Saturday, June 10, 2006

Reliable Recognition of Intelligent Agency.

Which of the following propositions do you agree with?

1. Human intelligent agency is a distinct type of causation which can be recognised and is recognised successfully as an integral part of our normal lives. The evidence left from some human acts is indistinguishable from other animals. The evidence left from other human acts is distinguishable from all other known animal activity. eg writing books and using a complex language.

2. Human intelligent causation can be recognised as having occured even in situations where we know nothing about the individual agents concerned. We believe in their existence solely on the basis of the recognition of human like intelligent causation.

3. Human intelligent causation is currently our only physical model for the whole field of intelligent causation...we have no other material intelligent agents to study yet.

4. It is possible to concieve of other different intelligent agents from ourselves. It is not impossible that such beings may exist.

5. It is legitimate to use human intelligent causation as a model for the whole field of possible intelligent causation-
(a) from different time periods
(b) from different planets.
(c) from other non-material/hyper material intelligent agents.

6. It is possible to come to a correct conclusion of intelligent causation when examining
(a) the universe as a whole
(b) particular instances of intelligent design e.g. a living cell or a flagellum.

32 Comments:

Anonymous Anonymous said...

1) Agree, subject to caveat over false positives and false negatives, leading in turn to a caveat over "distinct".

2) Disagree. The fact that the individual agents are human gives us considerable context as far as what they are capable of, and what their motives might be. Lacking this information, I don't believe that a conclusion of "human causation" is permissable.

3) Agree.

4) Agree.

5) Agree with strong caveats, that the farther the postulated intelligence is from "human", the less relevant our information on human intelligence is, so the more tentative our inference of non-human intelligence must be.

6) Disagree. The postulated examples of design are so far from human intelligence that such an inference, from what is known about human intelligence, is completely unreasonable. Such an inference would require first constructing a model of the intelligence that you were attempting to infer, including (for example) its motives and what the limits were on its capabilities.

An inscrutable, omnipotent intelligence is capable of anything, so to hypothesise one therefore explains nothing (as any conceivable observation would be consistent with such an intelligence).

12:06 pm  
Blogger Lifewish said...

1) Broadly agree, although I'd strongly emphasise the "known" in "The evidence left from other human acts is distinguishable from all other known [...] activity", and would probably disagree with you as to precisely what acts fall into this category.

2) Broadly agree, but I'd rephrase this as "the conjecture that humans were responsible for something can be useful even with comparatively little information about the humans in question". It's the phrase "know nothing" that's bothering me - if we know they're humans then we automatically know something about them.

3) Depends on your definition of intelligence.

4) Agree

5) Broadly disagree. There are two main elements that we look for when deducing that something was produced by a given group of humans: function and cultural references. So, for example, if we find a chipped flint we might note that it's sharp and that it bears the marks of a certain style of knapping.

The problem is that functionality is essentially an objective quality, so it's perfectly possible for unintelligent processes to produce it. That means that, when we're trying to deduce intelligent design in the situations where those processes operate (for example if the objects in question can reproduce), we're effectively limited to cultural references*. Which wouldn't tend to be recognisable when coming from a nonhuman intelligence.

6) Not in the case of the universe as a whole because we don't know enough about its context (how many universes are there, what proportion of different environments can life survive in, etc). In the case of living organisms it's technically possible, but only with knowledge of the cultural markers associated with the designer in question.

* For example, in the case of recognising that humans have genetically modified a given plant, we don't look at the survival effectiveness of the plant; we look for examples of the specific modifications that humans have made to plants - the cultural references.

1:28 pm  
Blogger William Bradford said...

Anonymous wrote:

6) Disagree. The postulated examples of design are so far from human intelligence that such an inference, from what is known about human intelligence, is completely unreasonable. Such an inference would require first constructing a model of the intelligence that you were attempting to infer, including (for example) its motives and what the limits were on its capabilities.

Why should advanced intelligence not have detectable properties not dependent on the nature of the intelligent source? Common properties of similar entities can be intelligently inferred through inductive reasoning and recognized deductively. This type of approach is common in science. Why would an expression revealing analytical or abstract thought not be considered a sign of intelligence even if a source is unidentified?

5:54 am  
Blogger Lifewish said...

Anonymous hasn't responded here, so I'll take up the slack :)

Why should advanced intelligence not have detectable properties not dependent on the nature of the intelligent source?

Why should intelligence possess such properties? The only reasons I can see relate to the efficiency of certain approaches. This has two problems:

1) as I mentioned before, efficiency is an objective quality and hence there's no intrinsic barrier to its production by objective (unintelligent) processes.

2) efficiency is only required when resources are limited, which becomes less of an issue as one's technology advances. Consider, for example, the gradual bloating of MS Windows :)

Common properties of similar entities can be intelligently inferred through inductive reasoning and recognized deductively.

Except that our sample size is very limited - we only really have one intelligence to examine. Attempting to make an inference based on that is therefore going to run into more or less unavoidable difficulties due to lack of data.

This type of approach is common in science. Why would an expression revealing analytical or abstract thought not be considered a sign of intelligence even if a source is unidentified?

Well, firstly you'd have to come up with a rigorous test for "analytical or abstract thought". Then you'd have to check that there could be no false positives (this would presumably be accomplished by mathematical means). Then you'd have to have your work carefully peer-reviewed to ensure that you hadn't made any daft mistakes.

Currently Dembski has only completed the first two steps. Given his stated views on peer review (i.e. it's not as lucrative as publishing books), and the views of other mathematicians on his work (written in jello), I hold out no hope for step 3 being completed any time soon. I'm not aware of anyone else attempting to take this approach.

12:21 pm  
Blogger Lifewish said...

I forgot to mention that the "rigorous test" of CSI is one that to the best of my knowledge only Dembski has rigorously applied. IIRC, no-one else can figure out how he's selecting such key components as the specification.

If anyone wishes to prove me wrong on this point, may I ask that they do so by performing a rigorous design test so that I can confirm that it doesn't require arbitrary decisions? Then I'll go away and check that the output of (say) genetic algorithms can't exhibit the same property.

5:23 pm  
Blogger William Bradford said...

My comments in italics.

Why should advanced intelligence not have detectable properties not dependent on the nature of the intelligent source?

Why should intelligence possess such properties? The only reasons I can see relate to the efficiency of certain approaches.

Then let me suggest another. Intelligence is detectable in the very nature of this exchange. It is possible to generate the alphanumeric symbols through a source unfamilar with English language encoding conventions but the result will be nonsense. Pets, inanimate objects and toddlers all have key compression capacity. They lack a capacity to generate intelligible messages. A biological counterpart is nucleic acids whose biological utility is a function of their sequential order. Rearranging the codon order of a functional DNA molecule will negate its function without changing its chemical nature. Function is not dependent on chemical identity which is the same for both functional and non-functional nucleic acids. It is related to their selective value; problematic in generating an initial genome, in the absence of intelligence, on prebiotic earth.

Common properties of similar entities can be intelligently inferred through inductive reasoning and recognized deductively.

Except that our sample size is very limited - we only really have one intelligence to examine. Attempting to make an inference based on that is therefore going to run into more or less unavoidable difficulties due to lack of data.

We have a broad array of intelligent capacity and examples of its expression upon which inferences can and have been made. Our sample size of genetic information carriers known to biology is limited to nucleic acids. Not a problem. You analyse what is before you.

This type of approach is common in science. Why would an expression revealing analytical or abstract thought not be considered a sign of intelligence even if a source is unidentified?

Well, firstly you'd have to come up with a rigorous test for "analytical or abstract thought". Then you'd have to check that there could be no false positives (this would presumably be accomplished by mathematical means).

The test entails the capacity of an unguided natural force to generate the sequential order of symbols in conformity with the code at hand to express either this message or the gene expression required of a functional genome.

6:20 pm  
Anonymous Anonymous said...

Sorry, this blog has been moribund, so I'd ceased browsing it, and so missed a response to my own comment here.

"Why should advanced intelligence not have detectable properties not dependent on the nature of the intelligent source?"

There is no reason, in principle, that they shouldn't. However, in arguing that they had any particular detectable property in common, you would first need to show why their shared intelligence would of necessity lead to this commonality. But while such a commonality is conceivable, until such a commonality has been hypothesised and substantiated, there is no reason to believe that such a commonality even exists.

"Common properties of similar entities can be intelligently inferred through inductive reasoning and recognized deductively."

Only if they are sufficiently similar. I would argue that similarity to a intelligence capable of 6(b) would be a bit of a stretch, and 6(a) quite simply incomprehensibly dissimilar (even assuming that said commonalities had been substantiated).

"Why would an expression revealing analytical or abstract thought not be considered a sign of intelligence even if a source is unidentified?"

How should a universe or a flagellum be considered as revealing "analytical or abstract thought"?

Given the hard-wired human instinct to find patterns, even extending to situations when such patterns don't exist, there should always be a wariness of false positives.

6:48 pm  
Blogger Lifewish said...

Intelligence is detectable in the very nature of this exchange.

Only because we have extra knowledge of the behaviour of specific intelligent entities. This is a classic example of the sort of cultural indicators I was talking about earlier.

Consider the case where we have no cultural knowledge - no knowledge of the language that two entities were speaking in. We don't even know whether it is a language - it might just be random static. How would we determine whether what we were looking at was indeed a product of intelligence?

The only way I can think of (please tell me if you're aware of any others) is to hypothesise that the signals are indeed a language and assess how effective they appear to be. For example, you could see whether the ability to communicate improved the entities' survival chances.

However, this reduces the situation to an efficiency question, and it's demonstrable that languages of this sort can actually evolve.

Function is not dependent on chemical identity which is the same for both functional and non-functional nucleic acids. It is related to their selective value; problematic in generating an initial genome, in the absence of intelligence, on prebiotic earth.

An initial genome would not have sprung fully-formed as from the head of Zeus; it would have been the result of evolution acting on populations of RNA. Unlike DNA, RNA can both reproduce and catalyse organic reactions. Originally, there would probably have been only one uber-RNA strand per "organism", but RNA breaks down much more easily than DNA so it would have had a stronger incentive to form mutually-supporting communities.

Eventually, the RNA communities would have "worked out" (excuse the teleologism) how to encode themselves in DNA form. Over the following billions of years, the less-specialised middleman would have been gradually cut out, leaving us with the current situation where RNA generally takes a back seat to DNA and proteins.

Et voila! A means by which the modern genome can arise without hitting significant chicken/egg issues.

The problem with learning about this sort of stuff has nothing to do with any fundamental conceptual problems; rather, it's due to the fact that the original RNA world was written out of the biological picture in a way that would make Stalin proud. We're still learning new things about the abilities of these molecules, and occasionally another piece of the puzzle falls into our laps. It's a slow task, made easier by tools such as in vitro evolution.

We have a broad array of intelligent capacity and examples of its expression upon which inferences can and have been made.

But they're all linked by common features unique to homo sapiens, and usually to specific cultures, that wouldn't necessarily hold for other intelligences.

Our sample size of genetic information carriers known to biology is limited to nucleic acids. Not a problem. You analyse what is before you.

Except that biologists don't attempt to generalise their results to cover all forms of life that could plausibly exist. ID, on the other hand, attempts to provide a general framework for differentiating the output of unintelligent and intelligent processes regardless of the actual details of those processes.

In those circumstances, lack of data does become an issue; even if Dembski's work is broadly accurate (which I consider unlikely), there could still be boundary cases where it breaks down.

The test entails the capacity of an unguided natural force to generate the sequential order of symbols in conformity with the code at hand to express either this message or the gene expression required of a functional genome.

OK, so how do you ensure that this isn't the case? Wouldn't such a test require enumeration of every unguided natural force in the universe?

7:09 pm  
Blogger William Bradford said...

Intelligence is detectable in the very nature of this exchange.

Only because we have extra knowledge of the behaviour of specific intelligent entities. This is a classic example of the sort of cultural indicators I was talking about earlier.

It is precisely this knowledge that enables us to rule out the possibility that an unintelligent source like a falling object or a pet walking across a keyboard generated the observed result. Natural unintelligent sources can be ruled out by the nature of the effect.

Consider the case where we have no cultural knowledge - no knowledge of the language that two entities were speaking in. We don't even know whether it is a language - it might just be random static. How would we determine whether what we were looking at was indeed a product of intelligence?

The only way I can think of (please tell me if you're aware of any others) is to hypothesise that the signals are indeed a language and assess how effective they appear to be. For example, you could see whether the ability to communicate improved the entities' survival chances.

Nice try at a selection paradigm. In assessing intelligence in signals one must consider the possibility that a natural force generated the signals. Consideration also requires the possibility that a natural (unintelligeent) source would be ruled out as an option. An encoded signal would be one whose symbolic sequences are not determined by a force of nature. If the next symbol in a sequence can be predicted based on it being an effect of a force of nature then one can rule out intelligence as a cause. Conversely if the sequential order of symbols is not predetermined by a force of nature, as is the case with this message, then one must look to either a random event or an intelligent source.

However, this reduces the situation to an efficiency question, and it's demonstrable that languages of this sort can actually evolve.

Efficiency is not the indicator of intelligence.

Function is not dependent on chemical identity which is the same for both functional and non-functional nucleic acids. It is related to their selective value; problematic in generating an initial genome, in the absence of intelligence, on prebiotic earth.


An initial genome would not have sprung fully-formed as from the head of Zeus; it would have been the result of evolution acting on populations of RNA.

That's easy to assert but meaningless in the absence of specification as to what the selection criteria is for a "population of RNA."

Unlike DNA, RNA can both reproduce and catalyse organic reactions.

Catalysis of RNA by RNA is likewise meaningless in an extra-cellular environment unless, as a minimal requirement, there is specification of a cause whose end result is a sequence specification having a biological encoding function and a means to express it.

Originally, there would probably have been only one uber-RNA strand per "organism", but RNA breaks down much more easily than DNA so it would have had a stronger incentive to form mutually-supporting communities.

What is the scientific basis for postulating the existence of an "organism"? What causes incentive?

Eventually, the RNA communities would have "worked out" (excuse the teleologism) how to encode themselves in DNA form.

Teleology is inevitable once you decide biological data requires a problem to accomodate a selection paradigm

Over the following billions of years, the less-specialised middleman would have been gradually cut out, leaving us with the current situation where RNA generally takes a back seat to DNA and proteins.

I'm familiar with the approach but this is so vague as to appeal only to those with a prior conviction that life must have somehow arisen.

Et voila! A means by which the modern genome can arise without hitting significant chicken/egg issues.

None of this addresses a generating cause for the nucleic acid property that is essential to a functional genome- sequential order and a genetic code enabling function.

The problem with learning about this sort of stuff has nothing to do with any fundamental conceptual problems; rather, it's due to the fact that the original RNA world was written out of the biological picture in a way that would make Stalin proud. We're still learning new things about the abilities of these molecules, and occasionally another piece of the puzzle falls into our laps. It's a slow task, made easier by tools such as in vitro evolution.

We're learning that function is not conferred by a stochastic process associated with the polymerization of nucleotides outside a cellular environment.

We have a broad array of intelligent capacity and examples of its expression upon which inferences can and have been made.

But they're all linked by common features unique to homo sapiens, and usually to specific cultures, that wouldn't necessarily hold for other intelligences.

Signals not generated solely as a consequence of a natural force result from intelligent input. The nature of the intelligence is a secondary issue.

Our sample size of genetic information carriers known to biology is limited to nucleic acids. Not a problem. You analyse what is before you.


Except that biologists don't attempt to generalise their results to cover all forms of life that could plausibly exist.

Of course they do. All life forms yield to particular biochemical generalizations namely, having nucleic acids and proteins whose function is linked to the sequential order of their base polymers.

ID, on the other hand, attempts to provide a general framework for differentiating the output of unintelligent and intelligent processes regardless of the actual details of those processes.

Untrue. Details are everything.

In those circumstances, lack of data does become an issue; even if Dembski's work is broadly accurate (which I consider unlikely), there could still be boundary cases where it breaks down.

Boundary issues are ubiquitous in biology.

The test entails the capacity of an unguided natural force to generate the sequential order of symbols in conformity with the code at hand to express either this message or the gene expression required of a functional genome.


OK, so how do you ensure that this isn't the case? Wouldn't such a test require enumeration of every unguided natural force in the universe?

It requires the evaluation of those forces connected with object of study. They would be those affecting reactions of organic and biochemical compounds.

1:39 am  
Blogger William Bradford said...

"Why should advanced intelligence not have detectable properties not dependent on the nature of the intelligent source?"

There is no reason, in principle, that they shouldn't. However, in arguing that they had any particular detectable property in common, you would first need to show why their shared intelligence would of necessity lead to this commonality. But while such a commonality is conceivable, until such a commonality has been hypothesised and substantiated, there is no reason to believe that such a commonality even exists.

As long as the following substitution also requires substantiation I have no problem with this line of reasoning:

But while abiogenesis is conceivable, until it has been substantiated, there is no reason to believe that it even occured.

"Why would an expression revealing analytical or abstract thought not be considered a sign of intelligence even if a source is unidentified?"


How should a universe or a flagellum be considered as revealing "analytical or abstract thought"?

The process by which the object in question was generated can be revealing. I'll let others make an argument for the universe if so inclined as I'm more at home with biochemistry and cellular biology. The process by which an initial functional genome was generated is better explained by an intelligent inference. The chemical nature of functional nucleic acids and non-functional nucleic acids is the same. The nitrogenous bases may vary but it is the sequential order of codons and their constituent nucleotides along with an encoding convention expressed through proteins and RNA, themselves the product of the very encoded DNA whose translation they enable, that provide evidence an intelligent source.

3:02 am  
Anonymous Anonymous said...

"But while abiogenesis is conceivable, until it has been substantiated, there is no reason to believe that it even occured."

Firstly, the Theory of Evolution neither contains Abiogenesis, nor does it require that Abiogenesis occured. Evolution (a fact) via the mechanisms of the Modern Evolutionary Synhthesis (a theory to explain this fact) could have occured whether the first reproducing primitive lifeforms came into existence due to Abiogenesis, infestation via a comet, deliberate seeding by small furry things from Alpha Centauri, or supernatural creation by the Flying Spaghetti Monster.

Secondly Abiogenesis, although itself highly speculative, simply happens to be the best substantiated scientific explanation of how it all started. While substantiation of it is tenuous, that substantiation could by no means be claimed to be non-existent.

"The nitrogenous bases may vary but it is the sequential order of codons and their constituent nucleotides along with an encoding convention expressed through proteins and RNA, themselves the product of the very encoded DNA whose translation they enable, that provide evidence an intelligent source."

Behind all the jargon, this appears to be the information=intelligence argument. At a conceptual level, I find it to be highly uncompelling (particularly given the wealth of research into areas of self-organisation). I lack the biochemical expertise to refute this particular instantiation of that argument, so will have to rely on the fact that the scientific consensus has found no version of the argument to be in the least bit substantiated.

7:05 am  
Blogger Lifewish said...

Before I respond, I'd note that the posts are getting longer and longer. As such, I'd recommend that Mr Bradford, should he respond, pick only the points he finds most interesting. I promise not to interpret that as my having won the other arguments.

It is precisely this knowledge that enables us to rule out the possibility that an unintelligent source like a falling object or a pet walking across a keyboard generated the observed result. Natural unintelligent sources can be ruled out by the nature of the effect.

OK, so if we find the complete works of Shakespeare encoded into an organism's DNA, we can reliably deduce that geneticists have a weird sense of humour. This doesn't appear to tell us much about general approaches to detecting intelligent action.

If the next symbol in a sequence can be predicted based on it being an effect of a force of nature then one can rule out intelligence as a cause.

But this brings us back to an approach involving comparison of specific hypotheses, rather than rarefied inferences. Which rather undermines the central idea of ID.

Efficiency is not the indicator of intelligence.

That's precisely my point. Efficiency merely indicates the presence of some kind of optimising processes. Cultural indicators are limited by our knowledge of a designer's culture. What other approaches to detecting intelligence are there?

That's easy to assert but meaningless in the absence of specification as to what the selection criteria is for a "population of RNA."

The same as the selection criterion for a population of cells (such as ourselves): the ability to replicate the entire group. This is precisely why things like cell membranes would have been necessary - a specialised community has to be transplanted en masse rather than just casting itself into the ocean and hoping to land somewhere nutrient-rich.

Hope I understood your comment correctly.

Catalysis of RNA by RNA is likewise meaningless in an extra-cellular environment unless, as a minimal requirement, there is specification of a cause whose end result is a sequence specification having a biological encoding function and a means to express it.

I'm sorry, I honestly have no idea what you mean here. Any chance you could clarify? Are you talking about the difficulties of setting up DNA-to-protein translation apparatus or something like that?

What is the scientific basis for postulating the existence of an "organism"? What causes incentive?

A clarification: I was using the word "organism" to describe the minimal self-replicating population. So, once specialisation had started to occur, the "organism" would become the community rather than the individual RNA molecule. IIRC, it's not particularly implausible for an ocean full of RNA bases to throw up a few self-replicators if left for long enough, so the creation of the initial "organism" (a single self-replicating strand) wouldn't be a problem.

I'm not sure what you mean by "incentive" here. The strands that were able to self-replicate most effectively would become predominant. This ability would be affected by factors including length, stability, efficiency and, most interestingly, ability to manipulate the environment. Even a fairly poor replicator can prosper if it can transform any pool it finds into a haven of useful proteins.

Teleology is inevitable once you decide biological data requires a problem to accomodate a selection paradigm.

Teleology is inevitable once you attempt to describe evolutionary concepts in the language of a culture that hadn't even been introduced to the concept until 150 years ago.

I'm familiar with the approach but this is so vague as to appeal only to those with a prior conviction that life must have somehow arisen.

However, even this sketchy hypothesis provides plausible explanations for a number of puzzling phenomena such as RNA-based viruses. It also provides us with a starting point for further investigation - for example by using in vitro evolution to investigate the plausibility of the intermediate steps and to fill in more detail.

If you can come up with an hypothesis that fits the facts more closely or has more predictive power, I'll happily listen to it, regardless of the number of supernatural entities it incorporates. The last I heard on this front, however, was "it's not ID's task to match your pathetic level of detail in telling mechanistic stories" (Dembski, 2002), which was somewhat disheartening.

None of this addresses a generating cause for the nucleic acid property that is essential to a functional genome- sequential order and a genetic code enabling function.

It certainly explains the sequential order (by which I assume you mean the existence of useful genes) - the DNA would be a direct copy of pre-existing RNA chains, which would by that point only exist if they could replicate (otherwise they'd have been broken down for spare parts by their fast-evolving neighbours).

I don't have a clue what you mean by a "genetic code enabling function".

We're learning that function is not conferred by a stochastic process associated with the polymerization of nucleotides outside a cellular environment.

Speak for yourself. I'm learning that replicators placed under selective pressure can do very cool things. As long as the replicators and the pressure exists, the exact environment is relatively irrelevant.

I'm happy to back this up with lots of genetic algorithm theory, if desired. Are you able to back up your statement?

Signals not generated solely as a consequence of a natural force result from intelligent input. The nature of the intelligence is a secondary issue.

But you were talking about looking at different intelligences and searching for common properties. How can we know the common properties of intelligence without having a few to look at? More significantly, since you appear to be using an eliminative approach, how can we know whether a natural force can produce a given effect without the impossible task of enumerating all natural forces?

I'd say that we can't, and hence the only valid approach is comparison of concrete hypotheses.

Of course they do. All life forms yield to particular biochemical generalizations namely, having nucleic acids and proteins whose function is linked to the sequential order of their base polymers.

Only all known life forms. If biologists were to generalise that to all life forms then for a start the outcry from religions (most of which believe that at least one life form is spiritual rather than corporeal) would be earthshakingly loud.

[In response to my comment about ID being detail-independent] Untrue. Details are everything.

But I thought the entire point of ID was that you could validly say that an object was not created by natural forces without actually having to discuss detailed hypotheses about how it might have arisen naturally?

Boundary issues are ubiquitous in biology.

But if there are boundary issues in ID, how do we know the life on our planet isn't a result of one of them?

It requires the evaluation of those forces connected with object of study. They would be those affecting reactions of organic and biochemical compounds.

OK, but now we're into discussion of specific flaws in specific hypotheses. Which means that general pronouncements of "natural forces can't produce that kind of effect" will in general not be valid.

I'm not complaining; I think that this is by far the best approach. But it seems somewhat at odds with the work of Dembski et al. It also means that, if they wish to claim that they're not merely attacking evolution, IDers will need to present their own concrete, testable, preferably predictive hypothesis.

So far, ID has appeared to limit its efforts on this front to a generic statement that the Designer did it. Whilst obviously appealing to the religious community, this statement is almost completely worthless when it comes to actually explaining stuff.

4:32 pm  
Blogger William Bradford said...

Firstly, the Theory of Evolution neither contains Abiogenesis, nor does it require that Abiogenesis occured. Evolution (a fact) via the mechanisms of the Modern Evolutionary Synhthesis (a theory to explain this fact) could have occured whether the first reproducing primitive lifeforms came into existence due to Abiogenesis, infestation via a comet, deliberate seeding by small furry things from Alpha Centauri, or supernatural creation by the Flying Spaghetti Monster.

Which misses the point of an intelligent inference. ID is not confined to an evaluation of evolution. The inference is strongest at the point of life's origin.

Secondly Abiogenesis, although itself highly speculative, simply happens to be the best substantiated scientific explanation of how it all started. While substantiation of it is tenuous, that substantiation could by no means be claimed to be non-existent.

There is no substantiation of the belief that a replicating cell arises in a prebiotic environment; only evidence of monomers of biochemical compounds found under very limited conditions. That hardly qualifies as substantiation.

"The nitrogenous bases may vary but it is the sequential order of codons and their constituent nucleotides along with an encoding convention expressed through proteins and RNA, themselves the product of the very encoded DNA whose translation they enable, that provide evidence an intelligent source."

Behind all the jargon, this appears to be the information=intelligence argument. At a conceptual level, I find it to be highly uncompelling (particularly given the wealth of research into areas of self-organisation).

Behind all that jargon is an erroneous belief that "research into areas of self-organization" provides evidence that functional genomes arise.

I lack the biochemical expertise to refute this particular instantiation of that argument, so will have to rely on the fact that the scientific consensus has found no version of the argument to be in the least bit substantiated.

Small peptides have been found to form outside cellular environments. It is a fact that the sequential order of their amino acids shows no relation to functional protein encoding sequences but rather appears random. There is no empirical evidence that DNA forms in extra-cellular environments and no evidence of a natural force that would direct polymerization in sequentially useful pathways.

6:27 pm  
Blogger William Bradford said...

It is precisely this knowledge that enables us to rule out the possibility that an unintelligent source like a falling object or a pet walking across a keyboard generated the observed result. Natural unintelligent sources can be ruled out by the nature of the effect.

OK, so if we find the complete works of Shakespeare encoded into an organism's DNA, we can reliably deduce that geneticists have a weird sense of humour. This doesn't appear to tell us much about general approaches to detecting intelligent action.

It demonstrates confidence in your ability to distinguish between an intelligently formed symbolic message and a random sequence of nonsense. You have ruled out the possibility that one of the unintelligent sources I cited is a cause. This indicates a means of distinguishing intelligent input in sequences once the encoding convention is known. An analysis of the steps involved and an application of them to any system governed by an encoding convention specifies the approach.

If the next symbol in a sequence can be predicted based on it being an effect of a force of nature then one can rule out intelligence as a cause.


But this brings us back to an approach involving comparison of specific hypotheses, rather than rarefied inferences. Which rather undermines the central idea of ID.

Wrong. It indicates encoded systems require independence from strict determinism. If a natural force of nature determines a codon inevitability of UAG at specific defined locci in a gene sequence the flexibility required for amino acid protein sequencing is lost.

Efficiency is not the indicator of intelligence.


That's precisely my point. Efficiency merely indicates the presence of some kind of optimising processes. Cultural indicators are limited by our knowledge of a designer's culture. What other approaches to detecting intelligence are there?

Cultural indicators are irrelevant to determining the genetic encoding convention and the means by which it is expressed. One need only apply scientific methodology.

That's easy to assert but meaningless in the absence of specification as to what the selection criteria is for a "population of RNA."


The same as the selection criterion for a population of cells (such as ourselves): the ability to replicate the entire group.

A capacity for which has been assumed rather than empirically demonstrated.

This is precisely why things like cell membranes would have been necessary - a specialised community has to be transplanted en masse rather than just casting itself into the ocean and hoping to land somewhere nutrient-rich.

Hope I understood your comment correctly.

I understand the necessity of a cellular membrane but point out the need to empirically demonstrate the plausibility of it forming in an extra-cellular environment.

Catalysis of RNA by RNA is likewise meaningless in an extra-cellular environment unless, as a minimal requirement, there is specification of a cause whose end result is a sequence specification having a biological encoding function and a means to express it.


I'm sorry, I honestly have no idea what you mean here. Any chance you could clarify? Are you talking about the difficulties of setting up DNA-to-protein translation apparatus or something like that?

Nucleic acid function is sequence dependent. Even if one shows the possibility of formation outside a cell there must at the same time exist an encoding convention linking codons to specific amino acids and a mechanism to translate the code.

I'm familiar with the approach but this is so vague as to appeal only to those with a prior conviction that life must have somehow arisen.


However, even this sketchy hypothesis provides plausible explanations for a number of puzzling phenomena such as RNA-based viruses.

It does not. Even viruses with RNA genomes have genetically encoded genomes and proteins involved in the replication process. The sketchy hypothesis does not account for this.

None of this addresses a generating cause for the nucleic acid property that is essential to a functional genome- sequential order and a genetic code enabling function.


It certainly explains the sequential order (by which I assume you mean the existence of useful genes) - the DNA would be a direct copy of pre-existing RNA chains, which would by that point only exist if they could replicate (otherwise they'd have been broken down for spare parts by their fast-evolving neighbours).

You have not explained sequential order until you specify what sequences are selected and why.

I don't have a clue what you mean by a "genetic code enabling function".

Every cellular function is directly or indirectly dependent on expressed genes operating in conformity with a genetic code. No code; no function.

7:42 pm  
Blogger Lifewish said...

It demonstrates confidence in your ability to distinguish between an intelligently formed symbolic message and a random sequence of nonsense.

But only in the context of cultural indicators - the reason it's a strong argument for intelligent intervention is that these indicators, being essentially arbitrary, are no more likely to be generated than any other possible set of indicators, and hence coming up with the same set twice is implausible.

Once you start throwing in features (for example the presence of specialised RNA for transcription of the genetic code) that have an objectively measurable effect (for example an improvement in the organism's ability to replicate), that all goes out the window.

You have ruled out the possibility that one of the unintelligent sources I cited is a cause. This indicates a means of distinguishing intelligent input in sequences once the encoding convention is known.

A better description would be that I give greater credence to the hypothesis that the source was an English speaker than to any of the alternate hypotheses of which I'm aware. This is still an issue of comparison of concrete hypotheses, not an abstract inference.

This, of course, only works when I have sufficiently detailed knowledge of the behaviour of all the plausible sources. It certainly can't be made in a vacuum, as Dembski appears to claim.

Wrong. It indicates encoded systems require independence from strict determinism. If a natural force of nature determines a codon inevitability of UAG at specific defined locci in a gene sequence the flexibility required for amino acid protein sequencing is lost.

I'd agree that this conclusion can also be drawn. However, going back to your original point, we can only rule out intelligence in the way you describe if we know how the extant natural forces work. In practice, we'd never know if we'd missed one.

Cultural indicators are irrelevant to determining the genetic encoding convention and the means by which it is expressed. One need only apply scientific methodology.

Again, that's precisely my point. When we recognise a work of Shakespeare as being intelligently produced, it's because of cultural indicators. When we recognise, say, a new type of vehicle as being intelligently produced, it's because of its efficiency. Neither of these arguments apply in the case of the genome; there are no cultural indicators that we're aware of, and efficiency can be adequately generated by evolutionary processes.

So what other approaches to making rarefied design inferences are there?

[With regard to replication of RNA groups] A capacity for which has been assumed rather than empirically demonstrated.

To start with, the groups would be of size 1. The ability of single RNA strands to replicate has been demonstrated. The interdependence between different substrains of the population would presumably start with some RNA molecules either making use of or being aided by the byproducts of other strains. It would be easy for this to become reciprocal - if strain A is helping strains B and C to multiply then strain B will tend to do better than strain C if it helps strain A.

The more interdependences of this sort that a population could sustain, the faster it would replicate. However, the larger number of necessary components would mean that the ability of individual strains to spread to other locations would be curtailed.

This barrier could be overcome by introducing cells. It's actually very easy to form cell-like structures - lipid spheres actually form naturally. Probably the first true cells were formed by accident, when an RNA strain stumbled across a way to encourage such protocells to form.

I understand the necessity of a cellular membrane but point out the need to empirically demonstrate the plausibility of it forming in an extra-cellular environment.

See above.

Nucleic acid function is sequence dependent. Even if one shows the possibility of formation outside a cell there must at the same time exist an encoding convention linking codons to specific amino acids and a mechanism to translate the code.

I'll need to read up more to produce any sort of accurate response, but off the top of my head the process could have gone something like this:

1) Some RNA molecules are able to catalyse the formation of proteins. Some of these proteins would have allowed the RNA to reproduce more efficiently, and hence these RNA would have been selected for.

2) Other strains of RNA would have found the same proteins useful. Even if they couldn't produce the proteins themselves, they would have been under selective pressure to make the production easier. So, for example, they could drag useful amino acids about the place.

3) The replicators and their assistants would have coevolved. For example, if the assistants tended to grab different amino acids, the replicators would do better if they were capable of grabbing the assistant with the acid they needed rather than blindly searching for such an acid. That would prompt the assistants to specialise further.

That's enough to take us to a point where we have "ribosomes" with hardwired genetic information, plus tRNA. The next step is figuring how the two functions of the "ribosomes" would have become separated.

4) One of the strains of protoribosome, instead of producing its own hardwired protein, develops the ability to figure out what another protoribosome is doing and to join in. This is effective because by this point all surviving protoribosomes will be producing useful proteins. It adds to the survival chances of the protoribosome, too, because it means it can potentially be shorter (RNA is unstable so this is significant). Over time, this new strain of protoribosome takes over all protein production, and the other strains dwindle to become more like messenger RNA.

We're not far off having a modern RNA genome here, so I'll leave it at that unless there's anything else you want me to provide hypotheticals for, or if you think you can rigorously demonstrate that any of the steps in this hypothetical are implausible.

This explanation is probably grossly mistaken in all sorts of interesting ways, but it demonstrates the fashion in which evolutionary processes can produce things like genetic codes. It's still rather sketchy, but it already has tons more detail than any explanation the ID community has produced.

10:50 pm  
Blogger William Bradford said...

Bradford: It demonstrates confidence in your ability to distinguish between an intelligently formed symbolic message and a random sequence of nonsense.

But only in the context of cultural indicators - the reason it's a strong argument for intelligent intervention is that these indicators, being essentially arbitrary, are no more likely to be generated than any other possible set of indicators, and hence coming up with the same set twice is implausible.

Bradford: The reason the symbols are generated is they are the symbols needed to convey the encoded message. There is nothing arbitrary about the symbols in this message or the symbols found in functional genes. There are codons in genes that are repetitive because they convey messages and need to be located at exactly the needed locus to confer gene function. There is no means of explaining how an initial genome would acquire this type of precision in the absence of intelligent input.

Once you start throwing in features (for example the presence of specialised RNA for transcription of the genetic code) that have an objectively measurable effect (for example an improvement in the organism's ability to replicate), that all goes out the window.

Bradford: Your explanations postulate rather than elucidate how organisms come about. You are begging the question.

Bradford: You have ruled out the possibility that one of the unintelligent sources I cited is a cause. This indicates a means of distinguishing intelligent input in sequences once the encoding convention is known.

A better description would be that I give greater credence to the hypothesis that the source was an English speaker than to any of the alternate hypotheses of which I'm aware. This is still an issue of comparison of concrete hypotheses, not an abstract inference.

Bradford: Your belief is based on a knowledge that there exists a correlation between the symbols and the message. The correlation was intelligently created. We observe the same thing in genomes and you arbitrarily reject a methodolgy that would direct you to the same conclusion.


Bradford: Wrong. It indicates encoded systems require independence from strict determinism. If a natural force of nature determines a codon inevitability of UAG at specific defined locci in a gene sequence the flexibility required for amino acid protein sequencing is lost.

I'd agree that this conclusion can also be drawn. However, going back to your original point, we can only rule out intelligence in the way you describe if we know how the extant natural forces work. In practice, we'd never know if we'd missed one.

Bradford: An unintelligent natural force, like, for example, chemical attraction generated by ions would produce a deterministic outcome. Forces of nature do not cause codes to be generated de novo. Natural selection can influence outcomes but only on existing genomes. One can imagine extra-cellular synthesis of RNA (chemical obstacles are considerable) but no selection process directs functional sequence specificity.

Bradford: Cultural indicators are irrelevant to determining the genetic encoding convention and the means by which it is expressed. One need only apply scientific methodology.

Again, that's precisely my point. When we recognise a work of Shakespeare as being intelligently produced, it's because of cultural indicators.

Bradford: The "cultural indicators" are exactly those found in functional genomes.

When we recognise, say, a new type of vehicle as being intelligently produced, it's because of its efficiency. Neither of these arguments apply in the case of the genome; there are no cultural indicators that we're aware of, and efficiency can be adequately generated by evolutionary processes.

Bradford: There is no linguistic difference in an initiation codon and the symbolic notation for such in any of hundreds of different languages. You are making an artificial distinction and are continuing to throw around phrases like "evolutionary processes" without defining what these are in a prebiotic environment.


[With regard to replication of RNA groups] A capacity for which has been assumed rather than empirically demonstrated.

To start with, the groups would be of size 1. The ability of single RNA strands to replicate has been demonstrated.

Bradford: Within cells. Where do the initial RNA molecules come from?

The interdependence between different substrains of the population would presumably start with some RNA molecules either making use of or being aided by the byproducts of other strains. It would be easy for this to become reciprocal - if strain A is helping strains B and C to multiply then strain B will tend to do better than strain C if it helps strain A.

Bradford: You're question begging again. You don't assume a complex of strains on prebiotic earth when you have yet to source the origin for them.


This barrier could be overcome by introducing cells. It's actually very easy to form cell-like structures -lipid spheres actually form naturally.

Bradford: These lipid polymers bear very little resemblance to cellular membranes. They do not allow for membrane function. I'll explain the details if you need them.

Probably the first true cells were formed by accident, when an RNA strain stumbled across a way to encourage such protocells to form.

Bradford: This is not a scientific explanation. Protocells are theoretical not empirical constructs.

Bradford: Nucleic acid function is sequence dependent. Even if one shows the possibility of formation outside a cell there must at the same time exist an encoding convention linking codons to specific amino acids and a mechanism to translate the code.

I'll need to read up more to produce any sort of accurate response, but off the top of my head the process could have gone something like this:

1) Some RNA molecules are able to catalyse the formation of proteins. Some of these proteins would have allowed the RNA to reproduce more efficiently, and hence these RNA would have been selected for.

Bradford: Catalytic RNA does not catalyze the synthesis of proteins. That is the function of tRNA amino acyl synthetases.

2) Other strains of RNA would have found the same proteins useful. Even if they couldn't produce the proteins themselves, they would have been under selective pressure to make the production easier. So, for example, they could drag useful amino acids about the place.

3) The replicators and their assistants would have coevolved. For example, if the assistants tended to grab different amino acids, the replicators would do better if they were capable of grabbing the assistant with the acid they needed rather than blindly searching for such an acid. That would prompt the assistants to specialise further.


That's enough to take us to a point where we have "ribosomes" with hardwired genetic information, plus tRNA. The next step is figuring how the two functions of the "ribosomes" would have become separated.

4) One of the strains of protoribosome, instead of producing its own hardwired protein, develops the ability to figure out what another protoribosome is doing and to join in. This is effective because by this point all surviving protoribosomes will be producing useful proteins. It adds to the survival chances of the protoribosome, too, because it means it can potentially be shorter (RNA is unstable so this is significant). Over time, this new strain of protoribosome takes over all protein production, and the other strains dwindle to become more like messenger RNA.

We're not far off having a modern RNA genome here, so I'll leave it at that unless there's anything else you want me to provide hypotheticals for, or if you think you can rigorously demonstrate that any of the steps in this hypothetical are implausible.

This explanation is probably grossly mistaken in all sorts of interesting ways, but it demonstrates the fashion in which evolutionary processes can produce things like genetic codes. It's still rather sketchy, but it already has tons more detail than any explanation the ID community has produced.

Bradford: I'll credit you with effort and imagination although the imagination is better suited for science fiction.

2:39 am  
Anonymous Anonymous said...

"The inference is strongest at the point of life's origin."

Naturally! Intelligent Design is an argument from ignorance, so of course it is strongest at the point where there is least data, and thus where scientific investigation is at its most speculative and least tangible. It is however an "inference" lacking both a substantive theory or any substantiation whatsoever.

Further, in side-tracking into Abiogenesis, you have avoided engaging my claim that there is no reason to believe that common detectable properties of intelligence (regardless of the intelligence) exist until such properties have been hypothesised and substantiated.


"Which misses the point of an intelligent inference. ID is not confined to an evaluation of evolution. The inference is strongest at the point of life's origin."

You were the one who wished to divert the discussion into Abiogenesis. I was merely pointing out that it is irrelevant to the wider debate.


"Behind all that jargon is an erroneous belief that "research into areas of self-organization" provides evidence that functional genomes arise."

As I said, I was arguing against the fallacy that information=intelligence generally (not for any specific mechanism of Abiogenesis).

3:07 am  
Blogger Lifewish said...

Bradford: The reason the symbols are generated is they are the symbols needed to convey the encoded message. There is nothing arbitrary about the symbols in this message or the symbols found in functional genes.

Heck yes they are. Why is a letter "a" the shape it is? Why is UGA a "stop" codon? Why do we English-speakers put the adjective before the noun?

All these are things that can and have been done differently elsewhere - the Japanese "a" looks like this, the French usually put the adjective after the noun, mycoplasma read UGA as coding for tryptophan.

Bradford: Your belief is based on a knowledge that there exists a correlation between the symbols and the message. The correlation was intelligently created. We observe the same thing in genomes and you arbitrarily reject a methodolgy that would direct you to the same conclusion.

Your reasoning here appears to boil down to "intelligent design implies correlation, hence correlation implies intelligent design". This is logically dodgy. Merely pointing to the presence of a genetic code and the fact that other codes have been produced by intelligent entities does not in and of itself imply that the genetic code was produced by intelligent entities.

An unintelligent natural force, like, for example, chemical attraction generated by ions would produce a deterministic outcome.

Sadly mistaken. For example, radioactive decay is caused entirely by unintelligent forces yet is the epitome of randomness. Protein folding is non-deterministic - it's possible for the same protein to fold up in multiple ways (this is the cause of prion diseases). And the purely chemical method of DNA replication is demonstrably prone to error.

Forces of nature do not cause codes to be generated de novo.

Are you speaking from personal experience here or what? I'd agree with the statement "forces of nature do not usually cause codes to be generated de novo", but your generalisation is gonna require a lot of support.

One can imagine extra-cellular synthesis of RNA (chemical obstacles are considerable) but no selection process directs functional sequence specificity.

Actually, IIRC there's quite a few ways for nature to polymerise RNA bases. Iron catalysts and certain types of clay spring to mind.

I have no idea what the shortest RNA self-replicator is, but by comparison with polypeptides (where the shortest known self-replicator is 32 units), the creation of such a chain probably wouldn't be that implausible. This gives us our initial "organism", which can then be acted on by natural selection as I described.

[Regards Shakespeare] The "cultural indicators" are exactly those found in functional genomes.

You miss my point. The types of cultural indicator may not differ that much between, say, DNA and morse code, but the basis of my assessment of the designedness of Shakespeare's work is that there are multiple different indicators that can exist for each type thereof. Hence the chances of a set that I'm already aware of being independently produced elsewhere are fairly slim.

The specific "cultural" indicators in DNA do not resemble those of any human language of which I'm aware, and hence this argument cannot be made. There may of course be a way to modify this argument appropriately, but I can't see any that aren't obviously fallacious.

There is no linguistic difference in an initiation codon and the symbolic notation for such in any of hundreds of different languages. You are making an artificial distinction and are continuing to throw around phrases like "evolutionary processes" without defining what these are in a prebiotic environment.

For the first point, see above. For the second point, the evolutionary processes would be acting on RNA chains in the fashion I described in detail when I was discussing one possible way that modern protein-production machinery could have formed. The selection pressures would come from the fact that non-reproducing chains would degrade fairly quickly, leaving no descendents, and that some chains would probably be breaking others down for spare parts.

If this isn't an adequate explanation, could you give a brief example of the form of definition you're after w.r.t prebiotic evolutionary processes?

Bradford: Within cells. Where do the initial RNA molecules come from?

See above comments about inorganic catalysis of RNA.

You're question begging again. You don't assume a complex of strains on prebiotic earth when you have yet to source the origin for them.

See above, and note that once one self-replicator strain had formed it would tend to accumulate errors over time, resulting in several distinct strains.

These lipid polymers bear very little resemblance to cellular membranes. They do not allow for membrane function. I'll explain the details if you need them.

I know they lack all the interesting ion channels and secretion systems and so on, but they'd be sufficient to transport communities of RNA from one rockpool to another. Once this approach had become institutionalised, there are many obvious improvements that would tend to have occurred. I personally can't see any reason why these improvements couldn't lead to the sort of cell we have today; please say if there's anything specific that you'd like me to address.

This is not a scientific explanation. Protocells are theoretical not empirical constructs.

I'm using the word "protocell" to refer to the aforementioned lipid capsule transplanting an RNA community, rather than anything more modern. Protocells of this type are definitely empirical constructs - see here for photos.

Bradford: Catalytic RNA does not catalyze the synthesis of proteins. That is the function of tRNA amino acyl synthetases.

At present, of course it is. Was this necessarily true during the formation of life? Probably not.

If I might use an analogy, the protoribosomes I've discussed are roughly equivalent to the clockwork music boxes that have existed for centuries, whereas the modern arrangement of ribosome, mRNA and tRNA is more equivalent to a full-fledged stereo system with player, CDs and speakers.

I'll credit you with effort and imagination although the imagination is better suited for science fiction.

Thanks for the compliment. Coming up with ideas for how something might have happened is the first step in determining how it did happen. I hope that my flight of fantasy has adequately demonstrated that, in principle at least, it is possible for codes to be produced by evolutionary processes (if you disagree, please point out the step that is in error).

I of course invite you to come up with a better hypothesis if you can think of one. This hypothesis should explain why life as we know it is more plausible than its complexity suggests. It should explain why life as we know it arose instead of any alternative form of life. Ideally it should be predictive, but mine isn't so we'll waive that clause :)

11:37 am  
Blogger William Bradford said...

"The inference is strongest at the point of life's origin."

Naturally! Intelligent Design is an argument from ignorance, so of course it is strongest at the point where there is least data, and thus where scientific investigation is at its most speculative and least tangible. It is however an "inference" lacking both a substantive theory or any substantiation whatsoever.

Bradford: Intelligent design is an argument based on our knowledge of cellular functions and biochemistry. It is the ignorance of some that allows the self- deceptive belief that a smattering of amino acids produced in spark discharge experiments has anything to do with the generation of cells. OOL is speculative because the data produced does not match the hopes of its adherents. To argue abiogenesis one must have an active imagination and a good deal of blind faith.

Further, in side-tracking into Abiogenesis, you have avoided engaging my claim that there is no reason to believe that common detectable properties of intelligence (regardless of the intelligence) exist until such properties have been hypothesised and substantiated.

Bradford: To the contrary, one of the reasons why abiogenesis was introduced was to illustrate the point that opponents of ID are willing to accept unsubstantiated hypotheses. There can be no absolute substantiation of an unobserved historic process. All we can do is offer the explanation that best matches the physical evidence.

1:54 pm  
Blogger William Bradford said...

Bradford: The reason the symbols are generated is they are the symbols needed to convey the encoded message. There is nothing arbitrary about the symbols in this message or the symbols found in functional genes.

Heck yes they are. Why is a letter "a" the shape it is? Why is UGA a "stop" codon? Why do we English-speakers put the adjective before the noun?

Bradford: Encoding conventions are evidence of choice not chemical necessity. Symbolic biological functions are evidence of design.

All these are things that can and have been done differently elsewhere - the Japanese "a" looks like this, the French usually put the adjective after the noun, mycoplasma read UGA as coding for tryptophan.

Bradford: All variation is consistent with intelligent assignment of representation.

Bradford: Your belief is based on a knowledge that there exists a correlation between the symbols and the message. The correlation was intelligently created. We observe the same thing in genomes and you arbitrarily reject a methodolgy that would direct you to the same conclusion.

Your reasoning here appears to boil down to "intelligent design implies correlation, hence correlation implies intelligent design". This is logically dodgy. Merely pointing to the presence of a genetic code and the fact that other codes have been produced by intelligent entities does not in and of itself imply that the genetic code was produced by intelligent entities.

Bradford: One of course also would examine the alternative- that symbolic correlations are produced from either stochastic processes or chemical necessity. Physical evidence debunks both alternatives.

An unintelligent natural force, like, for example, chemical attraction generated by ions would produce a deterministic outcome.

Sadly mistaken. For example, radioactive decay is caused entirely by unintelligent forces yet is the epitome of randomness. Protein folding is non-deterministic - it's possible for the same protein to fold up in multiple ways (this is the cause of prion diseases). And the purely chemical method of DNA replication is demonstrably prone to error.

Bradford: Radioactive decay does not lead to a biological encoding process. The eventual outcome of decay is predictable even if randomness is part of the process. It is not a symbolic linking process. Protein folding is determinsitc but the number of variables representing the different bonds is so large as to make quantification difficult. Still we are making great strides. Nevertheless all properties of functional proteins are determined by their aa sequences; problematic for an prebiotic world.

Forces of nature do not cause codes to be generated de novo.

Are you speaking from personal experience here or what?

Bradford: I'm referring to years of scientific data. Of course you can explain what chemical reactions generate codes.

I'd agree with the statement "forces of nature do not usually cause codes to be generated de novo", but your generalisation is gonna require a lot of support.

Bradford: It is an observation. If you have a scientific basis for believing they do come out with it.

Bradford: One can imagine extra-cellular synthesis of RNA (chemical obstacles are considerable) but no selection process directs functional sequence specificity.

Actually, IIRC there's quite a few ways for nature to polymerise RNA bases. Iron catalysts and certain types of clay spring to mind.

Bradford: All of which have nothing to do with generating sequence specificity.

I have no idea what the shortest RNA self-replicator is, but by comparison with polypeptides (where the shortest known self-replicator is 32 units), the creation of such a chain probably wouldn't be that implausible. This gives us our initial "organism", which can then be acted on by natural selection as I described.

Bradford: You have not described it despite repeated requests to specify what is selected and why in a precellular world. This is really the crux of the argument. Darwinism is constructed around the belief that changes are selected. The argument is clear when referencing existing cells. It is distinctly murky whyen referencing a prebiotic environment. If you wish to discuss protocells and other proto items you need to specify natural selection criteria that produces a minimal genome. Otherwise the comments are scientifically meaningless.

2:25 pm  
Anonymous Anonymous said...

"Intelligent design is an argument based on our knowledge of cellular functions and biochemistry."

No. Intelligence design is based on the ignorance of a religiously motivated Law Professor with a dislike of science. It has later been rationalised with some superficial gloss by some biochemists (among others), most notably Michael Behe, who are willfully ignorant of Evolution.

The vast majority of biochemists and cellular biologists find ID to be vacuous.

"To the contrary, one of the reasons why abiogenesis was introduced was to illustrate the point that opponents of ID are willing to accept unsubstantiated hypotheses."

Firstly, Abiogenesis has not been accepted as well-established science. It remains an explicitly speculative field, with many competing hypotheses. It is currently "science as process" more than it is "science as end-product."

Secondly, unlike ID, Abiogenesis has a well-established empirical research programme. Further, this programme has produced at least some (albeit limited) positive results.

But even if it were true that Abiogenesis were an "accepted unsubstantiated hypothesis," this would merely invalidate Abiogenesis - it would in no way validate ID! It thus in no way rebuts my previous assertion.

4:16 pm  
Blogger William Bradford said...

Bradford: Your inaccurate opinions of Philip Johnson and Behe are noted. Johnson does not dislike science. He dislikes the selective use of evidence for philosophical rather than scientific reasons. Behe is well aware of claims for evolution and has done an admirable job of illustrating the empirical shortcomings of the other side.

"To the contrary, one of the reasons why abiogenesis was introduced was to illustrate the point that opponents of ID are willing to accept unsubstantiated hypotheses."

Firstly, Abiogenesis has not been accepted as well-established science. It remains an explicitly speculative field, with many competing hypotheses. It is currently "science as process" more than it is "science as end-product."

Bradford: It is an exercise in futility that has produced very meager scientific data since Miller-Urey.

Secondly, unlike ID, Abiogenesis has a well-established empirical research programme. Further, this programme has produced at least some (albeit limited) positive results.

Bradford: The evidence produced illustates why the expectation that cells arise from chemical reactions is an exercise in blind faith.

But even if it were true that Abiogenesis were an "accepted unsubstantiated hypothesis," this would merely invalidate Abiogenesis - it would in no way validate ID! It thus in no way rebuts my previous assertion.

Bradford: It is true that abiogenesis is an unsubstantiated hypothesis. There is no conditional attached. Abiogenesis excludes intelligence as a causal agent. If it is invalidated the alternative is obvious. There are not a great many options here.

4:51 pm  
Anonymous Anonymous said...

"He dislikes the selective use of evidence for philosophical rather than scientific reasons."

Given that his "theistic realism" is nothing more than "the selective use of evidence for philosophical rather than scientific reasons," I find that claim to be utterly ludicrous!

Johnson in fact has a reputation (in common with many other Creationists) for being "selective" to the point of misrepresentation, on how he uses scientific evidence and quotes from scientists.

The only 'science' Johnson appears to appreciate is that which rationalises his own preconceived worldview.


"Behe is well aware of claims for evolution..."

Behe's ignorance of the evolution of the immune system was highlighted at the Dover trial. His complete failure to address, in the new edition of his Darwin's Black Box, any of the newly discovered evolutionary pathways undercutting his claims of Irreducible Complexity for certain systems, shows how far out of touch with ongoing evolutionary research he is.

How many peer-reviewed articles has Behe published on Evolution? That is generally considered the most appropriate indication of expertise in a field by the scientific community.


"It is an exercise in futility that has produced very meager scientific data since Miller-Urey."

"Meagre data" (even if that was a fair characterisation) is far less futile than the ID approach of "assume design, do nothing."

But as it turns out, the results of Abiogenesis since Miller-Urey are not meagre. Follow-up experiments:
Abelson 1956
Groth and Weyssenhoff 1957
Bahadur, et al. 1958
Pavolvskaya and Pasynskii 1959
Palm and Calvin 1962
Harada and Fox 1964
Oró 1968
Bar-Nun et al. 1970
Sagan and Khare 1971
Yoshino et al. 1971
Lawless and Boynton 1973
Yanagawa et al. 1980
Kobayashi et al. 1992

Alternative hypotheses:
The iron-sulfur-hypothesis, developed by Wächtershäuser in the 1980s and further elaborated by Martin and Russell.

Also numerous other smaller programmes.

And what has ID to show for itself in terms of hypothesised mechanisms, emprical testing and published results, to compare with this? Nothing!

The field of Abiogenesis is accepted as being science (but science-the-process, not science-the-end-result) because the people working in the field are doing science - making testable hypotheses and testing them. That is what science is about.

You may consider this to be "futile" - but this is what science is about. So I can only conclude that you consider science itself to be futile.

However speculative this may be, and however tentative and incomplete the results, this puts Abiogenesis head and shoulders above ID.


"If it is invalidated the alternative is obvious. There are not a great many options here."

I said if Abiogenesis were invalidated as an ACCEPTED hypothesis, not as a STILL VIABLE hypothesis! So no alternative is needed.

In any case there are plenty of alternatives: infestation via a comet, deliberate seeding by small furry things from Alpha Centauri, or supernatural creation by the Flying Spaghetti Monster. None of these are substantiated, and the last alternative isn't even scientific, but that puts even the FSM in no worse a position than ID.

6:03 pm  
Blogger William Bradford said...

You may consider this to be "futile" - but this is what science is about. So I can only conclude that you consider science itself to be futile.

Bradford: Science is indeed about testing so let's look at the results. Functional proteins- no. A cellular membrane- no. DNA-no. Metabolic pathways- no. A single enzyme identified in any metabolic pathway- no. Encoded RNA-no. A cell- are you kidding?

However speculative this may be, and however tentative and incomplete the results, this puts Abiogenesis head and shoulders above ID.

Bradford: Tentative and incomplete? You can't establish anything other than an ability to provide just enough testing to keep the true believers happy.

"If it is invalidated the alternative is obvious. There are not a great many options here."

I said if Abiogenesis were invalidated as an ACCEPTED hypothesis, not as a STILL VIABLE hypothesis! So no alternative is needed.

Bradford: What would falsify abiogenesis?

7:15 pm  
Anonymous Anonymous said...

"Science is indeed about testing..."

And ID proposes no testable hypotheses and thus tests NOTHING! The only conclusion therefore is that ID IS NOT SCIENCE!


"What would falsify abiogenesis?"

Abiogenesis is a field of research, not a specific hypothesis, to be falsified. I do not doubt that a number of hypotheses in this field have been tried and falsified over the years. History (and particularly historical summaries) tends to record science's successes, not its blind alleys, so I cannot name any specific falsified Abiogenesis hypothesis. I have however heard hearsay that the "prebiotic soup" hypothesis has been discarded in favour of a more heterogeneous hypothesis of the prebiotic environment.

I would also point out that you have still neither hypothesised nor substantiated any "particular detectable property" where "shared intelligence would of necessity lead to this commonality."

7:24 am  
Blogger William Bradford said...

I would also point out that you have still neither hypothesised nor substantiated any "particular detectable property" where "shared intelligence would of necessity lead to this commonality."

Bradford: The detectable property central to life has been mentioned by me repeatedly; namely, the correlation between nucleic acid function and a very small subset of sequence possibilities enabling nucleic acid function. As a test the following is proposed:

The helical nature of DNA results in a physical phenomenon known as supercoiling during essential functions of protein synthesis and cellular replication. The contemplated experiment is based on genetically engineering DNA so that the genes, encoding a protein complex which prevents deleterious effects of supercoils, are knocked out. A rapidly reproducing organism would be placed in an environment that allows for adaptation. To be generous to anti-IDers only one of the multiple protein encoding genes would be disabled. The hypothesis is no coping mechanism would evolve. Associated with the hypothesis is the contention that incremental Darwinian evolutionary changes do not generate this type of irreducibly complex system. Sequence specificity fitting function is evidence for intelligent causality.

6:25 pm  
Anonymous Anonymous said...

"I would also point out that you have still neither hypothesised nor substantiated any "particular detectable property" where "shared intelligence would of necessity lead to this commonality."

Bradford: The detectable property central to life has been mentioned by me repeatedly; namely, the correlation between nucleic acid function and a very small subset of sequence possibilities enabling nucleic acid function."


Thank you Bradford for answering a completely different question than the one I asked!

I asked about "particular detectable property where shared intelligence would of necessity lead to this commonality." Note that the question was about intelligence, not life! I would also point out that your answer may not even be correct even for life. It is not inconceivable that non-carbon-based life might exist - so that life being carbon-based may not be a necessity, but only the only life we have, as yet, observed.

7:58 pm  
Blogger William Bradford said...

Anonymous said...
"I would also point out that you have still neither hypothesised nor substantiated any "particular detectable property" where "shared intelligence would of necessity lead to this commonality."

Bradford: The detectable property central to life has been mentioned by me repeatedly; namely, the correlation between nucleic acid function and a very small subset of sequence possibilities enabling nucleic acid function."

Thank you Bradford for answering a completely different question than the one I asked! I asked about "particular detectable property where shared intelligence would of necessity lead to this commonality."

Bradford: Explain what you mean by "shared intellligence" and while you're at it commonality refers to exactly what? Evidence for abiogenesis and evolution is indirect and so too is evidence for intelligence. It must be so by virtue of the historic nature of the subject matter.

Note that the question was about intelligence, not life!

Bradford: I thought your question related to evidence for intelligence which would include living as well as non-living objects.

I would also point out that your answer may not even be correct even for life. It is not inconceivable that non-carbon-based life might exist - so that life being carbon-based may not be a necessity, but only the only life we have, as yet, observed.

Bradford: Any intelligent inferences refer to observable life on earth. Inorganic life forms are the stuff of science fiction not science.

2:58 am  
Anonymous Anonymous said...

"Explain what you mean by "shared intellligence" and while you're at it commonality refers to exactly what?"

This is in reference to your original comment:
"Why should advanced intelligence not have detectable properties not dependent on the nature of the intelligent source?"

The "shared intelligence" is the fact that intelligence is the only inherent commonality that we are assuming, and that you must substantiate any other common "detectable properties" that might derive from this shared feature.

7:13 am  
Blogger Lifewish said...

Bradford: Encoding conventions are evidence of choice not chemical necessity. Symbolic biological functions are evidence of design.

You have yet to provide any evidence for this proposition. All you've done is pointed out that all the codes we were aware of before we discovered the genetic code were the product of design. You've provided no plausible explanation of why it's valid to generalise this.

All variation is consistent with intelligent assignment of representation.

Even the fact that, depending on the physical structure of the generated mRNA, UGA can code for Stop or selenocysteine? If so, what wouldn't be consistent with intelligent assignment???

One of course also would examine the alternative- that symbolic correlations are produced from either stochastic processes or chemical necessity. Physical evidence debunks both alternatives.

So it's valid to "arbitrarily reject a methodology" that would lead me to infer design if it didn't adequately address these alternatives? Doesn't Dembski's CSI fall into that category?

Oh, and what "physical evidence" are you referring to? I accept that, as Pascal showed, there is valid physical evidence for abiogenesis not happening terribly often, but how on earth could one produce physical evidence demonstrating it to be impossible even in principle?

Radioactive decay does not lead to a biological encoding process.

The point I made wasn't intended to prove abiogenesis, but to debunk a specific point you made that abiogenesis was impossible because chemical processes were deterministic.

The eventual outcome of decay is predictable even if randomness is part of the process.

Ever hear of chaos theory? A single misfolded protein can kill a man - how predictable is that?

(And no, protein folding is not deterministic - what do you think prion diseases are? "Chemical" =/= "deterministic" or "predictable")

You have not described it despite repeated requests to specify what is selected and why in a precellular world.

Individual RNA molecules are selected on the basis of their ability to copy themselves (or get themselves copies) intact. In your basic soup of organic molecules, nothing there will be selected for. However, the probabilistic resources of the system are great enough to produce a very simple self-replicator.

Once you have the self-replicator, it will quickly copy itself many times over. Some copying errors will creep in, resulting in different strains. Some of these strains will be more effective self-replicators than others. RNA degrades fairly quickly, so there will be a strong selective pressure to reproduce quickly - sequences that don't do so will tend to die childless.

Is that a sufficient answer? If not, what would you like me to discuss? I'm running out of things I haven't described in depth, so I suspect I may be missing the point of your question.

If you wish to discuss protocells and other proto items you need to specify natural selection criteria that produces a minimal genome.

A minimal polypeptide genome would be <= 32 units. I don't know off the top of my head what a minimal RNA genome would look like but, given that RNA can also self-replicate, I can't see any reason for expecting it to be significantly longer. That sort of minimal genome can actually be achieved by random chaining, no natural selection needed.

Once this genome existed, the natural selection described above would kick in. I've already given a detailed description of one way that a more complex genome capable of producing proteins could in principle arise from this basic replicator.

Any questions?

One other point that you made in response to Anonymous:
Any intelligent inferences refer to observable life on earth. Inorganic life forms are the stuff of science fiction not science.

Since when is the Bible science fiction?

12:48 pm  
Blogger William Bradford said...

Bradford: Encoding conventions are evidence of choice not chemical necessity. Symbolic biological functions are evidence of design.

You have yet to provide any evidence for this proposition. All you've done is pointed out that all the codes we were aware of before we discovered the genetic code were the product of design. You've provided no plausible explanation of why it's valid to generalise this.

Bradford: Symbolic encoding conventions are known to be the product of intelligent design. Included are the symbols of this message and others enabling its transmission. It is not the matter or the electronic signals that constitute the information. These are the medium of expression. Applying this to evidence for intelligence is common. Evolutionists cite common genomic patterns as evidence for common descent. They have not observed the descent itself but claim that the outcome is consistent with the evidence cited. Similarly genetic patterns expressed by means of an encoded convention is evidence consistent with an intelligent cause.

All variation is consistent with intelligent assignment of representation.

Even the fact that, depending on the physical structure of the generated mRNA, UGA can code for Stop or selenocysteine? If so, what wouldn't be consistent with intelligent assignment???

Selenocysteine occurs in association with a SECIS element which plays a modifying role. What's the point?

One of course also would examine the alternative- that symbolic correlations are produced from either stochastic processes or chemical necessity. Physical evidence debunks both alternatives.

So it's valid to "arbitrarily reject a methodology" that would lead me to infer design if it didn't adequately address these alternatives? Doesn't Dembski's CSI fall into that category?

Bradford: CSI can be applied to stochastic processes. That appears to be its purpose.

Oh, and what "physical evidence" are you referring to? I accept that, as Pascal showed, there is valid physical evidence for abiogenesis not happening terribly often, but how on earth could one produce physical evidence demonstrating it to be impossible even in principle?

Bradford: Historic claims rely on a best explanation principle. Impossibility is not a currently utilized standard in a natural history context.

Radioactive decay does not lead to a biological encoding process.

The point I made wasn't intended to prove abiogenesis, but to debunk a specific point you made that abiogenesis was impossible because chemical processes were deterministic.

Bradford: My precise point was that deterministic processes are not consistent with encoding systems for which a successor symbol cannot result from chemical necessity. If alanine must follow lysine then encoding flexibility is lost.

The eventual outcome of decay is predictable even if randomness is part of the process.

Ever hear of chaos theory? A single misfolded protein can kill a man - how predictable is that?

(And no, protein folding is not deterministic - what do you think prion diseases are? "Chemical" =/= "deterministic" or "predictable")

Bradford: This is straying from the connection between encoding viability the need for options free of chemical determinsim. Determinism does not imply unchanging conditions.

You have not described it (the basis for selection) despite repeated requests to specify what is selected and why in a precellular world.

Individual RNA molecules are selected on the basis of their ability to copy themselves (or get themselves copies) intact. In your basic soup of organic molecules, nothing there will be selected for. However, the probabilistic resources of the system are great enough to produce a very simple self-replicator.

Once you have the self-replicator, it will quickly copy itself many times over. Some copying errors will creep in, resulting in different strains. Some of these strains will be more effective self-replicators than others. RNA degrades fairly quickly, so there will be a strong selective pressure to reproduce quickly - sequences that don't do so will tend to die childless.

Is that a sufficient answer? If not, what would you like me to discuss? I'm running out of things I haven't described in depth, so I suspect I may be missing the point of your question.

Bradford: Efficiency of replication is not connected with the generation of an encoding convention or particular sequence patterns needed for gene expression.

If you wish to discuss protocells and other proto items you need to specify natural selection criteria that produces a minimal genome.

A minimal polypeptide genome would be <= 32 units. I don't know off the top of my head what a minimal RNA genome would look like but, given that RNA can also self-replicate, I can't see any reason for expecting it to be significantly longer. That sort of minimal genome can actually be achieved by random chaining, no natural selection needed.

Bradford: A minimal genome is a functional one. Current research indicates that such a genome would entail hundreds of distinct genes.

Once this genome existed, the natural selection described above would kick in. I've already given a detailed description of one way that a more complex genome capable of producing proteins could in principle arise from this basic replicator.

Any questions?

Bradford: You have yet to address the need for sequence specificity. Your concept does not distinguish between a useless sequence of nucleotides and a sequence that could produce a functional chain of amino acids.

One other point that you made in response to Anonymous:

Any intelligent inferences refer to observable life on earth. Inorganic life forms are the stuff of science fiction not science.

Since when is the Bible science fiction?

Bradford: What biblical passage refers to inorganic life forms?

3:35 pm  
Blogger Lifewish said...

Sorry for the delay in response - a blogger malfunction ate my lengthy post yesterday, and I'm having trouble getting motivated to redo it. I'll (hopefully) reply tomorrow.

12:09 am  

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