p-value testing will never be the same again

[shunyadragon]

Surely not, what natural process will generate a given protein with 100% certainty?

Blessings,
Lee

Simply the Laws of Nature, and the fact that many amino acids simply occur naturally. The only criteria is the environment in which they form. The Miller-Urey and other similar experiments demonstrated how amino-acids formed naturally, and amino acids have been found in meteorites.

Source: https://en.m.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment

The experiment
The Miller–Urey experiment[1] (or Miller experiment)[2] was a chemical experiment that simulated the conditions thought at the time to be present on the early Earth, and tested the chemical origin of life under those conditions. The experiment supported Alexander Oparin's and J. B. S. Haldane's hypothesis that putative conditions on the primitive Earth favoured chemical reactions that synthesized more complex organic compounds from simpler inorganic precursors. Considered to be the classic experiment investigating abiogenesis, it was conducted in 1952[3] by Stanley Miller, with assistance from Harold Urey, at the University of Chicago and later the University of California, San Diego and published the following year.[4][5][6]

After Miller's death in 2007, scientists examining sealed vials preserved from the original experiments were able to show that there were actually well over 20 different amino acids produced in Miller's original experiments. That is considerably more than what Miller originally reported, and more than the 20 that naturally occur in life.[7] More recent evidence suggests that Earth's original atmosphere might have had a composition different from the gas used in the Miller experiment, but prebiotic experiments continue to produce racemic mixtures of simple to complex compounds under varying conditions.

© Copyright Original Source

Further research has demonstrated that live could have emerged near undersea vents in similar conditions as the Miller-Urey experiments, and the atmosphere is not the likely environment. Hot springs are another possibility.

[lee_merrill]

Simply the Laws of Nature, and the fact that many amino acids simply occur naturally. The only criteria is the environment in which they form. The Miller-Urey and other similar experiments demonstrated how amino-acids formed naturally, and amino acids have been found in meteorites.

But the laws of nature do not guarantee that a given protein will form, nor would an abundance of amino acids.

Blessings,
Lee

[shunyadragon]

But the laws of nature do not guarantee that a given protein will form, nor would an abundance of amino acids.

Blessings,
Lee

Guarantee is legal term for a legal contract for such things as the reliability of a manufactured product, and not a scientific term for physics, cosmology biochemistry, genetics, evolution nor any other science for that matter.

Nothing meaningful here. Again the not so subtle 'arguing from ignorance' will get you nowhere.

[lee_merrill]

Guarantee is legal term for a legal contract for such things as the reliability of a manufactured product, and not a scientific term ...

It means a 100% probability, as in fact, you stated...

Blessings,
Lee

[shunyadragon]

It means a 100% probability, as in fact, you stated...

Blessings,
Lee

Yes, all the given proteins necessary have a 100% probability of eventually forming to form the set of amino acids we have today. We had millions of years for this to take place, no problem.

[shunyadragon]

The following reference gives a detailed critique of William Dembski's book No Free Lunch, and it goes into more detail into my objections to Dempski's misuse of probability and statistics by asserting uniform probability over time of 'chance' and utter random combinations to come up with a low probability, or as asserted the impossibility of natural laws causing the universe, abiogenesis nor the evolution of life. This reference is heavily footnoted and referenced to document the objections to Intelligent Design.

Source: http://www.talkorigins.org/design/faqs/nfl/#unif

The aim of Dr William Dembski's book No Free Lunch is to demonstrate that design (the action of a conscious agent) was involved in the process of biological evolution. The following critique shows that his arguments are deeply flawed and have little to contribute to science or mathematics. To fully address Dembski's arguments has required a lengthy and sometimes technical article, so this summary is provided for the benefit of readers without the time to consider the arguments in full.

Dembski has proposed a method of inference which, he claims, is a rigorous formulation of how we ordinarily recognize design. If we can show that an observed event or object has low probability of occurring under all the non-design hypotheses (explanations) we can think of, Dembski tells us to infer design. This method is purely eliminative--we are to infer design when we have rejected all the other hypotheses we can think of--and is commonly known as an argument from ignorance, or god-of-the-gaps argument.

Because god-of-the-gaps arguments are almost universally recognized by scientists and philosophers of science to be invalid as scientific inferences, Dembski goes to great length to disguise the nature of his method. For example, he inserts a middleman called specified complexity: after rejecting all the non-design hypotheses we can think of, he tells us to infer that the object in question exhibits specified complexity, and then claims that specified complexity is a reliable indicator of design.

The only biological object to which Dembski applies his method is the flagellum of the bacterium E. coli. First, he attempts to show that the flagellum could not have arisen by Darwinian evolution, appealing to a modified version of Michael Behe's argument from irreducible complexity. However Dembski's argument suffers from the same fundamental flaw as Behe's: he fails to allow for changes in the function of a biological system as it evolves.

Since Dembski's method is supposed to be based on probability and he has promised readers of his earlier work a probability calculation, he proceeds to calculate a probability for the origin of the flagellum. But this calculation is based on the assumption that the flagellum arose suddenly, as an utterly random combination of proteins. The calculation is elaborate but totally irrelevant, since no evolutionary biologist proposes that complex biological systems appeared in this way. In fact, this is the same straw man assumption frequently made by Creationists in the past, and which has been likened to a Boeing 747 being assembled by a tornado blowing through a junkyard.

This is all there is to Dembski's main argument. He then makes a secondary argument in which he attempts to show that even if complex biological systems did evolve by undirected evolution, they could have only done so if a designer had fine-tuned the fitness function or inserted complex specified information at the start of the process.

The argument from fine-tuning of fitness functions appeals to a set of mathematical theorems called the "No Free Lunch" theorems. Although these theorems are perfectly sound, they do not have the implications which Dembski attributes to them. In fact they do not apply to biological evolution at all. All that is left of Dembski's argument is then the claim that life could only have evolved if the initial conditions of the Universe and the Earth were finely tuned for that purpose. This is an old argument, usually known as the argument from cosmological (and terrestrial) fine-tuning. Dembski has added nothing new to it.

Complex specified information (CSI) is a concept of Dembski's own invention which is quite different from any form of information used by information theorists. Indeed, Dembski himself has berated his critics in the past for confusing CSI with other forms of information. This critique shows that CSI is equivocally defined and fails to characterize complex structures in the way that Dembski claims it does. On the basis of this flawed concept, he boldly proposes a new Law of Conservation of Information, which is shown here to be utterly baseless.

Dembski claims to have made major contributions to the fields of statistics, information theory and thermodynamics. Yet his work has not been accepted by any experts in those fields, and has not been published in any relevant scholarly journals.

No Free Lunch consists of a collection of tired old antievolutionist arguments: god-of-the-gaps, irreducible complexity, tornado in a junkyard, and cosmological fine-tuning. Dembski attempts to give these old arguments a new lease of life by concealing them behind veils of confusing terminology and unnecessary mathematical notation. The standard of scholarship is abysmally low, and the book is best regarded as pseudoscientific rhetoric aimed at an unwary public which may mistake Dembski's mathematical mumbo jumbo for academic erudition.

© Copyright Original Source

[shunyadragon]

Well, constraining the set of events is not the same as constraining possible variables, and variables are constrained to reduce extraneous effects that are not of interest, not to increase the probability.

Does not make sense at all. The proper way to determine probability is to consider each cause and effect event to be constrained by the laws of nature, which is the reality of the nature of our physical existence. This procedure does not necessarily reduce the extraneous effects. The probability of each cause and effect event would consider extraneous effects as is done when probability and statistics are properly used in research experiments. Yes this proper use of statistics would increase probability, because it would not use the bogus 'Chance' of the whole chain of cause and effect events which assumes 'utter fandom combinations.'

The following from the other thread explains the problems in great detail with references.

Source: http://www.talkorigins.org/design/faqs/nfl/#unif

The aim of Dr William Dembski's book No Free Lunch is to demonstrate that design (the action of a conscious agent) was involved in the process of biological evolution. The following critique shows that his arguments are deeply flawed and have little to contribute to science or mathematics. To fully address Dembski's arguments has required a lengthy and sometimes technical article, so this summary is provided for the benefit of readers without the time to consider the arguments in full.

Dembski has proposed a method of inference which, he claims, is a rigorous formulation of how we ordinarily recognize design. If we can show that an observed event or object has low probability of occurring under all the non-design hypotheses (explanations) we can think of, Dembski tells us to infer design. This method is purely eliminative--we are to infer design when we have rejected all the other hypotheses we can think of--and is commonly known as an argument from ignorance, or god-of-the-gaps argument.

Because god-of-the-gaps arguments are almost universally recognized by scientists and philosophers of science to be invalid as scientific inferences, Dembski goes to great length to disguise the nature of his method. For example, he inserts a middleman called specified complexity: after rejecting all the non-design hypotheses we can think of, he tells us to infer that the object in question exhibits specified complexity, and then claims that specified complexity is a reliable indicator of design.

The only biological object to which Dembski applies his method is the flagellum of the bacterium E. coli. First, he attempts to show that the flagellum could not have arisen by Darwinian evolution, appealing to a modified version of Michael Behe's argument from irreducible complexity. However Dembski's argument suffers from the same fundamental flaw as Behe's: he fails to allow for changes in the function of a biological system as it evolves.

Since Dembski's method is supposed to be based on probability and he has promised readers of his earlier work a probability calculation, he proceeds to calculate a probability for the origin of the flagellum. But this calculation is based on the assumption that the flagellum arose suddenly, as an utterly random combination of proteins. The calculation is elaborate but totally irrelevant, since no evolutionary biologist proposes that complex biological systems appeared in this way. In fact, this is the same straw man assumption frequently made by Creationists in the past, and which has been likened to a Boeing 747 being assembled by a tornado blowing through a junkyard.

This is all there is to Dembski's main argument. He then makes a secondary argument in which he attempts to show that even if complex biological systems did evolve by undirected evolution, they could have only done so if a designer had fine-tuned the fitness function or inserted complex specified information at the start of the process.

The argument from fine-tuning of fitness functions appeals to a set of mathematical theorems called the "No Free Lunch" theorems. Although these theorems are perfectly sound, they do not have the implications which Dembski attributes to them. In fact they do not apply to biological evolution at all. All that is left of Dembski's argument is then the claim that life could only have evolved if the initial conditions of the Universe and the Earth were finely tuned for that purpose. This is an old argument, usually known as the argument from cosmological (and terrestrial) fine-tuning. Dembski has added nothing new to it.

Complex specified information (CSI) is a concept of Dembski's own invention which is quite different from any form of information used by information theorists. Indeed, Dembski himself has berated his critics in the past for confusing CSI with other forms of information. This critique shows that CSI is equivocally defined and fails to characterize complex structures in the way that Dembski claims it does. On the basis of this flawed concept, he boldly proposes a new Law of Conservation of Information, which is shown here to be utterly baseless.

Dembski claims to have made major contributions to the fields of statistics, information theory and thermodynamics. Yet his work has not been accepted by any experts in those fields, and has not been published in any relevant scholarly journals.

No Free Lunch consists of a collection of tired old antievolutionist arguments: god-of-the-gaps, irreducible complexity, tornado in a junkyard, and cosmological fine-tuning. Dembski attempts to give these old arguments a new lease of life by concealing them behind veils of confusing terminology and unnecessary mathematical notation. The standard of scholarship is abysmally low, and the book is best regarded as pseudoscientific rhetoric aimed at an unwary public which may mistake Dembski's mathematical mumbo jumbo for academic erudition.

© Copyright Original Source

And snowflakes are not designed because this is viewing the probability of a random arrangement after the fact.

No it is not. It is the probability of any one complex snowflake of the same number of events.

The probability of any given arrangement (of snowflakes, of taillights on a highway, of amino acid chains) after it happens is 100%.

The issue is NOT after it happens. Probability is a prediction before the result of the cause and effect outcome

Blessings,
Lee[/QUOTE]

[lee_merrill]

Source: http://www.talkorigins.org/design/faqs/nfl/#unif

This method is purely eliminative--we are to infer design when we have rejected all the other hypotheses we can think of--and is commonly known as an argument from ignorance, or god-of-the-gaps argument.

© Copyright Original Source

But we do validly infer design, with the process that Dembski outlines, this is not arguing from ignorance, it is based on knowledge of design.

Source: NFL page

Dembski's argument suffers from the same fundamental flaw as Behe's: he fails to allow for changes in the function of a biological system as it evolves.

© Copyright Original Source

But that is considered in the argument of irreducible complexity, the object of interest is non-functional if one part is removed.

Source: NFL page

In fact, this is the same straw man assumption frequently made by Creationists in the past, and which has been likened to a Boeing 747 being assembled by a tornado blowing through a junkyard.

© Copyright Original Source

So with irreducibly complex objects, they do have to appear all at once in order to be functional.

Source: NFL page

Although these theorems are perfectly sound, they do not have the implications which Dembski attributes to them. In fact they do not apply to biological evolution at all.

© Copyright Original Source

The NFL theorem is about fitness functions, which indeed do apply to evolution.

Blessings,
Lee

[lee_merrill]

Yes this proper use of statistics would increase probability, because it would not use the bogus 'Chance' of the whole chain of cause and effect events which assumes 'utter fandom combinations.'

Well, the question is whether a given chain of events has independent probabilities for each event.

No it is not. It is the probability of any one complex snowflake of the same number of events.

It is indeed viewing the probability of a given snowflake after the fact. But I don't understand your statement here, P(A|A) is 1, or stated in English, the probability of event A given that event A happened is 100%.

Blessings,
Lee

[shunyadragon]

Well, the question is whether a given chain of events has independent probabilities for each event.

The answer is an easy not. By the evidence the chain of the outcome of cause and effect events is dependent on the probability for each event constrained by the laws on nature.

It is indeed viewing the probability of a given snowflake after the fact. But I don't understand your statement here, P(A|A) is 1, or stated in English, the probability of event A given that event A happened is 100%.

Blessings,
Lee

No, probability is predictive by its nature, and any given snow flake with the same given complexity is only an a example after the fact. The probability of any given specific shape of a snowflake with the same complexity is not 100%. The probability of snowflakes forming with the same geometric crystal pattern determined by the chemistry of water is 100%.

Source: https://experimentalmath.info/blog/2009/08/misuse-of-probability-by-creation-scientists-and-others/

Along this line, consider snowflakes. Bentley and Humphrey’s book Snow Crystals [Bentley] includes over 2000 high-resolution black-and-white photos of real snowflakes, each with intricate yet highly regular patterns (a few of the Bentley-Humphrey photos are posted at Online article). The chances that one particular structure, with striking near-perfect 6-way symmetry, can form “at random” can be calculated as roughly one part in 10^(2500). Does this astoundingly small probability figure constitute proof that individual snowflakes have been intelligently designed? Obviously not. The fallacy, once again, is presuming a sudden, all-at-once random formation. Instead, snowflakes, like biological organisms, are formed as the product of a series of steps, acting under natural laws with some element of chance.

© Copyright Original Source

[shunyadragon]

But we do validly infer design, with the process that Dembski outlines, this is not arguing from ignorance, it is based on knowledge of design.

Actually my previous responses responded to all these assertions and inferences without objective verifiable evidence nor falsifiable hypothesis, which at this point none have been provided to support Intelligent Design.

Source: NFL page

Dembski's argument suffers from the same fundamental flaw as Behe's: he fails to allow for changes in the function of a biological system as it evolves.

© Copyright Original Source

But that is considered in the argument of irreducible complexity, the object of interest is non-functional if one part is removed.

In evolution if one part is removed the organism or the part of the organism fails, which is the natural course of evolution. Not all mutations result in a positive survival of the organism. Millions of years are available for successful mutations as one mutation or a series in evolution. As the evidence indicates the results are not highly optimal, but only optimal to the point of successful natural selection.

Source: NFL page

In fact, this is the same straw man assumption frequently made by Creationists in the past, and which has been likened to a Boeing 747 being assembled by a tornado blowing through a junkyard.

© Copyright Original Source

So with irreducibly complex objects, they do have to appear all at once in order to be functional.

Actually this only happens as described in human manufactured products and yes, they fail when something is missing.

This conflicts with the actual evidence that structures such as the flagellum and the eye evolve over millions of years, and do not appear all at once, as in the claim of alternate claim of complete randomness 'all at once,' which is not an option based on the evidence.

Source: NFL page

Although these theorems are perfectly sound, they do not have the implications which Dembski attributes to them. In fact they do not apply to biological evolution at all.

© Copyright Original Source

The NFL theorem is about fitness functions, which indeed do apply to evolution.

Actually the NFL theorem conflicts with evolution without objective verifiable evidence. It does not take into account that fitness functions can evolve over time, and do not have to fit all at once and all or nothing. It is based on the faulty probability assumptions of intelligent design and assumes a chain of the outcomes of all cause and effect events are random. This goes back to my original objections supported by references.

Source: https://en.wikipedia.org/wiki/No_free_lunch_theorem

However, note that NFL only applies if the target function is chosen from a uniform distribution of all possible functions. If this is not the case, and certain target functions are more likely to be chosen than others, then A may perform better than B overall. The contribution of NFL is that it tells us choosing an appropriate algorithm requires making assumptions about the kinds of target functions the algorithm is being used for. With no assumptions, no "meta-algorithm", such as the scientific method, performs better than random choice.

© Copyright Original Source

[Roy]

But we do validly infer design, with the process that Dembski outlines, this is not arguing from ignorance, it is based on knowledge of design.

Source: NFL page

Dembski's argument suffers from the same fundamental flaw as Behe's: he fails to allow for changes in the function of a biological system as it evolves.

© Copyright Original Source

But that is considered in the argument of irreducible complexity, the object of interest is non-functional if one part is removed.

Garbage. The irreducible complexity argument assumes a single, non-changing function.

So with irreducibly complex objects, they do have to appear all at once in order to be functional.

Garbage. Building an arch using scaffolding is a well-known counter-example. So well known that your unawareness of it shows that you're uncritically and unthinkingly swallowing ID clap-trap.

The NFL theorem is about fitness functions, which indeed do apply to evolution.

Garbage. The NFL theorem is about search functions, not fitness functions.

Your ignorance is not an argument.

[Roy]

Well here, the probability of a coin flip coming up heads is 50% if you view the coin flip before the event occurs. Viewing the event after the coin flip, the probability is 100% that it came up the way it did. So you can view an event such as protein production before the event occurred, and ask what that probability would be.

That would be "viewing the probability of a random arrangement after the fact" - which you just cautioned against for snowflakes, which you don't think are designed, but are content to do for proteins, which you want to show were designed. You're even content to 'calculate' the probability using a completely different production method than the one found in nature, making your supposed probabilities not just irrelevant but deliberately so.

You are a self-serving, inconsistent, double-standard-holding, dishonest hypocrite.

[lee_merrill]

The answer is an easy not. By the evidence the chain of the outcome of cause and effect events is dependent on the probability for each event constrained by the laws on nature.

Are you saying there are no such things as statistically independent events in nature? Coin flips are one example.

No, probability is predictive by its nature, and any given snow flake with the same given complexity is only an a example after the fact. The probability of any given specific shape of a snowflake with the same complexity is not 100%. The probability of snowflakes forming with the same geometric crystal pattern determined by the chemistry of water is 100%.

I'm not sure what you are saying, but the probability of a given snowflake pattern forming is not 100%.

Source: https://experimentalmath.info/blog/2009/08/misuse-of-probability-by-creation-scientists-and-others/

Along this line, consider snowflakes. Bentley and Humphrey’s book Snow Crystals [Bentley] includes over 2000 high-resolution black-and-white photos of real snowflakes, each with intricate yet highly regular patterns (a few of the Bentley-Humphrey photos are posted at Online article). The chances that one particular structure, with striking near-perfect 6-way symmetry, can form “at random” can be calculated as roughly one part in 10^(2500). Does this astoundingly small probability figure constitute proof that individual snowflakes have been intelligently designed? Obviously not. The fallacy, once again, is presuming a sudden, all-at-once random formation. Instead, snowflakes, like biological organisms, are formed as the product of a series of steps, acting under natural laws with some element of chance.

© Copyright Original Source

The fallacy here is miscalculating P(A|A), which is 100%.

Blessings,
Lee

[lee_merrill]

In evolution if one part is removed the organism or the part of the organism fails, which is the natural course of evolution. Not all mutations result in a positive survival of the organism. ...

Actually this only happens as described in human manufactured products and yes, they fail when something is missing.

But you just said that if one part is removed, at times the organism does not survive.

This conflicts with the actual evidence that structures such as the flagellum and the eye evolve over millions of years, and do not appear all at once, as in the claim of alternate claim of complete randomness 'all at once,' which is not an option based on the evidence.

So what is the evolutionary path to development of the flagellum?

Actually the NFL theorem conflicts with evolution without objective verifiable evidence. It does not take into account that fitness functions can evolve over time, and do not have to fit all at once and all or nothing.

Actually, the NFL theorem does apply to evolution, and a changing fitness function is not a problem, it has to do with all fitness functions.

Blessings,
Lee