Upright BiPed has been proposing what he has called a “semiotic” theory of Intelligent Design, for a while, which I have found confusing, to say the least. However, he is honing his case, and asks Nick Matzke…
…these three pertinent questions regarding the existence of information within a material universe:
- In this material universe, is it even conceivably possible to record transferable information without utilizing an arrangement of matter in order to represent that information? (by what other means could it be done?)
- If 1 is true, then is it even conceivably possible to transfer that information without a second arrangement of matter (a protocol) to establish the relationship between representation and what it represents? (how could such a relationship be established in any other way?)
- If 1 and 2 are true, then is it even conceivably possible to functionally transfer information without the irreducibly complex system of these two arrangements of matter (representations and protocols) in operation?
… which I think clarify things a little.
I think I can answer them, but would anyone else like to have a go? (I’m out all day today).
Way to avoid the questions, joe. Try again.
Here they are:
What if a person changes their worldview to believe that Fred the giant frog god designed and created the universe and everything in it? Would that be testable?
Exactly how would believing in or inferring a designer/creator god change the way science is done?
And you’ve avoided many other questions, including these:
Asteroids are an arrangement of matter. Specifically describe and demonstrate the non-material information, and the origin of the non-material information, in an asteroid that has never been detected or seen by humans or any other living thing.
After you do that, consider and respond to this:
An undetected asteroid is coming toward this planet. When it enters the atmosphere it ‘burns up’. It is no longer an arrangement of matter, is it? Where did the matter go? What happened to the non-material information? Does that non-material information still exist?
Well, of course the content of my post owes its existence in part to the forces at work in my CPU. It also owes its existence to a whole host of other material forces, like for example those at work in my brain and my hands. I don’t understand your point?
What part of the relationship between a bee’s dance and the other bees’ behavior is not material? As far as I can tell (and you yourself described), all the chemical and electrical processes of perception, signal transfer, and behavioral action taking place in the bees are perfectly material.
Describe and demonstrate the software, and the origin of the software, that is programmed into an asteroid.
How does that even follow from anything I have said?
You seem to have missed the word “process” that was in Allan Miller’s comment, and that OMTWO was responding to.
Then why are you pushing ID?
It’s funny that you nitpick the words other people use, yet your grasp of the English language and scientific terminology is laughable.
Joe, given that you just said
You are now an evo.
Nope- evos think that necessity and chance can construct new, functional multi-protein configurations whereas I say that requires design.
But anyway neitehr ID nor baraminology are anti-evolution in the broadest sense of the word.
1) No.
2) Yes. Autocatalysis.
3) Yes, it’s conceivable, and it happens.
Yep.
And he also finally admits that there’s a difference between the origin of life and biological evolution.
Yes there is a difference between the OoL and evolution. However if you decouple the two then you have nothing.
Ya see, as any child can tell you, how living organisms arose determines how they evolved. That means if living organisms arose by design then they evolved by design. And if living organisms arose from non-living matter via necessity and chance then necessity and chance is what drove their evolution.
Joe G,
Congratulations on walking across the floor to our side!
Your first assignment, should you decide to accept it, is to explain our position to kairosfocus.
Good luck!
LoL! ID is not anti-evolution. Even baraminology is OK with evolution is the broadest sense of the word.
I will NEVER just blindly believe that necessity and chance can give rise to a living organism from non-living matter nor will I believe necessity and chance can construct new functional multi-protein configurations.
Also I have explained your position to KF-
Father Time + Mother Nature + some unknown processes = living organisms and their diversity.
Joe is still missing the point of science I see. Nevermind the burden of proof fallacy, Joe seems not to understand that scientists are only going to investigate those phenomenon they a) perceive b) find interesting.
Scientists don’t study everything just to do so; we study what we find fascinating enough to want to understand and explain.
Thus far, NOBODY (and this includes Joe apparently) finds the idea of non-material information interesting enough. Heck, I’m not aware of any actual scientists who even perceive “non-material information”, so I can’t imagine why any would be trying to study it.
However, it is quite odd that if Joe perceives this “non-material information” phenomenon he isn’t testing. Until he does, no one is going to bother.
LoL! Non-material information runs our world Robin.
Information Technology relies on non-material information.
IOW once again you do not know what you are talking about, and it shows.
What do you mean it’s “not like a punch-card”? In old computers it was a stack of punchcards!
Or try this computer:
http://en.wikipedia.org/wiki/Dr._NIM
And that’s the point. If you assemble the molecules of a cell into a replica of some cell, it will work exactly like that cell. You don’t need to poof it into life after you’ve finished building it, you’ve already programmed it with the assembly of molecules.
Liz- with old computers punch cards had to be manually entered. We do not see that with living cells- meaning the cell’s information is self-contained.
And we have tried to do that- assemble the molecules and guess what? they do NOT work exactly like the molecules in a living cell.
There is no reason to couple them. Perhaps you should stop getting your conclusions from children.
Even if they arose by design, the designer could then simply piss off elsewhere – his science project was just to create a self-replicating system, and he got an A. They may have been designed to stay exactly the same, but he got that bit wrong and chance mutation took over. A-.
Alternatively, a ‘materialistic’ Ool may have been followed by an extended period during which nothing much happened until an Intelligent Designer happened upon these replicators and decided to guide the natural process to create something interesting.
No EVIDENCE for these scenarios, you say? Yeah well, not my problem. I think the Designer created Adenine but not Cytosine, whales and bats but not penguins or artichokes, Casey Luskin but not my mum, and designed rennet so we could make cheese. Using the Explanatory Filter, I win.
There is a reason to couple them and I provided it. And all I said is that the reason is so easy to understand that even children get it.
And guess what? Neil Shubin went to children to ask about Tiktaalik.
Also what you are saying is like saying that automobiles were designed, but the way they get around is just by chance gear interactions- it doesn’t make any sense at all. But you are welcome to it.
Guess what?
I don’t think you can cite any evidence to show that an exact replica of a functioning system doesn’t function.
Hundreds of thousands of times a day, scientists all over the place conduct in-vitro experiments using molecules extracted from living cells (or exact copies of those molecules)
And guess what? – the processes that ensue are exactly the same as in the living cells.
It’s called chemistry, Joe – chemistry and biochemistry. It’s what life is
Umm we tried that with a ribosome- that is we (humans) have synthesized a ribosome and it didn’t function.
Then we (humans) took the ribosome apart, synthesized one ribo RNA, put the ribosome back together and it did not function as it did before it weas tinkered with.
Also we tried genetic engineering in order to make proteins that we need. Yet strangely enough it only worked for a few proteins, like insulin.
Also why is it that no one has synthesized a living cell if, according to you and Liz, it should be easy to do?
Your choice of words is indicative of your confusion disorder but what you’re essentially saying is that no designer is detected or necessary. If the alleged “information” in a cell is “self-contained” and did not have to be “manually entered” there’s no need for a designer/programmer/enter-er.
Citation please.
“we”?? What part did you play in assembling molecules?
And there you go again with the time limit mindset. Do you think that assembling molecules is as easy as repairing toasters? Do you think that scientists have given up on assembling molecules into whatever assemblages they find interesting or useful? Do you think, at all?
Don’t bother with answering that last question.
LoL! The confusion is all YOURS, as usual.
What I said means the designer(s) does (do) not have to be around to keep entering the information. The point being is all the required information was designed in from the start.
And I have already provided the citation. Go figure….
In the broadest sense and in any sense, ID is okay with anything IDiots feel like conjuring up. That”s the thing about sky daddy magic; any assertion can be manipulated to fit with it.
Well goody for you. The things is, what you believe or not is of no interest to science or reality.
Nope, unlike your position ID has made its claims and has even told you how to test them.
YOUR position requires the magic- magical mystery mutations.
I understand that but your position doesn’t have anything to do with science nor reality. So what is your point?
Here is a rather cool paper, for those oddballs like me who find such things cool. It might help to scroll through this in conjunction with it, if one is unfamiliar with the relationships between amino acid structures.
It may seem a derail, but it is related to the ‘semiotic’ issue. It also sheds some light on apparently unrelated topics such as Common Descent and ‘Islands of Function’.
The authors, using a bit of educated guesswork, created a minimal amino acid set for a specific E Coli protein. They had to retain the ‘core’ conserved sequence, so that they could assay their results for function. Beyond that, they just chose additional acids for the set to be representative of their particular group, and then from this minimal set, they engineered genes coding for the appropriate peptides and checked them for function. They were able to get function from a reduced set of 13. Given that they have chosen a protein from a modern, 20-acid creature, this is much more impressive than it may sound. The huge numbers of combinations in this 213-acid protein means that they could not examine sequence space exhaustively – yet they still found function by randomisation, in what we may term a ‘natural genetic algorithm’.
So:
1) The code is not as ‘information-rich’ as it may seem.
2) Support is lent to the hypothesis that LUCA and the OoL do not mean the same thing.
3) You don’t need 20 acids for function. How many you do need as a minimum is not known, but the groupings of the modern set are very likely to preserve some ‘information’ from pre-LUCA days regarding historically more general codon assignments, from which the modern set crystallised. For example, with 3 exceptions a U in the middle position specifies ONLY Leucine, Isoleucine and Valine – 3 closely related amino acids sharing the same biochemical pathways and structures. An early code specifying just one of these, via 13 different codons, would be more error-tolerant, but less ‘informational’, than the modern derivative.
4) With an amalgamated acid set, the number of different DNA sequences that could code for the same functional protein is enormous. This gives a huge amount of sequence space doing more-or-less the same thing, rendering these bogus Hoyle-style ‘probability’ calculations somewhat … well, bogus.
5) Taking the above, if we find two proteins in different organisms, with very similar sequences, it is a very shaky position to say that they had to be that way because of “Common Design” or, even more laughably, “Convergence”. Such broad regions of functional sequence space render it highly unlikely that any explanation other than Common Descent is the correct one.
Allan, There isn’t any evidence that E. coli can evolve into anything but E. coli and your position can’t explain the 13 AA code. You can’t explain transcription and translation except to say “it just happened”.
And we observe common design in our world- it works. We have also observed convergence.
I concur. I’ve seen UB in action at a couple of venues, and he will use 5 paragraphs to answer a yes/no question. He gets it from his intellectual mentor of sorts, David Abel, who is a tremendous offender in that respect. wow them with volume when you have no facts on your side. And without analogies, this whole “theory” of his is nothing.
….. ah, just me, then!
The science of the genetic code less interesting than the opportunity it provides to peek into the mind of the Designer, or what a given word REALLY means!
What science of the genetic code?
yet you are now on record as saying the exact opposite:
http://theskepticalzone.com/wp/?page_id=651&cpage=10#comment-10686
So which is it Joe? You have to choose. Or explain the apparent contradiction, this holding of two mutually exclusive positions.
What contradiction? Are you saying that you are too stupid to understand that evolution can proceed by design? As in via some preprogrammed genetic algorithm.
Ya see OM your problem is that you equivocate so much you think that all evolution is blind watchmaker evolution. Typical but still sadly pathetic.
RB:
OMTWO:
It appears that UB has chosen door number three. Shame.
UB has realized that staying here is a waste of time…
Of course it can. Now all you have to do is show *any* evidence for that claim at all.
So your claim is that everything that life might have later needed was front loaded at the origin of life?
Is that your claim?
Whereas you of course are convincing all and sundry with your oh-so-clever arguments.
I am convincing the people who matter- high school students. OTOH your position can’t seem to convinve anyone but the willfully ignorant.
There any many fully sequenced organisms out there. Please show where in those sequences these preprogrammed genetic algorithms are that control future development.
Yup and the sequence doesn’t have anything to do with the programming and your position still has nothing to offer.
Upright has mentioned in the past he’s going to publish something or other at “Complexity Cafe”, if that’s a website or journal I’m not sure.
So perhaps he’s had enough “peer review” of his ideas for a re-write…
Joe G
Not sure how you expect that to be answered. Are you saying there is no science in the genetic code? Was it elucidated by computer programmers, comms engineers, lawyers and fridge repair men? Amino acids, their side-chain properties in terms of different charge and polarity and backbone bend restriction, the patterns of codon usage groupings, the correlations between codon groupings and the places in which the translated amino acids end up in ‘finished’ proteins, the clustering of departures from the ‘universal’ code’ … this is all relevant to such questions as:
- whether the code can legitimately be referred to as ‘semiotic’.
- whether it is reasonable to infer a precursor system with fewer acids, and if so, how few, and with what core properties?
- whether Common Design or Convergence are legitimate alternative hypotheses to Common Descent for DNA sequence similarity.
- whether function is isolated on narrow ‘peaks’/'islands’, or occupies much broader regions of sequence space than those that the ID-er would prefer.
These people, and others, have done some very painstaking work, to try and get some real answers, rather than spamming blogs with tedious irrelevancies. That science of the genetic code.
LoL! No one knows if Common Descent is legitimate. It can’t be tested, so it isn’t science.
And you have no idea what ID-ers prefer. All you have are strawmen that you keep erecting and refuting.
OMTWO,
It appears to be a rather defunct blog. The only other reference I could find was to a 2004 symposium on the evolution of complexity.
Toronto,
Look at what you’ve claimed is not arbitrary – the relationships between the representations, protocols, and effects – the very things that cause the song to play. If they are not arbitrary, then they are physically determined. What you’ve said is that the music box must exist, and it must play Hey Jude.
Suddenly, it’s no longer reducible to the music box after all… and it’s arbitrary.
Since when did hard-coded information stop being information? If I slip my Visa into a card reader, are you suggesting that it doesn’t transfer information if the reader contains the hard-coded protocols for reading the hard-coded information on the card? And “indirection”? Are you suggesting that the reader only transfers information if it decides for itself how the card should be read?
So the protocols for reading my card are an inherent property of the material the card reader is made of?
If you’re going to go, ya might as well go big, right? This is the granddaddy of misplaced objections. Every material thing in the cosmos operates under the material laws of nature. The transfer of Morse code across a wired network occurs by a material process; the CPU in your computer operates by a material process, your name spelled across a piece of paper is a material process. What these examples have in common is that the relationship between the representation and the effect cannot be reduced to the material properties of the representation or the effect. They each require a materially isolated arrangement of matter to physically establish that relationship. This is exactly what takes place in genetic information transfer.
So, the digital code physically instantiated in an MP3 player is not a part of the physical process that causes the player to play, and that’s why it’s information? But if it’s not part of the physical process, then how is the information transferred?
May simply suggest you study the argument a little more closely.
Recip Bill,
Foregoing rhetorical ploys, the only reason an objector would grant that the entailments are a proper and valid description of the material process, is if they could not demonstrate them to be false. If they cannot be demonstrated to be false, then it is up to the objector to logically demonstrate that a system exemplifying the same material characteristics is the sole result of the material constituents involved. This goes to the very heart of your objection; it does follow that “that representational or symbolic content is a necessary condition for the emergence of systems displaying [these] material entailments”. The observed relationship between the input of the system and the output of that system is either determined by the material make-up being input, or it is not. There is no third option. In genetic translation, the pattern of the input sequence alters the output, but it does not establish what that output will be. Nucleotides only order anticodons; they do not establish which amino acids will be associated with them. That is accomplished in complete material isolation from both the input sequence and the output effect.
Alternatively, you can claim that the system is the non-falsifiable product of chance. At which point the objector is obligated to provide some rationale to demonstrate that sheer chance is preferable to the causally-adequate interpretation of the system.
I am still waiting for you to demonstrate the material observations are false, or that the observations are reducible to the material involved. You may also at any time claim that the system is the product of non-falsifiable chance.
NOTE: Regarding the false claim in your objection… You suggest that all known instances of semiotic information transfer are human. For this to be true, it would require that a bee flying off in a particular direction from the hive (in response to seeing a pattern in the flight of a returning bee) is an inherent material property of that particular pattern in flight, not requiring a physical protocol to establish the relationship between the two.
Madbat,
Yes, one of the things your post requires is a mechanism capable of creating and establishing the immaterial relationships fundamentally required for the recorded information contained in your post to exist. To explain this, you point to an incredibly complex material object, your brain. Whether or not your mental faculties can be reduced to material is not of consequence in this instance; the fact remains that your brain didn’t exist until after billions of years of evolution. So what was the mechanism capable of creating and establishing the immaterial relationships required for the recorded information to exist which organizes inanimate matter into Life in the first place?
“It’s all material” is an objection that has been answered enough times to not need repeating.
Hello Allan,
I appreciate your thoughtfulness in dealing with the evidence itself, but you make a lot of unwarranted assumptions about me personally in the defense of your opinions. Your assumptions are no less warranted than your objections themselves. The argument I presented has nothing whatsoever to do with the size of the code. Cut the code in half, and it’s still the same argument; the material observation are the same. You’ve erected an army of strawmen, and then cut them down one by one, even as you ignore what was actually presented.
Dr Who,
Autocatalytic systems do not transfer recorded information as stated in #1. This objection was answered in the original conversation with Nick Matzke, as follows:
Arbitron,
Is there a material observation I’ve made which you are prepared to challenge? Which one will you claim to be false and then support your objection with material evidence? If there is not one, then your objection can be seen for what it is. Also, to my knowledge David Abel has not published any work that describes the physical entailments of recorded information. If you have information otherwise, I’d like to see it. In any case, my argument makes no reference to Abel’s work, so your comment can once again be seen for its inherent meaninglessness. As for having facts, Nick Matzke and several others (such as Elizabeth Liddle, who’s blog you are on) have agreed that it is inconceivable to record transferable information without utilizing an arrangement of matter to represent that information within a system. Do you agree with them? Do you think the genome contains recorded information in the form of nucleotides sequences which transfer information through a materially isolated protocol? Or, are these material (observable) facts non-existent?
Your observations seem irrelevant to the claims you want to claim are absolutely true. I find your claims re: aminoacyl synthetases to be particularly comical, for I had read your misrepresentation of their role get exposed on another forum (a forum which you have not, most interestingly, returned to since).
Right – so because one “new” aspect of your overall claim does not have Abel written all over it, your claims have nothing to do with Abel’s nonsense. OK.
Yes, but what I do not agree with is the notion that this information had to have a “writer.”
A “materially isolated protocol”? Interesting use of metaphorical language, no doubt intended to be taken literally. This is my primary argument against your unyielding series of assertions.
Thorton, Neil Rickert, and Cubist,
- – - – -
- – - – -
You must not be the “Thorton” or the “Neil Rickert” or the “Cubist” I have occasionally seen elsewhere on the web arguing from your position. As I recall it, those persons could at least form a coherent response, even if it was wrong. It is more than apparent from your responses here that neither of you fundamentally understand the argument enough to be making a response to it – much less being condescending.
- – - – -
Hotshoe,
I refer you to my response to Toronto.
Dr Liddle,
I answered your question in my response immediately after you asked it. I just checked, and you can still find my answer there, exactly as it existed prior to you claiming that you could not find it.
Dr Liddle, it is very clear you dispute that anything semiotic exists within genetic information transfer. The problem for you is that the process has been observed in terms of its physicality alone. Despite your personal preference to see it otherwise, it is those physical observations which you have been unable to challenge. Your situation has now been complicated by your admission that it is inconceivable to record transferable information without the utilization of an arrangement of matter to represent that information within a system, and further, that it is inconceivable to transfer that information without a second arrangement of matter to establish the relationship between the representation and its effect with that system.
It appears that, at this late date, you’d like to summarily wipe the slate clean and pretend as if the preceding 11 months of conversation never took place. Incredibly, you state above that you are prepared to be persuaded, but that I need to answer a specific question; a question that has been answered so many times that I have lost count, a question that would be quite literally insulting to anyone who had engaged it on your behalf the number of times I have. Even so, on this very thread I engaged it yet again, and you simply ignored it.
You created this blog partly in response to the conversation you and I had regarding information transfer going back to May of 2011. That discussion was the topic of your opening thread here, where you eventually recanted your claim to be able to create de novo information transfer within a simulation, claiming that my definition of information was unclear to you (even though you participated fully in the conversation and even complimented me on my definition being “more defensible” than others you were aware of) . You then later followed it up with another thread, which I referred to as an anthropocentric malaise. I backed that claim up with a substantial post going point-by-point in your response. You ignored that response and ceased participating in the thread, even after acknowledging it on more than one occasion – claiming that you would get around to responding at a future date when you had time (even though for months you maintained full participation among many other threads). Now you have made a third thread dedicated to the semiotic argument. Here again, you are claiming that you’ll get around to it someday, which is fair enough if you do. Yet thus far, it appears to be more of the same. You want me to respond to questions that have grown stale in their inability to penetrate the argument. I have absolutely no doubt that you’d love to turn to the physical evidence to challenge the argument before you – but you simply can’t. The material evidence is unavailable to you; and is resoundingly against you instead. It is the same for you as it was for Larry Moran, and Nick Matzke, and Robert Saunders, and Robert Collins, and Mark Frank, and everyone else I have engaged. So in response to your failed position, you seem willing to simply repose the incredible question of ‘what I think are the representations in genetic translation”.
This is the very nature of the argument Dr Liddle; you either do the empirically responsible thing and acknowledge the entirely coherent and observable evidence of the semiotic state in protein synthesis, or you bullshit about it instead. The modest conclusion of the semiotic argument is simply that the transfer of genetic information during protein synthesis materially demonstrates a semiotic state, and therefore requires a mechanism capable of creating it. You are on the wrong side of that evidence.
Upright BiPed,
Exactly.
There are software layers in a computer and hardware levels.
At the software layer, we have your “information”, but at the hardware level, we are working with material processes.
The software layer deals with “meaning”, (protocols and data), but at the hardware level, we are dealing with voltages.
One pin of an input port may be at 0.2V, and another at 0.15V.
We say they represent a “low” or 0 or FALSE.
Another pin may be at 4.9V and we call that “high” or 1 or TRUE.
But, if we have a pin at 1.2V and we are dealing with TTL levels, what does that mean and what information does that represent?
That value is not electrically valid and may even result in damage to a device.
That is what so many here are trying to tell you, that your “information” in a cell is limited in what it can “represent” by chemistry because it is part of the lower level process even though we “describe” it as “information”.
There are configurations of “information” in a cell that cannot exist because of chemistry and therefore the “search space” and “islands of functionality” they represent are much more limited and thus not truly reflected in “unrestricted” probability calculations.
Most likely represents an open-circuit to an IC input- OR a short-circuit conmnecting two or more points. And last but not least is there is a damaged device on that line.
What device would be damaged by 1.2V? Perhaps a damaged device was causing that low level.
Bt anyway I worked for a company that used non-zero and non-one levels for something- we called it a “code violation” and two sode violations followed by a specified sequence would alert the receiver that there was an incoming signal to respond to.
Upright BiPed,
The second error you make is to assume all “information” has “indirection” and must be somehow translated from a “symbolic” form to a “usable” one.
Imagine a switch hooked up to a transistor driving a relay.
If I flip the switch, no CPU or any such process needs to “decode” the voltage level at the switch to determine whether the relay should be energized or not.
The switch is directly hooked up to the transistor and is not “information” to the transistor, it is part of the process.
It is only “information” when we have to show someone what we have found in the working of this device.
In other words, it is “information” only to an observer, not to the devices actually in the circuit.
The information was in the design of the circuit.
Toronto, your response is incoherent with regard to the topic.
Your original objection was that the example of information transfer I gave didn’t actually transfer information because the information was “hard-coded” and therefore part of the system. But all information must be “hard-coded” in a material medium in order to exist at all, and that medium is necessarily part of the system it operates within.
So I asked you how information was transferred if it wasn’t part of a material system. You’ve responded by ignoring every single thing I posted, and simply returned with:
This does nothing to address the point. With software, you are still dealing with a material process. If you are not dealing with a material process, then please describe the nonmaterial process by which information is transferred within a system.
You also stated :
You’ve become quite lost in your argument. I never introduced the term “indirection” to the conversation – you did that yourself. My immediate response was that it has nothing to do with the issue at hand. The fact that you are now suggesting it is a fault on my part is simply stupefying.
One is left to wonder just what the hell you are talking about.
Quite frankly, it seems that following my last response to you, you are merely saying something in order to have something to say. Your response did not address a single thing I said, it only introduced another layer of unrelated babble. Given that this is the case, there is no longer a reason to respond to you.
UB:
That is factually incorrect. An excellent reason to grant your “material entailments” arguendo it to direct attention to a fatal flaw in the argument you build upon those claimed “entailments.” That flaw is lethal whether or not your “entailments” are true or false.
To wit: it would no more follow from an observation that all known instances of semiotic information transfer exhibit your “material entailments” that all systems exhibiting these “entailments” are necessarily semiotic, than it follows from the fact that all rainstorms make the ground wet that demonstrating that the ground is wet confirms the existence of a rainstorm – to repeat Thorton’s felicitous example (which recapitulates the logic of my comment vis murder.) It only follows that “Demonstrating a system that satisfies the entailments (physical consequences) of recorded information, also confirms the existence of a semiotic state” if you define a “semiotic state” as “a system that demonstrates these ‘entailments.’” In which case this “confirmation” is tautological.
Nothing in your reply addresses this objection.
UB:
Not “logically.” However, contemporary biology is tasked by its own foundational assumptions to elucidate how these relationships arose across history by natural means. Such questions are settled empirically, not logically. This is the stuff of empirical science, not logical sparing.
Yours is, however, a telling statement, in that it exhibits your apparent belief that you have shown “logically” that biological functions such as the transcription of DNA into proteins are semiotic, and therefore can’t have originated by unguided processes. And it exhibits your apparent belief that these questions can be settled from within an armchair.
In examining this, It is worth looking more closely at your misuse of the term “entailment.” “Material evidence,” independent of theory, doesn’t have entailments. Rather, definitions, propositions, and theories have entailments. As an example, It follows as an entailment of the definition of “bachelor” that each bachelor you encounter will be male. This relationship isn’t established or confirmed by means of “material observations,” – we don’t sex each bachelor we encounter to confirm that all bachelors are indeed male, as though another outcome was possible or the action is even intelligible. Rather, the result follows from the definition of “bachelor” within our culture, because definitions can have entailments.
Your “material observations” concerning the “transfer of recorded information” aren’t “entailments” at all. They are, at best, your proposed description of the minimum characteristics of the transfer of recorded information. By itself, it is an interesting description that may have merit. In a sense, these characteristics become your definition of “transfer of recorded information.” It is therefore no surprise that whenever you observe the transfer of recorded information as you define it it exhibits these characteristics.
However, your follow-on claim that systems that exhibit those minimum characteristics are also necessarily semiotic is no more than that – a claim. The only sense in which “semiotic status” follows as an entailment of your “material entailments of the transfer of recorded information” is in the sense that you have defined “semiotic state” as “a system that exhibit these minimum characteristics.” But nothing in that compels one to accept that definition, or that claim.
As I parse this, I am seeing more clearly where your argument goes off the rails (apart from the first logical train wreck I identified above.) Perhaps you think that a system that exhibits “the presence of these material characteristics” necessarily entails “a semiotic state” in the same sense that “the presence of a bachelor” necessarily entails “the presence of a male.” You certainly state your position with conviction that that is so. But that simply doesn’t follow. It certainly doesn’t follow from your description/definition of information transfer, and most of us would further argue that “semiotic” communication entails many characteristics, most often exemplified in human communication, that are wholly absent from your proposed minimal characteristics of the transfer of recorded information. Hence we argue that “semiotic” and your “material entailments” are not coterminal.
The reason for your inclination to prefer a definition of “semiotic” that is implicitly equivalent to “the presence of your ‘material entailments’” seems clear enough to me. You’ve been coy about it, but you obviously wish to claim that it is inherently, even logically impossible that semiotic information transfer can have originated without intelligent agency, and therefore it is impossible that information transfer from DNA to sequences of amino acids can have originated absent intelligent agency. But as an argument intended to compel that conclusion, your semiotic theory fails.
This paragraph nicely exemplifies a problem inherent in your argument, identified above. Specifically, it assumes – perhaps unwittingly – the necessary equivalence of “requires a physical protocol establishing a relationship (etc.)” and “semiotic” information transfer. You can propose that equivalence, but nothing in your argument entails or compels it – other than your definitions, which themselves are no more than claims. As does your entire argument, this statement assumes its conclusions.
Upright BiPed,
My purpose here is to show “onlookers” how bad your arguments are.
If a reasonable discussion can come out of it that’s fine, but not necessary.
Of course I introduced the term because you don’t seem to understand that “indirection” is a characteristic of transferring or storing “information”.
You can’t use the term “transferring information” without using “indirect references” to the “data”.
You claim to understand biology by making analogies to computers but you don’t even understand them well enough to even use the terms properly.
Joe G,
What I meant by this is that the “information” represented by 1.2V is ambiguous to a TTL level device that is reading it.
In 5V TTL, a low is 0.8V or below and a high is 2.2V or above.
So what does that represent to a healthy device reading it when the level is not in either window?
That’s what I was trying to say, that there are restrictions, at the hardware level, to what we can claim is valid information and the same applies to living cells.
Not all “information” is allowed and thus the “search space” and “improbability”, shrinks.
Upright BiPed to English Translation: “I couldn’t address the valid points raised against my pet hypothesis, so I decided to post a snarky non-answer and hope no one notices the difference.”
UB
It is true that the argument remains intact when you cut the code in half … and when you cut it in half again … and again … but ultimately, you are left one amino acid (for the sake of argument).
You have a ribosome, an RNA-based enzyme that takes two substrates (tRNA/mRNA) and condenses the amino acids into a peptide chain. It sits at the end of a biochemical pathway that includes an aaRS which charges the tRNA with the amino acid. That system is no different from many another biochemical pathway – a series of chemical inputs and outputs. Now, you may argue that all biochemical pathways are IC, but that is a different argument.
But what is added by calling that system ‘semiotic’? In the simplified version, there is no code; there is simply a chemical mechanism, somewhat convoluted, whose output is a molecule formed from condensation of repetitive units of one amino acid. It is no more (or less) informational than any other chemical system.
Now, I accept that this reduction may be a complete fantasy. There may never have been such a system. But the point was not to knock down straw men, but to unpack the argument to its chemical heart and then rebuild. A simple one-acid system would become a two-acid system by duplication of an aaRS. By increments, codon groups can become subdivided, until usage becomes critical. IF a simple one-acid system is not semiotic, how does a two-acid system become so? Or, are all interactive enzymatic systems semiotic?
I see the responses that were posted overnight, and will be happy to respond in the next 24 hours or so.
Thanks…
Thank you, Upright BiPed.
No, you did not. I asked:
Your response was:
It is utterly relevant. If you are going to appeal to semiotics in your argument then you need to explain how they map on to the process you are arguing about. And saying that a question is “not relevant” is not answering it.
I profoundly disagree that it is “not relevant”.
There are many kinds of information transfer in biology: from environment to population genome; from parental genome to offpring genome; from organism genome to organism phenotype; from cell to cell within a multicellular organism; from the environment to the sensory apparatus of an organism.
All these information transfer processes involve DNA, in lots of different ways. I see nothing “semiotic” about any of them, nor do I see any mystery about how the “information” is produced. For example, the information that is passed from the environment to my retina is simply generated by light reflected off, or given off by, objects. Nothing “semiotic” about that, until I start to recognise the pattern of light as one of your posts. Then it becomes vehicle of information transfer between an intelligent sender (you) and an intelligent receiver (me), and I recognise the information not merely as information about an object that I must avoid spitting at, but as information from an intelligent member of a community of symbol-users of which I am also one.
I dispute that the word “semiotic” is relevant to genetic information transfer. And you dispute that my dispute is relevant!
My situation is complicated by the fact that you have not been able to clarify what analogous roles to those played in a human semiotic transfer system are played by which players in a cell, or population of cells. Indeed, you have regarded this question as “not relevant”. And so I remain at a loss to know what your semiotic theory actually means.
What I would like, at this late date, is for you to present a coherent theory in which you actually lay out what you mean by “semiotic” in the context of biological information transfer, in, for example, the instances I have given above.
Well, not exactly. But I did hope it would host that conversation, as well as many others.
Upright BiPed, it seems to me that you are massively missing the point of my posts. I am not disputing the physical facts of what goes on in a cell. I am disputing your analogy with semiotic information transfer between intelligent members of a shared symbol-using community. I do hope you will engage with this point. In the mean while, I would ask you to stop casting aspersions on my willingness to engage with you, not to mention my integrity.
It is my view, Upright BiPed, that the phrase “semiotic state” as applied to protein synthesis is bullshit. I will remain of that view until you can lay out for me exactly how the relationship between two intelligent agents communicating information to each other using a shared symbol-system maps on to the relationships between biochemical entities.
You are not presenting “evidence” at all. You are presenting an analogy coupled with a non-sequitur, in my view.
And were I as ungenerous as you, I would regard your refusal to engage with my question as “evasion”. As it is, I honestly believe it is because you haven’t seen my point.
But I’d be grateful if you would try.
Stickied this for a bit, as Upright BiPed is back in town
Elizabeth,
You are not presenting “evidence” at all. You are presenting an analogy coupled with a non-sequitur, in my view.
I absolutely agree.
From my encounter with UB on another forum:
He did not reply.
OK, let’s try to lay this thing out.
Upright BiPed is talking, it seems, about the process by which the nucleotide sequence in a DNA molecule results in a specific protein being synthesised.
There are several stages to this process, but I will simplify: Firstly, the DNA acts as a template, essentially, on which a strand of messenger RNA is constructed. Leaving aside the editing of the mRNA strand, the mRNA bonds to a certain set of tRNA molecules. The tRNA molecules are themselves formed on the same templating principle as the mRNA, i.e. they are the set they are because of certain DNA sequences.
One end of each of these tRNA molecules binds to a specific triplets of mRNA and the other end binds to to an amino acid. Some members of the set of tRNA molecules share the same amino acid end, but have different mRNA triplet ends.
The result of all this is that we have a strand of mRNA bearing a sequence of tRNA molecules each carrying a specific amino acid, so we have a string of amino acids, the order determined by the sequence of nucleotide triplets in the mRNA, which in turn is determined by the sequence of nucleotides in the DNA. An RNA catalyst (the ribosome) then separates the amino acid string from the tRNA and outputs a connected folded protein.
Upright BiPed wants to describe this as a “semiotic” system, because many sets of tRNA molecules would do the job, as long as there was only tRNA molecule for each possible triplet, and that each tRNA molecule could only attach to one amino acid. It doesn’t matter, of course, if more than one tRNA molecule binds to the same amino acid, and that is in fact what we have.
So the system of tRNA molecules is a bit like a symbol system – each tRNA molecule “represents” an amino acid. Not only that, but the mRNA molecule also “represents” an amino acid, but that representation, like a human symbol system, is arbitrary – any triplet could “represent” any amino acid; the fact that any one triplet “represents” any one amino acid is simply an epiphenomenon of the particular set of tRNA molecules that the DNA molecule templates for.
An equally good system could work with a completely different set of tRNA molecules as long as the rule that there has to be only on tRNA molecule for each triplet, and each tRNA molecule has to be specific to one amino acid.
So let’s grant that such a system can be described as “semiotic” on the grounds that the mapping is arbitrary, not a matter of necessary chemistry.
In principle we could alter the DNA of a cell so that a different set of tRNA molecules was produced, and recode the protein coding portions of the genes into the new mapping, and get a perfectly well functioning cell. So in that sense the “language” of the cell is the “language” of a community of “shared symbol-users”, so that as long as the DNA in a community of cells conforms to the community symbol system, i.e. each cell’s DNA generates the same set of tRNA molecules, each cell’s DNA will be “read correctly” correctly by the cell’s tRNA molecules and the correct protein produced at the correct time.
And, it seems, all living things have (roughly) the same “symbol” system. In practice this means that all living cells have a stretches of DNA that form templates for the same set of tRNA molecules.
So far so good.
But UBP then draws two conclusions that are IMO quite unsupported. He says that:
which I will provisionally accept on the assumption that the “semiotic state” of “the transfer of genetic information” simply means that translation from mRNA sequence to amino acid sequence is achieved by means of a specific but arbitrary set of tRNA molecules templated by the DNA,
“and therefore requires a mechanism capable of creating it.”
Sure. There needs to be a mechanism by which that set, or an equivalent set, of tRNA molecules came to be templated by the DNA, and not some useless set in which one triplet could result in any one of a number of amino acids.
So?
Why shouldn’t evolutionary mechanisms result in such a set?
It’s an interesting challenge, and one that I would still like to rise to (although I am much shorter of time than I was when this conversation started). So perhaps someone else would like to take it on.
So here is my proposal to UBP:
If someone were to produce a virtual GA environment in which, evolved, starting with a population merely of self-replicating virtual organisms that produced no “proteins”, a coding system by which the virtual genomes coded for a set of “symbols” that in turn resulted in a “reading” of other parts of the genome to produce reproduction-enhancing “proteins” – would you accept the result as evidence that evolutionary mechanisms can result in the evolution of a “semiotic” system of information transfer?
I’m not saying I can, or will, do it, but I’d at least like to get agreement on what would constitute contradictory evidence for your claim.
Elizabeth, I’m a little confused by your use of the word “arbitrary” above. Doesn’t seem to fit, somehow.
Perhaps it’s the wrong word. “Fortuitous” maybe? What I mean is that any set would do as long as the set itself has certain properties.
The properties don’t lie in the molecules themselves, but in the set.
Like the arbitrary mapping of the symbol “b” to the sound “buh”.
Any symbol would do. So the mapping is arbitrary. Whereas the mapping of a left hand button to a left hand stimulus and a right hand button to a right hand stimulus isn’t “arbitrary”.