@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
@Faith:
Faith I admire your commitment to Sean and your confidence that he knows more in all areas of science than the thousands of scientists that have spent their lives working on honestly interpreting the data and with whom he disagrees.

You do of course realize that Sean has committed himself to leave the Adventist church and Christianity if he is at any time in the future convinced that the creation story cannot be sustained on a scientific basis. Talk about building you faith on sand.

In contrast I do not believe that the creation account can be at all sustained on the basis of the science without a selective distorted reading of the literature of science which I cannot do. I do however believe in the Bible as the inspired word of God and the doctrine of creation which is an essential part of the Judeo Christian tradition. In theology I am closest to the neo-orthodox and anabaptist views of Karl Barth, Dietrich Bonhoeffer and John Yoder and would see the core of Christianity in the incarnation event and the revelation of God in Jesus. A revelation that calls us to follow as disciples and enact the principles of the Kingdom.

Acceptance of the Christian understanding of the Grace of God is not based on some notion of Natural theology or science but on the revelation of Jesus that comes through the proclamation of the community of Faith and by reading the Word of God.

You may think that believing by faith in the revelation of God in the incarnate Christ is eroding belief in the Bible but I certainly do not view it that way and I suspect that Prof Kent does not but I will leave it to him to articulate his own belief.


WASC Reviews LSU’s Accreditation
@Sean Pitman:

Sorry Sean you say

Nowhere has the General Conference voted that Adventists must believe the Bible “at face value” without any empirical evidential support for its claim to be the Word of God.

What then is the basis for your crusade against academics who have not interpreted Genesis 1 at face value?


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.


Recent Comments by pauluc

LSU memorandum confirms Educate Truth’s allegations
@Sean Pitman:

To summarize the issues in your long response.

1] NHP as you have articulated do not offer any possibility of deciding between relatedness by descent and “God made it that way”

2] ID only hypothesis; Has never been formulated in any rigorous way that has been subject to testing. I do not even know what you mean by “ID-only”. Most scientists would understand ID as code for “We dont understand this except God did it”.

3] Hypothesis testing you say

“Real science demands that models be at least theoretically falsifiable. That means that a particular model can be shown to be false even if there is no other model with which to replace the current model. A false model is a false model. It’s as simple as that.”

Unfortunately it is nowhere near as simple as that as you would know if if you had bothered to try to understand science beyond your sectarian base. Although the poperian model of science as hypothesis testing and a requirement for falsifiability is still the dominant understanding it is much more complicated than that. The discussion by Alistair McGrath in “A scientific theology vol 3 theory” pg 192-214 of the Durham – Quine theory and the nature of hypothesis testing would be a useful start to understand hypothesis testing and falsifiability. In summary however the theory suggests that a thesis such as quantum mechansisms, origin of life by evolution by common descent is surrounded by a group of agregated interrelated hypotheses. These might include Darwinian natural selection. In reality as Jerry Fodor has suggested in his book “What Dawin Got Wrong”, the Darwinian hypothesis can be rejected based on evidence without at all rejecting the core evolutionary hypothesis. As he says in his eassy “Fodor against Darwinism” found on his website

“None of this should, however, lighten the heart of anybody in Kansas; not even a little. In particular, I’ve provided not the slightest reason to doubt the central Darwinist theses of the common origin and mutability of species. Nor have I offered the slightest reason to doubt
that we and chimpanzees had (relatively) recent common ancestors. Nor I do suppose that the intentions of a designer, intelligent or otherwise, are among the causally sufficient conditions that good historical narratives would appeal to in order to explain why a certain kind of creature has the phenotypic traits it does (saving, of course, cases like Granny and her zinnias.) It is, in short, one thing to wonder
whether evolution happens; it’s quite another thing to wonder whether adaptation is the mechanism by which evolution happens. Well, evolution happens; the evidence that it does is overwhelming. I blush to have to say that so late in the day; but these are bitter times.”

The response to data that would falsify one of the hyptheses is to change that hypothesis to better account for the new fact without at all changing the original thesis.

A recent review on evolution of cellular complexity by ratchet like mechansisms rather than selection also critiques Darwinian selection as the mechanism of generating complexity but does not question the well established rubric of evolution of cellular complexity. (Gray MW, Lukeš J, Archibald JM, Keeling PJ, Doolittle WF. Irremediable Complexity? Science 2010 Nov;330(6006):920 -921). This is the model of scientific advance you are confonting. Science could completely reject all darwinian mechanisms but the thesis of evolution would remain because of the absence of a better theory.

Your approach of pointing out the problems you see with some aspect of the evolutionary model completely misses this point. You are approaching science and knowledge from the approach to truth you hear from the pulpit and from fundamentalists like Bob Ryan. You cannot be a christian unless you believe in the literal creation. You cannot have a sabbath unless the literal creation is correct. There can be no second coming unless the creation is literally true. This is not the mindset outside the inclaves of fundamentalism. The pillar talk of people like this engender the idea that failure at a single point destroys the whole edifice. This does not pass the test of realism.

You cannot hope to change the scientific paradigm that is the thesis of evolution by pointing out even a multitude of errors or inconsistencies in the surrounding interrelated hypotheses without a compelling alternative core model. You have to provide both an overarching alternative to evolution as a thesis and to each of the surrounding interrelated hypotheses each of which provide support for the overall hypothesis.

I know you have taken the view that you can and must personally understand everything related to origins and have published critiques in all conceivably related fields. This is all well and good but these have to be both credible and well informed in each field.
for Eg do you seriously want us to believe that geo biodiversity can be accounted for by a model of plate tectonics that suggests that in 6000 years south america moved >11000 km from Gwondanaland. This is incredible; minimal rate of nearly 2 Km per year! The constraints imposed on the model, a 6000 year earth history makes your task of credibility virtually impossible. But if you move away from the “about 6000” of divine relevation you are on your own and well away from the mothership of the church.

You have a problem in that your core thesis that God created everything 6000 years ago was the dominant model some 150 years ago but this has been tested and progressively rejected as untenable because of accumulating evidence for the alternative model over the last 150 years. It is extremely unlikely that this will ever be a scientific thesis although it will always remain as a faith statement which is outside the magesteria of science and hypothesis testing. People like Prof Kent seem to recognize this.

4] The organization of the genome;

“Beyond this, your notion that the genome is a hodge-podge poorly planned jumbled mess is a view that is at odds with the currently emerging view of the genome”

I think it interesting that you would take a journalists view, albeit published in science, as the best evidence for “currently emerginf view of the genome”. Even given this caveat I do not read this review as supporting your contention of design on which it is completely silent. Unless of course you see in a Mandelbrot and all complexity the finger of God.

If you had read the chicken defensin gene paper you would have an example of what I mean by messy. Within this gene family
a] Why are the introns of different length ie different ?random intronic lengths
b] why are the intergenic distances variable?
c] why does the gal13 have partial repeat sequences
d] why is the orientation of the gene seemingly at random?

This does not to me seem the carefully ordered regular precise structure I would expect of intelligent design. If you suggest that we do not yet know but that all of this nonetheless reflect careful thought or that it reflects interference and corruption from the devil as David Read woudl suggest I would have to conclude that your ID concept is vaccuous has not explanatory value and is far from scientific.

In contrast the evolutionary model of common origin and ancestory has extraordinary explanatory and predictive value. It predicts that changes between species will reflect this history of origin by descent from common ancestors.

I ask you to take any published analysis of a multigene family and ask the same questions. Do they objectively support order and design or are they best accounted for by contingency and chance with a mere modicum of selection.

5] I have dealt with “real science” and new models above but your statement

” … but on the functional aspects associated with the NHP that cannot be explained by any known mindless mechanism while being within the realm of the powers of intelligent design at a very high level.”

is a faith statement, a non-sequitur that does not get to the point of this dialogue which was why the genome is as it is and can you honestly say it is best accounted for by “design”.

Pauluc


The End of “Junk DNA”?
@Sean Pitman:
“I’m a very strong supporter of the freedoms of religion, speech, and general expression within the confines of civil law and government………………church employment is an entirely different matter. Church employment is a privilege, not a basic human right. No one should expect payment from any particular organization, to include a church organization, just because one claims the name of that organization”.

Does your rhetoric and claimed principle really just come down to concerns about administrative process and control of thought by economic leverage? Do you have no respect for education as a process that involves academic freedom?
Your approach seems to be blind to the progressive history of Adventism. Adventist have no creed and what you believe about origins is not precisely what early adventists would believe. Adventism has had a doctrine of creation like all christians. Most have adopted a YEC view but that YEC in general has not always believed that the earth was old or that a big bang occurred. The idea that there has been a single standard of belief over the last 150 years is naive. Are you advocating that what you believe now in 2012 including your belief on natural mechanisms of macroevolution (as it is usually defined) and the age of the earth is the gold standard manifests to me a huge amount of hubris and lack of perspective. Have you not read the statement of fundamental beliefs and its preamble? What do you want to do. Sack people every time there is new perspective on mechanisms of creation? Do you have a purge your educational faculties with every change in administration? Doesnt seem to have worked very well for ADRA. Do you think you are the one who can determine the “truth” to which we must educate. How about a little academic freedom and acknowledgment of the true standard. Recognition of a doctrine of creation rather than judging people by the nuances of some theory of creation.

I do not really know the people who teach science at La Sierra but as Prof Kent has suggested it seems to me they may well have projected a lack of respect for traditional Adventist positions and heritage in the past but I suspect you are now beating a dead horse and the University has done what it can to be responsibly responsive to the expressed concern.

“The freedom of expression and the ability to hire only those who will most accurately reflect one’s views is also extended to the “ignorant”.”

Yes we are all ignorant it is a question of whether we are able to admit it and concede expertise to those who manifest it. I have never claimed to be brilliant, I simply try to practice my craft as honestly and consistently as I can and that means accepting the tradition and process of science as a window to understand the natural world and accepting the value and insight of both the Adventist tradition and the Christian faith as it has been practised by our spiritual fathers for 2000 years. I ask only that we practice charity rather than condemnation toward those who are trying to educate in science and in knowledge of God.


Southern Adventist University opens Origins Exhibit
@Sean Pitman:

Thanks for that. Wise choice, that I knew given your intelligence you would make despite you vigorous defence of your near perfect pair model of origins. We will pass over the assumption that there are no deleterious mutations and that you discriminate against animals with variant expression of FGF4 and consider it deleterious. Why the prejudice against short legs?
Lets recap what we do agree on

1] A genetically bottle-necked population such as 2 Daschunds lacks the genetic diversity to allow rapid selection of phenotypic novelty by selection among allelic variants. imposing a bottleneck on a non-bottle-necked population of wolves is also suspect so you choose 100 pairs.

2] In this you seem to be accepting the conventional scientific view that a bottle-necked population is undesirable as it has dramatically decreased repertoire in their gene pool and high levels of homozygosity. Lack of variation rather than deleterious mutation is the issue.

3] You accept that wolves and their subfamily dogs, foxes, jackal and coyotes are all derived from 2 animals living 4000 years ago. This by definition is a genetic bottleneck

4] These animals had 2 genomes and maximum of 4 haplotypes and alleles for every gene. Any additional alleles has arisen subsequently as random or non-random mutations.

5] The vast majority of the SNP (>2.5million) arose in the progeny of this pair by mutations over a period of 4000 years.

5] The multiple DLA alleles at the class II arose denovo since these 2 animals provided the 4 original alleles.

6] Similarly in man [assuming 8 people on the ark and that Noahs sons were the progeny of he and his wife, and that his daughter in laws were unrelated to each other and to Noah and his wife and were heterzygous] there were a total of 10 alleles at HLA B. this means that 1590 of the HLA-B alleles currently recognized by genotype in man have arisen denovo over the last 4000 years.

7] In this case if we accept Seans value of 1600 HLA-B allels then 99.3% of the variation seen today has arisen by chance mutations and selection.

8] If we conservatively estimate the HLA-B serological specificities associated with amino acid changes and differences in peptide binding are 60 and all of the 10 HLA-B alleles in the 8 people on the boat were associated with serological specificity then we can assume that at least 83% of the variation in the highly functional amino acid changes in HLA-B seen the current population were derived by chance mutations.

9] There seems little reason to argue that the same process that must occur in highly polymorphic systems such as the MHC do not occur in other gene systems.

9] If between 83% and 99% of the variation in the progeny of 2 animals and 8 humans arose rapidly over 4000 years and in the case of canines this acquired variation was able to generate at least the species wolves, coyote, foxes and Jackals, it is hard to then mount a consistent criticism that species can never arise by acquired mutations.

10] You can of course invoke miracles. Indeed I think it is the only logically consistent conclusion given your premises.
1] All species variation arose over 4000 years from an extremely bottle-necked population
2] Mutations account for any variation not present in the original near perfect pair.
3] These mutations cannot generate anything useful or novel that can contribute to the phenotypic development of breeds or species.

I have great faith in your ability to reconcile these but I do not have the intellectual horsepower to do so except by invoking miracles.


Southern Adventist University opens Origins Exhibit
@Sean Pitman:

You suggest

“Don’t sell yourself short! You think you’re just as right in your opinions and that I’m clearly mistaken. You’re certainly no less “gifted” in this regard than I am.”

No Sean this is really the core of the differences between you and me. It is not a matter of opinion but a matter of statistical probability. In almost all of what I have posted on this site I have reflected the evidence for the consensus view rather than my opinion.

Dismiss me as kowtowing to authority if you will. I have faith in the process of hypothesis driven science and the community of scientists that seeks to arrive at objective truth by free and open communication of ideas by publication and peer review. In this process I continue to participate for I do think it is one of the most noble human endeavours.

As a outsider to this process and as one who has never had formal training in science you uncritically accept the paranoid meme that says you must be somehow blessed by some scientific inner circle to have your papers accepted. You feel excluded but have you actually tried to participate?

I accept in good faith the work of scientists and the derivative consensus view in most areas of science but like all good scientist understand it is always a tentative synthesis. I maintain a cynical attitude which unfortunately taints the way I view your claims. I nonetheless can appreciate the elegance of a solution to a conundrum and an hypothesis that has huge explanatory value while still accepting its tentative nature. I understand my limitations and have some inkling of the extent of the biomedical literature. I recognise expertise and am therefore happy to defer to the expertise of others with an appropriate track record.

In contrast because of your religious views you do not accept the consensus view of scientists in a vast number of areas including geology, climatology and paleoclimatology, volcanology, oceanography, genetics, paleontology, cladistics, and molecular biology. In all these areas you imagine that you have more expertise and insight than the people who have dedicated their lives to the study of the content of these areas.

In spite of the way you construct it I am not suggesting I am more righter than you and I have only ever suggested that you have some respect for the history of the current consensus view in science and a little more realism in your perception of mastery of these areas. You may view this as a contest and that you easily best some fool from the antipodes but in rejecting my appeals to the evidence and the orthodox consensus view in areas in which I have some expertise you are essentially claiming you know it all.

[to save time I will acknowledge this space as containing some castigation from you or Bob Ryan such as “Gotta love the appeal to authority!!!”]

Which brings me to the question of probabilities. Statistically who do you think is more likely to be right? 1] An MD from Southern California whose ambition in life seems to be to extinguish any open discussion of views that do not align with his own views and interpretation of most all of science. 2] The consensus view of many scientists who in good faith attempt to understand the world through a process of hypothesis testing and experimentation and open communication of that information and interpretation.


A “Christian Agnostic”?
Sean

Concerning your fixation with the numerology I can use R and bioconductor probably better than the average biologist but like lawyer jokes the adage about “lies, damn lies and statistics” resonates because it has some basis in reality. Biologists use statistics to decide what is the likely among the possible processes and hypotheses. Statistics and mathematics are tool in biology not the reality. Particularly annoying I find the abuse of post hoc probabilities which are largely meaningless and depend on the rigor of your definition of the dependent variables proposed as precedent to the outcome. Bayes and the savy gambler understood the real purpose of statistics.