples, we start with a physical pattern of some kind (a performance, a melody, an organism) and we end with a recreation of that physical pattern (a rendering of that performance, the sound of that melody, a second organism). In the case of language we do not. There is no protocol that can create an apple from the word apple, although uttering the word may induce someone else to go fetch one.

    Okay, so maybe it didn’t occur to you that the effect of the sound pattern “apple” is not the sudden appearance of an apple coming from the pattern of the sound. The fact remains that the word “apple” has an effect, and the actualization of that effect (from the sound pattern of the word) follows the same dynamics as any other form of recorded information transfer.

    Again, remove yourself from the sample. Stop injecting issues that only pertain to you as a symbol-maker. Observations having to do with what a free agent can do with information does not change the physical dynamics observed in the transfer.

    This, it seems to me is because the word “apple” is a symbol, or, in Saussure’s term, a signifier that is linked to a signified (aka referent) in this case a specific kind of fruit. UBP appears to want to say that this linkage between signifier (word) and signified (fruit) is equivalent to the link between the sequence on a music box cylinder and the melody that emerges, and that therefore the music box cylinder (and therefore a base sequence in a polynucleotide too) is a symbol for the sound pattern that emerges from the music box in the same way as the word “apple” is a symbol for an actual apple.

    But it clearly is not. When I say the word apple, and you hear it, no apple is created, though you may reproduce my image of an apple in your own inner eye. But the referent for the signifier “apple” is not “the mental image of an apple” but an actual apple. So the linkage between signifier and signified in language (the relationship of a “sign”) is qualitatively different from the relationship between a recorded physical object or pattern and its reproduction.

    Well, it was obvious from the start this was where you were heading, and you’ve done me the favor of encapsulating your error in a single sentence: “But the referent for the signifier “apple” is not “the mental image of an apple” but an actual apple.” So my question to you is simple:

    Do you have an apple in your head -or- Do you have a “mental image of an apple”?

    Really, Dr Liddle. Have you been taught that when an animal communicates it doesn’t know it’s communicating, so it expects apples to appear as it gestures? And will you please take special note; none of this anthropomorphism has anything to do with the observed dynamics of information transfer, instead it revolves around a certain (repeating) disciplinary issue.

    I say again, you are a natural symbol-maker. You transfer information. This is what you do. Accept that, then to the best of your ability, remove yourself from the sample. Recorded information goes in a lot of different directions. It’s an anthropocentric error to continually describe a particular aspect of being human as if that aspect alters the observed dynamics. It doesn’t. I suspect that you probably know this, but are left to ponder the sudden appearance of apples. This is what the evidence of your rebuttal would indicate.

    It seems to me that UBP is defining recorded information as something that requires a discrete protocol, then regards it as noteworthy that all instances of recorded information require a discrete protocol.

    This is a question of the structure of the system. In order to make your case, it requires you to deal with what you’ve ignored in your objection. Recorded information is an abstraction (within a system) which is represented in an arrangement of matter/energy. For one thing to represent another thing within a system, it must be separate from it. If it is a separate thing, then there must be something that physically establishes the relationship between the two. That is what the protocol does. The dynamic involved is that all three of these physical things remain discrete, and this has been validated by observation.

    And finally, describing the parts of a system does not result in a circular argument.

    In other words, the table – an object with pattern – was being replicated with each layer of snow, with sufficient fidelity that an observer could extract from the layer of snow the information that the table had an umbrella hole. By evening there was about 4 feet of snow on the table, but there was still a dimple in the middle, indicating that the information that beneath the snow was a table with an umbrella hole had been faithfully recorded and transferred from snow-layer to snow-layer all afternoon. Yet in this case, the “representation” was also the “effect”.

    Your table wasn’t being replicated (or represented); that was just snow. What you say was a representation, wasn’t a representation. A representation is an arrangement of matter in order to cause an effect within a system. It wasn’t a representation you saw outside, it was table covered in snow. It had a hole in the center of it, which left a dimple in the snow. That dimple made you think of the hole. You then end this anthropic adventure by concluding the “representation was also the effect”. It wasn’t. The representation was a neural pattern going to your visual cortex and beyond. The end effect was “There’s a hole in the table”. Those are not the same thing – and – you’ve put yourself right back into the sample, making observations that only matter to a human.

    However, that seems to me to be the least of the problems with UBP’s case. The far bigger problem is that there is a qualitative difference between a sign (in the Saussurian sense), namely a linked signifier with signified pair, where the signified can be a physical object, and the signifier a symbol potentially renderable in a number of media, and where the transfer of information using the signifier does not result in the physical creation of the referent, and the information transfer in a musical box or in a reproducing organism whereby a physical pattern is recorded in such a way that it can be reproduced, which, at its simplest, can be layers of snow on a table.

    Here you say there is a difference between:

    a) A Saussurian sign [signifier+signified] where the signified can be an object and the signifier can be a symbol.

    …and

    b) where a “signifier does not result in the physical creation of the referent”

    ..and

    c) a music box or an organism where something can be reproduced, like layers of snow on a table.

    I respond:

    a) Firstly, a Saussurian“sign” [signifier+signified] is a linguistics concept that does not invalidate biosemiotics or information theory. In any case, a signifier cannot result in a signified without a protocol. That protocol may exist in a living interpreter (such as a human, or a bee), or it can be instantiated in a machine (such as a music box or a fabric loom). In each of these cases, the protocol will be separate from the signifier and the signified, and it will establish the relationship between the two.

    b) There is no principle involved which would require a representation to result in the production of a physical object; only a physical effect. This is at the central false premise of your objection. When a bee dances in flight in order to direct the other bees to the feeding grounds, it is not nectar that results from the dance, just a change in flight plan (which is an effect, not an object). And once again, you’ve injected yourself right back into the observation.

    c) A representation leads to an effect within a system, and those systems vary, as does their effects. And thoughts of layers of snow becoming a “representation”, is simply anthropocentric.

    BIPED: In this instance, the configuration of holes served as the representation, and the configuration of sensors served as the protocol, leading to the specified effects. Each of these is physically discrete, while sharing the immaterial relationship established by the protocol.

    Well, yes, but the discreteness is, as I’ve said, only arguably intrinsic to the concept of “recorded information” and in any case, does not render it semiotic.

    Here you say that discreteness is not intrinsic to recorded information, but is only arguably so. You also used the word “concept” which is a cognitive term, one which we generally use in order to know anything at all, so I will leave it aside. (If the existence of recorded information is in doubt, then that can be addressed separately).

    Now to your objection: Over the course of this conversation I have given many examples of the discreteness observed. These observations have been given in coherent terms. In all of those instances you have never shown that the observation is incorrect. This suggests that the ‘discreteness’ is inherent based upon logical observations, and is only arguably non-inherent (and is therefore falsifiable by any contrary evidence available). I have told you of the physical entailments which are evident in the transfer of recorded information. One of those qualities is a discreteness among the physical objects involved. You then return to me to say “that doesn’t make it semiotic”. But I have already challenged that objection, and am awaiting a reply. You may remember 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.

    BIPED: a) the existence of an arrangement of matter acting as a physical representation

    Well, maybe, though it’s a bit imprecise.  But sure, information transfer is going to entail physical arrangements of matter.  And let’s allow “representation” to be the thing-that-is-read, like DNA, or the cylinder of the musical box, or even the pattern of sounds making the word “apple” and let that representation be of something (a whole organism; a melody; an apple).

    …or a neural pattern related to an apple, resulting in a pattern of impulses being sent to the chest and larynx.

    BIPED: b) the existence of an arrangement of matter to establish the relationship between a representation and the effect it represents within a system (the protocol)

    Well, no. In the case of the linkage between the signifier “apple” and its referent, the piece of fruit, there is no “arrangement of matter”. There is some kind of “arrangement of matter” that links the signifier “apple” to the evocation of the idea of an apple in a hearer, but the “idea of an apple” is not the referent of the signifier “apple”.

    Translating first sentence: ‘In the linkage between the word apple and the fruit apple, there is no arrangement of matter.’

    If that is true, then each time you say the word “apple” you have the uncanny good fortune of inventing it from scratch. Otherwise, there is a pattern(s) in your brain that maps your knowledge of the fruit to the word and potential downstream effects on your vocal chords. And once again, you’ve plopped yourself right down in the middle of the observations. And still, none of this changes the dynamics of the transfer in any way. The apple is not the word, and neither of them is the pattern in your brain. Again, get out of the study.

    Translating second sentence: ‘There is an arrangement of matter that links the word apple to the thought of an apple in the hearer, but the thought of an apple is not what lead the speaker to use the word.’

    Again, do you have an apple in your head? You are going in circles, Dr Liddle, and I am feeling rather done with this.

    What links the word “apple” to apples is shared agreement among a community of speakers that “apple” means apple … And even if we allowed this as the “protocol” UBP refers to, no amount of cultural agreement that “apple ” means apple will make an apple assemble itself when someone says the word “apple”.

    Speechless.

    The problem seems to be entailment b, as it always has been. A semiotic system relates a signifier to a signified so that two members of a shared linguistic community can communicate ideas – i.e. one member of the community can evoke in the mind of another member the idea s/he is currently entertaining.

    When a “semiotic system relates a signifier to a signified so that two members of a shared linguistic community can communicate ideas” they exchange arrangements of matter (voice patterns) that represent effects within a system (an evocation: apple) and those arrangements of matter will achieve that effect by a second arrangement of matter – a neural pattern – which is the physical instantiation of an agreement among the participants that the sound of the word “apple” represents the red fruit with the white center and the little black seeds.

    So, the voice is not the thought, and the agreement is neither of those. Either that, or there is zero physical distinction between knowing what an apple is, and not knowing what an apple is.

    The thing you need to acknowledge Dr Liddle, is that this same dynamic happens in any transfer of recorded information, not just among members of a “shared linguistic community”. Again, remove yourself from the observation.

    The referents of my signifiers are not my thoughts, but real-world objects, and abstract concepts. Those real world objects and abstract concepts are not brought into actuality when I utter a word. Unfortunately.

    This is becoming silly. You apparently think that when you speak the word “apple” there is an apple in your head prompting you to say the word. This ridiculous deduction comes directly from someone who specifically disavows that neural patterns prompt her words – only, she says, real-world objects can accomplish that task. Well, I am a different person. I only have my sensory/cognitive systems prompting my words.

    Moreover, this is simply wallowing in an anthropocentric malaise. My background in research is certainly different than yours (we are humans measuring humans, so we tend to get out of the way). Consequently, this is not something I will continue to do. I now need to find a stopping point.

    In its entirety, your argument is based a false premise.

    You believe that you have identified a distinction in the effects of information transfer, and somehow by virtue of this distinction, the semiotic argument (based on observed physical dynamics) fails. So let us put your distinction in play and follow it to its logical end. Let us say that only information transfer that produces objects is semiotic. That would mean that the exchange of words is not semiotic. Obviously that is incorrect. So let us say that only information transfer that does not produce objects is semiotic. In that case, there is no such thing as machine code (as machine codes are specifically representations and protocols which produce things). This second view suggest that machine code cannot have anything to do with representations, protocols, and effects. In other words, 01100001 is not a representation of the letter “A” and will not result in the letter “A” in a system where 01100001 is the protocol for the letter “A”. Obviously, this is incorrect as well. So your distinction first fails at the observed real-world level, but the question remains “does it change the dynamics of the transfer”. It completely fails here as well. So as I said earlier, there is no principle that information transfer must or must not result in the production of an object in order to be considered semiotic. It’s only required to have a physical effect within a system following the dynamics as set out by the observations themselves. Therefore the underlying premise in your objection has entirely refuted.

    If I should choose not to continue engaging you in this dialogue, I would like you to know one of the reasons why. In my comments I said …

    Demonstrating a system that satisfies the entailments (physical consequences) of recorded information, also confirms the existence of a semiotic state. It does so observationally. Yet, the descriptions of these entailments makes no reference to a mind. Certainly a living being with a mind can be tied to the observations of information transfer, but so can other living things and non-living machinery.

    … and I substantiated each of these statements by the observation of evidence. At no time have you been able to show an error in these observations. I then went on to say:

    But Dr Liddle, you are deliberately confusing what is at issue. The output of a fabric loom being driven by holes punched into paper cards is “a physical object” as well – an object created by representations operating in a system capable of creating fabric. The nucleotides in DNA don’t know what leucine is, any more than the hole-punched cards of a fabric loom know what “blue thread” is. Or, any more than a music box cylinder knows what the key of “c” is. Observing the critical dynamics does not require any reference to a mind in any way whatsoever, yet you are repeatedly trying (as hard as possible) to inject a mind into the observations so that you can then turn around and claim that its all about a mind. In case you have not yet noticed, you have failed at this position every time you’ve tried it, and you will continue to do so. The reason for this is simple; the observations are correct and you are wrong

    So instead of successfully attacking the correctness of the observations, you introduced Saussure’s (specifically anthropic) concept of a “sign” and have used it as a definition that somehow isn’t required to address the observations. This has the net effect of allowing you to introduce a mind without regard to the observations being made. This is, of course, pure obfuscation of the evidence. Yet, having done so, you then go on to misrepresent the argument as if none of the preceding ever occurred. You say:

    [BiPed] seems to be saying: cell-reproduction is information transfer, and information transfer is semiotic, and semiotics require minds, therefore cell-reproduction requires minds.

    You say this even though you know it is an absolute misrepresentation of the argument I’ve made. The semiotic argument is simply that the information transfer in protein synthesis is not only physical (as in all other forms of recorded information transfer) but is also semiotic (as in all other forms of recorded information transfer). I do not say that semiosis requires a mind in those physical observations, nor do I have to in order to make those physical observations. I do not say so for a specific reason. That reason is because the source of the information is in question, so to make that assumption in the observations is a logical fallacy. In other words, I do not make that assumption as a matter of evidentiary discipline, and you have used it to smuggle in a mind without addressing that same evidence.

    Now certainly I have thick enough skin to be misrepresented, and each time I am I will endeavor to straighten it out. But you represent a special case for two reasons. Firstly, we have been talking rather consistently in and around these observations since May of this year. For you to start blatantly misrepresenting me at this late date is, well, uninteresting. And secondly, you present as someone who simply cannot, or will not, remove themselves from the observations. And that is an argument that I must concede; I cannot argue against it.

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    Mung says:

    Now might be a good time to roll out that refutation of ID you’ve been working on.

    http://www.uncommondescent.com.....n-of-life/

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