The Digital Demise Of Darwinism

[Eclogite]

Paul,

I appreciate that one problem you will face here is that different members wil try to move the discussion in particular directions. If it makes sense at some point to separate out a particular line to a separate thread please ask.

 

Now I am concerned that you are conflating Darwinism - or, as I prefer, the Modern Synthesis, with abiogenesis. You remarked in an early post that the failure to account for the origin of life was a weakness of Darwinism. It isn't. You seem to repeat this belief in directing Buffy to think about the origin of the genetic code. We are not interested in the origin of the genetic code when discussing evolution. The origin of the genetic code is more or less equivalent to the origin of life, a related, but distinctly different topic. Is there any possibility you could come to agree on this point?

[Moontanman]

this is a really interesting discussion, and i wish i was half as intelligent as the main protagonists and contributors. though i have my feet firmly planted in the natural evolution camp i like to think i am open minded enough to consider any other possibility. so if we are to consider this mind / creator scenario there are definitely questions that need to be asked that are thrown up by paul's above post. these are questions relating to the origin of the mind (the perennial creator problem), the length of time this mind was experimenting, and whether there are or have been other of these minds.

 

if we accept that this mind created life, and maybe the universe itself, where did it come from? we have to consider the idea that at some point there is an absolute origin. something had to spontaneously or randomly appear. if the fossil record shows a pattern of trial and error does it also show the point at which the mind stopped experimenting? or is it still experimenting? and if so, how can we sense it? as the search for exoplanets is revealing (or at least strongly suggesting) that planetary systems are the norm and not a rarity, we can extrapolate that there must be a huge number of rocky planets in stars' habitable zones and therefore conducive to life. might the same mind that made life on earth also have made life on those planets? or are there more of them? or did the one mind randomly choose planet earth?

 

 

You are correct, the concept of this "mind" does nothing to add to the sum of human knowledge and actually ads another layer of mystery to something already unknown... in fact something that can by definition never be known since it's evidently not part of perceptible reality...

[Moontanman]

 

This red herring does not apply and deserves no more comment.

 

 

 

 

Um... no... you don't get to claim that with out demonstrating why, I "could" just as easily claim it does but I want to hear why you claim it does not...

[clinkernace]

I'm almost afraid to say anything here after Buffy, reminds me of the delima of remaining quiet and be thought an idiot or opening my mouth and removing all doubt but Buffy knows I'm not smart enough to remain completely quiet. So here goes...

 

My thoughts on this is that Qdogman's ideas are nothing more than the old information argument ie DNA represents information and since information cannot come from anything but a mind then DNA must have been designed by a mind.

 

This fails on many levels but most importantly is that new information can indeed form by random chance coupled with a selection process. Language is a prime example of this, languages evolve via the addition of slang from place to place. This addition of slang has no direction and is random but it results in complex differences in a language. Latin is at the root of many languages, if you had taken a population of Latin speakers and isolated them for millenia you would come up with a unique romance language but you would never come up with a current romance language.

 

Evolution uses a random process, mutation, as raw material for natural selection, this is not random but highly deterministic. In fact the process of evolution can be used to design things like aircraft much better and faster than any human mind can and this is used in modern aircraft design.

 

Evolution is deterministic not random and the idea of information and design is something humans place on the process arbitrarily, this design does come from an outside source but not God or Gods.

 

 

Consider these two successive paragraphs, right out of your fingers...

 

"Evolution uses a random process, mutation, as raw material for natural selection, this is not random but highly deterministic. In fact the process of evolution can be used to design things like aircraft much better and faster than any human mind can and this is used in modern aircraft design. "

 

"Evolution is deterministic not random and the idea of information and design is something humans place on the process arbitrarily, this design does come from an outside source but not God or Gods."

 

Focus whatever passes in you for mind upon the boldfaced and accented excerpts of your own words, in context. Then have another drink, or smoke, or whatever you utilize before offering your tidbits of limited wisdom before barfing up another tidbit, chunk, hairball, or other partially digested morsel of insight.

 

You have done a great job of "removing all doubt."

Alas... I'd expected better.

[clinkernace]

Paul,

I appreciate that one problem you will face here is that different members wil try to move the discussion in particular directions. If it makes sense at some point to separate out a particular line to a separate thread please ask.

 

Now I am concerned that you are conflating Darwinism - or, as I prefer, the Modern Synthesis, with abiogenesis. You remarked in an early post that the failure to account for the origin of life was a weakness of Darwinism. It isn't. You seem to repeat this belief in directing Buffy to think about the origin of the genetic code. We are not interested in the origin of the genetic code when discussing evolution. The origin of the genetic code is more or less equivalent to the origin of life, a related, but distinctly different topic. Is there any possibility you could come to agree on this point?

 

Eclogite,

 

Before Paul weights in, I must ask...,

 

Do you regard abiogenesis as irrelevant?

 

Are you aware that the smallest genome yet discovered consists of an economical 160,000 base-pairs, and that the critter which survives with such a limited genetic vocabulary is a parasite that lives off of other critters and cannot survive on its own? If you had that information, as you do now, would you wonder how a basic cell might have come into existence from mud and primeval gook with the more than 160,000 base-pair genome required to actually survive and replicate in mud and gook on its own?

 

It would appear that Paul is far off the high end of the not-stupid spectrum. Asking him to agree upon an absurd point seems an exercise in futility. By way of alternative, would you consider the notion that you have been fed and programmed with a long line of pseudo-scientific BS? Are you even capable of considering an alternative, or are you run by your beliefs?

 

In the context of that remark, it might be helpful to know that I was once a serious and devout Roman Catholic. The most difficult part of my conversion to free thought was admitting that I'd been seriously conned, by well-meaning people, intelligent and educated good people, who believed the con. Later, I had the opportunity to work with brilliant people, men with hard-science Ph.D's, who tried their best to feed me the other end of the same con. But by then I'd developed a serious distrust of authority figures in all their forms.

 

You seem to have the potential to think for yourself, but at the moment your mind seems to be owned by unfounded belief systems which, like my outdated religion, rely upon agreement rather than logic or valid data to support the beliefs of their followers.

[Eclogite]

The theory of evolution, which is the matter under discussion does not deal with the origin of the universe, it does not deal with the origin of the solar system, it does not deal with the construction of the Earth, it does not deal with the flow dynamics of lava, it does not deal with quantum mechanics, and it sure as heck does not deal with the origin of life. It deals with the evolution of existing life. So, yes, abiogenesis is assuredly irrelevant to the present discussion.

[Buffy]

You are exactly right; this is the correct starting point. We (I) need to define terms. And, we are already past the starting point.

That we are! :cheer:

 

It does appear that this process of definition is exposing some clear misunderstandings on both sides that cloud the inner conflict.

 

You are correct that I "have restricted the meaning of "symbolism". This is in the spirit of mathematical usage as I just explained. But you are not quite correct in your statement of my definition.

 

I do not mean that symbolism is "anything that can be perceived as having any sort of mapping has a well-defined symbolic meaning." What I mean, and forgive me for not making this clear, is that symbolism is any mapping from a symbol to a physical entity, where 'symbol' is defined to be some specific arrangement of physical entities such that the mapping from the symbol to the physical entity (not the entity making up the symbol but the one referred to in the symbolism) constitutes meaning in some mind.

The interesting thing here is that even though you've done some restriction by that definition, the critical part of my statement still stands according to your revised definition: that is that it is "the mapping from the symbol to the physical entity...constitutes meaning in some mind," the essential point being that it is a mind that creates both the mapping and the symbol. The physical entities are "just sitting there" (well, actually they're quite active, but they're following "physical laws" which as you state in your essay do not involve symbolism, and I think we agree on that).

 

Minds create models, which consist of conceptual symbols, and the usefulness of the model as a tool to the person with the mind is that they allow understanding (or not), based on the closeness of the model to the physical system.

 

In orbital mechanics, Ptolemy's model of epicycles was a gross fit to observations, first improved by Copernicus' Heliocentric model with circular orbits, then Kepler's ellipticals, then Newton's gravitational model which explains interactions of multiple bodies, and finally Einstein which got rid of the errors in Newtonian Mercury's orbit.

 

While the mappings and symbols in people's minds changed radically, the planets themselves just kept on moving: the existence of the symbols or mappings had no effect on their movements. Their behavior is "encoded" in the underlying behavior of the elementary particles they consist of: how a Higgs boson and strong force create attraction, electromagnetic charges repel, and symmetry creates structure.

 

Of course this now requires the definition of 'meaning' and 'mind'. And, of course, that forces us to face the essence of the entire discussion of mind, consciousness, any putative God, and the questions related to life. So that's good; that's what we should be concerned with.

 

To define 'mind', (keep in mind, I get to make the definitions here because it is my concept that I am trying to communicate to you) I say it is the faculty that is able to experience what you, the reader, have at this very moment while you are reading and parsing this sentence. And of course, I mean the "mental" experience you are having trying to understand what I wrote, not the physical discomfort you may be experiencing because you happen to be sitting on a tack, although I believe that, too, requires a mind to some extent.

Actually, I think you should follow your own lead here and use a more restricted definition: let's say a mind is self-aware (e.g. sitting on a tack is bad) being that is capable of creating models and using them. That's to the point and I don't think it's a point of contention here.

 

The last one is the tough one. What is meaning? (It is occurring to me as I compose this, that this may very well be the very essence of the whole subject.) Here's my definition of 'meaning':

 

Meaning is the role a symbol plays in the process of a mind processing the input it receives (usually if not wholly from the physical world) in order to take willful action (OK I should define 'free will', but for the sake of brevity I'll take that as a primitive and let you imagine what it means to you.) to increase the probability of future physical states to match expectations (expectations are, of course, mental states that again I trust you understand what I mean without further definition.)

 

In short, meaning is a component of understanding which allows a thinker to take deliberate action to help cause something predictable to happen. (E.g. the thinker sees a symbol, say a big red octagon emblazoned with the word 'STOP', understands this to mean bring the vehicle to a stop, and takes the deliberate action of applying the brakes. The symbol means "Stop the car!)

No problem, except that I'd note that you are in this definition inextricably linking "mind" with "meaning": that is you need a mind to see a meaning in an abstract.

 

The implication inherent in this linkage is important. If I replace a human in that car with a typical self-driven car, there are two fundamentally different ways to have that car deal appropriately with that Stop sign:

 

• I with my human mind (using your definition) write a program that literally says "when a red octagon with the letters 'STOP' on them appear in the field of view, then stop before reaching the sign", then we have a perfect example of a "designed" physical system. They "physical laws" that drive the system literally say "look for bit patterns that come close to resembling this abstract symbol" and then do "stop".
  
• Conversely, I can put an untrained neural net in it, have it drive around for a while, and through evolutionary change, weights will be adjusted to cause the car to stop when a stop sign appears in it's field of view, NOT because it is red or octagonal or has the letters 'stop' in it, but simply because an autonomic response to a range of differentiable but unspecified (i.e. not "encoded") bit patterns become visible. The system's physical laws in this case have no "awareness" of any "symbolic meaning" or "mapping" on to any response.
  

The interesting thing is that these two systems make pretty clear which they use by both their structure and their behavior. The former always stops whereas the latter may sometimes not (it's "learned" its own way of avoiding collisions and we could spend endless years trying to divine it's "model" when it in fact has none!). The latter if given enough evolutionary generations, will operate far more efficiently, because it's been allowed to optimize its response without being tied to fixed rules ("stop at stop signs" "don't go if there's another car moving after you've stopped"), and through the overhead of first translating to the symbolic model, mapping to the response and then executing it: I know from experience with this exact problem that actually a neural network will start to brake as soon as there's *anything* red in the field of view; it doesn't wait to be able to resolve an octagon or letters.

 

What's important to take away from this issue is that you can have physical systems that are designed that perform what appear to be complex symbol recognition and mapping onto behavior, but not only can systems that are *undesigned* replicate all the functional requirements of the designed system and we with our minds and ability to perceive multiple models (as we did with orbital mechanics above) can actually tell the difference between the two, and as a result, not all systems that perform complex enough behavior have to be designed.

 

We'll come back to this later, as I've jumped ahead and need to "map" what I've just said onto your clarified definition of mapping (apologies if this is mapping a symbol onto a symbol):

 

Next, I have not defined 'mapping', instead taking it to have the customary mathematical definition. I have not done as you said; I have not "limited the definition of "mapping" in the sense of it having to be a priori-defined mapping, that is, you assume it is designed by a mind."

 

If I were to limit the definition of 'mapping', I would restrict it to mappings from symbols to physical entities. Mappings from symbols to symbols, or from non-symbolic physical entities to other physical entities are not ruled out, but they do not play an interesting role in my explanation of the necessary mental role in the establishment of the genetic code. The only interesting mapping in the context of my essay is the mapping between a codon and a specific amino acid group.

 

I have no real problem with your explanation here, I'd just like to clarify that I've use "mapping" in the preceding explanation to map onto actions in a physical system, and if you're into object oriented programming objects contain both data and methods and from the object's viewpoint, they're all the same. I don't think this violates anything in your definition here so I think we can proceed.

 

You might however want to think right now about what I've said in the preceding section about the *perception* of mapping, because it has a huge impact on your argument about mapping between codons and amino acid groups.

 

...The important question, Is a codon a symbol?

 

If you accept my definitions, then, as my argument spells out, mind is necessary in order to establish the symbolism in which the codon is a symbol.

Absolutely! :cheer:

 

Glad we can absolutely agree on that! Mainly of course because it's at this point that we have to get into the more contentious issue of what can be done with these definitions:

 

If you deny this conclusion, and maintain that a codon is not a symbol (in my sense of the term), then the three nucleotides comprising the codon are no more special than any other three nucleotides and their role and significance in the evolution (I'm talking Schrödinger evolution here, not Darwinian) of the various chemical structures in the cell is no more special than any other chemical action.

 

In the latter case, the genetic code is not a code after all. It is no more a code than the arrangements of the stars in the zodiac really map to bears, twins, etc. That is, the mapping between codons and amino acids, or stars to bears, are simply—what were your words?—"what a "mind" consciously either creates out of whole cloth, or perceives in existing physical systems,". The symbolism is all imaginary and has no impact or effect on any physical system.

 

There is no genetic "code", but simply the purely physical interactions of very complex molecules, because "code" implies a mapping and mappings are purely mental constructs which don't interfere with physical or chemical processes.

 

This is where I think you are completely missing the very important distinction I have been trying to make in the preceeding grafs:

 

I absolutely agree with the notion that a codon is a "symbol" ONLY when a mind intervenes to identify it as a symbol. But you're missing the fact that context is exactly what the mind uses to perceive the symbol from its physical representation: What is "CAT"? A codon? Computerized Axial Tomography? A small furry animal? Before you complain that I'm violating your definition by dealing with mapping symbols to symbols (and remember that you said that was kind of okay, but it wasn't your concern), I'd like to point out that you've *already* done that: WE define what a codon is as a combination of 3 nucleotides, and nucleotides as a combination of some sugar and phosphate groups and we put all these names (symbols) on them because it makes it easier to understand. But for the physical system, it's just a whole bunch of atoms that hang together because physics says they can.

 

So in when you claim that I'm saying that "The symbolism is all imaginary and has no impact or effect on any physical system," you got it. Absolutely! :cheer:

 

But this is exactly what you just claimed you believed: that a mind is necessary to map a symbol onto a physical system. Any physical system can be observed by a mind to produce any number of arbitrary mappings on to symbols and we can go further to utilize those symbols in a model and make predictions about what might happen in that physical system under various conditions.

 

And what I've been at pains to point out is that these two things are not at all contradictory, precisely because there is no implication for the physical system on the symbols we impose on it with our minds. Simply by thinking about the physical system we can invent mappings between specific patters of atoms to define symbols for "groups", "nucleotides", "codons", "amino acids" to our heart's content, but the physical system does not care. We happen to *choose* these divisions precisely because we build models using these particular symbols because we then run experiments and find that those symbols produce correct predictions. But as with the case of orbital mechanics above, if we use symbols (e.g. epicycles) that actually don't at all make accurate predictions, the physical system happily ignores that error in our mind's activity of mapping onto symbols.

 

What you appear to be doing here is to try to say that if a mind can identify a "symbol" in a physical system, then the existence of that symbol is intrinsic evidence that that the physical system onto which it maps was created by a mind.

 

The problem is that what you've said, "If you accept my definitions, then, as my argument spells out, mind is necessary in order to establish the symbolism in which the codon is a symbol." which is--as I said my previous post--an implication that I agree with. But you have tried to turn this into an equivalence (logic terms, that is asserting the reverse implication) by saying that since a codon is a symbol, it is evidence that the codon must have been designed.

 

Useful for your purposes, but any logician would tell you, if "if A then B" is true you still have not proven that "if B then A" is true. You need to provide evidence.

 

It would obviously be easier if you could just bootstrap this (that is, use a circular argument) to just assume that the second statement is true, but I'm not going to let you off that easy.

 

But mappings are incredibly maleable: if you're familiar with the volumnous amount of work done on Bible Codes, you'll see this application of "perception of mappings" in action:

This red herring does not apply and deserves no more comment.

 

Mother Nature has built mechanisms that actually have no idea what they're doing.

Most true. But the question at hand is whether or not Mother Nature knew what she was doing.

Here's the thing: if you've been following what I've been saying and keeping an open mind, you'd see that my Bible Code example from the previous post was not at all a red herring, in fact it is interesting precisely because it resembles very closely the exact example you are trying to use: the perception of codons as symbols and my contention that that perception is simply the activity of a mind doing the perception. For the physical system, it is all just letters, we can see all sorts of stuff in it that may or may not have anything to do with the physical system's operation.

 

So, did "Mother Nature know what she was doing?" Well, it is *certain* that the physical world does not *require* her to have known.

 

 

Now I sense at this point that you at least recognize this unconsciously, because in your last post, your argument shifts at this point from trying to provide a conclusive proof to dealing with the plausibility of the argument as the alternative, and to be fair, I am going to logically adhere to my last sentence--which is an implication--and recognize the validity of this weaker rhetorical goal on your part.

 

Yes, your neural nets are impressive; simple initial conditions lead to surprisingly complex results. There is an even more breathtaking example from mathematics: the Mandelbrot Set. I've heard it claimed that the M'set is the most complex structure known in reality (probably claimed by a mathematician).

 

But in any case, the M'set, your neural nets, molecular biology, the question we are exploring here is not how and whether such complex systems evolve once they get started, but the question of what was required in order for them to get started at all.

 

The Mandelbrot set requires that a series of computations be performed according to an exceedingly simple formula. Some mind was necessary to come up with that formula and to implement ways of doing the calculations.

 

Your neural nets run fine unattended once you configure them and apply the power. But some mind was necessary to figure out how to wire up and program the thing in the first place.

 

Is it totally out of the question that molecular biology also required a mind to get it started? I think we should open our minds to the possibility that this provides the most plausible explanation for the origin of life.

 

As a preface to this, I find that I need to reiterate a point I made in a previous post: The fact that simple systems like these that we can manipulate (indeed, that in the case of neural nets we can actually even take through an evolutionary process) and show that they can replicate the extreme complexity of natural systems like molecular biology, forces the question of whether a mind was necessary to create them back from the really hard stuff (like evolving eyes), further and further back to the most primitive stages of evolution. This is something that CraigD alluded to in his earlier post when describing the fact that we keep closing the gaps, but there's always enough space in the gap to allow some to claim that those gaps can only be filled by a "mind".

 

Unfortunately as we expand our knowledge of these systems, the mechanisms become clearer. Craig also pointed out that as we've seen here your focus really homes in on trying to describe problems in abiogenesis, and oddly enough there was an annoucement today of yet another experiment showing that one of the problems that have been claimed about the formation of self-replicating RNA because of it's soluability in water has been shown to be solvable in a natural environment. The darn scientists will keep chipping away at this.

 

Oh and to those of you who've read this far, happy Charles Darwin's birthday.

 

So some clarifications on these examples:

 

Neural networks start out with "all zero initial conditions". You train them by throwing in the water and letting them modify themselves using randomized changes to weights (a simple built-in algorithm) that are forced by feedback over many generations from the output of the network. In practical applications, we usually start with a whole set of predefined inputs that produce "good" and "bad" outcomes, but this is done ONLY because it reduces the training time: the "throw it in the water and see if it swims" technique works just as well, it just takes more generations. Because the probabilities with neural nets are just as lacking in probabilistic independence as molecular biologic systems, it's been shown that this is still not computationally intractable.

 

A single neural net is very simple: here's an example:

 

Source: Wikipedia

 

Each of the arrows has a weight and the nodes are the values at the three stages of the net: Input, "Hidden" and "Output" a simple multiplication of the weight is done to move from one node to the next from the input to the output. That's it, that's all there is. In an actual neuron, this is the exact operation that's performed, with the "multiplication" being done by chemical/electrostatic reactions deciding if the input impulses will cause the outputs of the cell to fire.

 

In the case of the Mandelbrot set, here's the equation that produces all those pretty pictures you've seen:

 

[math]z_{n+1} = z^2_n + \sqrt{(-1)}[/math]

 

Anyone who's taken physics or chemistry will tell you that first off the "imaginary number" (the square root of -1) shows up all over the place in physical systems, so that oddity is not at all odd, as do squares (the inverse square law is everywhere) and well, what's complicated about addition? And just about everything in nature from leaves to trees to mountains actually obeys variations of this simple computation.

 

So of course this is a great example of a situation where we use all sorts of symbols and manipulate them and as we've said, symbols require a mind, so it's fair enough for you to propose that a physical system that seems to map onto our symbolic language of math might require a mind to start it off.

 

But as I've hopefully fully demonstrated in the preceeding arguments, a mind is not *required* to create such a physical system.

 

Thus the reason I did not address this, is precisely because it's a fairly simple physical system in terms of its *operation*. The mechanisms of tRNA are a very simple Turing machine--although only when we humans go through the step of imposing our own mapping of what it's doing onto something we're familiar with, that just so happens to have been created by a mind--but tRNA does not have any "understanding" of the coding: it follows a sequence--because it's chemical bonds cause it to--and that physical sequence has the evolved effect of constructing DNA in a way that *appears* to us to be symbol translation, but the process is just a bunch of chemical reactions going on because over time, the positive outcomes of having that combination of chemicals around make it persist and regenerate. None of these molecules floating around care what they're doing, even over generations.

Well I guess that's strike two against me. I have still failed to get you to see and focus on the correct issue. The *operation* of the system is not the issue. And whether the operation or mechanism is simple or not or resembles a Turing Machine, has no bearing. To paraphrase, none of the telegraph machines nor the electrical impulses modified by them, care what they are doing, even over the entire globe where they were active. Those devices and pulses do not have any "understanding" of the Morse Code.

 

The issue is whether a mind was required to establish Morse Code (which it obviously was) and whether a mind was required to establish the genetic code. You have focused on the operation of the genetic mechanisms and have ignored, or at least not commented on, the way in which the genetic codebook is stored physically, and the possible ways in which the *codebook* was established at the outset.

 

And the reason I have "not commented" on it is that as I've said, a mind is not *required* to create the "initial codebook", as I've tried to show examples of simpler (although just as awe-inspiring) systems.

 

As I mentioned in my previous post, it took 3 billion years just to get cells to the point where they had most of that "codebook" working for the very simplest multi-cellular organisms. From a probailistic analysis perspective, this is tremendously interesting, because there is MUCH more independence in the probabilities of creating each of the individual advances to get to a single replicating cell than the *very* highly interdependent probabilities that are involved from getting from a flatworm to homo sapiens. That's why we have 3 billion years to get the cells going and only 1.5 billion years for *everything* else. Using "random", non-mind-driven processes.

 

As a result, the notion of a "codebook" in the sense that you're using it is imposing a human mapping onto a system that really doesn't need it, doesn't understand it, and can't be shown to be "impossible" to evolve in the absence of such a "codebook."

Hmmm...I think I'm beginning to see our difficulty. You seem to think that what I refer to as the "codebook" is a construct in my mind that I am overlaying onto the chemical processes. Not at all. By 'codebook' I mean (I would quote myself if I could easily find what I said earlier but I'll try to reproduce it faithfully) the 60-some-odd sequences within DNA which when replicated into tRNA molecules produce the 60-some-odd species of tRNA molecules.

 

The "codebook" IS those sequences of DNA.

Yes, but I'll point out that by continuing to use the term "codebook" you miss the point I'm making which is that as far as the physical system is concerned it is *not* a "codebook". There's a bunch of chemicals floating around; they do what they do because chemistry and physics make it happen. I know that you think that this is me focusing on the process, but it's really me pointing out the fact that you're continuing to try to make the symbolic meaning that we apply to of the 60 tRNA molecules an *intrinsic property* of the physical system, and it's not. As you do say, symbols don't exist without a mind. Take the mind away and it is indeed a bunch of chemicals floating around doing what they do. They do amazing things, but there's no symbols there and as far as the molecules are concerned, no "codebook."

 

The related easy question is how do you explain the varieties of tRNA. Well, the easy and obvious answer is that the first one got replicated 60 or so times, with some minor (by count) changes occurring along the way.

 

The hard question is how those minor changes got effected into the sequences. Keep in mind that in order to get it right, the special codon near the middle of each sequence has to match (i.e. according to the assignment in the genetic code, a purely abstract conceptual thing you will find in textbooks.) the pattern of nucleotides at one end of the sequence which just happens to have the chemical structure necessary to bond with the proper (in the sense of the code assignment) amino acid group.

 

Getting all 60 of those right somehow in some primitive cell without a mind seems impossible to me. I would love to hear you outline some plausible mindless method.

3 billion years is an incredibly long time. It's really quite mind-boggling, at least for us humans. Now take into account that just the number of molecules in the earth's oceans has been calculated to be something far north of [math]10^{45}[/math]. Now as Craig pointed out, there hasn't been a lot of research into this to a great extent because the payback from research in how the systems we've got now work has a much bigger payoff than the long-gone early earth environment that generated the first archea. But as the link I provided above shows (and I encourage you to look at the link) we're filling in more and more of the gaps in our knowledge about how the basic pieces of the whole DNA mechanism evolved.

 

In your specific question, really the issue is that there could be billions of failed combinations before one match was produced. Since by that point we already had the molecules forming strands, with so many of the floating around, you get enough trials in this gigantic parallel processor called "the ocean" that while it takes a while, you do get instances that work. And once the chemical process has a combination of molecules that aid the self-replication process, the "probabilistic independence" of random events starts to dive, and the whole process accelerates because all of the constituents reinforce each other.

 

While I am not an evolutionary microbiologist, and cannot reproduce for you the exact probabilities of each of the stages in the evolution of the DNA mechanism, I have had direct experience with systems like neural nets which show declining probabilistic independence in complex systems when evolution is applied. Because of that experience, for me it is not at all hard to understand how this can be driven "randomly."

 

You are probably as mystified by my conclusion in this respect as I am that "getting all 60 of those right...without a mind seems impossible" to you.

 

Now when you try to make that happen with an "intelligent designer" you have two choices: you can either front-load the design step--that is just DNA was designed and the rest happened purely due to physical processes, in which case the most interesting parts of evolution still stand as showing how much Mother Nature can do on her own, and pretty much proving that that initial step of "designing the codebook" of DNA is pretty trivial for her to do too--OR there has to be constant meddling with DNA and cell structure and selection and explaining branches of life that would (a) keep a designer very busy and (b ) leave plenty of data around in terms of biology, and evolution that shows pretty clearly that there really wasn't any meddling, nor again, a need for it. Thus while you claim that a "designed" interpretation is "easier", in fact it starts to create a situation where the observable data is very hard to fit into that interpretation.

Oh I think the observable data would be very easy to fit into that interpretation. We could use the tactic you accuse us of anyway, that if there is a "God" involved, then we can imagine any scenario happening.

 

But you raise interesting questions that I think should be explored. For example, what hard problems could easily be explained by an interventionist mind? How about protein folding as a frequent requirement in which a little help could be used? And the question at issue, How about mental intervention in establishing the genetic code?

 

The problem, as I see it, is the extreme reluctance on the part of scientists to even entertain the notion of some mentality being involved in the origin and processes of life. And when they have the courage to do so, they invariably adopt the (IMHO) ludicrous "almighty" attributes for that mind. How about considering a limited mind who couldn't get it right the first time and had to fumble around with many tries over billions of years to arrive at what we see now.

That's actually an interesting point, one that I think proves my point: It's taken our humble species less than 200 years to develop models that explain how much of the microbiology of life works. We don't have it all worked out, but there's certainly a lot of work with "artificial life" going on, and most of what's stopping us is not that we *can't* do it but that it may cause all sorts of nasty side-effects if we do it without thinking it through.

 

And you're saying an intelligence capable of getting a universe off the ground took 3 billion years to do it? That seems like an awfully long time! Especially when you consider the fact that this designer could be doing these experiments on trillions of earth-like planets in the universe, and had 9 billion years before the earth was even formed.

 

I won't comment on possible conclusions from that.

 

But basically your complaint here is simply that "a designer could have done it and it's closed-minded not to consider the possibility." The problem with this is that since we don't--and if you listen to most philosophers, *can't*--know about any sort of "outside of the physical laws of the universe designer," the scientific method has always eschewed appeals to a designer as a basic precept. For some, especially in the past, this is a variation on "rendering unto Caesar that which is Caesar's" but as a practical matter, it is a cop-out for the lazy, and is extremely prone to producing models and results that fail.

 

It's just really not a good idea, and most people ask "why would you *want* to appeal to a designer?"

 

I think also there is a innate human distaste for this approach that shows up in popular culture. Among critics going back to ancient Greece, one of the most devastating accusations you can hurl at a work of literature or drama is Deus ex machina, for the same reason as appealing to a designer in the natural world: it shows the author either did not care enough or simply wasn't smart enough to figure out what to do with the plot.

 

So I think the answer is simply, no thank you. Appealing to a designer as a cause to solve "hard" scientific problems is not only unappealing, it's a really bad idea.

 

 

In the beginning the Universe was created. This has made a lot of people very angry and has been widely regarded as a bad move, :phones:

Buffy

[Moontanman]

Consider these two successive paragraphs, right out of your fingers...

 

"Evolution uses a random process, mutation, as raw material for natural selection, this is not random but highly deterministic. In fact the process of evolution can be used to design things like aircraft much better and faster than any human mind can and this is used in modern aircraft design. "

 

"Evolution is deterministic not random and the idea of information and design is something humans place on the process arbitrarily, this design does come from an outside source but not God or Gods."

 

Focus whatever passes in you for mind upon the boldfaced and accented excerpts of your own words, in context. Then have another drink, or smoke, or whatever you utilize before offering your tidbits of limited wisdom before barfing up another tidbit, chunk, hairball, or other partially digested morsel of insight.

 

You have done a great job of "removing all doubt."

Alas... I'd expected better.

 

 

greylorn, i honestly am disappointed, insult is no way to further your argument but such dishonest discourse is a hallmark of creationist tactics. when you have no evidence your only move is to either concede you are wrong or try to misrepresent your opposition, your insults and misdirection does nothing to support your nonsensical arguments... but it helps my position by making yours look weak...

[clinkernace]

The theory of evolution, which is the matter under discussion does not deal with the origin of the universe, it does not deal with the origin of the solar system, it does not deal with the construction of the Earth, it does not deal with the flow dynamics of lava, it does not deal with quantum mechanics, and it sure as heck does not deal with the origin of life. It deals with the evolution of existing life. So, yes, abiogenesis is assuredly irrelevant to the present discussion.

 

Eco,

 

I must assume that you have read P. Martin's essays before generating this reply, but with all due respect, it seems that your reply does not reflect an honest or thorough perusal.

 

His essay is all about the relationship between codons and the cellular mechanisms, the ribosomes, that use the information contained in codons to convert a tRNA sequence into a functional and properly folded protein. Without such mechanisms somehow appearing within the first living, self-replicating cell, there would not have been a first cell.

 

These arguments are entirely about abiogenesis!

[Eclogite]

I have read the essay. I have also read the title of this thread, which I take to be an executive summary of the topic. The origin of the genetic code is not about Darwinism, or biological evolution, or the Modern Synthesis. If Paul, or you, wish to debate about the competing hypotheses for the origin of life I am happy to entertain this, but do not call it a discussion about Darwinism, etc. It wouldn't be.

[clinkernace]

greylorn, i honestly am disappointed, insult is no way to further your argument but such dishonest discourse is a hallmark of creationist tactics. when you have no evidence your only move is to either concede you are wrong or try to misrepresent your opposition, your insults and misdirection does nothing to support your nonsensical arguments... but it helps my position by making yours look weak...

I am sorry that you are disappointed, but hardly surprised, since you've yet to do anything but complain about whatever I post. Another complaint is hardly a surprise.

 

Judging from your profile photo (can't tell who is you, but both guys look equally scruffy (not an insult--- the people I trust are scruffy, but clean up well for the weekend dance), you are an independent kind of guy, at least at the physical level. But I'm getting the sense that at the mental level, you are better at dishing it out than taking it. All I did here was quote you, and point out your self contradictions. That seems to be an affront to you. No insult was intended, although clearly one was taken. You and I would probably get along much better over a mountain campfire and a favorable supply of beer, where we could read eyes and expressions. And, that's not the format.

 

But man, if you cannot abide having someone point out your own confusions (as people often do with me), what are you doing on a forum full of cognitively adept individuals? I'm certain that others noted your contradictory statements, but were too kind to point them out in public. My pointing them out was actually a service to you, although not one that you value.

 

Consider the possibility that a friend is someone who takes the trouble to point out that you have a nasty looking green booger lodged in your mustache, and that those who neglect to convey that information do not care about you at all, or--- they know that you will be angry at them because of their observation, and prefer to avoid confrontation. So far, you strike me as a fellow who likes to dish out vague and non-specific criticism but cannot take a pointed criticism in return. Your choice. That's just IMO, and of course I am wrong and confused. Be at peace anyway.

[LaurieAG]

If Paul, or you, wish to debate about the competing hypotheses for the origin of life I am happy to entertain this, but do not call it a discussion about Darwinism, etc. It wouldn't be.

Don't be so hasty Eclogite,

 

From a pure mathematical perspective you can build some very simple but extremely complex encryption systems from Very Large Scale Finite State Cellular Automata. With 3 simple variables, Alphabet length, number of cycles and a translation table you can scramble a simple message so much that you can only get it back if you know how to decode it. It's just pure discrete math.

 

http://en.wikipedia.org/wiki/Cellular_automaton

http://en.wikipedia.org/wiki/Blowfish_(cipher)

http://en.wikipedia.org/wiki/Enigma_machine

 

The first reference note from the Cellular Automaton wiki leads to http://en.wikipedia.org/wiki/Darwin%27s_Dangerous_Idea

 

Darwin's Dangerous Idea: Evolution and the Meanings of Life (1995) is a book by Daniel Dennett which looks at some of the repercussions of Darwinian theory. The crux of the argument is that whether or not Darwin's theories are overturned there is no going back from the dangerous idea that design - purpose or what something is for - might not need a designer. Dennett makes this claim because he thinks that natural selection is a blind process which is nevertheless sufficiently powerful to explain the evolution of life. Darwin's discovery was that the generation of life worked algorithmically, that processes behind it work in such a way that given these processes the results that they tend toward must be so. Dennett thinks that by, for example, claiming that minds cannot be reduced to purely algorithmic processes, many of his eminent contemporaries are claiming that miracles can occur.

[Eclogite]

Given that the extract from the wikipedia article is in error I fail to see what relevance your post has to my preference to justifiably exclude discussions of abiogenesis from one on Dariwnism, or - alternatively - not to label an origin of life discussion as having to do with evolution.

 

In case you didn't spot the error, it is here: Darwin's discovery was that the generation of life worked algorithmically, that processes behind it work in such a way that given these processes the results that they tend toward must be so

 

The problem lies in the word generation. Darwin spoke only of the generation of life in his now well known letter to Joseph Hooker in which he spoke of the "warm little pond". Substitute the word evolution for generation and we return validity to the sentence, while simultaneously robbing it of relevance for your argument.

 

 

Note that there are very likely aspects of evolution that were involved in the advances in pre-biotic chemistry, but that is not at all the same as conflating abiogenesis with evolution.

[Moontanman]

I am sorry that you are disappointed, but hardly surprised, since you've yet to do anything but complain about whatever I post. Another complaint is hardly a surprise.

 

Judging from your profile photo (can't tell who is you, but both guys look equally scruffy (not an insult--- the people I trust are scruffy, but clean up well for the weekend dance), you are an independent kind of guy, at least at the physical level. But I'm getting the sense that at the mental level, you are better at dishing it out than taking it. All I did here was quote you, and point out your self contradictions. That seems to be an affront to you. No insult was intended, although clearly one was taken. You and I would probably get along much better over a mountain campfire and a favorable supply of beer, where we could read eyes and expressions. And, that's not the format.

 

But man, if you cannot abide having someone point out your own confusions (as people often do with me), what are you doing on a forum full of cognitively adept individuals? I'm certain that others noted your contradictory statements, but were too kind to point them out in public. My pointing them out was actually a service to you, although not one that you value.

 

Consider the possibility that a friend is someone who takes the trouble to point out that you have a nasty looking green booger lodged in your mustache, and that those who neglect to convey that information do not care about you at all, or--- they know that you will be angry at them because of their observation, and prefer to avoid confrontation. So far, you strike me as a fellow who likes to dish out vague and non-specific criticism but cannot take a pointed criticism in return. Your choice. That's just IMO, and of course I am wrong and confused. Be at peace anyway.

 

 

Dude, careful how far you bend over, your creationism is showing...

[Moontanman]

Consider these two successive paragraphs, right out of your fingers...

 

"Evolution uses a random process, mutation, as raw material for natural selection, this is not random but highly deterministic. In fact the process of evolution can be used to design things like aircraft much better and faster than any human mind can and this is used in modern aircraft design. "

 

"Evolution is deterministic not random and the idea of information and design is something humans place on the process arbitrarily, this design does come from an outside source but not God or Gods."

 

Focus whatever passes in you for mind upon the boldfaced and accented excerpts of your own words, in context. Then have another drink, or smoke, or whatever you utilize before offering your tidbits of limited wisdom before barfing up another tidbit, chunk, hairball, or other partially digested morsel of insight.

 

You have done a great job of "removing all doubt."

Alas... I'd expected better.

 

 

greylorn is there any chance you can refute what i said with anything but derision? I can support what i said.

 

http://www.sciencedaily.com/releases/2007/11/071119123929.htm

 

 

Now either refute that with something other than "I can't understand it so it must be false" or apologize for being so condescending... btw that pic you seem to be obsessing on is 40 years old, my grandfather is dead and I am a white headed old man... go figure huh?

Edited February 14, 2013 by Moontanman

[Eclogite]

@greylorn

Taking up your objection to Moontanman's points, I am perplexed why you would disagree with him if you have ,as you imply, a reasonable understanding of conventional evolutionary theory.

 

Simply put the source of evolutionary change, largely from mutations, is essentially random.

The overall process of evolution is certainly not random, since it is directed (priamrily) by natural selection.

 

These two points are very straightforward, lie at the heart of the Modern Synthesis, and form the consensus view of the vast majority of biologists. If you wish to challenge these you have to do considerably more than denigrate the intellect of a member who is simply reminding you of these points. I look forward to seeing your justification for rejecting these cornerstones of the Modern Synthesis.

[Qdogsman]

 

My thoughts on this is that Qdogman's ideas are nothing more than the old information argument ie DNA represents information and since information cannot come from anything but a mind then DNA must have been designed by a mind.

 

 

If that's all you got out of my essay and the following discussion, then I humbly suggest you read it again a bit more carefully.