@pauluc: “There has only been a few hundred generations since …

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


“There has only been a few hundred generations since our original parents.”

This is based on a particular exegesis of religious text not published data derived from experiment.

I personally see a great deal of empirical evidence to suggest that life on this planet, to include human life, is of recent origin – consistent with the claims of the Bible, to include the claims of Jesus Himself who is quoted as saying that He had personally witnessed pre-history and was/is The Creator of it all.

“While we are in fact heading downhill genetically, in each generation”,

This is based on exegesis of religious text and you have not yet provided any compelling direct evidence from data on genomics beyond showing the rate of new mutations from generation to generation which we all can accept.

We know far more than just the rate of mutations. We also know the minimum rate of detrimental mutations vs. beneficial mutations and the death rate that would be required to effectively remove the detrimental mutations from the gene pool in a manner that would keep them from building up over time. I’ve presented what seems to me to be very compelling evidence that the detrimental mutation rate is far far too high for natural selection to cope with in any sort of meaningful way (even based only on the SNP mutation rate). The death rate required to remove the detrimental mutations from the gene pool as fast as they are entering it in each generation would be far beyond the reproductive capacity of humans or any other slowly reproducing species.

What of the rate of loss of mutations from the generation to generation within a family?

As you know, or at least as you should know, detrimental mutations are not lost or removed nearly as fast as they are gained in each individual in each generation. That is why no known naturalistic mechanism comes remotely close to solving this devastating problem for neo-Darwinism.

After all only half the genetic material and the newly acquired maternal of paternal mutations are transmitted to a single progeny. Your calculation of never-ending accumulation of detrimental mutations seems to be oblivious to this constant gain and loss of new genetic material.

One problem, of course, is that the genetic material from both parents sustains detrimental mutations in each generation at a rate far far higher than the coping potential of natural selection or any other naturalistic mechanism. I’m really not sure what you think you gain from your argument here? After all, even if mutations only occurred in one parent, instead of both parents, the number of mutations transferred to any given child would still be far far too high for natural selection to deal with in slowing reproducing populations. As I’ve already explained many times now, the real problem here is the minimum required death rate that natural selection would need to effectively deal with the detrimental mutation rate. Regardless of how you look at the problem, the required death rate would still be far far too high.

Obviously, you still have yet to sit down and actually deal with the statistics involved with this particular problem.

In talking of mutation you seem to infer SNP as the variation driving selection and evolution but seem to exclude the other sources of variation that any biologist would accept; indels, VNTR, variation in transposable elements, and CNVs.

Not true. I did mention indel mutations and other forms of genetic mutations, but I thought I’d give you a huge benefit of the doubt by only considering SNPs. In any case, all forms of genetic mutations are almost always detrimental. Very rarely will any kind of mutation be selectably beneficial – and always at a low level of functional complexity.

Together these account for 0.5% sequence diversity between individuals identified in hapmap. To put this in perspective two random, apparently unrelated individuals selected from geographically different regions are likely to differ by up to 15,000,000 bases in sequence. What is 100 more against that level of variability?

Indeed. Prior estimates of average human similarity of around 99.9% didn’t take into account all the various types of mutational changes that occur. The current estimate you cite of around 0.5% diversity is based on this consideration.


This variability has built up over generations and has been enhanced over what SNPs could alone achieve – as you correctly point out. However, this only adds to my point that the human gene pool is degenerating over time – even faster than what could be assumed using only the SNP mutation rate. In other words, the total number of nucleotide changes resulting from all forms of genetic mutations combined is far higher than the SNP mutation rate of <100 per person per generation. Again, of those that affect function, the vast majority are detrimental to one degree or another.

Now against this backdrop of existing variability found in hapmap what happens if we introduce a model of homogenization of the genetic repertoire with a genetic bottleneck of 2 individuals [or in the case of man 5 genetically distinct individuals] in 2349-2348 BC and I think we do have significant problems. You must then postulate that most of the inter-individual variability averaging 15E6 bases was introduced to the human gene pool over a period of 4360 years. Assuming a generation time of 30 years that translates to accumulation of variation at a rate of 103211 bases per generation.

For argument’s sake, let’s assume that all the current inter-individual variability started, say, 5000 years ago (since there were certainly mutational differences between the individuals on Noah’s Ark):

So, 15e6 / 5000 = 3000 mutation differences per year or ~1500 per individual per year since random mutations are unlikely to affect the same spot in unrelated lineages. As far as the length of an average generation, “For much of human history the average generation length has been determined socially by the average age of women at first birth, about 16 years.” But, let’s round up a bit and use a generation time of 20 years. Given a generation time of 20 years, there would be ~30,000 mutational differences per person per generation.

Although substantially less than your calculation, 30,000 mutational variations per generation still seems like a very large number. How can all of these DNA differences be produced in such a short time?

Well, the per-generation mutational nucleotide rate of change is roughly as follows for the various types of mutations listed below:

Nucleotide substitutions: ~70
Satellite mutations: 3,000
Deletions: 5,000
Duplications/ insertions: 5,000
Inversions/translocations: 10,000
Conversions: 10,000

As you can see, a per generation variation rate is reasonably over 30,000 nucleotide variations per generation within each individual. Note that this would produce over 60,000 nucleotide differences on a person-per-person comparison between different lineages in each generation.

Again the measured 102-120 per generation pales into insignificance at that level of postulated inter-generational variability.

I agree…

The problem as I see it is you want to propose there was a miraculous origin by Divine Fiat Creation 4004 BC and a Divine intervention with a miraculous worldwide flood in 2349 BC but you want the biology to exclude miracles? Where is the logic in that? I cannot see why you seem averse to any miracles in the biological realm. Are you just contrary and because I say that I can only understand the literalist position by invoking miracles at the time of the flood to explain the existing biodiversity and the existing speciation you feel compelled to disagree and say no it is all by natural mechanism and we do not need to invoke miracles. The logic totally escapes me.

Perhaps the logic escapes you because you’re not considering the evidence properly? Again, note that you’re the one arguing for Divine intervention here, not me. There simply is no need to invoke Divine miracles or any other kinds of intelligent intervention to rationally explain the features you think require vast periods of time to explain.

The mutation rates and allelic diversity that currently exists can be explained via known naturalistic mechanisms acting over a very short period of time.

I’m sorry, but you’re the one who has yet to present anything that would require a Divine miracle to explain – short of the origin of the informational complexity of life itself. The degenerating nature of all slowly reproducing gene pools necessitates the “front-loading” the informational complexity of life on this planet via a very very intelligent and creative Mind. It could not have been produced any other way that is known to modern science.

This insistence that there is no miracles in biology beyond the original creation raises the question of where you actually are in terms of the belief in origins. Are you saying that origin of species is by highly accelerated natural mechanisms?

No significant acceleration is needed beyond the current rates observed for mutational changes and divergence within isolated gene pools.

You seem to accept the ID paradigm and postulates but unlike most of the adherents to ID want to put it into a short time frame of a few thousand years. From reading your responses in the posts here on canid evolution you accept macroevolution (change beyond the species level) of the canid species by a natural process of genetic variation and natural selection.

I don’t like the terms “micro” or “macro” evolution because they aren’t well defined as far as any kind of predictable limit to evolutionary progress is concerned. The same is true for the “species” concept. That is why I prefer to define unique “kinds” of gene pools based on differences in functional complexity at higher levels of functional complexity (i.e., beyond the level of systems requiring more than 1000 specifically arranged amino acid residues). I do admit that this concept is fairly unique. IDists have some great ideas, of course, but I find ID arguments significantly limited in this particular regard.

You however constrain this process by saying that any mutations that arise enabling speciation must be at very very low levels of complexity. This seems quite a disconnect to me. Are you insisting that the genetic basis of speciation is genetic changes of very very low levels of complexity?

Yes. It is indeed my position that no novel systems of function are or have ever been produced by RM/NS which require a minimum of more than 1000 specifically arranged amino acid residues. There isn’t a single observable example of such within all of scientific literature and statistically such an event is extraordinarily unlikely this side of a practical eternity of time.

It is all very puzzling and makes me very curious how you would actually commit yourself in terms of a position on origins.
Wikipedia http://en.wikipedia.org/wiki/Creationism#Types_of_creationism classifies creationism as
1] YEC
2] Gap Creationism
3] Progressive creationisms
4] Intelligent design
5] Theistic evolution or evolutionary creationism.

As I’ve already explained to you several times now, I’m a young-life creationist. I think that all life on this planet was created less than 10,000 years ago by God. Before this time, no life existed on this particular planet. I do, however, believe that the universe itself and even the material of this planet may be very old indeed.

Of course you do know that people like David Read, Bill Sorenson or Kevin Paulsen might consider you a heretic since you do depart from the YEC of GMP. Not unlike the way you consider Lee Grismer a heretic for perhaps being somewhere further down the list than you are. As always I worry as Christians within the Adventist community we completely miss the point of our eternal need of the Grace of God. We forget the message of the mote and beam and wanting to justify ourselves seem to see people as heretically different rather than fellow sinners redeemed by His power but struggling to live the life of discipleship as honestly as we can.

Again, this has to do with Biblical credibility. When it comes to the literal 6-day creation week of all life on this planet within recent history, all who support the Seventh-day Adventist view on origins are in agreement. There may be disagreements on other issues, but this is the key fundamental position of the church when it comes to origins. Those like Lee Greer or Lee Grismer who actively undermine the church’s position on this topic within our own schools (like La Sierra University) are misrepresenting their employer and what their employer has expressly hired them to do. That’s simply wrong in anyone’s book. It would be far more honest and forthright for those who disagree with the church’s perspective on such a fundamental issue to go and work in the public sector for an employer who is more than happy to pay to promote the popular philosophies of most modern scientists.

Sean Pitman

Sean Pitman Also Commented

The End of “Junk DNA”?

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

The End of “Junk DNA”?

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

The End of “Junk DNA”?

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

“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

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

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

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

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

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

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