Powerful evidence for Design?

[rossum]

Extrapolating from our data and from modest sequence constraints on interhelical turns (23, 28–30), we can estimate that if every position in the protein had been randomized, a library of ˜10^24 members would have been needed to obtain AroQ mutases. (colour added)
pnas.org/content/98/19/10596.full#ref-30

This is discussing evolution. Since every ancestor has to be functional enough to reproduce, then the assumption of random bases for the entire protein is incorrect. In any evolutionary process we know (not assume) that the protein is functional enough to allow the organism carrying it to survive long enough to reproduce. If the organism does not reproduce, then that particular protein configuration will not be carried on into the next generation. Evolution is an iterative process.

That is often the reason simple probability calculations are not useful in this area. It is much easier to calculate completely random probabilities, but in real life, the process of natural selection greatly constrains the range of possibilities that are actually found. Incorrect mathematical models lead to incorrect results.

Quoting further from your PNAS reference, this point is borne out:
reference:

Our estimate of the low frequency of protein catalysts in sequence space indicates that it will not be possible to isolate enzymes from unbiased random libraries in a single step. The required library sizes far exceed what is currently accessible by experiment, even with in vitro methods (31, 35). Instead, as in natural evolution, the design of new enzymes will require incremental strategies in which, for instance, a suitable scaffold is first generated, binding and catalytic groups are subsequently added, and the ensemble is optimized in an iterative fashion. Our two-stage approach to binary-patterned mutases and work on the redesign of existing enzymes (36–38) demonstrate the power of stepwise and modular procedures for directing the course of evolution.

Your own source is telling you that single step methods will not work, while “incremental strategies” “as in natural evolution” will succeed.

You need to look at your own sources more thoroughly. Incremental, stepwise, strategies, such as evolution, require a different mathematical treatment from the single step “tornado in a junkyard” strategies, often used as strawmen by the ID side.

rossum

 

[tonyrey]

Your own source is telling you that single step methods will not work, while “incremental strategies” “as in natural evolution” will succeed.

You need to look at your own sources more thoroughly. Incremental, stepwise, strategies, such as evolution, require a different mathematical treatment from the single step “tornado in a junkyard” strategies, often used as strawmen by the ID side.

The use of the term “strategies” is an implicit acknowledgement of the incoherence of the unplanned-development hypothesis. Buddhism is based on belief in spiritual development - which entails insight - yet physical development is explained as a sequence of accidents!

In other words a series of incremental steps up an immense staircase which just happens to exist for no reason whatsoever and leads the bodies ascending the staircase to precisely nowhere yet the minds linked with those bodies are supposed to have a destination towards nirvana! It seems there are two disparate worlds which are totally unrelated and have absolutely nothing in common…

It would be more economical to opt for materialism or idealism rather than attempt to divorce mind and matter without achieving an intelligible strategy - in the true sense of the term. In other words choose a rational system or an absurd concatenation… (But of course the latter excludes the power of choice.

 

[tonyrey]

You’re saying "No – there is zero evidence that intelligence was involved in the development of life or the universe. Everything is reducible to science alone (scientism). Everything can be explained as the product of chance, matter and natural law.

On the contrary – it is demanded. I already pointed it out to you that it was infallibly defined in Vatican Council I. If you’re willing to reject that teaching, then I hope you really think long and hard about it. You strike me as a believer and as one serious about the teaching of Christ. Importantly, you cannot accept the divine character of Christ without accepting also the Argument from Design. He pointed to it Himself:
“the very works that I do bear witness of me …” We observe the works – the lame can walk, the sick are healed, the blind can see. These are evidence in nature. They bear witness. Of what? Merely a good person? – no, they bear witness of the supernatural – of something that transcends nature, not reducible to a science lab. The power of God – the purpose of God – and that is His Design which is evident.

It’s because the universe is constant and predictable that we have math and science. You cannot use these rational processes to argue against the knowability of the universe. The fact that the universe corresponds in a very high degree to mathematical modelling itself is strong evidence in the Argument from Design.

Fine-tuning in the universe is real. Even atheists fully recognize it.

It always boils down to the choice between the primacy of Reason or the primacy of unReason - but of course Unreason excludes the element of choice!

 

[reggieM]

This is discussing evolution. Since every ancestor has to be functional enough to reproduce, then the assumption of random bases for the entire protein is incorrect. In any evolutionary process we know (not assume) that the protein is functional enough to allow the organism carrying it to survive long enough to reproduce. If the organism does not reproduce, then that particular protein configuration will not be carried on into the next generation. Evolution is an iterative process.

Origin of life speculations have to move from inert chemicals to the first cell so those papers give an idea of what it takes for the development of de novo proteins. Evolution has nothing to work with if there is no organic life available yet.

That is often the reason simple probability calculations are not useful in this area. It is much easier to calculate completely random probabilities, but in real life, the process of natural selection greatly constrains the range of possibilities that are actually found. Incorrect mathematical models lead to incorrect results.

I’ll only disagree that it’s not that easy to calculate the random probabilities involved with abiogenesis either since it might be impossible to accurately create or model the conditions of pre-biotic earth. That’s one of the reasons why in vitro experiements with RNA are opposed by a number of prominent origin of life researchers (Shapiro, Orgel, Koonin …)

Incremental, stepwise, strategies, such as evolution, require a different mathematical treatment from the single step “tornado in a junkyard” strategies, often used as strawmen by the ID side.

Abiogenesis claims have to explain both how chemical evolution and biological evolution can develop the first self-replicating cells.

 

[reggieM]

The use of the term “strategies” is an implicit acknowledgement of the incoherence of the unplanned-development hypothesis. Buddhism is based on belief in spiritual development - which entails insight - yet physical development is explained as a sequence of accidents!

Good point. The term “strategies” is the language of design – since strategies are oriented towards a future state.

There is a spiritual world in Buddhist cosmology and that world cannot be explained as a product of natural processes.

Buddhism versus Materialism

 

[rossum]

Origin of life speculations have to move from inert chemicals to the first cell so those papers give an idea of what it takes for the development of de novo proteins. Evolution has nothing to work with if there is no organic life available yet.

The paper your referenced was not dealing with abiogenesis, but with evolution. If you wish to discuss the probabilities of abiogenesis, then it would be better to refer to a paper dealing with abiogenesis. As the paper pointed out, the presence of evolutionary mechanisms changes the mathematical model to be used. What applies to one does not apply to the other.

Abiogenesis claims have to explain both how chemical evolution and biological evolution can develop the first self-replicating cells.

Indeed, and scientists are still working on it. Intelligent Design has to explain the origin of intelligence and of life and hasn’t even started yet. So far, abiogenesis is in the lead.

rossum

 

[rossum]

Good point. The term “strategies” is the language of design – since strategies are oriented towards a future state.

There is a spiritual world in Buddhist cosmology and that world cannot be explained as a product of natural processes.

Buddhism versus Materialism

Indeed. I use material science to explain the material. For the spiritual world I use spiritual explanations. Buddhism is far less prescriptive of what we should believe about the material world than the Abrahamic religions:

1. *]It exists.
   *]It is impermanent.
   *]It can be escaped.
   
   Beyond that, all the details can be left to science.
   
   rossum

 

[reggieM]

The paper your referenced was not dealing with abiogenesis, but with evolution. If you wish to discuss the probabilities of abiogenesis, then it would be better to refer to a paper dealing with abiogenesis. As the paper pointed out, the presence of evolutionary mechanisms changes the mathematical model to be used. What applies to one does not apply to the other.

Abiogenesis has to explain the origin of proteins so it can be helpful to look at the statisitcal probability for functional proteins to arise de novo. The RNA World proposal has to incorporate evolutionary mechanisms since the proposal starts with self-replicating ribosomes and then claims that proteins and DNA emerge from that starting point through evolutionary mechanisms.

Indeed, and scientists are still working on it. Intelligent Design has to explain the origin of intelligence and of life and hasn’t even started yet. So far, abiogenesis is in the lead.

Intelligent Design doesn’t propose to explain the origin of intelligence. It’s a research project that works within limits and begins with some assumptions – just as Darwinian theory has limits and doesn’t attempt to prove the origin of natural laws or the origin of chance.

But ID does explain that there is evidence that intelligence was involved in the origin of life – and that is a far more reasonable explanation than any of the dozens of conflicting origin of life speculations that science offers today.

 

[reggieM]

Indeed. I use material science to explain the material. For the spiritual world I use spiritual explanations. Buddhism is far less prescriptive of what we should believe about the material world than the Abrahamic religions:

1. *]It exists.
   *]It is impermanent.
   *]It can be escaped.
   
   Beyond that, all the details can be left to science.
   
   rossum

1. 
   Well, not all of the details since science cannot determine the boundary between the material and spiritual and it cannot explain the effect that the spiritual has on the material – it cannot explain how the material can be escaped, what that means, how it happens, and it cannot explain how and why the material world is impermanent – or what that actually means with regards to the science of origins.
   
   Existence, permanence and transcendence are all aspects of Buddhist cosmology and are actually all very good support for the Argument from Design itself.
   
   Chance and natural laws can only operate on the material world.
   Buddhism posits a spiritual world.
   Therefore, something beyond chance and natural processes is required to explain the origin of the world in the Buddhist view.
   If not chance and natural law – then purposeful design.

 

[tonyrey]

The paper your referenced was not dealing with abiogenesis, but with evolution. If you wish to discuss the probabilities of abiogenesis, then it would be better to refer to a paper dealing with abiogenesis. As the paper pointed out, the presence of evolutionary mechanisms changes the mathematical model to be used. What applies to one does not apply to the other.

Since** all mechanisms are supposed to have originated in inorganic objects
it is necessary to explain how** they have become radically different.

Indeed, and scientists are still working on it.

The standard response from materialists who have no explanation yet have irrational faith in the power of irrational processes.

Intelligent Design has to explain the origin of intelligence and of life and hasn’t even started yet. So far, abiogenesis is in the lead.

Intelligent Design explains the origin of everything with the factor on which all rational beings rely implicitly to reach their conclusions…

 

[Sair]

The standard response from materialists who have no explanation yet have irrational faith in the power of irrational processes.

I realise I’m just leaping in here, but surely this response is better than saying, “Scientists haven’t discovered/demonstrated an explanation yet, therefore I’ll have irrational faith in a transcendental magic man”?

Intelligent Design explains the origin of everything with the factor on which all rational beings rely implicitly to reach their conclusions…

That’s the whole problem - it doesn’t explain the origin of intelligence - it merely assumes this complex process as a brute fact, rather than something that warrants an explanation in its own right.

 

[tonyrey]

The standard response from materialists who have no explanation yet have irrational faith in the power of irrational processes.

A crude description of theism that reveals an irrationally aggressive mentality…

Philosophers, scientists and all** rational **beings - use intuition and personal experience but primarily the power of reason to reach all their conclusions. It is hardly an insignificant by-product of irrational processes…

Intelligent Design explains the origin of everything

with the factor on which all rational beings rely implicitly to reach their conclusions… That’s the whole problem - it doesn’t explain the origin of intelligence - it merely assumes this complex process as a brute fact, rather than something that warrants an explanation in its own right.

Only materialists regard insight - on which intelligence is based - as a complex process because they are dominated by an atomistic interpretation of reality. The mind cannot be divided into bits and pieces like physical objects. It is an entity which functions like the director of an organisation or the conductor of an orchestra. No one asks “Which part of you reached that conclusion?” because “I reached that conclusion” is an adequate answer - provided that we give a reason (but the reason is not a part of us).

Materialists believe things are brute facts whereas theists believe persons are basic facts. That is the essential difference. What is more reasonable: to be a person or a collection of things? The fatal flaw of the analytic approach is its failure to see the wood for the trees…

 

[rossum]

Abiogenesis has to explain the origin of proteins so it can be helpful to look at the statisitcal probability for functional proteins to arise de novo.

Not necessarily. If the particular model of abiogenesis has proteins arising de novo, then it does. If the particular model of abiogenesis does not have proteins arising de novo then it does not. The RNA world hypothesis does not have proteins arising de novo for example.

The RNA World proposal has to incorporate evolutionary mechanisms since the proposal starts with self-replicating ribosomes and then claims that proteins and DNA emerge from that starting point through evolutionary mechanisms.

Indeed. The term “chemical evolution” is sometimes used in this context. Again, we need to use mathematical models of the appropriate evolutionary processes. Models of purely random processes do not apply at this stage.

Intelligent Design doesn’t propose to explain the origin of intelligence.

However, its basic premise does assume that it is possible for intelligence to arise without design.

But ID does explain that there is evidence that intelligence was involved in the origin of life – and that is a far more reasonable explanation than any of the dozens of conflicting origin of life speculations that science offers today.

ID claims that there is evidence. However, so far actual scientific evidence has been notably lacking. Behe’s IC has been shown to be evolveable by indirect methods, and Dembski’s CSI has not been calculated for anything more than toy examples. For instance, has any ID scientist calculated the CSI of a human and the CSI of a chimp to determine if it is possible for a human and a chimp to have evolved from a common ancestor? Or indeed for any pair of closely related species. It is not as if we don’t have the complete genome sequences of many species.

rossum

 

[rossum]

Since** all mechanisms are supposed to have originated in inorganic objects
it is necessary to explain how** they have become radically different.

Water is a liquid and is “radically different” from its gaseous constituent elements, Hydrogen and Oxygen. Radically different emergent properties are easily observable even within the domain of inorganic chemistry. Similar effects can be observed in organic chemistry.

The standard response from materialists who have no explanation yet have irrational faith in the power of irrational processes.

We have examples of the power of irrational processes. Many models show just how powerful such processes can be.

Intelligent Design explains the origin of everything with the factor on which all rational beings rely implicitly to reach their conclusions…

False. ID does not explain the origin of the Designer, nor does it explain the origin of intelligence.

rossum

 

[reggieM]

Not necessarily. If the particular model of abiogenesis has proteins arising de novo, then it does. If the particular model of abiogenesis does not have proteins arising de novo then it does not. The RNA world hypothesis does not have proteins arising de novo for example.

The tornado in a junkyard analogy was used to describe certain models of abiogenesis. So, it’s important to see what that really means in terms of probability. As for the RNA world hypothesis, one criticism is as quoted: “That world of nucleic acids could not have existed if not tethered to proteins”. So, the origin of proteins still has to be explained somehow.

However, its basic premise does assume that it is possible for intelligence to arise without design.

Could you explain that further?

ID claims that there is evidence. However, so far actual scientific evidence has been notably lacking. Behe’s IC has been shown to be evolveable by indirect methods, and Dembski’s CSI has not been calculated for anything more than toy examples. For instance, has any ID scientist calculated the CSI of a human and the CSI of a chimp to determine if it is possible for a human and a chimp to have evolved from a common ancestor? Or indeed for any pair of closely related species. It is not as if we don’t have the complete genome sequences of many species.

Again, you’re shifting this conversation to evolutionary processes when we were talking about abiogenesis.

We have direct, conclusive evidence that intelligence can modify DNA for new cellular function.
We have no evidence that undirected natural processes can do the same.

So, the ID proposal that some intelligence was involved in the origin of the first life form is the most reasonable explanation.

 

[reggieM]

doesn’t

explain the origin of intelligence - it merely assumes this complex process as a brute fact, rather than something that warrants an explanation in its own right.

As I explained above, Evolutionary theory does not explain the origin of natural laws. It “merely assumes that constant, predictable laws as a brute fact, rather than something that warrants an explanation”.

So, you have to use the same standard in judging one from the other.

Evolutionary theory relies on a number of assumptions – about rationality, logic, the scientific method, interpretation of evidence, purposefulness, causality and human capabilities – among many other things.

 

[reggieM]

False. ID does not explain the origin of the Designer, nor does it explain the origin of intelligence.

rossum

If I can jump in – we have to be careful about not confusing Intelligent Design science with the Argument from Design.

 

[reggieM]

Indeed. I use material science to explain the material. For the spiritual world I use spiritual explanations.

Going back so we don’t lose these points …

In the above, you cite spiritual explanations. That sounds good except that there is a middle ground between material and spiritual explanations – and those are philosophical explanations. That’s metaphysics, the use of reason to explain aspects of reality. One does not have to rely on spiritual revelations for those kinds of explanations.

From the Buddhist perspective, the mind cannot be reduced to matter/natural laws alone. It is part of the spiritual cosmos - and thus cannot be comprehended by science.

Since every human being possesses a mind and a spiritual, non-material destiny in worlds which are also non-material, then it is not possible to explain human origins without considering the non-material aspect of human beings.

From the Buddhist perspective, therefore, science cannot fully explain human origins.

1. Chance and natural laws can only work in a material universe (and on matter)
2. Since human beings possess a non-material component (mind), something other than natural processes (evolution) is required to explain their origin.
3. Mind/intelligence is something other than natural laws and matter.
4. Therefore, a reasonable explanation for the origin of the spiritual nature of human beings is mind or intelligence.

 

[reggieM]

Only materialists regard insight - on which intelligence is based - as a complex process because they are dominated by an atomistic interpretation of reality. The mind cannot be divided into bits and pieces like physical objects.

Exactly – and that is supported in the Buddhist view also (which regards mind as non-material). There are no physical parts in a conscious awareness (a flash of insight, for example).

It is an entity which functions like the director of an organisation or the conductor of an orchestra. No one asks “Which part of you reached that conclusion?” because “I reached that conclusion” is an adequate answer - provided that we give a reason (but the reason is not a part of us).

The fact that we recognize what the “I” in in that example indicates something universal in human experience – it’s not reducible to physical parts.

 

[Sair]

A crude description of theism that reveals an irrationally aggressive mentality…

“Aggressive”? Really? I suspect the only reason you interpret my remarks as aggressive, in light of the nature of many of your own, is due to the enculturated respect traditionally afforded religious faith.

Philosophers, scientists and all** rational **beings - use intuition and personal experience but primarily the power of reason to reach all their conclusions. It is hardly an insignificant by-product of irrational processes…

You are are the one claiming it is insignificant if it’s not a product of supernatural design.

Only materialists regard insight - on which intelligence is based - as a complex process because they are dominated by an atomistic interpretation of reality. The mind cannot be divided into bits and pieces like physical objects. It is an entity which functions like the director of an organisation or the conductor of an orchestra. No one asks “Which part of you reached that conclusion?” because “I reached that conclusion” is an adequate answer - provided that we give a reason (but the reason is not a part of us).

Materialists believe things are brute facts whereas theists believe persons are basic facts. That is the essential difference. What is more reasonable: to be a person or a collection of things? The fatal flaw of the analytic approach is its failure to see the wood for the trees…

What’s the difference between a brute fact and a basic fact? Both are assumed, if your usage is anything to go by, apparently without recourse to explanation. And the difference between the naturalist and the supernaturalist view - as I’ve elucidated before - is that the former tends to regard the mind (in light of the present extent of study) as an emergent property of the brain, whilst the latter regards it (in light of religious dogma and philosophical idealism) as a fully developed independent entity that merely interacts with the body and the external world through means of the brain (though adherents of supernaturalism tend to remain stubbornly obscurantist as to any explanation of how this happens). I’ve also discussed in a previous post (actually on another thread) why the supposition that a naturalist view of the mind is “reductionist” is patently erroneous. To offer a crude analogy, that is like claiming that your computer would operate without multiple transistors to process and store information; or like claiming a recipe would taste just the same without the proper balance of ingredients. No-one - except supernaturalists trying to denigrate science - seriously thinks that minds can be “reduced” to the components that interact to give rise to them. A less crude analogy might be that of music - it is utterly dependent upon sound waves and the matter through which they must travel, but no-one supposes that a Beethoven symphony is “reducible” to its individual component parts, not even the musicians in the orchestra while they’re practising their separate lines of the score.