@Sean Pitman: You suggest I have not read the paper …

Comment on WASC Reviews LSU’s Accreditation by pauluc.

@Sean Pitman:
You suggest I have not read the paper and offer a proof text. I make a living reading and writing papers in the research literature so I think I have developed some skill. Let me give you some pointers on approaching scientific literature. First lets see what you have read into this paper. You seem to have skipped the statement that encapsulates the basis of this paper;

“Population size was extremely efficient in ameliorating fitness decline, its effect highly significant across all
traits and population-size treatments in both assays.”

pg 1272 in the first section of the results with its accompanying figures 1, 2 and 3 that plot the data supporting this statement. Instead you fixate on the statement in the results on pg 1274 which says as you have correctly indicated

“Notably, no lines in the long-term natural MA experiment have ever been observed to significantly improve beyond the control with respect to the typically measured fitness-related characters.”

You seem to not understand what is the control in this experiment. In context this simply says that the worms with homozygous defect in the Msh2 DNA repair enzyme were never phenotypically fitter than the control N2 worms with normal Msh2 DNA repair. This may seem so blindingly obvious that you might say why did they even say that? The explanation lies in the next section “Observed vs. expected fitness decline in populations of different size:” and in their figure 4 data. Here they compare their results with the predictions based on the Bateman-Mukai method that “relates changes in the mean and among line variance of a character experiencing mutation to the genome-wide mutation rate and average mutation effect”. The prediction being that ” ..under a model of constant, large mutation effects, our calculations (see materials and methods) indicate that no decline in productivity or r due to fixations of new mutations would be expected in these larger populations”

As figure4 shows there is a residual effect asymptotic to the x axis that indicated an effect that persists despite increasing population size. Hence their statement that it was never better than control. They further explain this in the discussion

“The decline in fitness with decreasing population size suggests that the majority of the mutational variance discernible in the benign environment of the lab is due to mutations producing large, negative effects as population sizes of three were able to maintain fairly high fitness levels relative to the control over the course of the study. This result is congruent with our estimates of average mutational effects (Table 1). (The fact that the msh2 strain began the experiment with fitness well below the N2 control may place a bound on how large a population-size effect could be detected in this experiment.)”

“However, even the largest population-size treatments show a slight trend toward reduced fitness compared to the control. Our comparisons of observed vs. expected declines in fitness correlates (Figure 4) show that fitness reduction observed in the larger-population-size treatments was greater than that expected on the basis of our B-M estimates of average mutation effect, while the decline observed in smaller population sizes closely matched the expectations. There are at least two possible explanations for this observation: (1) a fraction of small-effect mutations managed to reach fixation in the large population lines or (2) the reduced fitness at the larger population sizes is due to still-segregating mutations that arose during the experiment.” pg1276-1277

I did expect better of you and though they would teach you how to read a research paper as a medical student? You cannot approach research with the proof text approach. You have to ask what is the theme of this paper, What does the data show? You will learn little if you come to a paper to selectively pick out the conclusions that you have already arrived at as seems to be what you have done here.

Though some might think you are being deceptive in quoting out of context but I do not think you are at all dishonest, simply subject to mortons demon selectively reading and accepting data unconsciously so that certainty remains. We all tend to do this.

Why have I spent so much time on this process which I am sure has bored some of your readers from the first sentence. I do it because I value honestly and truth. I worry that I could extrapolate and find similar selective reading of almost any piece of primary peer reviewed literature that you might cite. I think when it comes to faith we should forget about trying to prove the science and simply accept the revelation of God through Jesus Christ and the community of faith that communicates that to us. You can call it blind faith if you will but that is the basis of salvation.

pauluc Also Commented

WASC Reviews LSU’s Accreditation
@Sean Pitman:
Thank your for your response. You state

“The problem, of course, is that the per generation detrimental mutation rate still is and always was far far too high for natural selection to keep up (for creatures with few offspring per generation). Also, as already explained above, the relative strength of natural selection has absolutely nothing to do with this problem.”

And here is the nub of the problem. You and Sandford state have accepted a faith position of biblical inerrancy and literalism which affects your reading of the scientific literature.

You accept by faith a 6000 year earth history and the genetic models must follow. You accept that there must be genetic degradation because it must be so according to your a priori assumptions on the innerrancy of EGW and the bible. You have of course given us mutation rates that are consistent with the literature and which I do accept in good faith, but then go on to calculate a required death rate. Nowhere have you provided real evidence that this death rate is correct and is inadequate in the real world rather than in your flawed theoretical models predicated as they are on your core belief in the degradation from a perfect genome in Eden circa Oct 4004 BC.

You nonetheless have the temerity to claim that this model is endorsed by modern populations geneticists.

When I suggest that at least one population geneticist who sees the issue as being a man made genetic crisis he then becomes “Your professor Lynch”. How insulting.

Sean as always despite your endorse of science as the source and basis of your faith you seem to manifest an underlying disdain for scientists and their integrity. In virtually any discipline we talk about you are right and they are clearly wrong. Sorry I do not trust you.

We will just have to revisit all this in 10-20 years time and see if your perspective has moved. I would hope by then you have realized that Christianity is not about science but is all about faith in the revelation of God in Jesus and our response as disciples.

Grace to you.


WASC Reviews LSU’s Accreditation
@Sean Pitman:

I am not arguing this I am simply saying this is what Lynch in his lecture on being elected to the academy of science was arguing if you read his paper.

Further he argues that human compared to other non-mammalian animals have greater fidelity in somatic cell replication and so have a lower rate of somatic cell mutation. What do you suppose accounts for that? Perhaps error correction mechanisms that are present in higher mammals. Do we have a complete understanding of these. I think not but does your model allow for that?

It is not that I do not trust the math but it is as in programming that other most useful area of math; GIGO.

I do not trust that you have the biology correct. As I more and more see how you read the literature I am no more sanguine.

We can argue on the math as much as we want but until you actually provide evidence of increasing deleterious gene accumulation over non-modern times I do not think we have a basis for your argument.

I would have no argument that humans are currently accumulating genetic damage but I would tend to agree with Lynch’s argument that this reflects human manipulation of the environment and removal of selection pressure that previously existed. Indeed he argues this is akin to Global warming.


WASC Reviews LSU’s Accreditation
@Sean Pitman: Sorry I havent responded earlier to your last missive.

We agree that natural selection is a mechanism that removed deleterious mutations in small creatures. You however continue to point to the mutations accumulating in humans and then ask me to give a mechanism for removal of deleterious mutations and more importantly near neutral mutations in long lived animals like humans. You imply that there is none and that human genetics is winding down from a perfect creation some 6000 years ago to a genetic meltdown.

You imply that the lack of published explanation is somehow the populations geneticists dirty little secret.

As usual you seem to be reading the literature with your own peculiar slant. After having looked at some of the literature I find that Lynch PNAS 2010 107:965 is simply expressing the predominant view among population geneticists when he writes:

“Dating back to Muller (49), considerable thought has been given to the potential for a cumulative buildup of the deleterious-mutation load in the human population (2, 3, 50, 51). The motivation for this concern is the enormous change in the selective environment that human behavior has induced during approximately the past century. Innovations spawned by agriculture, architecture, industrialization, and most notably a sophisticated health care industry have led to a dramatic relaxation in selection against mildly deleterious mutations, and modern medical intervention is increasingly successful in ensuring a productive lifespan even in individuals carrying mutations with major morphological, metabolic, and behavioral defects.”

How you can honestly read this as saying there is no mechanism for removal of mutations is beyond me.

They are simply saying that we are in a difficult situation as man made changes in the enviroment and heath care has removed most of the strong selection pressures that would purify a population. Ie infectious disease with historically high mortalities as both McNeil (Pagues and people) and more recent Diamond (Guns germs and steel) have cataloged.

They are not at all saying that they cannot image a mechanism for removing near neutral mutations they are saying that we have removed most of these.


Recent Comments by pauluc

Avondale College Arguing in Favor of Darwinian Evolution?

Bob Helm: With that said, I find your views to be spiritually dangerous and often scientifically weak. I detect a lot of smoke in your posts, but very little light. I hope you will continue to ponder these issues and try to have an open mind.

You are most welcome to your opinion and I know you would like nothing better than that anyone who takes Christianity and the Bible seriously but not literally to just go away. It is much better not to know of any possible problems with one current views. It very hard to get to the science when we cannot even agree on what is science. What passes as science on this site is so completely dismissive of its methodological basis and history and is entrained in a specific supernatural world view that allows arbitrary acceptance of any observation as miraculous. I think Roger’s paper may well be relevant to Adventist that believe that Christianity has and must respond to a careful study of physical reality by reconsidering its interpretations of the word of the Lord, but as Sean has indicated you are exception to that characterization. I still do not really understand why you should be interested at all in any science. It seems a bit messy to worry about facts. It really seems an unnecessary bother to argue whether the precambrian/cambrian boundary or the upper cenzoic (is that really what you meant?) as the evidence of a divine intervention.

Dont worry I do have an open mind which is why I still peruse this site to see how more knowledgable fundamentalist Adventists think. I wont worry you further.


Avondale College Arguing in Favor of Darwinian Evolution?

Sean Pitman: So, you do see the need for a police force and a military to maintain civil society, but somehow Christians should not provide what is an otherwise necessary part of that civil society? I’m with Abraham Lincoln on this one when he noted the inconsistency of such a position – like Orthodox Jews paying others to turn their lights on for them on Sabbath

On that logic you should not have any issue with working on Sabbath in any profession serving 24/7. Be that computer support, utilities firefighters. Those giving up those jobs because of inability to have sabbath observance were all deluded. They as Christians should be prepared to “provide what is otherwise a necessary part of civil society”

You cant have it both ways. You cant because of a moral postion claim that Adventists should have exception from working on Sabbath and at the same time deny me the right to consider immoral some occupations that may be very utilitarian in a world full of selfishness and the human acts of evil that comes from that.

Lets for a moment step back from lala land. Where are we and where did we come from on this thread?

1] You posted a rehash of all your usual arguments in response to an article about the more mainstream Adventist positions that may impact the way Adventism reacts to conventional science. All very straight forward.
2] The contention was that Adventism has accepted process for the orgin and evolution of the inanimate world. The birth and death of galaxys and stars and planets in black holes supernova and impacts of spiralling planets. This is where it gets really strange.
3] You contend that Adventism has always accepted the conclusions of that process but then expand on your view of the process which involves a little bit of order and natural law but large amounts of magic. God waited a few billions years until the interstellar material generated by the big band condensed into planets onto which God created life mature and complete. This included Heaven the place of his throne-room which he populated with physical being angels which it is implied have both mass and composition and metabolism.
4] When it was suggested that the same processes and natural law resulted in life on this planet this was claimed inconceivable and would never be done by any process involving life and death. Instead the life we see now is in reality designed to live for ever and has be chemically changed because it is deprived of a particular form of nutrient from a tree that existed on the Earth some 6000 years ago.
5] The inconguity of practicing medicine by the principles of process of natural law and the technology resulting from both the processes of the innanimate and the animate world rather than accepting the much more important process of divine intervention seems to be completely obsure.
6] When someone says that the process of life and death that gave us the physical substance of our universe is also the basis of the creation of life here he must be animal hating sadistic psychopath who cannot belieive in a God of love and grace and is lying when he says that non-violence characterizes the children of the heavenly father for one must always recognize that peace and freedom are only obtained over the bodies of 1/3 of the angels of heaven and the eternal physical and violent struggle against those who would practice violence.

I really cannot understand you Sean. Your ways are way beyond me. I am just sorry that Bob seems to be drawn into your twighlight zone.

Grace


Avondale College Arguing in Favor of Darwinian Evolution?
@Sean Pitman: sorry but your curious amalgam of magic and biology is not really comprehensible to me as a biologist or as a Christian . it. is neither logical or biologically feasible


Avondale College Arguing in Favor of Darwinian Evolution?

Sean Pitman: However, according to the Bible and Ellen White, before the Fall God specifically directed nature so that all sentient life was protected in a manner that there was no suffering or death. By eating from the “Tree of Life” God provided constant renewal and regeneration that worked against what would otherwise be inevitable entropic changes, decay, and death. It was by deliberately stepping away from the true Source of eternal life that mankind stepped away from God and into the full workings of mindless natural law alone – which does in fact inevitably lead to suffering and death.

And this interpretation is precisely why you need a theodicy. Where is the justice in killing all for the sake of the sins of one woman+man? It makes no sense logically. If they were conditionally immortal because of eating of the tree of life then did all the animals in all the world congregate around this tree like beasts around a water hole on the serengeti. how exactly do you as you are wont to do translate the account into a literal reality. And which beast had to come and eat. Or was it symbolic? Oh now that’s a thought.


Avondale College Arguing in Favor of Darwinian Evolution?

Sean Pitman: Come on now. Even I can imagine limitations to reproduction or the turnover of sentient carbon-based life. Surely you can at least imagine something similar? I know God can since such a world is described in the Bible and in the writings of Ellen White. Think about it…

Of course I have. This is not simply about reproduction. That is trivial. This is about metabolic process. Show me a carbon based life form that does not grow or metabolize anything and I will show you an organism in stasis as a spore “living” millions of year in amber. That is; effectively dead.

Real life cannot exist without metabolic process in a carbon based world and God has sanctified all this by a process of making good out of evil from the death of one comes life for others. Just as in the biological world so in the spiritual. By his death we have life. Just as God sanctified the practice of sacrifice of appeasement practiced by most cultures for thousands of years before and showed that in the Judeo-Christian tradition these same acts of sacrifice were emblematic of a monotheistic God that would become incarnate and bring life from death. So also he took the preceding accounts of creation derived as they were of the mesopotamian valley and recast it as an account of the monotheistic God who is above all but comes and dwells among us to become one of us. Participating in our life and death but showing us the importance of the transcendent life of the spirit that supercedes carbon based life and its inherent death. It is no fairy tale of 6 impossible things before breakfast. It is not pie in the sky by and by. It is rooted in a real world and it is about the transcendence of love and grace that is acted out in a real physical world by the incarnate God and us as we follow as His disciples.

That is the message I get from the images and visions of the Canon and EG White. But of course I read it for the message that it conveys not as a scientific text. That is where we fundamentally differ.