@pauluc: We return again to wonderland and to unique definition …

Comment on The End of “Junk DNA”? by Sean Pitman.

@pauluc:

We return again to wonderland and to unique definition of species and argument;

Why do you continually misrepresent my position? As I’ve explained to you and Professor Kent several times now, I’m not presenting a new definition of “species” – not at all. The mainstream definition of species works just fine for its intended purpose and does have value. My definition is a definition of unique “kinds” of gene pools that contain qualitatively unique functionality that cannot be evolved by RM/NS. This is not the same thing as the species concept and I’m not sure why you both continue to try to equate the two? That is why different species can indeed evolve, quickly evolve, over short periods of time while different “kinds” of biological systems cannot evolve beyond very low levels of functional complexity regardless of how much time is allotted this side of a practical eternity of time.

Note also that you’ve presented several demonstrably false assertions so far in this particular thread. You started off with the claim that the increasing mutation rate for men with age is clearly too high to consider the Bible’s claim for antediluvian reproductive life spans of several hundred years remotely tenable. You were wrong. You also claimed that other forms of mutations besides SNP-type mutations are too high to be consistent with the Biblical model. You were wrong. And, your claim that deleterious mutations can be effectively removed from slowly reproducing gene pools (via some form of genetic recombination?) is also clearly mistaken.

Why not just admit that Neo-Darwinism is obviously bankrupt and move on? Still clinging to your top-down approach “as Darwin did”? How is that valid “science” when your mechanism is so obviously bankrupt?

Your glory seem to be that classification of phenotypic and genotypic diversity “means what I say it means” completely disregarding the conventions of 150 years of biology and biologist who have gone before.

Not at all. The classification conventions of 150 years of biology are just fine for what they do. However, they do not, as you well know, draw a distinction between what can and cannot evolve via the Darwinian mechanism of random mutations and natural selection (RM/NS). My definition of qualitatively unique “kinds” of biological systems at various levels of functional complexity does draw this distinction and is not a redefinition of the species concept – despite your repeated attempts to paint it as such. The reality is that mine a unique concept that is independent of the species concept.

What is on the line here is the neo-Darwinian mechanism of random mutations combined with natural selection vs. the Biblical model of origins.

Does the mechanism of RM/NS have limitations that can be clearly defined? The answer to that question is yes. Any qualitatively novel system of function that requires a minimum of more than 1000 specifically arranged amino acid residues has not been observed to evolve and statistically is extremely unlikely to evolve this side of a practical eternity of time.

As a practical illustration, let’s say that we are comparing eukaryotic vs. prokaryotic motility systems for single-celled organisms. One type is based on a rotating flagellar system while the other is based on a back-and-forth sliding system. These two systems are qualitatively unique and they both require a minimum of far more than 1000 specifically arranged amino acid residues to work as motility systems. It is quite safe to say, then, that these two populations did not share a common ancestor – unless one wishes to propose that the common ancestor of both had both types of motility systems “front-loaded” in the original parental gene pool.

Another example would be the different kinds of vision systems in existence from a single light-sensitive cluster of cells to a cup-shaped “eye” to a compound eye to an eye with an inverted retina to an eye with a verted retina to an eye with a lens, etc. All such visions systems are qualitatively unique beyond the level of 1000 specifically arranged residues. Therefore, any comparison between gene pools containing codes for vision systems with such differences would suggest that these two gene pools do not share a common evolutionary ancestor – unless one wishes to propose that the original parental gene pool contained codes for both types of vision systems being compared… etc.

The other issue in play here, of course, is the credibility of the Bible. Has the Biblical account of origins been effectively falsified by the claims of modern scientists so as to require a non-testable Divine miracle to overcome? So far, based on what you’ve personally presented, the answer to this question is clearly no. You’ve not come remotely close to falsifying the Biblical claims regarding origins or even calling them into serious question. If anything, you arguments have ended up supporting the Biblical model. In short, the significant weight of the empirical evidence that we currently have in hand fits very very well within the Biblical model while effectively falsifying the neo-Darwinian perspective on origins.

“The biosystems themselves within different gene pools are what can be evaluated as far as levels of functional complexity are concerned. This is not beyond the capabilities of modern science.”

Indeed that is true but as far as I can see it so far has been beyond you to use the tools of modern science to evaluate your hypothesis. Certainly you do not even seem to have attempted to do so. There are complete genomes of at least 30 mammalian species as I have given reference to before. You seem to believe that there are differences between the mammalian species that would conform to your criteria of limits insuperable by an evolutionary process. Most biologist have long since past the point of worrying about these supposed limits so you cannot rely on someone else to do your research. Sit down at your computer and use the available free online resources and compare these genomes and tell us what and where are the 1000faar limits in these genomes that unequivocally destroy the argument that these mammalian species have arisen from a common mammalian ancestor.

I have given you multiple examples of qualitatively unique systems that could not have evolved by RM/NS. Any such systems in any gene pool would be beyond the powers of Darwinian mechanisms. What you seem to want is an analysis of innumerable gene pools with published dividing lines for each. That simply isn’t needed before the basic concept becomes clear – that there is a limit to the creative powers of RM/NS to very low levels of functional complexity and a steady devolution of slowly reproducing gene pools.

If you really think I’m wrong, you’re the one who needs to show how the high level qualitatively unique systems within modern species of plants and animals could actually have evolved given only a few billion years (a drop in the bucket compared to what the average time needed to achieve anything beyond the 1000saa level)? – and get rid of detrimental mutations faster than they are currently entering all slowly reproducing gene pools? That is the just-so story telling fairytale that is beyond scientific tenability.

“All the Pitta species can interbreed and produce viable and virile offspring. Therefore, they share the same basic “kind” of gene pool.”

Pardon my scepticism but I am reluctant to take this on your say so. Please provide a reference for the statement “All the Pitta species can interbreed”.

There are many examples of hybrids between Pitta bird species and no reason to think that any particular Pitta cross breed would be genetically impossible.

http://www.bird-hybrids.com/engine.php?search=pitta&searchby=nomenclature&nomenclature=ALL&family=ALL

This is simply obfuscation and a restatement of your postulate and does not at all respond to the question. Of course there is incomplete lineage sorting as is included for example in the Scally et al paper on comparison of primate genomes (Nature 2012 483:169). You cannot however use this mechanism to say that the 1000fsaar differences have been lost from all the sequenced genomes. Either the differences between mammalian species includes genes or DNA sequences fulfilling your criteria of 1000fsaar or it does not. I find it hard to accept that there are 1000fsaar differences that limit evolution somewhere beyond the species level but at the same time that you insist that all extant canid species arose over 4000 years from 2 animals by a process of mutation and natural selection. You seem to be insisting there is a rapid natural mechanism for speciation and that speciation occurs by multiple minor mutations (very very low complexity) yet there is some profound barrier at some arbitary point that you then use to define a kind.

I’m afraid I do not follow you here? I don’t see that you’ve presented any barrier to rapid canid speciation or any example of any kind of qualitatively unique system within various species of canids that is beyond low levels of functional complexity?

I also don’t see where you’ve presented any example of any qualitatively novel system of function evolving beyond low levels of functional complexity or how this might even be statistically tenable?

I also don’t see where you’ve explained how any naturalistic mechanism can deal with the very high detrimental mutation rate that is realized in every individual in every generation within slowly reproducing gene pools?

Where then is the “science” behind your position?

Oh, you want to me to list off distinct differences innumerable gene pools that could not be evolved. To a limited, but sufficient degree, I’ve already done this – as noted above. Other examples I’ve discussed with you include various qualitatively unique differences between reptiles and birds at high levels of functional complexity (like the breathing system for instance). Or, what about the qualitatively unique differences between human and ape brain structure and function that are based on unique genetic sequences?

I really don’t see why I need to get much more detailed here to get my basic point across? If no higher level system can evolve via RM/NS and slowly reproducing gene pools are devolving, not evolving, over time, then Neo-Darwinism is rationally and scientifically untenable while the claims of the Bible are right in line with the significant weight of the scientific evidence that is currently in hand.

I am happy you can accept as a faith position these extraordinary contradictory positions because of a particular literal reading of the biblical text. But to say

“All that mainstream scientists really have to prop up this concept are fantastic just-so stories that have no more scientific value than fairytales for children.”

and to imagine that even a fraction of the genomic and genetic data supports your unique and peculiar models without even actually examining the genomic data with a view to testing your models compels me to think that you have little understanding of the process of science or the explanatory value of natural process.

It is not a blind faith position to recognize the clear limitations of the Darwinian mechanism of RM/NS or to see that humans and all other slowly reproducing species are devolving toward eventual extinction over time.

All of you who accept the claims of mainstream scientists at face value without considering the limitations of the proposed Darwinian mechanism are not buying into science, but into a popular philosophy of mainstream scientists – a fairytale story that should have no more status in science than any other fairytale told to children at bedtime…

Sean Pitman
www.DetectingDesign.com

Sean Pitman Also Commented

The End of “Junk DNA”?
@Ethan:

It does seem like this feature would probably have an effect on the odds, but I’m not sure what additional significance this would bring to the table since the odds of evolving anything qualitatively novel that requires a minimum of more than 1000 specifically arranged amino acid residues would require trillions upon trillions of years of time.

Sean Pitman
www.DetectingDesign.com


The End of “Junk DNA”?
@pauluc:

You tout reason as trumping faith but do not appear to see that the enlightenment enterprise took precisely the position you think desirable.

I didn’t say that reason trumps faith. What I said was that faith does not trump reason. There’s a difference. What I’ve also said many times in this forum is that a useful or rational faith must go hand in hand with reason. One cannot exist in any kind of meaningful or useful way without the other. Even science itself is dependent upon making leaps of faith into that which is not absolutely known or knowable. Faith and reason are equals in my mind, both created by God. I believe that God gave us our reasoning minds for a reason and He does not expect us to then forgo its use (to paraphrase Galileo).

The logical and consistent end of that road is nihlism. That people like Richard Dawkins and the new atheists unlike the old atheists arrived at a faith position of meaningfulness in humanism rather than meaningless nihlism I think reflects the essential desire in all man for meaning and some higher meaning or faith.

There is no doubt that all mankind desires meaning. However, a desire for meaning is just wishful thinking if desire isn’t backed up by evidence. The same is true for faith. Faith, without the backing of evidence-based reasoning is nothing but wishful thinking.

Also, if God is the God of reason as well as faith, the honest and sincere use of the Divine gift of reason will lead one toward the God of reason; not nihilism.

“You will seek me and find me when you seek me with all your heart.” – Jeremiah 29:13 NIV

Motivation is vital, but given the sincere motivation of the heart, the Divine miracle is that God steps in and interacts with Human reasoning capabilities to guide the mind, based on evidences He has provided, toward Himself. God never asks for acts of faith without first providing evidence as a rational basis for the act or leap of faith. We are even asked to test various claims, to “test the spirits” to see what is and what isn’t from God. (1 John 4:1 NIV) Throughout the Bible God is constantly providing evidence as a basis for His claims and a reason to follow, serve, and worship Him. Nowhere is God portrayed as expecting blind faith in any naked claim coming from His mouth. The claims are always backed up by some form of evidence or prior experience with God and evidence of who He claims to be.

God understands the importance of evidence and the natural human desire for evidence. After all, He’s the one who made us this way.

Sean Pitman
www.DetectingDesign.com

“I do not feel obliged to believe that the same God who has endowed us with senses, reason, and intellect has intended us to forgo their use and by some other means to give us knowledge which we can attain by them.” – Galileo Galilei


The End of “Junk DNA”?
@pauluc:

What is clearly not acceptable is that there is generation of any new “information” as that would clearly play into the hands of the evolutionists. As we discussed in detail concerning the vast predominance of allelic variation in canids and man that must have arisen de novo from the breeding pair or breeding 5 do you or do you not think that new allelic variation contains new “information”?

The vast majority of allelic mutational changes do and did not produce qualitatively new information – only changes to the degree of expression of pre-existing systems (i.e., more or less of the same thing). More or less of the same thing isn’t what I would call “new” information.

However, there are relatively rare examples of truly new information that is qualitatively unique entering the gene pool. The problem, of course, is that all such examples are at very very low levels of functional complexity (i.e., requiring less than 1000 specifically arranged amino acid residues).

So, its relatively easy to evolve a novel beneficial system that is based on a specified 3-character sequence. It’s exponentially harder to evolve a truly novel system that is based on a minimum of 20 specified characters. And, it is effectively impossible to evolve a qualitatively novel system that requires at least 1000 specifically arranged characters (regardless of the type of information system you’re dealing with).

If you say yes then you are certainly outside the current YEC convention. If you say no then you are suggesting that species with very different phenotypes can evolve without any new information. A position that most biologist would find surprising.

I have been invited to speak in numerous venues, to include those largely populated by YECs and YLCs – as you can imagine. Yet, after I present evidence for low-level evolution the vast majority of creationists I’ve spoken to respond very favorably – even enthusiastically. After all, it simply makes good sense that the random discovery of novel beneficial sequences within sequence spaces would be exponentially easier to achieve when you’re dealing with 3-character sequences vs. 20 character sequences. It just makes sense to most people – including well-educated creationists.

Sean Pitman
www.DetectingDesign.com


Recent Comments by Sean Pitman

Science and Methodological Naturalism
Very interesting passage. After all, if scientists are honest with themselves, scientific methodologies are well-able to detect the existence of intelligent design behind various artifacts found in nature. It’s just the personal philosophy of scientists that makes them put living things and the origin of the fine-tuned universe “out of bounds” when it comes to the detection of intelligent design. This conclusion simply isn’t dictated by science itself, but by a philosophical position, a type of religion actually, that strives to block the Divine Foot from getting into the door…


Revisiting God, Sky & Land by Fritz Guy and Brian Bull
@Ron:

Why is it that creationists are afraid to acknowledge the validity of Darwinism in these settings? I don’t see that these threaten a belief in God in any way whatsoever.

The threat is when you see no limitations to natural mindless mechanisms – where you attribute everything to the creative power of nature instead of to the God of nature.

God has created natural laws that can do some pretty amazing things. However, these natural laws are not infinite in creative potential. Their abilities are finite while only God is truly infinite.

The detection of these limitations allows us to recognize the need for the input of higher-level intelligence and creative power that goes well beyond what nature alone can achieve. It is here that the Signature of God is detectable.

For those who only hold a naturalistic view of the universe, everything is attributed to the mindless laws of nature… so that the Signature of God is obscured. Nothing is left that tells them, “Only God or some God-like intelligent mind could have done this.”

That’s the problem when you do not recognize any specific limitations to the tools that God has created – when you do not recognize the limits of nature and what natural laws can achieve all by themselves.

Sean Pitman
www.DetectingDesign.com


Revisiting God, Sky & Land by Fritz Guy and Brian Bull
@Bill Sorensen:

Since the fall of Adam, Sean, all babies are born in sin and they are sinners. God created them. Even if it was by way of cooperation of natural law as human beings also participated in the creation process.

God did not create the broken condition of any human baby – neither the physical or moral brokenness of any human being. God is responsible for every good thing, to include the spark or breath of life within each one of us. However, He did not and does not create those things within us that are broken or bad.

“The owner’s servants came to him and said, ‘Sir, didn’t you sow good seed in your field? Where then did the weeds come from?’ ‘An enemy did this,’ he replied. “The servants asked him, ‘Do you want us to go and pull them up?'” Matthew 13:27-28

Of course, all humans are indeed born broken and are in a natural state of rebellion against God. However, God is not the one who created this condition nor is God responsible for any baby being born with any kind of defect in character, personality, moral tendency, or physical or genetic abnormality. God did not create anyone with such brokenness. Such were the natural result of rebellion against God and heading the temptations of the “enemy”… the natural result of a separation from God with the inevitable decay in physical, mental, and moral strength.

Of course, the ones who are born broken are not responsible for their broken condition either. However, all of us are morally responsible for choosing to reject the gift of Divine Grace once it is appreciated… and for choosing to go against what we all have been given to know, internally, of moral truth. In other words, we are responsible for rebelling against the Royal Law written on the hearts of all mankind.

This is because God has maintained in us the power to be truly free moral agents in that we maintain the Power to choose, as a gift of God (Genesis 3:15). We can choose to accept or reject the call of the Royal Law, as the Holy Spirit speaks to all of our hearts…

Remember the statement by Mrs. White that God is in no wise responsible for sin in anyone at any time. God is working to fix our broken condition. He did not and does not create our broken condition. Just as He does not cause Babies to be born with painful and lethal genetic defects, such as those that result in childhood leukemia, He does not cause Babies to be born with defects of moral character either. God is only directly responsible for the good, never the evil, of this life.

Sean Pitman
www.DetectingDesign.com


Revisiting God, Sky & Land by Fritz Guy and Brian Bull
@Ron:

Again, your all-or-nothing approach to the claims of scientists isn’t very scientific. Even the best and most famous of scientists has had numerous hair-brained ideas that were completely off base. This fact does not undermine the good discoveries and inventions that were produced.

Scientific credibility isn’t based on the person making the argument, but upon the merits of the argument itself – the ability of the hypothesis to gain predictive value when tested. That’s it.

Sean Pitman
www.DetectingDesign.com


Gary Gilbert, Spectrum, and Pseudogenes
Don’t be so obtuse here. We’re not talking about publishing just anything in mainstream journals. I’ve published several articles myself. We’re talking about publishing the conclusion that intelligent design was clearly involved with the origin of various artifactual features of living things on this planet. Try getting a paper that mentions such a conclusion published…

Sean Pitman
www.DetectingDesign.com