@pauluc: I am sorry but my prose seems to have …

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

@pauluc:

I am sorry but my prose seems to have allowed you to parse my comments but miss the intent. In response to your suggestion that we are devolving and accumulating mutations at a dangerously high rate and that we are in eminent danger of genetic meltdown I simply asked you to factor in paternal age as a mitigating factor in allaying your concerns. I made no comment on the veracity of the Bible’s claims of paternal longevity other than to point to similarity in paternal age to that in the existing Sumarian book of the kings. I still do not see that your argument that the yearly mutation rate is the same whether the generation time is 29.7 or 800 years has any value for the person who may have gained 1600 mutations and has high risk of autism as the original research suggested, but that is beside the point.

I’m sorry, but it seemed to me like you presented this argument to question the ability of humans to actually live and reproduce for almost 1000 years. What you still don’t seem to understand is that it isn’t the per generation mutation rate that matters as far as the gene pool is concerned or even the number of detrimental mutations for the offspring born in a given year (compared to some reference point in time). It is the yearly mutation rate that matters when it comes to the gene pool as a whole and the risk for new offspring. This yearly rate stays the same regardless of the generation time. A child born at any given point in time has the same risk of inheriting detrimental mutations regardless of if his father had lived 800+ years or if he/she was born after 800+ years worth of paternal generations. The detrimental mutation load would be essentially the same. I’m really not sure why you’re having such difficulty with this concept?

Also, autism and other genetically-based diseases would not have been as significant a risk when mankind was fresh from the Creator’s hand. Deleterious mutations had not built up to their current levels and associated genetic-based disease risks. Again, such genetic-based diseases will only get more and more prominent as our collective gene pool continues to degenerate over time.

“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.”

I see your model as based on selective biblical literalism if not inerrancy which to me is incomprehensible outside multiple continuing divine interventions to make the world the way it is. I am happy to concede you are Christian and Adventist though you do not believe the same as me on some points. To me issues of mutation rate are orthagonal to my Christian belief which is based on following Christ as the incarnation of the God of Grace.

Again, the Biblical authors who wrote Genesis clearly intended to be taken literally – to be describing real historical events. The question is, were they right or wrong in their testable statements regarding empirical reality? If they were wrong, the credibility of the metaphysical statements of the Bible also declines – to include claims regarding the life, death, and very nature of Jesus Christ (especially given that He personally confirmed the historicity of the Genesis account of origins).

So, what about your challenges to the credibility of the Bible’s claims regarding historical times and events? You’ve thrown out a multitude of arguments that supposedly falsify the Biblical narrative of history. The problem, of course, is that your claims are the ones that have turned out to be false. The hypothesis that the Bible’s claims regarding origins is empirically tenable remains intact and more vindicated in modern times than ever before. Why then do you try so valiantly to undermine the empirical basis for faith in the credibility of the Bible? Why do you even think Jesus existed and acted in the manner described in the Bible at all if you yourself pick and choose what you will and will not believe? How is this different than wishful thinking?

“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.” – Sean Pitman

Beyond process of natural selection I do not know how deleterious mutations might be removed from the gene pool but I am intrigued that long lived animals have lower rates of mutation. Sexual reproduction diploidy is clearly important but I do not at all imagine that we know all about the rate of removal of deleterious mutations despite your modelling assuming we do. What I am not convinced of is that you are correct that death is the only mechanisms of removal and that your conclusion that we are on track for genetic meltdown, subject as it is to huge pressure for confirmational bias from your assumption of devolution, is correct.

Natural selection does not work without the premature death of individuals within a population. And, genetic recombination doesn’t solve this problem (as discussed below).

Also, long-lived animals do not have significantly lower rates of gene pool mutation compared to humans – even with regard to animals demonstrating negligible senescence. In other words, the overall yearly mutation rate for the gene pool as a whole is not significantly different among all types of long-lived animals.

As far as sexual vs. asexual reproduction is concerned, the problem remains even for sexually reproducing species. This is because genetic recombination during meiosis is a random process that does not preferentially select to remove detrimental mutations vs. beneficial or neutral mutations. The only advantage genetic recombination provides is a statistical chance that a percentage of the offspring will have less detrimental mutations compared to their peers. In other words, when it comes to sexually reproducing populations, the ability for genetic recombination during the formation of gametes makes it possible to concentrate both good and bad mutations.

For example, let’s say we have two individuals, each with 2 detrimental mutations. Given sexual recombination between these two individuals, there is a decent chance that some of their offspring (1 chance in 32) will not have any inherited detrimental mutations. But what happens when the rate of additional detrimental mutations is quite high – higher than 3?

To look into this just a bit more, consider another example of a steady state population of 5,000 individuals each starting out with 7 detrimental mutations and an average detrimental mutation rate of 3 per individual per generation. Given a reproductive rate of 4 offspring per each one of the 2,500 couples (10,000 offspring), in one generation, how many offspring will have the same or fewer detrimental mutations than the parent generation?

Inherited…….After Ud = 3
7……………901
6……………631
5……………378
4……………189
3……………76
2……………23
1……………5
0……………0.45
< or = 7........2202 This Poisson approximation shows that out of 10,000 offspring, only 2,202 of them would have the same or less than the original number of detrimental mutations of the parent population. This leaves 7,798 with more detrimental mutations than the parent population. Of course, in order to maintain a steady state population of 5,000, natural selection must cull out 5,000 of these 10,000 offspring before they are able to reproduce. Given a preference, those with more detrimental mutations will be less fit by a certain degree and will be removed from the population before those that are more fit (less detrimental mutations). Given strong selection pressure, the second generation might be made up of ~2,200 more fit individuals and only ~2,800 less fit individuals with the overall average showing a decline as compared with the original parent generation. If selection pressure is strong, so that the majority of those with more than 7 detrimental mutations are removed from the population, the next generation will only have about 1,100 mating couples as compared to 2,500 in the original generation. With a reproductive rate of 4 per couple, only 4,400 offspring will be produced as compared to 10,000 originally. In order to keep up with this loss, the reproductive rate must be increased or the population will head toward extinction. In fact, given a detrimental mutation rate of Ud = 3 in a sexually reproducing population, the average number of offspring needed to keep up would be around 40 per breeding couple (2 * 1 / e^-Ud) – for two to survive without an increase in detrimental mutations. Humans simply don’t reproduce that fast and cannot tolerate a 95% death rate per generation. Even within mainstream literature clear limitations to mutation rates are known because of this particular problem. Even rapidly reproducing bacteria and viruses have a fairly small limit to the number of mutations that can be sustained per generation. Based on research coming out of Harvard University, that number is less than 6 mutations per individual per generation - for bacteria and viruses as well as most other living things! This is a total number of mutations affecting functional regions of DNA - counting detrimental, beneficial, and neutral varieties. Eugene Shakhnovich Eugene I. Shakhnovich

If enough mutations push an essential protein towards an unstable, non-functional structure, the organism will die. Shakhnovich’s group found that for most organisms, including viruses and bacteria, an organism’s rate of genome mutation must stay below 6 mutations per genome per generation to prevent the accumulation of too many potentially lethal changes in genetic material. (Link, Link-2, Link-3)

For viruses in particular, the limiting mutation rate was found to be just 2.5 mutations per genome per generation (Link). This is the total mutation rate, not just the detrimental mutation rate. Also, the population here is assumed to be infinite in size. For finite populations the maximum tolerable mutation rate would obviously be smaller. The smaller the population, the lower the mutation rate that can be tolerated without an eventual genetic meltdown.

But what about the effect of beneficial mutations?

“Whitlock included beneficial mutations and calculated that N-crit ~(U-deleterious/U-beneficial)^1/3, which depends only on the balance of beneficial to deleterious mutations and not on the mutation rate itself. Both of those examples contradict our results, which show that N-crit and τ depend dramatically on |U|. The dominant reason for the discrepancy is that those authors assumed that deleterious mutations occur “one at a time,” which is not true when the rate that mutations are introduced (U) exceeds the rate at which selection removes them (~1/s). When U/s≫1, the population experiences “Hill-Robertson interference”, which both accelerates extinction and also makes analytic solutions intractable.” (Link)

The nail in the coffin, of course, is the realization that the detrimental mutation rate is significantly higher than Ud = 3 or even Ud = 6 for humans. The original estimate of Ud = 3 was based on the notion that over 95% of the human genome is not functional. Of course, we now know that this notion is mistaken. The majority of the human genome is functional to one degree or another. That means that the detrimental mutation rate is much closer to the overall mutation rate for humans – i.e., at least several dozen detrimental mutations per person per generation (if one limits one’s self to only considering the SNP mutation rate. As we both know, the actual nucleotide mutation rate is much much higher than the SNP mutation rate). Now, we’re talking about trillions of offspring needed per couple in each generation to keep up with even the minimum likely detrimental mutation rate.

The conclusion is quite clear to anyone who considers this problem with a candid mind. All slowly reproducing species are inevitably headed for eventual genetic meltdown and extinction. This is simply no rational naturalistic means to explain this very clear problem away. You simply haven’t done the math for yourself or considered this problem in any real detail.

“That you allow for this toxic accumulation as the basis for speciation and generation of allelic variation to me is a glaring contradiction.” – Pauluc

Where is the contradiction? While beneficial allelic variants can and do evolve all the time (especially in large populations), they are vastly outnumbered by detrimental allelic mutations and other mutations within non-coding DNA. There is no contradiction here. These are well-established facts.

That there is a paucity of research on this suggests that the arguments you advance have no traction in genetics perhaps because as I have said many times before is theoretical not real.

What do you mean by “real”? Do you not realize that all scientific theories are, by definition, theoretical? The conclusion of a devolving gene pool is very “real” as far as a scientific theory is concerned – just as “real” as any other scientific theory is “real”. You do realize that science is based on hypotheses and theories, not direct absolute demonstration? – right? There is always the potential for any scientific theory to be wrong – to end up being falsified. Science isn’t about absolute proof, but about statistical probabilities of a theory being correct based on the less than complete information that is currently in hand.

The research that is in fact in hand regarding the build-up of detrimental mutations is quite clear. It is really beyond any serious debate that the vast majority of mutational changes that have a functional effect on DNA are deleterious to one degree or another. This not only makes intuitive sense, it has been demonstrated over and over again under laboratory conditions. As far as removing these detrimental mutations from the gene pools in a meaningful manner, many suggestions have been forwarded, such as eliminating detrimental mutations in clusters. However, no one has come up with a naturalistic mechanism by which such preferential clustering of detrimental mutations might be achieved.

The fact that you do not recognize any way to falsify your notions on this topic removes your ideas from the realm of science. If you really want to call yourself a scientist, there really is no way around the conclusion that the current evidence we have in hand strongly supports the theory that our gene pool is degenerating over time – as are the gene pools of all other slowly reproducing species on this planet.

Sean Pitman
www.DetectingDesign.com

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


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Thank you Ariel. Hope you are doing well these days. Miss seeing you down at Loma Linda. Hope you had a Great Thanksgiving!


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Thank you Colin. Just trying to save lives any way I can. Not everything that the government does or leaders do is “evil” BTW…


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Only someone who knows the future can make such decisions without being a monster…


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Where did I “gloss over it”?


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I fail to see where you have convincingly supported your claim that the GC leadership contributed to the harm of anyone’s personal religious liberties? – given that the GC leadership does not and could not override personal religious liberties in this country, nor substantively change the outcome of those who lost their jobs over various vaccine mandates. That’s just not how it works here in this country. Religious liberties are personally derived. Again, they simply are not based on a corporate or church position, but rely solely upon individual convictions – regardless of what the church may or may not say or do.

Yet, you say, “Who cares if it is written into law”? You should care. Everyone should care. It’s a very important law in this country. The idea that the organized church could have changed vaccine mandates simply isn’t true – particularly given the nature of certain types of jobs dealing with the most vulnerable in society (such as health care workers for example).

Beyond this, the GC Leadership did, in fact, write in support of personal religious convictions on this topic – and there are GC lawyers who have and continue to write personal letters in support of personal religious convictions (even if these personal convictions are at odds with the position of the church on a given topic). Just because the GC leadership also supports the advances of modern medicine doesn’t mean that the GC leadership cannot support individual convictions at the same time. Both are possible. This is not an inconsistency.