@Brad: I am probably going to

Comment on Elliot Sober: Just Don’t Call the Designer “God” by Sean Pitman.

I am probably going to write far too much but if you want the conclusion, it is that Sean Pitman is completely and utterly wrong in everything he says in his comments and displays a great ignorance of proteins and their structure and function.

And:

I hope the above short essay on protein structure and function is useful even to Sean Pitman who needs to stop being obsessed with computer-based numerology and do some reading and talk to some practical protein scientists.

From David Dryden of the University of Edinburgh. See: http://groups.google.com/group/talk.origins/msg/a7f670c859772a9b

Ah, so you’ve read Dryden’s arguments…

Where did Dryden point out my ignorance of protein structure and function? I am, after all, a pathologist with a subspecialty in hematopathology – a field of medicine that depends quite heavily on at least some understanding of protein structure and function. Yet Dryden says that I’m completely and utterly wrong in everything I say on this topic? Sounds just a bit overwrought – don’t you think?

In any case, where did Dryden substantively address my argument for an exponential decline of evolutionary potential with increasing minimum structural threshold requirements? Dryden himself only deals with very low level examples of evolution in action. He doesn’t even consider the concept of higher levels of functional complexity and the changes in the ratios of beneficial vs. non-beneficial sequences that would be realized in sequence space.

Dryden also completely misunderstands the challenge of the structural cutoff of systems that require a minimum of at least 1000 specifically arranged amino acid residues to work to do a particular function. He also flatly contradicts Axe’s work which suggests that it is not an easy thing to alter too many amino acid residue positions at the same time and still have the system in question work to do its original function. There is some flexibility to be sure, but there is a limit beyond which this flexibility cannot by crossed for protein-based systems. And, as this minimum limit increases for higher level systems, the ratio of beneficial vs. non-beneficial does in fact decrease exponentially. Dryden seems completely clueless on this particular all-important point.

This cluelessness is especially highlighted by Dryden’s comment that the bacterial rotary flagellum isn’t very complex at all:

These increasing degrees of functional complexity are a mirage.
Just because a flagellum spins and looks fancy does not mean it is
more complex than something smaller. The much smaller wonderful
machines involved in manipulating DNA, making cell walls or
cytoskeletons during the cellâ€™s lifecycle do far more complex and
varied things including switching between functions. Even a small
serine protease has a much harder job than the flagellum. The
flagellum just spins and spins and yawnâ€¦

I really couldn’t believe that Dryden actually said this when I first read it. Dryden actually suggests that a small serine protease is more functionally complex than a bacterial flagellum?! – just because it is used more commonly in various metabolic pathways? – or more interesting to Dryden? He completely misses the point that the bacterial flagellum requires, at minimum, a far far greater number of specifically arranged amino acid “parts” than does a serine protease – thousands more.

And Dryden is your “expert” regarding the potential of RM/NS to create protein-based systems beyond very low levels of functional complexity? Why not find somebody who actually seems to understand the basic concept?

Here’s another gem from Dryden. In response to my comment that, “The evidence shows that the distances [in sequence space] between
higher and higher level beneficial sequences with novel functions
increases in a linear manner.” Dryden wrote:

Reply: What evidence? And if importance of function scales with
sequence length and the scaling is linear then I am afraid that 20^100
is essentially identical to 2 x 20^100. Also a novel function is not a
new function but just one we stumble upon in doing the hard work in
the lab. Itâ€™s been there a long timeâ€¦

Dryden doesn’t grasp that in the debate over the creative potential of RM/NS that a novel functional system is one that the evolving population is looking for – not some lab scientists. It is only there in the potential of sequence space. It is not found until random mutations within the gene pool discover it by pure luck.

Dryden also doesn’t understand that this discussion isn’t over the “importance of function” but over levels of beneficial functionality – regardless of there “importance”. He also doesn’t understand that if a system requires a minimum sequence length or size (to include multiprotein systems) and a minimum degree of specific arrangement of amino acid residues within that minimum size, that a linear increase in this minimum structural threshold requirement does not result in a linear increase in average number of random mutations needed to achieve success. The linear increase in structural threshold results in an exponential decrease in the ratio of potentially beneficial vs. non-beneficial. This, obviously (to the candid mind anyway) will result in an exponential increase in the average number of random mutations needed to achieve success at the higher level.

Really, I would love to hear your take on Dryden’s paper in the light of a complete lack of evolution in action beyond very very low levels of functional complexity – i.e., minimum structural threshold requirements. I’m sure you could do better than he did…

Sean Pitman
www.DetectingDesign.com

Table of Contents

1 Sean Pitman Also Commented
- 1.1 Recent Comments by Sean Pitman
2 Related

Sean Pitman Also Commented

Elliot Sober: Just Don’t Call the Designer “God”
@Professor Kent:

My understanding is that, historically, Adventist fundamental beliefs have shifted in ways that individuals holding one particular position, including Ellen White herself at times, could have been expelled from the Church by those holding another particular position. There was a time when those of the Church held different views on what 24-hour period of the day should be kept as Sabbath (it wasnâ€™t always sunset to sunset); the Godhead (we once rejected the trinity); and righteousness by faith (we once believed in righteousness by works).

These disagreements occurred before certain agreed positions were so settled in the minds of the founding fathers and mothers of the SDA Church that they became “fundamental” pillars of the SDA faith. The current list of fundamentals was not always as it currently stands. It grew and developed over time. It is only expected that as more information comes clearly to light that the list of important “fundamental” beliefs would also expand over time.

And, as the early Church founders soon discovered, without the maintenance of internal order, discipline, and government within the Church, as based on the concept of “present truth”, as understood by the organized body of believers, the organization soon begins to fragment towards chaos and irrelevance…

Sean Pitman
www.DetectingDesign.com

Elliot Sober: Just Don’t Call the Designer “God”
@Professor Kent:

Sean, while I could agree with your statement on a prima facie basis, I think one needs to dig a bit deeper here. This statement basically says that we donâ€™t need the Bible or any type of falsifiable evidence or even beliefs to gain admission to heaven, which seems to contradict what you often state (not to mention the purpose of this website). I could be wrong, but I believe that God is able to claim souls who lack knowledge in Him because he can judge whether they would accept Him and Christâ€™s sacrifice if they had representative knowledge of Him.

Exactly…

It just goes to show that it is motive, not current knowledge or beliefs, that is important when it comes to judging if a person is or is not savable.

This idea does not contradict my efforts to uphold truth as I see it. Just because knowledge is not the basis of salvation does not mean that it isn’t important. Knowledge is the basis of the solid conscious hope of the Gospel message. While one can be saved without ever having a conscious knowledge of this future glory while here on Earth, it sure would be nice to have known while here – right?

Iâ€™m not convinced that God saves them because they have â€œlove;â€ after all, many animals give well-documented evidence of having love, which is an instinct written in the genes of many life forms, including most humans (Iâ€™ve met a few who could be exceptions). I suspect that He who knows us in the womb can discern much more than our love, and recognizes what our choice would be given an opportunity to know Him and serve Him.

Our moral choices are based on motive, not knowledge. While animals do express love and devotion to their masters, they cannot appreciate moral freedom as we humans can. They have not been given moral responsibility or choice as we have been given it. Free moral choices are based on the motive of love – of doing unto others as you would like to be treated because of your love for your neighbor.

Remember, it was Jesus who pointed out that all the Law and the Prophets were built on the single “Royal Law”, and James put it, of Love – love to both God and toward our neighbors. Matthew 22:39-40 NIV.

And, as Paul points out, those who love their neighbors as themselves fulfill the Law and are therefore savable – regardless of their knowledge or lack thereof regarding the particulars of God’s existence, the life and death of Jesus, His true character, or any other doctrinal truths while in this life. Romans 13:8-10 NIV.

Sean Pitman
www.DetectingDesign.com

Elliot Sober: Just Don’t Call the Designer “God”
@Professor Kent:

Like the vast majority of readers here, I donâ€™t need a scientific basis for my faith, and I believe I can be saved by it however â€œblindâ€ it may be.

Salvation is based on love, not blind faith – or faith of any kind for that matter. It is for this reason that even those who have never heard the name of Jesus or had any real concept of God can be saved according to how they expressed the Royal Law of Love toward their neighbors – a law which has been written on the hearts of all. This is why I believe that there will be a number of very surprised atheists in Heaven someday…

Faith or belief is the basis of conscious hope, but not of salvation. If you have faith that can move mountains, but have not love, you have gained nothing… 1 Corinthians 13:2 NIV.

Sean Pitman
www.DetectingDesign.com