1) Do you see a difference …

Comment on The Adventist Accrediting Association to Approve LSU’s Accreditation by Sean Pitman.

1) Do you see a difference between evolution between 3-character sequences and 20-character sequences?

Yes but it is totally irrelevant to the discussion of the relationship between humans and other great apes and the the evidence for any historical relationship.

What difference do you see between evolution between systems that require a minimum of 3 vs. 20 character sequences?

You seem to agree that function-based selection, when it comes to evolution in the English language system, is limited to very low levels of functional complexity because of the exponentially decreases ratio of potentially beneficial vs. non-beneficial with each increase in the minimum size requirement. However, you don’t seem to think this same situation translates into protein-based or DNA-based systems.

Why not? What’s different about protein and/or DNA-based systems of function? Are the functions that result not based on a specific arrangement of characters? – exactly like the English-language system? Do not random mutations have the potential to alter, change, or destroy functionality? – exactly like the English-language system?

Where then is the fundamental difference?

It seems to me like all language/information systems work the very same way – regardless of if you’re talking about English, Russian, German, Chinese, computer code, Morse code, proteins, or DNA. They all experience an exponential decrease the ratio between potentially beneficial vs. non-beneficial with each increase in the minimum size requirement of the sequence of characters. It is for this reason that mindless evolutionary algorithms will not replace authors or computer programmers or God.

2) Do you think that Dawkins’ famous “Weasel” evolution algorithm uses function-based selection?

I am happy to concede that it is a pretty pathetic model for selection based on outcome. The outcome is clearly contrived and is not convincing to me.

Great! We seem to be on the same page so far…

Now if we want to examine linguistic evolution which is what you are actually talking about with sequences of letters and meaning I would be fascinated to know how you think languages creoles and dialects evolve. After all there are innumerable languages which make no sense to me either as oral or written language. I would be fascinated to see any data you can muster on this.

Human languages don’t evolve by random mutations and function-based selection. They evolve by intelligent design…

3) What is the difference in the ratio of meaningful vs. meaningless sequences that are 3-characters long vs. 20-characters long?

I am not sure this is a meaningful scientific question. Maybe for linguistics as I have esuggested but certainly not to my interest and research in biology. I have not studied it and cant find anything meaningful in the scientific literature beyond the linguistics.

Why then do you think most random mutations are either detrimental are neutral with respect to functionality?

In a paper published in 2000, Thirumalai and Klimov make the following relevant comments:

The minimum energy compact structures (MECSs), which have protein-like properties, require that the ground states have H residues surrounded by a large number of hydrophobic residues as is topologically allowed. . . There are implications of the spectacular finding that the number of MECSs, which have protein-like characteristics, is very small and does not grow significantly with the size of the polypeptide chain.

The number of possible sequences for a protein with N amino acids is 20^N which, for N = 100, is approximately 10^130. The number of folds in natural proteins, which are low free energy compact structures, is clearly far less than the number of possible sequences. . .

The number of protein structures is far less than the number of sequences. By imposing simple generic features of proteins (low energy and compaction) on all possible sequences we show that the structure space is sparse compared to the sequence space. Even though the sequence space grows exponentially with N (the number of amino acid residues [by 20^N]) we conjecture that the number of low energy compact structures only scales as lnN [The natural logarithm or the power to which e (2.718 . . . ) would have to be raised to reach N] . . . The number of sequences for which a given fold emerges as a native structure is further reduced by the dual requirements of stability and kinetic accessibility. . . We also suggest that the functional requirement may further reduce the number of sequences that are biologically competent.

So if, as sequence space size grows by 20N the number of even theoretically useful protein structures only scales by the natural log of N, this differential rapidly produces an unimaginably huge discrepancy between potential target and non-target systems. For example, the sequence space size of 1000aa space is 20^1000 = ~1e1301. According to these authors, what is the number of potentially useful protein structures contained within this space? It is 20ln1000 = ~1e9. And, since only a tiny fraction of sequences are able to make any useful protein structure, you can clearly see that the ratio of stable, much less useful or beneficial, protein sequences declines exponentially with each increase in the minimum size/specificity requirement.

This is identical to what happens with any language/information system were meaning is based on a specific sequence or arrangement of characters or basic building blocks or parts. All such systems experience the very same exponential decay in ratio with each linear increase in the number of specifically arranged characters or parts required.

4) Do you think this ratio differences has anything to do with the rate of evolution? – Yes or No and why…

Yes. Obviously the the bigger the changes or specific sequence you demand the less likely this will occur by chance. Dawkins weasely example was merely trying to say that a large change can occur by some mechanism of incremental selection.

What if the selection mechanism is based on function, not on a sequential match to a pre-existing sequence? Then, the ratio of functional vs. non-function sequences becomes very important because it suggests a growing non-beneficial gap distance between islands of function within sequence space. As the minimum distance between one island and the next increases linearly, the “random walk” distance increases exponentially – as does the average time to success.

5) Why did you reference the immune system as an example of evolution when you “already knew” that it works within ~20aa sequence space? – if you already knew that it’s a very low-level template matching example of RM/NS?

Sorry I obviously did not make it clear but I was merely giving an example of the way random changes generate the repertoire from which natural selection can decide outcome. I did suggest that this was one of the evidences that biologists found compelling as an example of variation and natural selection.

At least for MacFarlane Burnet who with peter Medawer received his Nobel prize for clonal selection theory thought this process was basic to all biology and went on as I am sure you will have read in his subsequent books that random generation of diversity and natural selection were both the basis of purposeful immunological responses and evolution of species.

Yes, but you’re in a discussion with me here and you already know that I accept low-level examples of evolution in action via RM/NS. I’d hardly call evolution within 20aa sequence space anything close to the level of 1000 saars that I keep telling you is the statistical limit to evolutionary progress. There are hundreds and thousands of such low-level examples in literature. Why then do you feel the need to continually list these low-level examples off when I’m only asking you for higher level examples?

There is obviously a big difference between our perspective on limits of changes

That is because you admittedly haven’t even considered the problem of changing ratios of potentially beneficial vs. non-beneficial sequences at different levels of functional complexity. That is why your perspective is based on what you imagine must be possible without any real basis in empirical information or science.

You have defined the limit as 1000fsaar. I do not see any difference between micro and macroevolution and think that macroevolution derives from small incremental changes over long periods of time.

Based on what evidence for the statistical tenability of your mechanism to cross the non-beneficial gap distances in sequence spaces at this level and beyond?

Short of you demonstrating the 1000 fsaar limit in some system that differs between humans and great apes I will consider your scenario lacking scientific credibility

Why humans vs. apes? Why not deal with systems where a bit more is known about the functional differences?

Also, there are functional differences between humans and apes that are based on structures that requires far more than 1000 specifically arranged amino acid residues – like human brain structure and function for example.

Sean Pitman Also Commented

The Adventist Accrediting Association to Approve LSU’s Accreditation
This is the same language used by the Bible. Whatever “wiggle room” the Bible leaves open is still open when one uses this language. The Bible is not clear that the “creation of the heavens and the earth” means that the material of the Earth itself was created during creation week. Quite the opposite is true. The Bible seems to suggest that something was here prior to creation week. Or, at the very least, leaves this question open.


The Adventist Accrediting Association to Approve LSU’s Accreditation
Oh please. You do realize that there are difference kinds of “heavens” in Hebrew understanding? This is not a statement arguing that God made the entire universe…


The Adventist Accrediting Association to Approve LSU’s Accreditation
The question is if you or anyone else has even tried to explain how the evolutionary mechanism (RM/NS) can tenably work beyond very very low levels of functional complexity. The answer to that question is no. This means that this mechanism is not backed up by what anyone would call real science. It’s just-so story telling. That’s it. There is nothing in scientific literature detailing the statistical odds of RM/NS working at various levels of functional complexity. And, there is no demonstration beyond systems that require a few hundred averagely specified residues.

What is interesting is that no one who controls the mainstream journals will publish any observations as to why a real scientific basis for the Darwinian mechanism is lacking. The basic information is there. Contrary to Pauluc’s claims, a precise definition of “levels of functional complexity” has been published, along with what happens to the ratios of potential beneficial vs. non-benficial sequences. What no one is allowing to be published is the implications of this information.

Regardless, the implications should be clear to you. The math is overwhelmingly clear. If the ratio of beneficial vs. non-beneficial goes from 1 in 100 to 1 in 1,000,000,000,000 the fact that the average time to success will decrease quite dramatically doesn’t take a rocket scientist to figure out. Evolutionists, who have actually seriously considered this problem must recognize the implications here, but seem to be trying to brush it all under the rug because no one knows of any other viable mechanism (again, despite Pauluc’s unsupported claims to the contrary – to include his “life enzymes”).

In any case, it is possible for you to move beyond blind faith in the unsupported claims of your “experts” and consider the information that is available to all for yourself. Start at least trying to do a little math on your own and you will no doubt recognize the problem for yourself regardless of what your experts continue to claim – without any basis in empirical evidence or science.

Sean Pitman
www.DetectingDesign.com


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