@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.

http://www.usatoday.com/news/health/2007-09-03-dna-differences_N.htm

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
www.DetectingDesign.com

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Sean Pitman Also Commented

The End of “Junk DNA”?
@pauluc:

Lots of non-Adventist individuals and organizations are committed to Jesus Christ – like the Catholics, Baptists, Lutherans, Mormons, etc. However, the simple criteria of being committed to one’s own personal view of Jesus Christ does not qualify one as being a paid representative of the Seventh-day Adventist Church.

Now, this isn’t to say that being committed to Jesus Christ and His example, as detailed in the Bible, isn’t a good thing. It’s a very very good thing and the motive of love behind such a decision is the very basis of salvation. However, even being in a saving relationship with Jesus is not enough to qualify an individual to be an effective representative of the Seventh-day Adventist Church in particular.

The Adventist Church takes on basic Christianity as well as an additional mission – a mission which includes upholding before the world some 28 doctrinal beliefs which the church considers “fundamental” or crucial to its primary goals and mission during the last days of Earth’s history.

Now, one may be saved without being a part of the Adventist mission or church – thank God! In fact, the vast majority of people who will be saved in Heaven one day will never have even heard of Seventh-day Adventists. So, this isn’t an issue of salvation. It is an issue of appropriately representing the primary goals and mission of an organization as that organization defines itself.

You, weather you like it or not, are not in line with many of the primary goals and ideals of the Seventh-day Adventist Church. That doesn’t make you good or bad or outside of the saving love and grace of God. It just means that you cannot adequately represent the Seventh-day Adventist Church as a paid representative. Your representation would be counterproductive to the stated goals and missions of the church as an organization.

That is why it would be much better for you, and for more honest, if you were to take on a label that more accurately represents your current world views…

Sean Pitman
www.DetectingDesign.com

The End of “Junk DNA”?
@Professor Kent:

When empirical evidence and God’s word go different directions, you will choose the evidence, whereas the SDA Church always has and always will prioritize God’s word.

During the founding of the Seventh-day Adventist Church the founding fathers took on the position that the Bible prophesied that Jesus would return in 1844. The empirical evidence proved this notion wrong. And, these founding fathers were forced, by the empirical evidence, to admit that their faith in what they thought the Bible said was mistaken.

You see, the SDA Church, from its very beginnings, has been forced to recognize the interplay between faith and evidence for the rational mind. One cannot rationally argue that one’s faith in what one thinks the Bible says, or even the origin of the Bible, is entirely independent of the weight of empirical evidence.

It is for this reason that the modern Seventh-day Adventist Church is actually concerned over what is being taught at La Sierra University regarding the topic of origins. If all that mattered was a fideistic faith in the Bible and our own special interpretation of the Bible, the church wouldn’t care what people thought of the empirical evidence. It wouldn’t care what was being taught in science classes within its own schools. This simply isn’t the case.

You are delusional to believe that the SDA Church will agree to disembody and disavow itself of God if the accumulated evidence goes against its present interpretation of scripture.

But the church has changed its mind before regarding its views of the Bible based on the weight of empirical evidence (as noted above).

Again, God does not ask us to believe or have faith without the weight of evidence. He does not expect us to believe in something that has no more evidential backing than the Tooth Fairy or Santa Claus. That simply wouldn’t be reasonable on the part of God nor would it be fair for Him to act in such a manner…

Sean Pitman
www.DetectingDesign.com

The End of “Junk DNA”?

There is a great gulf between You and I. Where does one start in trying to find common ground and responding to your very concrete thought structure. Its as if the last 200 years have not happened. Your view of natural theology may have been accepted by William Paley but is not an approach to God thought valid by most modern theologians with any acquaintance with science.

One of the problems I personally have with your perspective, and that of many modern theologians, is that it seems to me to be inconsistent with itself. You yourself describe your own position as “irrational”! You reject the authority of the Scriptures when the Biblical authors describe the miracle of God creating life on this planet in just six literal days (clearly what the author of the Genesis account was trying to convey to his readers)… because of what you view as the contrary evidence of modern science. Yet, at the very same time, you accept the claims of the Biblical authors when they describe the miraculous virgin birth, life, death, and Resurrection of Jesus. You accept this portion of the Scriptures contrary to the claims of the vast majority of modern scientists who claim that such things are impossible.

Does this not then mean that your internally derived “faith” allows you to pick and choose what you will and will not believe independent of the influence of anything else? It isn’t a matter of consistent Biblical interpretation for you because you simply aren’t consistent in how you interpret the Bible or determine what is or isn’t true. You pick and choose based on your own individual desires for what you want to be true. That is why your faith is inconsistent with itself and is, as you yourself explain, completely irrational to the point of overt fideism. You take on a form of fideism that is its own evidence independent of any influence outside of your own mind and your own feelings and desires – to include any consistent influence from the Bible itself.

What argument can you or any modern theologian present to make what you yourself claim is an irrational position appear remotely attractive to those who appreciate rational thought and careful consistent investigation of fantastic claims?

It is not the 19th century and we are called to preach the grace of God to a secular world. Your vision shows no imagination or understanding of spirituality or the reality and value of vision, myth and abstract concepts that may have no correspondence in concrete realities.

But I do find value in various myths, legends, allegories, and fairytales. Even Jesus used such stories to teach various truths about the existence of realities that are not yet seen. However, it makes a great deal of difference if one believes that the life, death, and resurrection of Jesus is a good moral fable vs. true empirical historical reality. If the disciples of Jesus had believed His claims to be the Son of God simply allegorical, rather than empirical reality, they would not have put their own lives on the line. No rational person, who is naturally prone to avoid a martyr’s death, is going to put his life on the line for stories that he believes are mythical or allegorical – devoid of any “correspondence with concrete realities”.

They key point here is that if Jesus had not been raised from the dead and His disciples had not personally witnessed the empirical reality of this event, there would be no Christian Church of any kind today. All of Christian faith hinges on the literal reality of the Resurrection. Without this reality, there is no mystical experience with God that can rationally support the claims of Christianity.

Do you agree with Martin Luther in his statement about scripture trumping observation:

“People gave ear to an upstart astrologer who strove to show that the earth revolves, not the heavens or the firmament, the sun and the moon. Whoever wishes to appear clever must devise some new system, which of all systems is of course the very best. This fool [or ‘man’] wishes to reverse the entire science of astronomy; but sacred Scripture tells us that Joshua commanded the sun to stand still, and not the earth.”
– Martin Luther, Table Talk

If you truly privilege scripture over science you should really revamp this web site to be consistent with the supremacy of scripture along the lines of the site http://www.fixedearth.com/ A site that is at least absolutely consistent with biblical literalism as Luther saw it.

Even though we who live in this modern age know that the Earth does in fact revolve around the Sun, we still speak in everyday terms as the Sun “rising in the east” and “setting in the west” or the “Sun going down”. Such are terms of perspective. In context, therefore, no further interpretation is necessitated in the Bible’s description of Joshua speaking from his own Earth-bound perspective. Surely you can understand the difference between such passages and passages in Genesis where it would be very very difficult to misinterpret the observation of “evenings and mornings” separating the “days” of creation – regardless of perspective. In such passages the author is clearly claiming that God showed him that the days of creation were separated by what clearly appeared to be “evenings and mornings” from his Earth-bound perspective. There’s a big difference here.

As far as Martin Luther is concerned, he was a great reformer and he did advance important truths for his time. However, he was no prophet and received no privileged revelation regarding such things. He forwarded and acted upon a great many points of misunderstanding regarding the meaning of many Scriptural truths which the Seventh-day Adventist Church has since realized – to include those truths revealed to us by God speaking in a very privileged manner through Ellen White.

Now, you can either accept or reject the Adventist perspective on such things, but it is very difficult to call yourself an Adventist or a true representative of the Seventh-day Adventist Church when you are actually fighting against numerous doctrinal ideals that the Adventist Church, as an organization, still holds to be fundamentally important. It would be much better and far more honest for you to describe yourself in terms that more accurately reflect your true beliefs.

The reality however is that both you and I interpret the scriptures. As I have said before you appear to practice naturalistic evidence based medicine contrary to the biblical description of healing but then pretend that you are following the plain text of scripture when reject entirely naturalism when it comes to origins. You claim;

“You pick and choose what elements you will use to build your own image of “christianity”… which is quite different from the Biblical claims.”

But do not at all seem able to see that you are in fact doing exactly what you project in accepting evidence based medicine contrary to a plain reading of scripture but claiming origin by divine fiat and miracle on the basis of one particular reading of scripture.

There is actually good support for evidence-based medicine in Scripture. Just because the Scriptures also point out the power of prayer and God’s willingness to supernaturally intervene, on occasion, in our lives does not mean that the Scriptures are opposed to evidence-based medicine. Such a notion is completely contrary to the position of the Bible, Mrs. White, and the Adventist Church on the topics of health and medicine in general where the laws of nature, set in place by God, are to be dealt with on a routine basis in the practice of medicine and healthful living.

You continue to misconstrue the point of my discussion of Santa Claus and Christmas. Children can and do grow in their understanding of reality and are able to see beyond the concrete events of Christmas to see it as a representation of a worthy abstraction that is not invalidated by rejecting a fictitious Santa Claus. You seem unable to move from the concrete to the abstract and yet again claim you will reject Christ if your biblical interpretation is found not to be consistent with a simplistic reality. As though your superior mind trumps any non-rational revelation of God.

A non-rational revelation of God would not, by definition, make rational sense – right? (any more than a desire to believe in the reality of existence of Santa Claus or the Flying Spaghetti Monster?) Why then should I believe in any irrational “revelation” that makes no sense to me? Can you provide any rational answer to this question? Wouldn’t any response you might submit be irrational by definition? That’s why your position makes no sense to me. Why even try to argue for what you yourself are arguing has no rational explanation?

Your arrogance is unceasingly amazing.
You claim:

“And, so far, the organized Adventist Church agrees with me. Of course, you can call yourself whatever you want. But, again, that doesn’t mean that the church is going to recognize your claims as actually representing the church’s view of reality. So, why would you expect anyone holding views that undermine the fundamental goals and ideals of the church, the ‘fundamental beliefs’, to be paid by the church”

You are of course right if you think the church that is being rebuilt by Ted Wilson and Clifford Goldstein with their militant fundamentalism and unsavoury and ungracious political manouvering is the legitimate heir of traditional Adventism but I do not.

Where did Ted Wilson or Clifford Goldstein set up the fundamental doctrinal ideals of the Seventh-day Adventist Church? You give them far too much credit! These fundamentals were set up well before they came on the scene…

At the very least, you must admit that you are strongly opposed to many of the clearly stated doctrinal positions that the Seventh-day Adventist Church has long held, and currently holds, to be “fundamental” to its very existence. You fundamentally disagree with both the founders and the current leaders of the church on many key points of doctrine. You disagree with many of the modern and historical doctrinal positions of the SDA Church as an organization.

You are really more of a “social Adventist” who was raised in the Adventist Church but who really doesn’t subscribe to many of the doctrinal positions of the church as an organization. Why then do you wish to continue to take on the title of “Seventh-day Adventist” when this title doesn’t really do you justice? – when it doesn’t truly represent who you really are and what you really believe? And, why on Earth would you expect anyone who holds similar views to your own to be hired by any organization who claims to be fundamentally opposed to what you actually believe and are willing to teach/preach?

Wouldn’t it be far more honest and ethical for you and those of like mind to more clearly present yourselves and what you stand for and then go and work for those who are more than willing to pay to have such ideas taught in their schools and preached from their pulpits? Why the aversion to completely open and honest transparency here?

And, if the Seventh-day Adventist Church, as an organization, really has no problem with those from your perspective preaching and teaching on the church’s dime, why then hasn’t the Adventist Church come out in open support of such efforts? Why has the Adventist Church, as an organization, gotten so worked up over Neo-Darwinism being so openly promoted as La Sierra University? – if the church really is as supportive of your position as you seem to suggest?

Sean Pitman
www.DetectingDesign.com