Excuse me but no, the mind was present all the time. The mind of the scientists that did the selection. They are the ones that were intelligently selecting/designing the outcome.

No, they weren't designing the outcome, they were just ensuring that an outcome they were looking for from the experiment could be detected using a marker. To add to this, the artificial selection that you talked about was again with the process of demonstrating that random mutations acting on the components of translational machinery could produce alternate genetic codes. There was no guarantee that this selection could take place unless the requisite mutational events actually took place first, and those are stochastic.

PS - Is your stance one of guided evolution?

No, this is an outdated assertion.

Science advances quicky, so it better be outdated as new knowledge comes along. But on the other hand, does that statement in any way impact the notion of FSC in any way? If not, than why even bring it up?

[1] 8 - 10 again? Outdated claim but I will give him the benefit of doubt given it is an old paper.
[2] No bridge? I think such a bridge for an inorganic template is not necessitated anymore, the evidence refuting [1] also does away with requirements for an inorganic template.

Again, the point being, does thins claim affect the notion of FSC in any relevan way? I believe not.

Yes, point being? Any assertions about complexity often fail to take into account the Mullerian two-step for the evolution of Irreducible Complexity.

The point is that generation of FSC can not be explained by natural laws. Only it's transmission can. Since natural laws are deterministic in their nature, they can't produce anything other than they are supposed to produce.

Evolved function there.

Let's take a closer look at this paper. As we can clearly see from the quote. The function was modified to gaina higher fidelity. This is much different than gainign a completely new function. Not only that, but this was not produced by natural laws, as Abel rightly claims that they are not capeable of doing so. But as we can see, it is the scientists, with their intelligent input, that have been doing the selction and they are the ones that produced the higher fidelity of the said function.

The primary selective step involved the isolation of ribozyme polymerase-encoding genomes possessing correctly extended PT complexes. After incubating the emulsion, the aqueous fraction was recovered, the nucleic acid was denatured, and an excess of a biotinylated capture probe, having a sequence similar to the template used in the PT complex, was added (Table 2). Upon renaturation, this material was applied to streptavidin magnetic beads and washed so as to retain only those DNA pool sequences whose RNA primers had been correctly extended by a polymerase ribozyme. These retained DNA genotypes were then eluted and amplified by PCR. This new pool was subsequently digested using BtgI and ligated to the selection DNA/RNA primer (Table 1) before undergoing another Round of selection. A purification factor of 100 could easily be obtained by this hybridization approach (Fig. 4).

And there, just to name two instances.

What exactly was produced here?

And this assertion in the paper is [1] Uncited [2] Evidentially unsupported.

Actually, just atke a look at your computer screen. Can you show me an equation for your computer? Is there a way you can derive it's struture from it's material parts, just like you can do for crystals that from from the material itself under certain conditions? I guess not. Therefore, it is clearly an unsupported claim that any configurable switch can be reduced to the material that it is comprised of.

Nope, the fitness landscape necessarily isn't one peaked, selection works by eliminating lethal mutants.

Necessarily it does not have to be, but is it? What kind of fitness function do we have in nature for evolving new biological information?

And he makes no references to where biologists actually propose this strawman caricature where the whole of metabolism just popped into place. But yes, there is substantial evidence to suggest that there are ribozymes that can carry out functions such as peptide bond formation et cetera, there are self replicating ribozymes, there are translational ribozymes of a very small length.

Even if it takes along time, we can basicly say that it "just happened" if there was no direction to it.

I close this post with

Those two articles are fine, but they only address the formation of the RNA, the material that is. They do not address how it gained biological functions. The first paper just says that the Darwinian evolution is just supposed to take on from there.

Mechanical actions? since when did chemistry become a matter of solely mechanical actions?

I'm simply trying to be as general as possible. We can describe chemistry as electrical physical interactions, right?

The analogy fails when we talk about Turing machines et cetera, since there is direct evidence of humans building these Turing machines, otherwise the analogy would still fail given that there is no rigorous method for the verification of design.

The fact that we saw something get designed is irrelevan at this point. Not everything we infer design for gets to be observed. What is relevent is that computers and biological systems are functionally equivalent. So the analogy is valid. Regardless of biology being designed or not. The point is that the analogy is valid.

And I disagree when you say mutations involve transmission from parent to offspring, the offspring don't exist until purported transmission through reproduction is complete. In other words you cannot transmit to a receiver that only starts existing after the message has been received without involving storage until the latter happens, but since DNA is a storage molecule itself briging in transmission here is rather superfluous to requirements.

The fact that DNA is being copied is a form of transmission in the first place. You can also look at it this way, the notion of a receiver is already built in. When a male passes it's genetic material to the female, one is the transmitter, the other the receiver.

Also, mutations do not add noise in the process of purported transmission during reproduction, because these mutations happen prior to reproduction. Reproduction is an imperfect process because the imperfections are introduced through mutations before it occurs.

The point is rather that the copy is not perfect, therefore, by definition that is called noise. It does not matter when they happen. They happen, that's the main point, and they change the input sequence, so in the end it's not the same as as it originally was.

Since when did Macs and spectrums begin to reproduce? Or mutate stochastically?

Since when do Macs or Spectrums have eyes or ears? They don't. It's irrelevant. It's a non sequitur. The fact remains that they are intelligently designed, and they are functionally equivalent to biological systems. They lack the ability to self-reproduce but so what? If they had such an ability, would that mean that they were not designed? Obviousy not. So neither does it mean that biological systems are not designed, just because they can reproduce.

No, they weren't designing the outcome, they were just ensuring that an outcome they were looking for from the experiment could be detected using a marker.

And with each and evry step of the way, the scientists were selecting the right individuals. Teh ones they wanted, and by doing so, they were the ones who were inducing an artificial fitness function, on which selection could work. Thus the outcome is intelligently designed.

To add to this, the artificial selection that you talked about was again with the process of demonstrating that random mutations acting on the components of translational machinery could produce alternate genetic codes.

Which is a fact of life and nobody I know would argue otherwise...

There was no guarantee that this selection could take place unless the requisite mutational events actually took place first, and those are stochastic.

Indeed they are. Which still just shows that you need an intelligent agent do do the selction on stochastic events to evolve non-trivial amount of biological functions.

PS - Is your stance one of guided evolution?

It's a nice idea. I personally only think that microevolution is the only thing that there is evidence for right now, as far as any form of evolution is concerned.

Царь Славян wrote:

No, this is an outdated assertion.

Science advances quicky, so it better be outdated as new knowledge comes along. But on the other hand, does that statement in any way impact the notion of FSC in any way? If not, than why even bring it up?

Abel postulated that on the premise that a prebiotic template had to exist as a source of functional information and used that to critique the then extant hypotheses on the origins of life.

[1] 8 - 10 again? Outdated claim but I will give him the benefit of doubt given it is an old paper.
[2] No bridge? I think such a bridge for an inorganic template is not necessitated anymore, the evidence refuting [1] also does away with requirements for an inorganic template.

Again, the point being, does thins claim affect the notion of FSC in any relevan way? I believe not.

It does, since that was the setting in which he defined the term in an effort to suggest that the then extant hypotheses for OOL were inadequate. All it means is that some configurations have functions, some do not.

Yes, point being? Any assertions about complexity often fail to take into account the Mullerian two-step for the evolution of Irreducible Complexity.

The point is that generation of FSC can not be explained by natural laws. Only it's transmission can. Since natural laws are deterministic in their nature, they can't produce anything other than they are supposed to produce.

This is manifest nonsense, mutagenic processes can generate functional complexity, and even in cases of what you have been terming "intelligent selection" the de novo functionality of the entities involved are down to mutagenic processes, or in other words products of bog standard natural laws.

Evolved function there.

Let's take a closer look at this paper. As we can clearly see from the quote. The function was modified to gaina higher fidelity. This is much different than gainign a completely new function. Not only that, but this was not produced by natural laws, as Abel rightly claims that they are not capeable of doing so. But as we can see, it is the scientists, with their intelligent input, that have been doing the selction and they are the ones that produced the higher fidelity of the said function.

Abel didn't say FSC cannot be produced by natural laws, if you notice, he said they cannot be produced by self-ordering, I suggest you read the paper again. Again, no one is suggesting that everything popped into place at once so that statement is irrelevant.

The primary selective step involved the isolation of ribozyme polymerase-encoding genomes possessing correctly extended PT complexes. After incubating the emulsion, the aqueous fraction was recovered, the nucleic acid was denatured, and an excess of a biotinylated capture probe, having a sequence similar to the template used in the PT complex, was added (Table 2). Upon renaturation, this material was applied to streptavidin magnetic beads and washed so as to retain only those DNA pool sequences whose RNA primers had been correctly extended by a polymerase ribozyme. These retained DNA genotypes were then eluted and amplified by PCR. This new pool was subsequently digested using BtgI and ligated to the selection DNA/RNA primer (Table 1) before undergoing another Round of selection. A purification factor of 100 could easily be obtained by this hybridization approach (Fig. 4).

And there, just to name two instances.

What exactly was produced here?

Nothing was produced in the selection process, which you quote, which was used just to trap mutants which had evolved functionality, they produced, by mutation, a novel RNA polymerase ribozyme that had acquired the functional information to produce more high-fidelity replicated sequences, firstly, and also acquired the functional information required to produce copies of longer templates than the predecessor.

The scientists did not have any role in the generation of those novel properties at all.

And this assertion in the paper is [1] Uncited [2] Evidentially unsupported.

Actually, just atke a look at your computer screen. Can you show me an equation for your computer? Is there a way you can derive it's struture from it's material parts, just like you can do for crystals that from from the material itself under certain conditions? I guess not. Therefore, it is clearly an unsupported claim that any configurable switch can be reduced to the material that it is comprised of.

And since when did computers become self replicating, mutable entities subjected to natural stochastic variation?

Nope, the fitness landscape necessarily isn't one peaked, selection works by eliminating lethal mutants.

Necessarily it does not have to be, but is it? What kind of fitness function do we have in nature for evolving new biological information?[/quote]

Better reproduction, that is it. Anything that increases reproducibility will result in a trait being selected for, however, a large part of evolution is also fundamentally predicated on genetic drift, which is not under any fitness pressure.

And he makes no references to where biologists actually propose this strawman caricature where the whole of metabolism just popped into place. But yes, there is substantial evidence to suggest that there are ribozymes that can carry out functions such as peptide bond formation et cetera, there are self replicating ribozymes, there are translational ribozymes of a very small length.

Even if it takes along time, we can basicly say that it "just happened" if there was no direction to it.

And you have a citation to support this viewpoint?

I close this post with

Those two articles are fine, but they only address the formation of the RNA, the material that is. They do not address how it gained biological functions. The first paper just says that the Darwinian evolution is just supposed to take on from there.

The first paper, computationally, carries out a survey of the RNA mutational space and explains that functions stem from secondary structure, notably hairpin loops, which is especially notable, which of course is the case with ribozymes in general, and secondary structures are a function of base pairing.

RNA forms ----------------> RNA folds due to base pairing , just like proteins fold due to chemical bonding and chemical interactions such as hydrophobicity and hydrogen bonding et cetera, this folding allows RNA to function, biological functionality is also a function of the laws of physics and chemistry.

Царь Славян wrote:It's a nice idea. I personally only think that microevolution is the only thing that there is evidence for right now, as far as any form of evolution is concerned.

And despite your best effort, your whole facade of trying to come about as informed on the matter of biological evolution breaks apart, now that you made this comment.

Царь Славян wrote:

Mechanical actions? since when did chemistry become a matter of solely mechanical actions?

I'm simply trying to be as general as possible. We can describe chemistry as electrical physical interactions, right?

No, simply being general as possible does not convey adequate coverage.

The analogy fails when we talk about Turing machines et cetera, since there is direct evidence of humans building these Turing machines, otherwise the analogy would still fail given that there is no rigorous method for the verification of design.

The fact that we saw something get designed is irrelevan at this point. Not everything we infer design for gets to be observed. What is relevent is that computers and biological systems are functionally equivalent. So the analogy is valid. Regardless of biology being designed or not. The point is that the analogy is valid.

Natural snowflakes and artificial snowflakes (http://pubs.acs.org/doi/abs/10.1021/ed007p1682.1) are functionally equivalent, therefore the analogy of having a twerp sitting in the clouds tweaking a laboratory setup is a valid analogy, therefore there is indeed a clown who produces snowflakes in the clouds above, yeah right

And I disagree when you say mutations involve transmission from parent to offspring, the offspring don't exist until purported transmission through reproduction is complete. In other words you cannot transmit to a receiver that only starts existing after the message has been received without involving storage until the latter happens, but since DNA is a storage molecule itself briging in transmission here is rather superfluous to requirements.

The fact that DNA is being copied is a form of transmission in the first place. You can also look at it this way, the notion of a receiver is already built in. When a male passes it's genetic material to the female, one is the transmitter, the other the receiver.

Said noise doesn't happen during transmission but before it, and therefore Shannon information which is defined as a function of actual transmission of signals doesn't happen, that is it. Noise acts DURING transmission in Shannon information.

Also, mutations do not add noise in the process of purported transmission during reproduction, because these mutations happen prior to reproduction. Reproduction is an imperfect process because the imperfections are introduced through mutations before it occurs.

The point is rather that the copy is not perfect, therefore, by definition that is called noise. It does not matter when they happen. They happen, that's the main point, and they change the input sequence, so in the end it's not the same as as it originally was.

See above, the point is not whether it could be considered noisy. The point is that even if one were to treat it as noise, it wouldn't fall under the remit of Shannon information theory.

Since when did Macs and spectrums begin to reproduce? Or mutate stochastically?

Since when do Macs or Spectrums have eyes or ears? They don't. It's irrelevant. It's a non sequitur. The fact remains that they are intelligently designed, and they are functionally equivalent to biological systems. They lack the ability to self-reproduce but so what? If they had such an ability, would that mean that they were not designed? Obviousy not. So neither does it mean that biological systems are not designed, just because they can reproduce.[/quote]

What you do not realize is that you can have natural processes introducing variation and then interactions with the environment altering which copies survive in the face of competition for resources in the case of biological organisms.
The evolvability of organisms through natural mutagenic and selective processes means that the requirements for extraneous design do NOT apply to organisms as they do to computers. As far as functional equivalence is concerned look at the snowflakes counter.

No, they weren't designing the outcome, they were just ensuring that an outcome they were looking for from the experiment could be detected using a marker.

And with each and evry step of the way, the scientists were selecting the right individuals. Teh ones they wanted, and by doing so, they were the ones who were inducing an artificial fitness function, on which selection could work. Thus the outcome is intelligently designed.

And in nature the fitness function is naturally imposed, think predation, reaction rates, competition for food, metabolic efficiency, disease, immunity. The number of selection pressures can be as high as the number of interactions possible with the environment, the natural fitness space is very high.

To add to this, the artificial selection that you talked about was again with the process of demonstrating that random mutations acting on the components of translational machinery could produce alternate genetic codes.

Which is a fact of life and nobody I know would argue otherwise...

What it does is that the functional complexity for coding for an amino acid can result from the natural processes of mutation, something which your erroneous interpretation of Abel's work (which was more about prebiotic settings than extant organisms, and even then based on science that has moved on) asserted cannot do.

There was no guarantee that this selection could take place unless the requisite mutational events actually took place first, and those are stochastic.

Indeed they are. Which still just shows that you need an intelligent agent do do the selction on stochastic events to evolve non-trivial amount of biological functions.

Organisms without antibiotic resistance in the presence of antibiotics will go kaput, can you show me where intelligence is involved here? Limp animals that cannot run away because of developmental deformities brought about by stochastic mutation may get eaten by predators, where is your intelligent agent here? or organisms which can synthesize some of their own metabolites can free themselves from environmental constraints and reproduce better, where is your agent there?

Mutants interact with the environment differently while striving to reproduce in a setting of limited resources, this results in differential survival of said mutants, thus fixing mutants and allowing further mutations to act on extant pools because they still exist, where is your intelligent agent there?

It is always hilarious when people "infer" entities that have not been shown to exist or offer any evidence at all.
Can you demonstrate that there is clear, substantive evidence for design and devise a method to differentiate between natural and designed entities without producing evidence of the design process per se?

PS - Is your stance one of guided evolution?

It's a nice idea. I personally only think that microevolution is the only thing that there is evidence for right now, as far as any form of evolution is concerned.

Define microevolution, you are in for a literature based bombing run on this.

Abel postulated that on the premise that a prebiotic template had to exist as a source of functional information and used that to critique the then extant hypotheses on the origins of life.

Fine, does that impact the notion of FSC in any way?

It does, since that was the setting in which he defined the term in an effort to suggest that the then extant hypotheses for OOL were inadequate. All it means is that some configurations have functions, some do not.

It doesn't impact it in any way, and yes it does mean that some configuration have functions and some not.

This is manifest nonsense, mutagenic processes can generate functional complexity, and even in cases of what you have been terming "intelligent selection" the de novo functionality of the entities involved are down to mutagenic processes, or in other words products of bog standard natural laws.

If that is so then you will have no problem in providing the equation and naming the natural law that produces FSC in those cases. I will tell you right now that you can not. But just to give you an example of what you should provide, take a look a this.



This is the Avrami eqution and it describes how crystals form. You can describe any crystal's structure with that equation with ofcourse the addition of impurities, that shape it's structure. The point being is that this is a product of natural laws. Under certain conditions crystals will form. But no, under no known conditions, computers will not form. The reason is becasue they have FSC unlike crystals which have not. The same goes for DNA sequences that have biological functions. So if you can, then please show me the equation for a biologically relevant DNA sequence.

Abel didn't say FSC cannot be produced by natural laws, if you notice, he said they cannot be produced by self-ordering, I suggest you read the paper again. Again, no one is suggesting that everything popped into place at once so that statement is irrelevant.

You should be more careful. By self-ordering, Abel actually means natural laws acing on matter under certain conditions. On the other hand Self-organization would be something that you need to describe biological systems, yet Abel claims that it is not possible.

Self-ordering phenomena should not be confused with self-organization. Self-ordering events occur spontaneously according to natural “law” propensities and are purely physicodynamic. Crystallization and the spontaneously forming dissipative structures of Prigogine are examples of self-ordering. Self-ordering phenomena involve no decision nodes, no dynamically-inert configurable switches, no logic gates, no steering toward algorithmic success or “computational halting”. Hypercycles, genetic and evolutionary algorithms, neural nets, and cellular automata have not been shown to self-organize spontaneously into nontrivial functions.

link

And since when did computers become self replicating, mutable entities subjected to natural stochastic variation?

They aren't and it's irrelevant. Even if they were made to be self-replicating, they would still be designed.

Better reproduction, that is it. Anything that increases reproducibility will result in a trait being selected for, however, a large part of evolution is also fundamentally predicated on genetic drift, which is not under any fitness pressure.

So, now you tell me, is the fitness function of nature well suited for production of new biological functions?

And you have a citation to support this viewpoint?

It was a more of a logical deduction and a common sense notion. Anything that is not directed by an intelligent agent is either produced by chance or necessity.

The first paper, computationally, carries out a survey of the RNA mutational space and explains that functions stem from secondary structure, notably hairpin loops, which is especially notable, which of course is the case with ribozymes in general, and secondary structures are a function of base pairing.

RNA forms ----------------> RNA folds due to base pairing , just like proteins fold due to chemical bonding and chemical interactions such as hydrophobicity and hydrogen bonding et cetera, this folding allows RNA to function, biological functionality is also a function of the laws of physics and chemistry.

I agree. How does that explain how natural selection acting upon random mutations produced all the diversity of life we see today? Obviously it does not.

No, simply being general as possible does not convey adequate coverage.

If you want to be as general as possible then yes it does.

Natural snowflakes and artificial snowflakes (http://pubs.acs.org/doi/abs/10.1021/ed007p1682.1) are functionally equivalent, therefore the analogy of having a twerp sitting in the clouds tweaking a laboratory setup is a valid analogy, therefore there is indeed a clown who produces snowflakes in the clouds above, yeah right

No, since we have the knowledge of how snowflakes can form by natural means. We do not know how computers form by natural means. Oh, and snowflakes have zero FSC.

Said noise doesn't happen during transmission but before it, and therefore Shannon information which is defined as a function of actual transmission of signals doesn't happen, that is it. Noise acts DURING transmission in Shannon information.

Well, you do know that random mutations can also happen during replication, right? Radiation has been known to be mutagenic.

See above, the point is not whether it could be considered noisy. The point is that even if one were to treat it as noise, it wouldn't fall under the remit of Shannon information theory.

See above. Noise can be introduced while the DNA strand is being copied.

What you do not realize is that you can have natural processes introducing variation and then interactions with the environment altering which copies survive in the face of competition for resources in the case of biological organisms. The evolvability of organisms through natural mutagenic and selective processes means that the requirements for extraneous design do NOT apply to organisms as they do to computers. As far as functional equivalence is concerned look at the snowflakes counter.

Actually it does apply, since the information had to be inputed in some way from the start. If there is no self replicating mechanism that can translate the code, then there is no evolution. And no, snowflakes are not functional.

And in nature the fitness function is naturally imposed, think predation, reaction rates, competition for food, metabolic efficiency, disease, immunity. The number of selection pressures can be as high as the number of interactions possible with the environment, the natural fitness space is very high.

That's true. But in the lab, the scientists directed the outcome to a specific goal. Is there a goal to the fitness function in nature? Is the goal the evolution of new biological functions?

What it does is that the functional complexity for coding for an amino acid can result from the natural processes of mutation, something which your erroneous interpretation of Abel's work (which was more about prebiotic settings than extant organisms, and even then based on science that has moved on) asserted cannot do.

I'm sorry but you never showed such a thing actually happening. What you showed is intelligent agents, the scientists, producing new FSC, not nature itself.

Organisms without antibiotic resistance in the presence of antibiotics will go kaput, can you show me where intelligence is involved here? Limp animals that cannot run away because of developmental deformities brought about by stochastic mutation may get eaten by predators, where is your intelligent agent here? or organisms which can synthesize some of their own metabolites can free themselves from environmental constraints and reproduce better, where is your agent there?

Mutants interact with the environment differently while striving to reproduce in a setting of limited resources, this results in differential survival of said mutants, thus fixing mutants and allowing further mutations to act on extant pools because they still exist, where is your intelligent agent there?

Those are all pre-existing functions that have to be accounted for. Just like in the computer. A computer can render a movie all by itself. A person does not have to move every single bit every step of the way. But the point is that that functionality of the computer was designed in the first place.

It is always hilarious when people "infer" entities that have not been shown to exist or offer any evidence at all.
Can you demonstrate that there is clear, substantive evidence for design and devise a method to differentiate between natural and designed entities without producing evidence of the design process per se?

I'm sure you know Dembski's notion of Specified Complexity. It's a pattern that is easily describeable, yet hard to reproduce by chance. It is based on Fisher's notion of statistical hypothesis testing.

Define microevolution, you are in for a literature based bombing run on this.

There are lot's of different definitions. For me it's the change in frequencies of alleles in a population.

Царь Славян wrote:

Abel postulated that on the premise that a prebiotic template had to exist as a source of functional information and used that to critique the then extant hypotheses on the origins of life.

Fine, does that impact the notion of FSC in any way?

It impacts FSC applied to evolution, yes, because the prebiotic template he uses didn't have any functions associated with modern cells which are under darwinian evolution.

It does, since that was the setting in which he defined the term in an effort to suggest that the then extant hypotheses for OOL were inadequate. All it means is that some configurations have functions, some do not.

It doesn't impact it in any way, and yes it does mean that some configuration have functions and some not.

Good, now known biochemical processes can produce novel configurations, different configurations can have different functions, while some do not, mutational processes produce new configurations and as a consequence new functions, whether that function is preserved or not is subject to selection pressures and processes. Evolution is perfectly capable of generating FSC.

This is manifest nonsense, mutagenic processes can generate functional complexity, and even in cases of what you have been terming "intelligent selection" the de novo functionality of the entities involved are down to mutagenic processes, or in other words products of bog standard natural laws.

If that is so then you will have no problem in providing the equation and naming the natural law that produces FSC in those cases. I will tell you right now that you can not. But just to give you an example of what you should provide, take a look a this.

[/quote]

When did I say everything boils down to one equation? Is base pairing a result of natural laws? Substitution? Transversion? Transposon activity? Gene Duplication? Whole Genome Duplication? Heard of them? All known natural processes that can produce FSC by producing various configurations of DNA, and consequently a subset of functional configurations.

This is the Avrami eqution and it describes how crystals form. You can describe any crystal's structure with that equation with ofcourse the addition of impurities, that shape it's structure. The point being is that this is a product of natural laws. Under certain conditions crystals will form. But no, under no known conditions, computers will not form. The reason is becasue they have FSC unlike crystals which have not. The same goes for DNA sequences that have biological functions. So if you can, then please show me the equation for a biologically relevant DNA sequence.

You want an equation? RM + NS

Abel didn't say FSC cannot be produced by natural laws, if you notice, he said they cannot be produced by self-ordering, I suggest you read the paper again. Again, no one is suggesting that everything popped into place at once so that statement is irrelevant.

You should be more careful. By self-ordering, Abel actually means natural laws acing on matter under certain conditions. On the other hand Self-organization would be something that you need to describe biological systems, yet Abel claims that it is not possible.

And those conditions happen to be, in this case, a prebiotic templating system, which is superfluous to requirements given some of the more recent study in the field.

Self-ordering phenomena should not be confused with self-organization. Self-ordering events occur spontaneously according to natural “law” propensities and are purely physicodynamic. Crystallization and the spontaneously forming dissipative structures of Prigogine are examples of self-ordering. Self-ordering phenomena involve no decision nodes, no dynamically-inert configurable switches, no logic gates, no steering toward algorithmic success or “computational halting”. Hypercycles, genetic and evolutionary algorithms, neural nets, and cellular automata have not been shown to self-organize spontaneously into nontrivial functions.

link[/quote]

This again is a strawman caricature that assumes genes and everything must pop into place spontaneously. All you need is configurations to arrive at self replication first, and self replicating systems have been evolved in vitro
See http://www.pnas.org/content/99/20/12733.abstract and http://www.pnas.org/content/91/13/6093.full.pdf

Replication ----> more copies ----> mutation ------> new functions ------> selection ------> diversification.

And since when did computers become self replicating, mutable entities subjected to natural stochastic variation?

They aren't and it's irrelevant. Even if they were made to be self-replicating, they would still be designed.[/quote]

As I think I already explained, it is very relevant, since evolution is predicated on inheritance.

Better reproduction, that is it. Anything that increases reproducibility will result in a trait being selected for, however, a large part of evolution is also fundamentally predicated on genetic drift, which is not under any fitness pressure.

So, now you tell me, is the fitness function of nature well suited for production of new biological functions?[/quote]

Yes, for instance the emergence of drug resistance in cancer, or the de novo origination of antifreeze glycoproteins in fish, or the evolution of novel enzymes like nylonase. I would say it is excellently suitable.

And you have a citation to support this viewpoint?

It was a more of a logical deduction and a common sense notion. Anything that is not directed by an intelligent agent is either produced by chance or necessity.[/quote]

I'll give you a bit of logic, for processes to be explanatory, the entities involved must exist first.

The first paper, computationally, carries out a survey of the RNA mutational space and explains that functions stem from secondary structure, notably hairpin loops, which is especially notable, which of course is the case with ribozymes in general, and secondary structures are a function of base pairing.

RNA forms ----------------> RNA folds due to base pairing , just like proteins fold due to chemical bonding and chemical interactions such as hydrophobicity and hydrogen bonding et cetera, this folding allows RNA to function, biological functionality is also a function of the laws of physics and chemistry.

I agree. How does that explain how natural selection acting upon random mutations produced all the diversity of life we see today? Obviously it does not.[/quote]

Since life is an extension of chemistry, it does it rather well, you may find it very convenient to shove that argument from incredulity back up where it came from.

New fish?

Царь Славян wrote:

No, simply being general as possible does not convey adequate coverage.

If you want to be as general as possible then yes it does.

I do not want to be as general as possible.

Natural snowflakes and artificial snowflakes (http://pubs.acs.org/doi/abs/10.1021/ed007p1682.1) are functionally equivalent, therefore the analogy of having a twerp sitting in the clouds tweaking a laboratory setup is a valid analogy, therefore there is indeed a clown who produces snowflakes in the clouds above, yeah right

No, since we have the knowledge of how snowflakes can form by natural means. We do not know how computers form by natural means. Oh, and snowflakes have zero FSC.

And we have knowledge of how novel functionality can evolve by natural processes.

Said noise doesn't happen during transmission but before it, and therefore Shannon information which is defined as a function of actual transmission of signals doesn't happen, that is it. Noise acts DURING transmission in Shannon information.

Well, you do know that random mutations can also happen during replication, right? Radiation has been known to be mutagenic.

It still is not transmitted until after replication is completed, when telophase occurs and your receiver (the daughter cell) is produced, still cannot apply Shannon information.

See above, the point is not whether it could be considered noisy. The point is that even if one were to treat it as noise, it wouldn't fall under the remit of Shannon information theory.

See above. Noise can be introduced while the DNA strand is being copied.[/quote]

See above.

What you do not realize is that you can have natural processes introducing variation and then interactions with the environment altering which copies survive in the face of competition for resources in the case of biological organisms. The evolvability of organisms through natural mutagenic and selective processes means that the requirements for extraneous design do NOT apply to organisms as they do to computers. As far as functional equivalence is concerned look at the snowflakes counter.

Actually it does apply, since the information had to be inputed in some way from the start. If there is no self replicating mechanism that can translate the code, then there is no evolution. And no, snowflakes are not functional.[/quote]

Random variation in space ----> Some configurations are functional -----> no prior input required.

And in nature the fitness function is naturally imposed, think predation, reaction rates, competition for food, metabolic efficiency, disease, immunity. The number of selection pressures can be as high as the number of interactions possible with the environment, the natural fitness space is very high.

That's true. But in the lab, the scientists directed the outcome to a specific goal. Is there a goal to the fitness function in nature? Is the goal the evolution of new biological functions?

NS doesn't have goals, what it does is have an influence on how allele frequencies change. To ask what the goal of NS is is to beg the question? What is the goal of gravity? or nuclear fission? Evolution is just a large subset of chemistry.

What it does is that the functional complexity for coding for an amino acid can result from the natural processes of mutation, something which your erroneous interpretation of Abel's work (which was more about prebiotic settings than extant organisms, and even then based on science that has moved on) asserted cannot do.

I'm sorry but you never showed such a thing actually happening. What you showed is intelligent agents, the scientists, producing new FSC, not nature itself.[/quote]

Nonsense, picking up a card combination from a lot does not mean that the combination was produced by the one who picked it up, care to learn this elementary distinction anytime soon? Replicating natural processes in the lab (with just the selection pressure being different) does not constitute intelligent input.

From a random sequence, for the evolution of FSC that enabled a virus to gain steadily infectivity, with the fitness pressure being the naturally occuring one of differential reproduction you may want to read Hayashi et al (http://www.plosone.org/article/info:doi ... ne.0000096) or Cheng et al (http://www.nature.com/nature/journal/v4 ... 443a0.html) for novel functionality being gained.

Organisms without antibiotic resistance in the presence of antibiotics will go kaput, can you show me where intelligence is involved here? Limp animals that cannot run away because of developmental deformities brought about by stochastic mutation may get eaten by predators, where is your intelligent agent here? or organisms which can synthesize some of their own metabolites can free themselves from environmental constraints and reproduce better, where is your agent there?

Mutants interact with the environment differently while striving to reproduce in a setting of limited resources, this results in differential survival of said mutants, thus fixing mutants and allowing further mutations to act on extant pools because they still exist, where is your intelligent agent there?

Those are all pre-existing functions that have to be accounted for. Just like in the computer. A computer can render a movie all by itself. A person does not have to move every single bit every step of the way. But the point is that that functionality of the computer was designed in the first place.

Computers cannot mutate or reproduce, your analogy still is a bucketload of fail.

It is always hilarious when people "infer" entities that have not been shown to exist or offer any evidence at all.Can you demonstrate that there is clear, substantive evidence for design and devise a method to differentiate between natural and designed entities without producing evidence of the design process per se?

I'm sure you know Dembski's notion of Specified Complexity. It's a pattern that is easily describeable, yet hard to reproduce by chance. It is based on Fisher's notion of statistical hypothesis testing.

Will let Just A Theory deal with this.

Define microevolution, you are in for a literature based bombing run on this.

There are lot's of different definitions. For me it's the change in frequencies of alleles in a population.

That is evolution in general. Micro is within populations, macro is species and above, as defined in scientific parlance.

http://www.rationalskepticism.org/creat ... biogenesis

You may want to go through that thread where it has been demonstrated that information cannot be specified AND complex.

Edit 2 - A critique of Dembski's Specified Complexity also appeared in peer reviewed literature, and the paper can be downloaded here http://www.springerlink.com/content/a1l08u041t72m227/

The abstract follows

Abstract Intelligent design advocate William Dembski has introduced a measure
of information called “complex specified information”, or CSI. He claims that CSI is
a reliable marker of design by intelligent agents. He puts forth a “Law of Conservation
of Information” which states that chance and natural laws are incapable of generating
CSI. In particular, CSI cannot be generated by evolutionary computation. Dembski
asserts that CSI is present in intelligent causes and in the flagellum of Escherichia
coli, and concludes that neither have natural explanations. In this paper, we examine
Dembski’s claims, point out significant errors in his reasoning, and conclude that there
is no reason to accept his assertions.

Haha was just about to look for that link. Bet me to it ;D

It impacts FSC applied to evolution, yes, because the prebiotic template he uses didn't have any functions associated with modern cells which are under darwinian evolution.

Well, that would just mean that the first FSC had to come from somewhere in the first template.

Good, now known biochemical processes can produce novel configurations, different configurations can have different functions, while some do not, mutational processes produce new configurations and as a consequence new functions, whether that function is preserved or not is subject to selection pressures and processes. Evolution is perfectly capable of generating FSC.

Intelligent evolution yes, darwinian evolution no. Though I would have to say no, only to the extent that all life would be accounted for. Let's take a model of life on Earth as follows: population size 10^30, replication rate every 30 minutes, mutation rate 1000 bp per replication, average genome size 10^5, trials in about 4 billion years 10^13. So in total we would have about 10^42 trials for evolution. We convert thins to bits and we get is about 140 bits of FSC (fits). So reasonably, you can't expect nature to produce more than 140 bits of FSC.
And now let's take a look at some measurement of FSC in living organisms. A lot of them are over the bound of 140 bits, ranging up to 2146 bits. This can not be accounted for by evolution.

table

table

When did I say everything boils down to one equation? Is base pairing a result of natural laws? Substitution? Transversion? Transposon activity? Gene Duplication? Whole Genome Duplication? Heard of them? All known natural processes that can produce FSC by producing various configurations of DNA, and consequently a subset of functional configurations.

They are not producing anything. They are transmitting already existing information.
We can model natural laws as functions. Then we have a function f(x) = y. Any input, that is, any number for the x, there will always be an output y. And also for any output y, there will always be an input x. Nothing new is produced, there is only a transformation of an already existing input to the output.
If the equation is f(x) = x + 3. What else can the function produce but 5, if x = 2? Obviously noting. And also when we take the inverse of this function we get 5 – 2 = 3. Which means nothing new was generated in the process.

You want an equation? RM + NS

Derive some biological function from that. Just like you can do with a falling object. You have an altitude of 1 meter, and an object of 1 kg. If I tell you that I'll drop the object, you can use the equation v = s/t, and your knowledge of gravity, that is 9,81 m/s^2, to tell me exactly what and when the outcome is going to be. You can't do that with RM + NS. One is an equation, the other is not.

And those conditions happen to be, in this case, a prebiotic templating system, which is superfluous to requirements given some of the more recent study in the field.

The point is that FSC should be present, not the material.

This again is a strawman caricature that assumes genes and everything must pop into place spontaneously. All you need is configurations to arrive at self replication first, and self replicating systems have been evolved in vitro
See http://www.pnas.org/content/99/20/12733.abstract and http://www.pnas.org/content/91/13/6093.full.pdf

Replication ----> more copies ----> mutation ------> new functions ------> selection ------> diversification.

Yes, by intelligent agents. Has it happened in some other case?

As I think I already explained, it is very relevant, since evolution is predicated on inheritance.

I'm not talking about the evolution of computers. I'm saying that they were designed. And they have some specific features by which we can tell that. So do the biological systems. The fact that living organisms can change does not in any way imply they were not designed.

Yes, for instance the emergence of drug resistance in cancer, or the de novo origination of antifreeze glycoproteins in fish, or the evolution of novel enzymes like nylonase. I would say it is excellently suitable.

None of those have been shown to be over the bound of 140 bits of FSC, that is the first problem. The second problem is that all of those instances are either a gene expression or a reduction of FSC. Oh, an the nylonase has been already know to be a product of a transposon, and not a random mutaion.

I'll give you a bit of logic, for processes to be explanatory, the entities involved must exist first.

I agree, your point is?

Since life is an extension of chemistry, it does it rather well, you may find it very convenient to shove that argument from incredulity back up where it came from.

Life as an extension of chemistry is an assumption. Therefore I stand by my argument.

If I was intelligently created then there should be a barcode or 'made in Proxima 9' label on me somewhere, surely?

I do not want to be as general as possible.

Just a second ago you called life an extension of chemistry. It seems you do.

And we have knowledge of how novel functionality can evolve by natural processes.

If you mean intelligently evelove, then yes we certainly do.

It still is not transmitted until after replication is completed, when telophase occurs and your receiver (the daughter cell) is produced, still cannot apply Shannon information.

Why not?

Random variation in space ----> Some configurations are functional -----> no prior input required.

How does the first sequence come about?

NS doesn't have goals, what it does is have an influence on how allele frequencies change. To ask what the goal of NS is is to beg the question? What is the goal of gravity? or nuclear fission? Evolution is just a large subset of chemistry.

If that is so, you can't claim that nature's fitness function is well suited for producing new biological functions.

Nonsense, picking up a card combination from a lot does not mean that the combination was produced by the one who picked it up, care to learn this elementary distinction anytime soon? Replicating natural processes in the lab (with just the selection pressure being different) does not constitute intelligent input.

That is precisely what it is. Becasue the scientists are the ones that are inducing a new fitness function. They are not using the one that nature induces.

From a random sequence, for the evolution of FSC that enabled a virus to gain steadily infectivity, with the fitness pressure being the naturally occuring one of differential reproduction you may want to read Hayashi et al (http://www.plosone.org/article/info:doi ... ne.0000096) or Cheng et al (http://www.nature.com/nature/journal/v4 ... 443a0.html) for novel functionality being gained.

In the first paper the functionality is being lost not gained.
In the second paper, we are dealing with gene regulation not evolution of new genes. The information came from non-coding regions. It was already there from the start, it simply got up-regulated in colder waters.
http://www.eurekalert.org/pub_releases/ ... 033106.php

Computers cannot mutate or reproduce, your analogy still is a bucketload of fail.

I know they can't. They also don't have eyes, so what!? Nothing. Why you simply choose to pick this one function is beyond me. If a self replicating computer was produced, would that mean it was not designed? Obviously not. Again, try to follow me here. Replication is just one function of living organisms, as is sight or digestion, that you have to explain. You can't explain it by replication because that's circular logic. Computers also have various functions, they are explained as designed.

That is evolution in general. Micro is within populations, macro is species and above, as defined in scientific parlance.

That's the only thing I consider observed and tested.

http://www.rationalskepticism.org/creat ... biogenesis

You may want to go through that thread where it has been demonstrated that information cannot be specified AND complex.

Edit 2 - A critique of Dembski's Specified Complexity also appeared in peer reviewed literature, and the paper can be downloaded here link

The abstract follows

I'm not debating them, I'm debating you. Please provide relevant quotes as to why CSI fails.

Царь Славян wrote:Great paper. It clearly shows how people, ie. Intelligent agents, can manipulate the genetic code.

The code manipulated itself(mutations happened naturally, they weren't engineered), the mutants were selected by people. Please provide a rigorous, empirically verified reason for why nature could not select for this itself. Until you do this, the base assumtion that nature could select for this, is logically valid.

Царь Славян wrote:

GenesForLife wrote:In this case, they used mutant tRNAs to encode cysteine instead of isoleucine and methionine, they noted that the inclusion of cysteine instead of the other amino acids was not deleterious because of the nature of the amino acid.
But that is rather superfluous to requirements here, the important thing to note is that mutant tRNAs can cause different amino acids to be incorporated for the same codon on mRNA, they had therefore, by mutation and artificial selection, evolved a new codon assignment, in other words, they'd fundamentally changed the genetic code by evolution.

At this juncture I would also like to cite/present another paper, showing that such an approach is applicable to other amino acids too, in this case Tyrosine.

Again, a great paper, showing how scientist, ie. Intelligent agents can modify teh genetic code as they see fit.

Again, please provide a rigorous, empirically supported reason for why nature could not select for this function itself.

Царь Славян wrote:

GenesForLife wrote:The abstract and the full paper can be found here at http://uregina.ca/suhdaey/courses/04%20 ... 20coli.pdf

In this particular case, they chose to reconfigure a stop codon (UAG) into one that would code for Tyrosine.
I now move on to quote what in my opinion are the relevant (to this discussion) snippets of the paper.

What follows is an example of sheer scientific elegance in ensuring that the new modified code was orthogonal (i.e did not affect the translation of the native genetic code in E.coli) and building in selectability.

So, you are saying that they intelligently manipulated, that is, they intelligently selected the specific codons? Yes, I would have thought so. A pretty nice example of what intelligent agents can do.

No, you should have read the paper.
GenesForLife specifically said "[3] They subjected these to mutation and selection and evolved the new codon assignment, the method of selection they used follows below."

Please provide a rigorous, empirically validated reason for why nature could not select from naturally ocurring mutants itself.

Царь Славян wrote:

GenesForLife wrote:[1] The problem of orthogonality was solved by importing the tRNA that carries tyrosine and the coresponding aminoacyl tRNA synthetase pair from the bacterial species Methanococcus jannaschii

[2] This choice was made due to two primary reasons, one - the elements that the synthetase uses to identify the amino acid was different to the one the synthetase present in E.coli uses. In other words, the E.coli native synthetase would not recognize the tRNA from Methanococcus and two- that the said synthetase has minimal interactions with the anticodon loop, which means it could still recognize the tRNA for Tyrosine and attach the amino acid to it. Just to help you grasp the work being discussed you may refer to the diagram of tRNA below.
The anticodon arm binds to mRNA by complementary base pairing, in this case, they had to reconfigure said mRNA by altering the anticodon loop on the Tyrosine tRNA such that it bound to the amber codon on mRNA instead of the native codon for Tyrosine, and this is where the importance of the second reason becomes apparent.

[3] They subjected these to mutation and selection and evolved the new codon assignment, the method of selection they used follows below.

A perfect example of an intelligent agency producing the final design from it's starting idea. They wanted to produce the different populations with different allele frequencies, and for that they used their intelligent to select those individuals that were most fit.

Mutations happened on noone's command and by no intentional manipulation, ie. they were natural mutations. They simply happened and were selected. Once a-fucking-gain.
As nature does all the time. Mutations happen in nature all the time, and increased fitness is constantly, naturally selected, all the time. Please provide a rigorous, empirically supported reason for why you think this is not so.

Царь Славян wrote:

GenesForLife wrote:ug = (Mu)g = Micrograms, just thought I should make that clear.

Just expressing the mutant tRNA alone resulted in an extremely low treshold for survival in the presence of ampicillin, and this was no more than the survival if the amber mutation were not suppressed, in other words, the native synthetases from E.coli had no effect (no codon reconfiguration in other words)

Adding both the imported synthetase and the best mutant tRNA they selected from the library led to dose tolerance that was 36 times higher, in other words, reconfiguration successful, new codon assignment successfully evolved.

The paper then goes on to describe the incorporation of unnatural amino acids, but I'll let the discerning reader figure it out themselves

I also said I would illustrate how modifying the ribosome can change the genetic code. I will let Chin et al do the job.

The abstract follows...

Yes it did evolve. It was ntelligently evelved, which is a great example of intelligent design and what it can produce.

Which is an implicit admission that mutations generated functional changes that could easily be selected by increased fitness in nature. Please provide a rigorous, empirically supported reason for why you think this is not so.

Царь Славян wrote:

GenesForLife wrote:They developed new orthogonal ribosomes through mutations such that they read in fours instead of threes, firstly, and followed it up by adding two unnatural amino acids to the newly evolved quadruplet code using the new blank codons that were generated. They now have loads of codons to work with just by changing the nature of the code, and they are heralding a new era in synthetic biology where we can write stuff into the genome without affecting any of the native translation of the recipient cells.

The full paper is indeed available for this and I would encourage the discerning reader to read this, and the link is
http://ase.tufts.edu/chemistry/kumar/jc ... n_2010.pdf

Empirical demonstrations of the evolvability of the genetic code, without a mind directing said changes. Just mutation and selection. (the selection here was artificial because they were applying it with a specific purpose in mind, therefore they chose to determine which mutant genetic code would survive.

Excuse me but no, the mind was present all the time. The mind of the scientists that did the selection. They are the ones that were intelligently selecting/designing the outcome.

You are not excused because, fucking yes.
Nobody was fucking thinking mutations into place. Mutations just fucking happened, and people did the selection. Nature does the same all the time. Please provide a rigorous, empirically supported reason for why you think this is not so.

Царь Славян wrote:

GenesForLife wrote:we have seen evidence that

[1] Mutating the peptidyltransferase subunit of ribosomes as in the work of Chin et al leads to codons being read in fours instead of threes.
[2] Mutant tRNAs incorporate different amino acids even when the same codon assignment is maintained, by virtue of mutability of the chemistry of the interactions of the binding of amino acids with tRNA and their synthetase enzymes.
[3] Mutant tRNAs can incorporate an amino acid in response to another codon assignment.

I totally agree, and all of those eveidence was produced by intelligently selecting them.

No, they weren't "produced" by intelligence, they were selected. Nature selects for appropriate fitness all the time. Here scientisist just decided what was "fit" for survival. Mutations happened and were selected. You can drop your useless ID canard now because it's manifestly not applicable to the research revealed in those papers. In order for your ludicrous contention to be valid, the scientists would have had to intentionally physically manipulate the correct mutations into place at the correct positions in the genes.
They didn't. The mutations happened naturally, scientists just did the selecting part. Evolution took place, get over it. Or alternatively, please provide a rigorous, empirically supported reason for why you think this is not so.

Please play special attention to the "empirically supported" part of my requests. If you can't do so, the conclusion remains valid. That's how science works.

Царь Славян wrote:They are not producing anything. They are transmitting already existing information.

Bullshit. By definition a duplication followed by any type(substitution, deletion or insertion) of a single-base, point mutation, will have produced a reading-frame shift and if the resulting protein has any function at all, it is manifestly new information by any rigorous definition of information.

Царь Славян wrote:

It impacts FSC applied to evolution, yes, because the prebiotic template he uses didn't have any functions associated with modern cells which are under darwinian evolution.

Well, that would just mean that the first FSC had to come from somewhere in the first template.

Sequence space for self replicating entities.

Good, now known biochemical processes can produce novel configurations, different configurations can have different functions, while some do not, mutational processes produce new configurations and as a consequence new functions, whether that function is preserved or not is subject to selection pressures and processes. Evolution is perfectly capable of generating FSC.

Intelligent evolution yes, darwinian evolution no. Though I would have to say no, only to the extent that all life would be accounted for.

Nothing of any substance from proper peer reviewed literature to back this up, in other words, a good old ex-recto blind assertion.

Let's take a model of life on Earth as follows: population size 10^30, replication rate every 30 minutes, mutation rate 1000 bp per replication, average genome size 10^5, trials in about 4 billion years 10^13. So in total we would have about 10^42 trials for evolution. We convert thins to bits and we get is about 140 bits of FSC (fits). So reasonably, you can't expect nature to produce more than 140 bits of FSC.

Where do you draw your sources from? I need them to be backed up by citations, models that aren't in accord with the natural processes being tested are rejectable. What is the rationale for the parameters of your model.

Secondly, your mutation rate doesn't include anything other than point mutations, have you heard of gene duplications, whole genome duplications? If you have n bp, after following a whole genome duplication you get 2n bp. This alone renders your model nonsense. Throw in events of polyploidy and that number can be increased to further exponents.

And now let's take a look at some measurement of FSC in living organisms. A lot of them are over the bound of 140 bits, ranging up to 2146 bits. This can not be accounted for by evolution.

table

table

Care to post links properly? Dodgy inferences from dodgy models are dodgy, that is bleeding obvious. Care to try something else soon?

When did I say everything boils down to one equation? Is base pairing a result of natural laws? Substitution? Transversion? Transposon activity? Gene Duplication? Whole Genome Duplication? Heard of them? All known natural processes that can produce FSC by producing various configurations of DNA, and consequently a subset of functional configurations.

They are not producing anything. They are transmitting already existing information.

Manifest nonsense, as the Cheng paper will show, or the Hayashi paper.

We can model natural laws as functions. Then we have a function f(x) = y. Any input, that is, any number for the x, there will always be an output y. And also for any output y, there will always be an input x. Nothing new is produced, there is only a transformation of an already existing input to the output.

You are free to show that this is the case with evolution, starting with evolutionary dynamics, and where no information is produced, go on, I am all ears, as long as you use proper peer reviewed sources instead of numbers you pulled out of your arse.

If the equation is f(x) = x + 3. What else can the function produce but 5, if x = 2? Obviously noting. And also when we take the inverse of this function we get 5 – 2 = 3. Which means nothing new was generated in the process.

Very clever, that is a first order linear equation, for this retarded attempt to apply you must show that evolution follows first order linear equations.

You want an equation? RM + NS

Derive some biological function from that. Just like you can do with a falling object. You have an altitude of 1 meter, and an object of 1 kg. If I tell you that I'll drop the object, you can use the equation v = s/t, and your knowledge of gravity, that is 9,81 m/s^2, to tell me exactly what and when the outcome is going to be. You can't do that with RM + NS. One is an equation, the other is not.[/quote]

skip.

And those conditions happen to be, in this case, a prebiotic templating system, which is superfluous to requirements given some of the more recent study in the field.

The point is that FSC should be present, not the material.[/quote]

The material defines the FSC, what part of this do you not get?

This again is a strawman caricature that assumes genes and everything must pop into place spontaneously. All you need is configurations to arrive at self replication first, and self replicating systems have been evolved in vitro
See http://www.pnas.org/content/99/20/12733.abstract and http://www.pnas.org/content/91/13/6093.full.pdf

Replication ----> more copies ----> mutation ------> new functions ------> selection ------> diversification.

Yes, by intelligent agents. Has it happened in some other case?[/quote]

You are free to demonstrate where in some of the instances already quoted, including Cheng and Hayashi, the generation of FSC per se was intelligent. It would also help if you could present something of proper credibility instead of ex-recto obfuscatory nonsense you are pulling out of your orifices.

As I think I already explained, it is very relevant, since evolution is predicated on inheritance.

I'm not talking about the evolution of computers. I'm saying that they were designed. And they have some specific features by which we can tell that. So do the biological systems. The fact that living organisms can change does not in any way imply they were not designed.

No, but it permits a whole new class of naturally known phenomena to act on living things that do not act on computers, thus rendering computers a bad analogy.

Yes, for instance the emergence of drug resistance in cancer, or the de novo origination of antifreeze glycoproteins in fish, or the evolution of novel enzymes like nylonase. I would say it is excellently suitable.

None of those have been shown to be over the bound of 140 bits of FSC, that is the first problem. The second problem is that all of those instances are either a gene expression or a reduction of FSC. Oh, an the nylonase has been already know to be a product of a transposon, and not a random mutaion.[/quote]

Your estimation is flawed, firstly , secondly do you know that the integration of transposons is random? and I think you will find nylonase was a frameshift and not a transposon. Do check your sources first, rearrangement at a single base resulted in a new function being formed.

I'll give you a bit of logic, for processes to be explanatory, the entities involved must exist first.

I agree, your point is?[/quote]

Your postulated agents haven't been demonstrated, that is the point.

Since life is an extension of chemistry, it does it rather well, you may find it very convenient to shove that argument from incredulity back up where it came from.

Life as an extension of chemistry is an assumption. Therefore I stand by my argument.

Parroting canards ad nauseam doesn't make them facts, biology per se is studied through biochemical entities and the interactions thereof with the chemistry of the abiotic component of the environment, and this fundamentally underpins all of biochemistry today.

The code manipulated itself(mutations happened naturally, they weren't engineered), the mutants were selected by people. Please provide a rigorous, empirically verified reason for why nature could not select for this itself. Until you do this, the base assumtion that nature could select for this, is logically valid.

Nature can also select, but the question is, what can it produce while selecting. The whole diversity of life we see today? Nope, unreasonable. The probability is just too low. Nature could account for about 140 fits as explained before.

Again, please provide a rigorous, empirically supported reason for why nature could not select for this function itself.

Becasue it's not reasonable. Please explain why chance in a form of randomly coliding air molecules is not a reasonable explanation for self-combustion of buildings. Becasue the probability is too low.

No, you should have read the paper.
GenesForLife specifically said "[3] They subjected these to mutation and selection and evolved the new codon assignment, the method of selection they used follows below."

Which is?

Please provide a rigorous, empirically validated reason for why nature could not select from naturally ocurring mutants itself.

It can, who said that it can't?

Mutations happened on noone's command and by no intentional manipulation, ie. they were natural mutations. They simply happened and were selected. Once a-fucking-gain.
As nature does all the time. Mutations happen in nature all the time, and increased fitness is constantly, naturally selected, all the time. Please provide a rigorous, empirically supported reason for why you think this is not so.

I never said otherwise, I said that it can happen.

Which is an implicit admission that mutations generated functional changes that could easily be selected by increased fitness in nature. Please provide a rigorous, empirically supported reason for why you think this is not so.

Why should I when I never claimed otherwise?

You are not excused because, fucking yes.
Nobody was fucking thinking mutations into place. Mutations just fucking happened, and people did the selection. Nature does the same all the time. Please provide a rigorous, empirically supported reason for why you think this is not so.

But I'm not talking about mutations. They are random. The detail and the main point to grasp is the selection. That is where the intelligent input is occuring.

No, they weren't "produced" by intelligence, they were selected.

Who did the selecting? Human intelligence or nature? It was intelligence, so yes they were produced by an intelligence.

Nature selects for appropriate fitness all the time. Here scientisist just decided what was "fit" for survival. Mutations happened and were selected. You can drop your useless ID canard now because it's manifestly not applicable to the research revealed in those papers. In order for your ludicrous contention to be valid, the scientists would have had to intentionally physically manipulate the correct mutations into place at the correct positions in the genes.

False. It's applicable, becasue mutations is not where intellignet input takes place, it's the selection.

They didn't. The mutations happened naturally, scientists just did the selecting part. Evolution took place, get over it. Or alternatively, please provide a rigorous, empirically supported reason for why you think this is not so.

Please play special attention to the "empirically supported" part of my requests. If you can't do so, the conclusion remains valid. That's how science works.

The empirical support is in the articles themselves. The scientists are inputing information for selecting the right sequences.