@Sean Pitman: Sean your response includes several excellent descriptors of …

Comment on LSU memorandum confirms Educate Truth’s allegations by pauluc.

@Sean Pitman:

Sean your response includes several excellent descriptors of your assessment of the indaquacy of the paper and evolutionary models. The following give a flavour of your response.

“The assumption isn’t true.”

“…. there really are no “foolproof” genetic markers of common decent.”

“…..conclusive evidence for common descent has not held up”

“…..has also been shown to be false”

“….it still poses a problem for standard evolutionary theory.”

“…..do not falsify the ID-only hypothesis since they do not even address the origin of high
levels of functional information within the genomes of living things.”

“They are declining in quality – i.e., they are headed for extinction at a fairly rapid rate. ”

“Such evidence calls into serious question the validity of these just-so stories of mainstream scientists”

Nowhere however do you answer the real question that was posed to David Read. You are implying that the creationist argument is correct simply because the alternative is deficient. I know this is the SOP but I had hoped that you would be proactive in telling me whey this data is best interpreted from a creationist perspective which was David Reads contention ie

“I can also see how most of the actual facts fit better in a creationist framework”.

How can the apparently unplanned but cobbled together and functional mess that is the genome be best explained in a creationist framework? It cries out chance and contingency which is precisely what evolution would predict and why it is increasingly seen as the most compelling by most genome scientists. As you know you will not replace this dominant model by carping about minor or major deficiencies because in science you know a model is not replaced because it is deficient but because there is a better model.

The onus is on you to produce a better more compelling model. As Clausen has indicated they are currently lacking. For these published observations on the distribution of alu repeats you must show the superiory of you model not the inadequacy of the existing model. To be real science you must then go on to test the predictions of your model experimentally.


pauluc Also Commented

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”.


LSU memorandum confirms Educate Truth’s allegations
@David Read:

“What I know about myself is that when I read any book or article written by Darwinist, I can very easily spot assumption resting upon guesswork, resting upon unproven axiom. I can also see how most of the actual facts fit better in a creationist framework”.

Good then perhaps you could give us your analysis of this paper and how the data supports your creatonist perspective?

1. Liu GE, Alkan C, Jiang L, Zhao S, Eichler EE. Comparative analysis of Alu repeats in primate genomes. Genome Res 2009 May;19(5):876-885.


What are the “actual facts” here?
What is the guesswork and what is the unproven axiom.
What is the creationist interpretation of this?

I have no doubt that you will be able to generate a convincing response to this question as you are a lawyer and you are trained not for any objective analysis of data but to use the material that you can gather to produce the best available response. Your highly developed skill in this is manifest in your book on dinosaurs. But is it science?


Recent Comments by 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”?

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.

Southern Adventist University opens Origins Exhibit
@Sean Pitman:

“There is no need to invoke God to explain the phenotypic diversity of living things beyond His original programming of the parental population – His “front-loading” of the gene pools if you will.” – Sean Pitman

I clearly lack your gift. It must be wonderful to be always right even when I’m wrong.

It seems that your position is that in creationism there are no miracles except when there are miracles. I can accept that. but lets consider the turtles.

God created ex nihilo in 6 24hr contiguous days. We can of course define that as natural if we want.
This life was totally unlike the carbon based life form we see today as there was no death so there is none of the normal concepts of ecology we understand today.

He then miraculously introduced death associated with the many genes associated with cellular and organismal control of death (apoptosis and necrosis). Or maybe this was created by a alternative bad creator with similar power to the original good creator

He then dispersed the animals terrestial from a boat in the middle east to the rest of the world over a period of a few thousand years, 500 year of which was an ice age with an ice sheet covering all of the northen and southern regions of the planet. Truly a miracle.

He miraculously altered all concepts of genetics so that a population of 2 had enough genetic information and were so perfect (apart from the aforementioned introduction of death pathogens and immunity) that they could give the total diversity of the large number of species that exist now derived as they were from a few baramin that populated the ark.