I thought I would give a comment by a poster with the handle “ericB” a little more publicity as it was buried deep in an old thread where it was unlikely to be seen by passing “materialists / evolutionists”.
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Calling all evolutionists / materialists! Your help is needed! Alan Fox has not been able to answer a particular challenge, but perhaps you know an answer.
The issue is simple and the bar is purposely set low. The question is whether there exists one or more coherent scenarios for the creation of a translation system by unguided chemicals.
The translation system in cells indicates intelligent design. I would submit that, regardless of how many billions of years one waited, it is not reasonable to expect that unguided chemicals would ever construct a system for translating symbolic information into functional proteins based on stored recipes and a coding convention.
[I realize people have thoughts about what happened earlier (e.g. that might not need proteins, for example) and what happened later (e.g. when a functioning cell provides the full benefits of true Darwinian evolution). For the purposes here, attention is focused specifically on the transition from a universe without symbolic translation to construct proteins to the origin of such a system. Whatever happened earlier or later, sooner or later this bridge would have to be crossed on any path proposed to lead to the cells we see now.]
One of the key considerations leading to this conclusion is that a translation system depends upon multiple components, all of which are needed in order to function.
+ Decoding
At the end, one needs the machinery to implement and apply the code to decode encoded symbolic information into its functional form. (In the cell, this is now the ribosome and supporting machinery and processes, but the first instance need not be identical to the current version.) Without this component, there is no expression of the functional form of what the symbolic information represents. The system as a whole would be useless as a translation system without this. Natural selection could not select for the advantages of beneficial expressed proteins, if the system cannot yet produce any. A DVD without any player might make a spiffy shiny disk, but it would be useless as a carrier of information.
+ Translatable Information Bearing Medium
There must be a medium that is both suitable for holding encoded information and that is compatible with the mechanism for decoding. Every decoding device imposes limitations and requirements. It would be useless to a DVD player if your video was on a USB thumb drive the DVD player could not accept instead of a suitable disk. In the cells we see, this is covered by DNA and ultimately mRNA.
+ Meaningful Information Encoded According to the Same Coding Convention
One obviously needs to have encoded information to decode. Without that, a decoding mechanism is useless for its translation system purpose. If you had blank DVDs or DVDs with randomly encoded gibberish or even DVDs with great high definition movies in the wrong format, the DVD player would not be able to produce meaningful results, and so would have no evolutionary benefit tied to its hypothetical but non-functioning translation abilities. In the cell, this information holds the recipes for functional proteins following the same encoding convention implemented by the ribosome and associated machinery.
+ Encoding Mechanisms
This is perhaps the least obvious component, since the cell does not contain any ability to create a new store of encoded protein recipes from scratch. Indeed, this absence is part of the motivating reasons for the central dogma of molecular biology. Nevertheless, even if this capability has disappeared from view, there would have to be an origin and a source for the meaningful information encoded according to the same coding convention as is used by the decoding component.
(For the moment, I will just note in passing that the idea of starting out with random gibberish and running the system until meaningful recipes are stumbled upon by accident is not a viable proposal.)
So there has to be some source capable of encoding, and this source must use the same coding convention as the decoding component. To have a working, beneficial DVD player, there must also be a way to make a usable DVD.
+ Meaningful Functional Source Material to Represent
It would do absolutely no good to have the entire system in place, if there did not also exist in some form or other a beneficial “something” to represent with all this symbolic capability. If you want to see a movie as output, there needs to be a movie that can be encoded as input. If you want functional proteins as output, there needs to be access to information about proper amino acid sequences for functional proteins that can serve as input. Otherwise, GIGO. Garbage In, Garbage Out. If there is no knowledge of what constitutes a sequence for a functional protein, then the result produced at the end of the line would not be a functional protein.
+ Some Other Way To Make What You Want The System To Produce
If we supposed that the first movie to be encoded onto a DVD came from being played on a DVD player, we would clearly be lost in circular thinking, which does not work as an explanation for origins. Likewise, if the only way to produce functional proteins is to get them by translating encoded protein recipes, that reveals an obvious problem for explaining the origin of that encoded information about functional proteins. How can blind Nature make a system for producing proteins, if there has never yet been any functional proteins in the universe? On the other hand, how does blind Nature discover and use functional proteins without having such a system to make them?
The core problem is that no single part of this system is useful as a translation system component if you don’t have the other parts of the system. There is nowhere for a blind process to start by accident that would be selectable toward building a translation system.
The final killer blow is that chemicals don’t care about this “problem” at all. Chemicals can fully fulfill all the laws of chemistry and physics using lifeless arrangements of matter and energy. Chemicals are not dissatisfied and have no unmet goals. A rock is “content” to be a rock. Likewise for lifeless tars.
The biology of cells needs chemistry, encoded information, and translation, but chemicals do not need encoded information or biology. They aren’t trying to become alive and literally could not care less about building an encoded information translation system.
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I’m hoping ericB will find time to respond to any comments his challenge might elicit.
We couldn’t get him to look at Life’s Ratchet by Peter Hoffmann.
There are some interesting details about the motion of RNA polymerase in Chapter 7. Hoffmann writes:
Just doing that little high school chemistry/physics exercise would give some appreciation of what is happening here. (Well, maybe not to an ID/creationist.)
Ah, but RNA polymerase is a protein! 🙂
The relevance of force to the nucleic acids is a particularly interesting one. Single-stranded xNA, if template polymerised, becomes double stranded xNA, because complementary strands hybridise (and there’s nothing more complementary than the strand you’ve just synthesised!). Stopping that hybridisation is the problem, if you really do want a single strand (eg mRNA or a ribozyme). The easiest way to stop it is to keep another complementary strand handy – ie, to transcribe from double stranded xNA. Which is (conceptually) easy to make – polymerise and let ’em anneal, assuming the process did not zip them up as it went along.
Same goes for reproduction. Generate one free strand from another free strand and they will hybridise, not separate. Even if you forced them apart, the free strand would fold, and be susceptible to hydrolysis due to its bendiness. And only one would be a functional genome. So you keep, and replicate, the strands in pairs, to generate separable identically functional products with the side benefit of reduced chain-bend-mediated hydrolysis, and the possibility of ligation repair should damage actually occur, due to additional ‘pins’ from interstrand hydrogen bonds. And, inherent in that both-strands replication process is a chain reaction of geometric increase, powers of two setting the stage for evolution. Though I don’t think it was designed, it is damned elegant!
I was trying to emphasize that we can actually measure forces at this level. In fact, a gradient of about 0.01 eV over a distance of a nanometer is about a piconewton. Energies of interaction are typically on the order of a hundred times bigger.
No “vital force” is going to escape detection in these processes. The ratcheting processes are well understood.
However, as I understand it, RNA does have the ability to catalyze reactions. Hoffmann mentions this discovery took place in 1982; so there is no excuse for an ID/creationist not knowing about it. About ten years later, it was demonstrated that the RNA in the ribosome does all the work; proteins not needed.
If one has something like an RNA molecule already doing such work, it would seem plausible that a complimentary RNA molecule might come along and meet its “mate” and we would be off and running. A little frame-shifting would quickly find a “match.” I would think it wouldn’t even have to be a perfect match. Snip it and go. Whatever it coded for might not be around today; but, hey, evolution.
Yes, I was jokily anticipating what a UD response might be!
I think nucleic acid complementarity lies right at the heart of the OoL. I find it hard to see how bases could have ever functioned in a ‘single-stranded’ manner, only later being purified for those forming complementary pairs when oriented antiparallel. But stochastically generated complementary sequence could locate partners, forming stable, extensible paired structures where poor fits (including nucleotides that have no complementary molecule) would be exposed to degradation. Early selection, chemical selection, was for stability, not replicating ability or catalysis IMO. But this stability, and its fixing on complementary bases, provides the essence of many of the neatest ‘tricks’ of life: RNA folding, transcription, replication, repair, recombination, small-RNA gene regulation – and translation.
You seem to have misread the definitions. “poly” means “many”. The term “polypeptide” is never restricted to applying “below a certain threshold of number of residues”. If there is ever any restriction in length, it is only toward applying above a threshold that is just enough to be called “many”. As stated, in practice,
Since, by definition, no protein can have too many amino acids to be a polypeptide, your idea “that polypeptides are a subset of proteins” is clearly false and untenable.
Alan, since you were the one who brought this up, I’m amazed that you seem unwilling to concede to your own observation…
Your quoted definition about “enzyme” backed up my own use as being conventional. (Thanks for that.)
So it seems strange to me that you so resist using the terms protein vs. polypeptide as they are “normally accepted and understood (in the particular field of study)” and instead choose “to step outside well-understood and accepted conventions”.
Proteins are a subset of polypeptides. Polypeptide is obviously the more general and inclusive term, i.e. any many-peptide sequence. As Allan Miller’s comments also support, nothing is to be gained by trying to deny common and accepted usage.
Actually, I think you are fully able to realize the answer to this yourself, but perhaps got carried away in the moment. The answer is simple and obvious once one stops to think about it.
Whenever designers design — whether it is an author writing text, or a programmer programming, or an engineer at work, or you yourself writing your next post — this is never a physical search through a large physical space for a physical, preexisting object. No writer or programmer considers all possible sequences of letters.
Designs are created according to the intentions and goals of the designer, who employs their knowledge about cause and effect, and of symbols and meaning. Causes are creatively arranged to achieve the desired effects.
Consider, for example, the designing work of Craig Venter et al as they advance the state of the art for creating synthetic organisms, e.g. by designing, artificially creating, and implanting a customized genome.
Are you one of those ID/creationists who believes that if there exist N molecules with which to make something, and if there is a chain of these molecules of length L, then the probability of forming that chain is 1 out of N^L?
Well, protein usually means a biological molecules consisting of one or more polypeptides, and are highly folded. Polypeptide refers to the unbranched chain of peptides. Saying that proteins are a subset of polypeptides is like saying that a knot is a subset of pieces of string.
Eric
My original point was that proteins and polypeptides are linear sequences of amino acid residues linked by peptide bonds. I ask again, when is a protein not a polypeptide and when is a polypeptide not a protein. I am saying “protein” and “polypeptide” are words labelling essentially the same thing. It maybe the current convention to use “polypeptide” as a descriptive for a section of a protein under consideration and I would use polypeptides to describe the result of exposing a protein to a digestive enzyme such as trypsin but that does not affect my point.
If you think “polypeptide” and “protein” are not synonymous, then give me a counterexample – a protein that isn’t a polypeptide or a polypeptide that isn’t a protein.
And, no, I don’t think the issue is at all important other than an illustration of our difficulty in communicating clearly.
I don’t contest that “protein” could refer to biological molecules consisting of more than one polypeptide. Nevertheless, for the cases of proteins consisting of one polypeptide, even your own description points to a subset relationship with regard to the set of proteins consisting of one polypeptide vs. the set of polypeptides. The latter obviously includes the former, but the former set obviously does not encompass the latter.
To use your own analogy, it would be more correct to say that a protein was comparable to “knotted string” rather than simply the concept of a “knot” (as divorced from the string that is knotted). The set of knotted strings is indeed a subset of the set of strings (whether knotted or not). 😉
More importantly and more to the point of the context for the remarks, your description excludes Alan Fox’s attempt to claim that “protein” and “polypeptide” are synonyms. My comments on this point are in the context of responding to that incorrect idea (i.e. to indicate they are not synonyms), and my original and fuller statement was more careful to explicitly qualify that proteins are “at best” a subset of polypeptides.
Now, if you want to correct my allowance that proteins are at best a subset of polypeptides, I wonder why you’ve had no expressed objection to the claim that “protein” and “polypeptide” are synonyms. If that equivalence were accepted, your own description would become a self-referencing confused knot.
It should be quite simple, Eric, for you to tell me what differentiates a polypeptide from a protein if they are not synonymous terms.
Some of Allan Miller’s recent comments seemed to suggest that the conditions of the challenge excluded replication and/or any natural selection, leaving him with no options. But if so, I’m not sure how to understand that in light of the fact that I again explicitly granted as free assumptions without need of justification…
…replication of strands of DNA or RNA, either doubly or singly stranded
…the specifically sequenced ribozyme(s) needed to implement that replication
…random variation in the process of building or copying DNA or RNA
…and consequently a type of prebiotic natural selection deriving from the fact that some sequences of xNA may be more or less likely to be replicated and therefore increase or decrease in the frequency of their copies.
Thus, the starting point is an uncoordinated, replicating colony of xNA strands subject to natural selection against strand sequences that are less likely to be replicated. For example, strand sequences that tend to become less available for replication (e.g. due to their own folding tendencies that might inhibit replication or to tendencies to be bound with something else) will tend to be weeded out, while the more available sequences will tend to multiply and increase in relative frequency.
Other comments by Allan seemed to imply that I’ve forbidden certain options. In reality, what I’ve forbidden is simply assuming what one needs beyond the givens, e.g. that one could just assume feasible access to producing whatever sequencing one needs in an xNA strand (other than for the freebie of the ribozyme(s) for strand replication), or that one could assume a pseudo-cellular organism (where the unit of reproduction has become the pseudo-cell rather than the given of independent xNA strand replication) or the assumption of working non-protein substitutes for any needed components that are fulfilled using proteins in current cells. That doesn’t exclude proposing such things provided they have sufficient justification regarding the means available to overcome obstacles to their origin.
One point of mine that was not clear enough:
Apparently keying off the phrase “anything more than an RNA or DNA strand at a time“, Allan responded at length about how multiple strands could be processed concurrently. That’s not the issue I was raising. There is no suggested obstacle to having many such replications going on concurrently.
My point is that every one of those replication operations always only produces a reversed complementary strand of xNA as its output. There is no capacity to directly reproduce a complex structure of any kind or indeed any object at all that is not more xNA. One cannot reliably replicate something that one cannot replicate at all.
What you get for free is strands of xNA producing more strands of xNA. The inherent nature of the process itself requires this. To go beyond this to something more (e.g. that you might want to have for a pseudo-cell) would require justification.
This presents difficulties if you want to suppose, for example, the emergence of xNA structures that take the place now held by proteins. Strands of xNA whose bases are bound to something are not presently available for replication. To make such a strand available for replication requires detaching it from whatever structural arrangement it had (thereby breaking those bonds).
If you will permit an analogy simply to illustrate the idea, you could copy the parts of a clock by taking it apart and copying each part. But you couldn’t do that without disassembling the clock. You cannot replicate the clock as an intact whole. You couldn’t still have a working clock as it parts were being copied.
Meanwhile, strands of xNA whose bases are not bound to anything would be available for replication. As natural selection operates on the members of the colony of strands, the obvious tendency will be to replicate those strands that are available for replication. Their sequences will increase in frequency, while the sequences that dispose a strand to being unavailable for any reason will decline in relative frequency.
I didn’t say that “with transcription into functional RNA (ribozymes, riboswitches, etc)” is an automatic given that can be merely assumed. (Recall my points about not assuming any sequence you needed.)
In what I described above, the “consistent reproductive advantage” is ready availability for replication. Those that are more often available for replication will increase in relative frequency. Strands that tend to be not as available will tend to be left behind in frequency.
BTW, as a side observation, this is a point where a scientist operating by artificial selection can do what would not happen by natural selection. A scientist who might be looking for the property of binds-strongly-to-X could design an experiment to filter out xNA sequences that have that property to any extent. Then the scientist, who is working according to a goal, could artificially choose to keep just those sequences, free them from being bound to X, and then multiply them exclusively and repeat the process, rather than multiply those that by nature did not become bound-to-X (and so remained unattached and more available for natural replication).
The same technique is used by any breeder who wants qualities that the natural environment would not have promoted or would even have selected against.
I didn’t miss that. I understood “might” even while I chose to share the quote.
It would be a great advance to dialogue and reflection if more dogmatic evolutionists would begin to seriously consider even the possibility that mindless chemicals that don’t know where they are going might not get “there”, i.e. to where evolutionists assume they must have gone and would have needed to go to support the desired and presumed conclusion. The prevalence of dogmatic faith that a mindless path to the cell must exist is an obstacle to serious scientific evaluation.
So I would gladly welcome the positive development of accepting the possibility that unguided natural processes might not get there. That by itself would be a big step toward meaningful dialogue and consideration. As it is, for many the possibility is not even seriously on their radar.
Elsewhere I’ve pointed out that my challenge cannot show that undesigned intelligent life is not possible. By itself, it doesn’t rule out the possibility there might be some other path not involving cells with translation systems. (You would think that a materialist would have no problem acknowledging this, since materialism itself would require this, if our cells are designed. Yet, you still find some who balk at acknowledging this.)
Do we want to continue to argue about polypeptide v. protein or do we want to concentrate on the challenge. 🙂
Alan, if you really want to pursue it, feel free to start a new thread.
lol@mike
No, he’s not “that kind” of CREATIONIST, since “that kind” of CREATIONIST doesn’t exist.
Can you tell us why we should believe your post wasn’t generated by some sort of nonsense-generating mechanism?
Not so much that as I don’t think you realise what is consequent on ‘conceding’ replication and natural selection. If an xNA genome is replicatively competent, produces ribozymes, and yet performs no translation, it has replication and transcription. These are all it needs to have Natural Selection – genotype and phenotype. And they are all it needs to perform peptide synthesis, initially uncoded. You appear to wish to hamstring these organisms in some way that prevents them evolving, with talk of ‘free strands’. But if it can replicate and transcribe, it can free ’em. They rebind on their own; it’s one of the most fundamental facts of nucleic acid chemistry. Not if the strand is bound by a complement, of course. But if they can replicate, they can separate and synthesise a complement.
Replication and transcription are pretty much the same thing, conceptually. If you can do one, there is little to stop you doing the other.
ericB,
Actually, in your rush to be patronising, I think you missed the point, and in the process illustrate why English text and computer programs are completely inappropriate models for macromolecules. Engineering is a little better, but not much.
And neither – does it surprise you to learn? – does evolution.
People playing the ‘Hoyle card’ assert that there is a minimal size to a particular functional configuration. That is trivially true, but the point is to make the spaces so big, and function so rare, that evolution would still be trying to get the first one, but for Good Old Design.
If the length of that minimal configuration is n, and there are v different subunits, the total space has v^n members. If there are t such targets in that space, the probability of hitting a target is t/(v^n) if you search randomly.
Let’s take a 100-acid peptide. The space is 20^100 or 1.26^130. Hoyle’s arithmetic assumes that only one configuration would work – t=1. That is, even if you were one step away from the magic configuration, you might as well be anywhere else in the space; it’s a dud. t=1 is a little unrealistic, but that does not matter too much here.
So this is the configuration that a designer can possibly shortcut his way to. But how? Consider English. Allowing 26 characters, space and 3 punctuation marks an equivalently-sized space would be given by an 88-character sentence. But get any single letter wrong, and you have not made the target. And, because only the target is functional, you could be one step away and not even know it. You have nothing to guide you. So, I hope you can see, English is a useless analogy. And I hope you can see why – it’s inert. The same goes for programming – the equivalent-sized ‘space of programs’ would be given by 429 binary bits, and you would have no way of knowing that you were one step away from Hoyle’s unique target (or one of several targets in a more realistically-populated space).
Now of course we’d agree that ‘things aren’t like that’. But they ‘aren’t like that’ in a way that is affects both explanations. If the designer from experience elsewhere (how gained, I wonder?) knows that combination of subfunctions in smaller spaces leads to a desired effect, blind nature can also combine such subunits rather more clumsily but ultimately no less effectively. And Nature has one extra trick up its sleeve: it doesn’t give a damn what ‘function’ is. It throws, in a fairly controlled manner, all manner of crap at the wall and sees what sticks. Functional improvement, and novelty, can come from anything, anywhere. In a genome of 20,000 genes, and continual environmental feedback, the combinatorial explosion is crippling to all but omnipotent deities. But by the simple expedient of empirical testing against a very simple criterion – survival/reproduction – genomes find out what combinations work in their most recent environments. And it’s notable that this, not base-by-base detailed design, is what people do when they want to generate novel ribozymes and peptides – they mass-produce random peptides or xNA strings, and let the functional ones make themselves known by mass screening. That‘s sound design – what Nature does! It doesn’t always work in the marketplace, but it does in the wild.
Trying to generate consequences, except in certain areas, is a recipe for disaster – combinatorial explosion, and unintended consequences, are typical results of design, not exquisitely functioning nanomachines. People who worship at the altar of Design have obviously worked on much better projects than I ever have.
Craig Venter is, at best, reverse engineering.
Mike Elzinga:
Proteins not needed FOR WHAT?
THE RIBOSOME can perform it’s function without proteins. Period. That’s your claim?
Can you point us to a specific example of a ribosome that can “perform it’s function” in the complete absence of any protein?
Not that I count this site as any particular sort of authority, perhaps Mike can do better, but:
oh, that’s rich.
so i’m scratching my head now.
If the function of the ribosome is to synthesize proteins, how can it possibly function without them? The very idea is self-contradictory.
The RNA in the robosome does all the work OF WHAT? Protein synthesis?
No proteins needed? Really?
I said it wasn´t important. No reason for me to mention it again if you and Eric are no longer asserting there is some fundamental difference between “protein” and “polypeptide”.
Good one, Mung. Oh, you’re not joking … ? It’s like saying if the function of a pasta machine is to make pasta, how can it function without pasta?
The protein Mike refers to is the structural protein in the ribosome complex. It was assumed to be catalytic, since just about every other major bit of catalysis is performed by protein, but it turns out that the RNA in the ribosome is doing the catalysis of peptide bond formation.
It’s not a question of dogmatism or ‘faith’, but it is at least possible that people are conceptualising things in a way that is entirely rational, but you aren’t grasping the weight of those concepts – you don’t know everything they know (and vice versa, of course). Certainly, what I know has a considerable influence upon what I consider possible. And I know a fair bit about the nuts and bolts of what is under discussion.
At the least, you could grant that I don’t hold my position despite what I know; ‘dogmatism’ is not the only way to rationalise why I hold the views I do.
Hey, ericB! You’ve been going on about this ‘translation system’ thingie. And you’ve repeatedly made use of fallacious, bullshit not-arguments to buttress your repeated assertion that this ‘translation system’ thingie is the product of Intelligent Design. Are you ever going to get around to supporting said assertion with real arguments that actually do support it? I’d ask for evidence in support of your position, but you haven’t provided any such evidence, nor yet have you provided any reason to believe that you ever will provide any such evidence… so.
If you want people to accept the logical possibility that this ‘translation system’ thingie could conceivably be a product of Intelligent Design: Not a problem. I, for one, already accept that logical possibility. I just don’t think it’s anything more than a logical possibility; in particular, I don’t think there’s any good reason to believe that this specific logical possibility is something that actually does exist.
Um… you do recognize that “X is logically possible” is not an interchangeable synonym for “X actually does exit”, don’t you, ericB?
So. Got evidence, ericB?
Failing that, got a non-fallacy-ridden argument in support of your proposition?
ericB,
This is confusing. I think there are three main issues:
1) Failure to differentiate genotype and phenotype
2) The mechanism of transcription.
3) The relation between transcription and replication.
4) The Role of the Complementary Strand.
Four! Among the issues are …
1) Genotype is always that which is replicated, in any cell or any organism anywhere. You don’t take the organism to bits and replicate it, you replicate the nucleic acid from which, ultimately (translated or not), its entire – and temporary – essence is constructed. That ‘essence’ includes such things as the replicative cycle, cytoplasm, cell membranes, catalysts, structural units, fundamental behaviour (howsoever primitive). Phenotype is basically everything that isn’t genotype (raw sequence). So you never replicate the ‘clock’, you replicate the elements that, when copies are made, assemble into a clock. You throw the clock away.
2). Because one is taking the sensible precaution of keeping xNA double stranded in my model, it is not perennially folding up into its ribozymal configuration. This double stranded configuration has other consequences as well, which is why I felt the need to make extended points about it. When a ribozyme is required, the relevant portion of genotype is copied. All a ribozyme is is “a reversed complementary strand of xNA as output” from a subgenome version of whole-genome replication. You obviously need to copy the correct strand to get the correct ribozyme – it needs some control. Another advantage of the double strand here is that it, rather than your freshly-minted ribozyme, hybridises with the sequence you have copied, freeing it to fold. And folded RNA is what ribozymes are. And you can make as many of these copies as you want. And chuck them afterwards. Because the ‘master copy’ sits snug in your double stranded genome. Which you can subsequently replicate and create TWO copies of your ‘successful’ genome (if such it was).
3) Replication vs transcription. Well, I’ve pretty much covered this. If you can template polymerise your xNA, you can transcribe parts of it by exactly the same method.
4) In both, you need to consider the stoichiometry of strands. At this point, I feel the need to draw a diagram, but just consider the relevance of a second strand of complementary xNA to both replication and translation. If ‘all you are doing’ in replicating strand A is creating a complement B, the strand you separated to allow that must have been itself a B. Replicate that and you have an A. As if by magic, you have two ABs, both with all the ribozyme sequences neatly tucked away. You have geometric increase: a chain reaction. And you can get those ribozymes out by partial replication – ie transcription. If xNA were always single stranded, you couldn’t make a ribozyme because it would hybridise with the parent sequence. (Well, you could make one ‘sacrificial’ hybrid strand and then you’d have double stranded DNA anyway!)
I also wonder if you regard replication as something that comes from outside the strands themselves … ? Your talk of strands ‘being available’ for replication, or not, hints at that.
Allan Miller:
Yes, Allan, it’s that simple. Absent PASTA, what is the function of a pasta machine? Doorstop? Decorative conversation piece? Imaginary pasta maker? If it doesn’t make pasta, what sense does it make to call it a PASTA machine?
Making proteins (oh heck, let’s say making polypeptides, shall we?) is the function of the ribosome. Do you dispute this? Does it perform some other function? Given the Darwinian story there’s no reason to think the ribosome would even exist otherwise, is there? If it wasn’t selected for it’s ability to make proteins, what was it selected for?
Take it out. See how the ribosome functions without it.
Mike Elzinga:
O look, a PASTA MACHINE! It was demonstrated decades ago that it was a human turning a crank that does all the work. No PASTA required!
cubist:
You see, ericB, I can just type on this keyboard here and the text I type can appear on your screen there, and anyone with access can view it by visiting this blog here, and this proves beyond any shadow of a doubt that you’re only talking about what is logically possible.
And if there’s any translation or encoding or decoding going on, well, a person would have to be a fool to believe that. A monkey banging rocks together can achieve the exact same effect.
Mung is right and you are wrong and he loves the truth!
Absent pasta, the function of the pasta machine is to make the pasta that is otherwise absent.
“Stephen Meyer is a Liar for Jesus,” is an ad hominem. It’s not an argument. But when that’s all you have…
The question isn’t whether or not “translation” or “encoding” or “decoding” is going on. The question is whether or not the aforementioned activity could occur without some sort of Intelligent Design(er)’s intervention, somewhere along the way. ericB has argued that Intelligence must have been involved with the advent of the ‘translation system’ in living cells, on the analogical grounds that Intelligence is involved with the advent of every other ‘translation system’ known to Man—but since it’s human Intelligence which has been involved with the advent of every other ‘translation system’ known to Man, ericB’s argument is either (a) strongly supportive of the proposition that human beings were involved with the advent of the ‘translation system’ in living cells, or else (b) just plain bogus.
Apart from that, ericB hasn’t established that there’s anything in a living cell for which the term ‘translation system’ would be anything more than an inappropriately-reified metaphor.
Mung, do you think you can succeed where ericB has failed, and pony up some actual evidence and/or valid argument(s) in support of the proposition that Intelligence was involved with the advent of the ‘translation system’ in living cells? If so, I invite you to do this thing.
wow, what a change in tone.
cubist, faced with the obvious absurdity of your position, you’ve moved the goalposts!
When you type on a keyboard, you hit a key with a symbol inscribed on the key, assuming what? That it will generate nonsense? Hardly.
No, when you hit the key with the ‘M’ symbol on it while also holding down the ‘Shift’ key you expect a specific response from an otherwise mechanical system. But why would you even care if you were not attempting to communicate?
You folks kill me, you really do.
So right in front of your face is a system of encoding/decoding and translation, but instead of admit it, you prefer to deflect it.
Try to communicate without it, I dare you. Assert that the system you use to post here at TSZ does not require intelligence.
Here was your initial challenge:
Well, your own posts here at TSZ provide the evidence you claim does not exist and cannot exist. Your objection to ericB is self-refuting.
cubist:
Asked and answered.
There is a mathematical definition of a code. The “genetic code” meets that definition. There’s no reification involved.
Absent a pasta machine, pasta could not exist.
Mung, let me introduce you to a perhaps-relevant bit from the OP:
That is the question at hand: Is it possible for the ‘translation system’ in living cells to have been generated by ‘unguided chemicals’? If the biochemical ‘machinery’ in living cells does not, in fact, contain an actual, sho’nuff ‘translation system’, the question is moot. But even if the biochemical ‘machinery’ in living cells does, in fact, contain an actual, sho’nuff ‘translation system’, anybody who wants to argue for the position that the advent of said ‘translation system’ involved Intelligence has to… you know… argue for that position. That’s argue for said position, as opposed to baldly asserting it, or assuming up front that said position is correct, or disgorging obfuscatory verbiage in the general direction of an argument.
As to your verbiage about what does or doesn’t happen when someone types on a keyboard: To the extent I understand what you wrote, said verbiage appears to be a reply to someone who was attempting to argue the (transparently silly) position that no Intelligence was involved with the advent of any ‘translation system’ whatsoever, or perhaps the related (and even more transparently silly) position that no form of Intelligence was involved with the advent of a specific ‘translation system’ whose advent is, in fact, known to have involved (human) Intelligence. Since I was not attempting to argue either of those positions, it is not clear to me why this comment of yours is directed to me, as opposed to being directed to whichever person was attempting to argue that no Intelligence was involved with the advent of any ‘translation system’ whatsoever.
Again, you are responding to some other person than me, a person whose position, as best I can reconstruct it from your comment, seems to be that no Intelligence was involved with the advent of any ‘translation system’ whatsoever. Since that person is not me, it is, again, not clear to me why your comment is directed to me, as opposed to being directed to whichever person was arguing for that position.
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Asked and replied to, yes. Asked and answered, no.
Since this is simply a bald assertion of the truth of your position, bald assertion is all the response that is called for: No, the ‘genetic code’ does not meet that ‘definition’. And yes, there is reification involved.
Mung, feel free to advance the discussion by, you know, providing evidence to support your view—or even a good, solid, non-fallacy-ridden argument in support of it. Or not. Either way is fine by me…
When I wrote about the prevalence of dogmatism, I was not making a specific reference to you and I don’t make the claim that you hold your conclusions merely out of dogmatism in spite of what you know. If a shoe doesn’t fit, you don’t need to feel any obligation to wear it, and I’m not trying to make the case that it fits you.
I am referring to those who specifically hold a dogmatic position — as an axiom that is not subject to evidence — that an undirected, materialistic source for life must have been the original source. That being so, any present inability to reconcile this with what we’ve learned from chemistry must simply be due to our current ignorance. It cannot be seriously considered that it might reflect a failure of the hypothesis precisely because it never was considered a mere hypothesis. It is an axiom. No amount of apparently contrary evidence can ever defeat an axiom. It will always simply mean we don’t understand something yet. Thus it remains perpetually insulated from falsification.
In other words, some see that assumption as inherently baked into the rules of the game. The outcome of the matter has been predetermined from the start.
If you don’t embrace that type of dogmatism, good for you. May many more come to see that as antithetical to the true spirit of science.
Virtually no one in the scientific community holds that position. What is actually said is that there is zero evidence for any non-materialistic origin of life, and lots of positive evidence for a materialistic origin.
You Creationists do love you some dumb strawman arguments.
Here again you insert an assumption that I’ve explicitly pointed out is not one of the freebie hand-waved assumptions, i.e. “produces ribozymes”.
You understand how PCR works. It doesn’t require an “organism” to do the replicating of strands. Nor is the necessary enzyme for replication (whether protein or in the case under discussion a ribozyme) any necessary part of the strands being amplified.
I’ve freely granted to you a starting point intended to be devoid of teleological assumptions, including assumptions about organisms that might be programmed in advance to produce whatever ribozymes one might wish to imagine. The explicit exception is the hand-waved enzyme(s) needed to replicate xNA strands, which are assumed to have existed within the colony of xNA strands that results. I’ve also granted for free the idea of random transcription of random portions of any strand.
That doesn’t preclude you from justifying that a mindless process could lead to what you want. Just keep in mind that the unit of replication is xNA strands (or subportions thereof that are initially random).
Thus, you don’t start out merely assuming there is control over transcription, or the ability to produce a cell with a functional cell membrane, etc.. As I’ve mentioned, other than the explicitly granted free assumptions, you can’t freely assume that something done now in cells in ways that depend on proteins would already be an accomplished and functioning feature done by something other than proteins as part of your starting point.
In short, if cells need proteins to do X now, you cannot merely assume X is being done by something else as your starting point (other than strand replication and random transcription). Instead, the point is to see if the natural processes of mindless chemicals are “causally adequate” to justify the process that supposedly leads to the translation system (and then to proteins).
If you then revisit my points about the limits of strand replication / transcription, you will begin to see the problem I am referring to, i.e. how to get off that merry-go-round and start to build a functional cellular organism (without the help of preprogrammed translation).
It seems to me that your difficulty understanding my concerns about changing the unit of replication without justification come from your repeatedly assuming you are already starting from a fully operational cellular organism as a free assumption (e.g. already having the acquired ability to generate all the ribozymes needed to construct cell membranes that are not lethal).
I don’t read minds, but I would have to guess that is a strawman. I do not know anyone who takes the kind of position you criticize. But I’ll grant that some take stronger positions in that direction than I would.
Here’s my puzzle. ID proponents push the case for “fine tuning”. Yet, “fine tuning” would seem to call for something like deism — a god that created the cosmos in just the right way at the start, and then allowed nature (that finely tuned nature of the deities design) to take its course. It seems to me that a proponent of fine tuning should be a proponent of the view that the cosmos was so finely tuned that it was certain that life would emerge from that finely tuned nature.
“If Y occurs …”
My point is that you cannot assume that Y will occur, and nothing about the failure of X implies that any Y solution will arise naturally to be selected (e.g. any simplistic cell membrane that is not detrimental with the result of being weeded out).
The failure of X does not imply that the working and beneficial Y alternative is directly discoverable. It may be that every stepwise path to Y passes through detrimental intermediate configurations that would be weeded out just as X was weeded out.
I am pointing out that the belief that Y will arise at all cannot rest merely on assumption, and is not enhanced or improved in any way by the fact that X fails. Of itself, the fact that X is weeded out doesn’t add any support to the unguided appearance of a working Y.
I would not expect that anyone with that position would describe it in the blatant terms that I have. They would certainly choose to put it another way. Yet, it is real and can be seen, for example, in how people respond when issues of the apparent inadequacy of material explanations are raised. For some, there are only two possibilities that can be seriously considered.
A) Materialist explanations are adequate or reasonably so.
B) We are merely looking at an instance of our ignorance. Perhaps someday we will be able to see the materialist explanation (i.e. option A).
There is no option C on the table.
Consider, for example, the difference between saying that science is limited to studying material objects and processes vs. the stipulation that everything in the universe is in principle explainable by the material processes that science can study. The former is a defensible limitation on what science can do because of the tools and methods it has access to. The latter is an axiomatic declaration about the nature of the universe and what it contains, rather than a limitation on what science can learn. Some take the latter as part of the definition of science, i.e. as axiomatic.
I understand your point and it is a good question. In fact, there is no shortage of people who do in fact combine the two ideas and suppose that all the design needed was front loaded from the beginning, making any further intervention to create life unnecessary. If it ever became clear that living organisms could be produced by natural processes, I could consider taking that very viewpoint myself.
For the sake of answering your reasonable and worthwhile question, I’ll offer a couple explanatory thoughts. But I don’t plan to make a digression off topic to make an involved discussion of it.
With the exception of living organisms, the rest of what we see in nature seems in principle to allow explanation based on law+chance. Law is causally adequate to account for order and regular arrangements. Chance is causally adequate to account for unspecified complexity and meaningless irregularities.
Yet living organisms are different in documented ways that cannot be reasonably denied. They are systems based upon specified complexity. We’ve never found anything else in the universe (other than artifacts) to have that property.
Side observation: If someone tries to explain the origin of cellular translation beginning with a reproducing cellular organism that produces ribozymes from a genome as the starting point, they are preferring to start with a system that already has functional specified complexity packed in and working.
The short of it is that space+time+law+chance doesn’t provide causal adequacy for the origin of the massive extent of specified complexity that we see, for example, especially during the Cambrian Explosion.
BTW, those who treat a materialist explanation as an axiomatic assumption are likely to insist in one way or another that Stephen Meyer’s books (and his earlier peer reviewed article on this theme) should not be given serious consideration. But those who treat Meyer’s arguments dismissively or with ad hominem attacks simply remove themselves from the realm of persuasive discourse.
If Meyer is right that the specified complexity uniquely found in living organisms (and in the artifacts of intelligence) requires an infusion of specified information, then law+chance explanations are not going to be adequate. I don’t intend to side track onto discussing his books or his points, but if you sincerely want to understand the answer to your own excellent question, there is no substitute for personally reading and reflecting on what he has to say for yourself (not filtered through antagonists).
Thanks for your thoughtful questions.
The way that I look at it, is that explanations don’t really explain. We explain x in terms of y, but we leave y unexplained. In the process of doing this, we gain some ability to control x, and that pragmatic consideration is what drives science.
I don’t say either. Science is limited to studying that for which we can find reliable evidence. If you took what is known about quantum particles, and could take that back on a time machine to 200 years ago, people at that time would probably see it as talk of the immaterial. I don’t think the word “material” has a fixed (i.e. unchanging) meaning.
Yes, living things are different from, say, rocks. But what is that difference?
An important difference is that they consume energy. An automobile consumes energy, but we control it. A fire consumes energy and can easily be out of control. A biological organism consumes energy, and seems to have some degree of self-control.
Compared to fire, the energy consumption is better controlled in biology, and there is a great deal of self-control. But, in some ways, biology is a bit like fires. Nobody questions that fires are natural. Somehow, primitive biochemical reactions may have gained the feedback mechanisms to assert the kind of control that we see in biology.
While living things are different, it seems at least plausible that they arose naturally. I certainly don’t claim this is proved, or even that it is certain.
I remain unconvinced that “specified complexity” is a meaningful term. But let’s suppose it is. The complexity of a human adult far exceeds the complexity that could have been specified in the DNA. An automobile is far more completely specified than is a biological organism.
The way you ID-pushers use the term “Specified Information”, and the related term “Complex Specified Information”, those terms are meaningless noise. I realize that a devout ID-pusher like yourself, ericB, will not accept that assertion, but come on… get real, already. You ID-pushers can’t even identify the presence of (C)SI there is in stuff we damn well know to be products of (Human) Intelligence (see also: bowling balls, chocolate cake, etc), so why should anybody believe you ID-pushers when you claim to have identified the presence of (C)SI in stuff whose origin is very much not known?
Back to the immediate issue at hand: Does Meyer define this ‘specified information’ thingie as something which can only be produced by intelligence? If so, he damn well better justify the proposition that living organisms are a product of intelligence before he declares living organisms to be exemplars of SI. Because if he’s using the putative SI of living organisms as his evidence to support the proposition that living organisms are a product of intelligence, he’s assuming his conclusion.
If, on the other hand, Meyer <doesn't assume up front that SI is evidence of intelligence, then okay. Fine. Living organisms have SI. Now, what’s your evidence that living organisms are a product of intelligence?
Apart from all that, I note that you are… still… making use of the bullshit not-argument “every example of X with a known origin is due to Intelligence, therefore it’s reasonable to think that an example of X with an unknown origin is due to Intelligence”. Do I really need to remind you that your bullshit non-argument is stronger support for the proposition the ‘translation system’ in living cells is a product of human Intelligence than it is for your favored the ‘translation system’ in living cells is a product of some sort of unspecified Intelligence proposition?
There are no doubt many ways in which biological organisms may be similar to other entities. No objection there. Nevertheless, your question was about why the situation with living organisms is different from the situation with other parts of nature (where a deistic front loaded design might suffice).
Despite all similarities shared with other objects, there is nothing else in the universe that we have ever found (apart from what are known to be artifacts) that depends on reading a sequence and interpreting its meaning by a code. Some will try to quibble about labels and semantics, but that is entirely irrelevant. Anyone can put any reasonably descriptive and accurate label on it that they want. Regardless of labels, the reality is that this is unique and without counterpart in any other aspect of the known natural universe. That is something obviously noteworthy and in need of explanation. Something has been produced in this case that no natural feedback mechanism has produced in any other context that we know of.
I’m not sure I’m catching your point here. I think you would need to help me out a bit with more elaboration.
About specified complexity, it’s helpful to distinguish attempts to measure and quantify it (e.g. Dembski’s work) from the core concept itself. Complexity simply refers to the irregularity that does not follow any concise pattern. Any system with randomness can produce lots of merely random complexity, as both Orgel and Davies realized. Their point in making the distinction of (tightly) “specified” complexity is simply that the particular arrangement of this irregularity matters a great deal. It is vital to specifying function. For example, a very small difference in the specification can be the difference between a living or a dead organism.
Well said. So would it be correct to understand that you affirm the cell does perform translation / decoding by a code (with the understanding that I’ve made all along starting with my very first post that the use of these terms (e.g. translation, symbolic, codes, decoding, encoding) does not of itself inherently or automatically imply design)?
Not only is it relevant, it’s critical for the semantic games you keep playing. You have not established that genetic sequences have *meaning* which implies a message purposely transmitted between a sender and receiver. Genetic sequences don’t “mean” proteins any more than Na + Cl “means” table salt.
Sorry but you haven’t identified any specification either. A specification is a before-the-fact document detailing the requirements a designed object or system must meet. All you have is an after-the-fact *description* of a complicated chemical reaction. Calling it a specification is just one more silly semantic game the IDiots love to play.
Exactly.
But I’m not usually polite enough to allow them the modest covering of “semantic game”.
At least as far as the conmen like Meyer and Behe, the correct term is “lie”.
They know better, but they do it anyways (for money, mostly) and they hope no one will notice. Their followers never do notice. Too bad.
And from this we are supposed to infer that no one posting here at TSZ holds that position?
Well Mung, you *could* ask. I know that’s expecting a lot from a Lover Of Truth.
cubist:
Yet that is exactly the point that some people here at TSZ are unable or unwilling to concede. Surely you’ve noticed.
Encoding and decoding would seem to require a code. Translation would seem to require an alphabet and a language.
Only if your argument is 100% dependent on the use of analogy as its only “positive” evidence.
Some day the Creationists will realize that argument by analogy doesn’t work in science. But apparently not today.
A language implies words and syntax. That means that you can read the statements for meaning. Give me an example of reading a gene for meaning without doing the chemistry.
Just one example of decoding the abstract meaning of a novel code sequence without doing the chemistry.
If it’s an abztract code you will have no trouble. If you can’t do it, it’s just chemistry.