Sean Well this column has got it all and we …

Comment on The God of the Gaps by pauluc.

Sean

Well this column has got it all and we are barely over 35 comments. Glowing peer review from Holly, Specious arguments about laws of thermodynamics, The strawman argument; ie Scientitist practice methodological naturalism are really practicing God of the Gaps because they are not eclectic in their definition of causal mechanisms, so the use of ID must be quite scientific. Forced analogies about icecream and epistemology. Laments about the unjust claims of science to objectivity, paranoia about the scientific cartel including veiled references to the martyrdom of Richard Sternberg at the hands of those dastardly “high priesthood of science”, continuing misquoting of Paterson that is impervious to reason or correction, “forensic scientists, anthropologists, or even SETI scientists” as elite practioners of ID.

For good measure follow this with the transmutation of the anthropic principle to imply that Paul Davies, Roger Penrose, Arno Penzias, Freeman Dyson, Charles Hard Townes, Fred Hoyle and Chandra Wickramasinghe are supporters of literal YEC and its most recent incarnation ID.

If you got out more and actually talked with practicing scientists who accept that the basis of science is the method of hypothesis testing you would find that all except the fundamentalist and evangelical atheists are happy to admit the limitations of science and to simply say we dont know. We use our ignorance as a spur to discovery not as a bullet point to strengthen and support prejudices as Ken has rightly pointed out. We are ashamed of our ignorance more than proud of our scant knowledge as we live with uncertainty and as clinicians live with clinical equipoise.

I do not know how many forensic scientists, anthropologists, or even SETI scientists you know who would say their practice is all about intelligent design. They are scientist in that they propose hypotheses and test them be searching for evidence or generating data by experiment. ie for SETI the hypothesis is that if there is life and intelligence in space then there will be a signature in some output from that source which is similar to those humans as intelligent material beings produce. Seeing a signature of intelligence in this context is fine but do you then assume that any signal is from a supernatural source as you seem to want to do for origins? According to the cut and post of ID for literal creationism that seems precisely what you are arguing. I would confidently wager that SETI scientists at Berkley and Harvard would not. As scientists they would look for natural cause and would continue to look for natural albeit extraterrestial causes not for supernatural causes. (see Fred Hoyle and Chandra Wickramasinghe quotes below)

Similarly how often do anthropologists or forensic scientist conclude that an artifact is generated by supernatural means?
It is a far cry from recognizing artifacts as products of intelligent humans to say that because there is an artifact it must be from God which is what you want us to do for origins.

You cite several scientists arguing from the anthropic principle but none appear in the discovery institute list (http://www.dissentfromdarwin.org/) of scientist supporting creationism or at least opposing Darwinian evolution;

Paul Davies:
“Yes, the universe looks like a fix. But that doesn’t mean that a god fixed it” The Guardian 2007-6-25
“We may never have all the details but I’m sure that there is a physical pathway leading from a mixture of mindless molecules to something as wonderful as a simple living cell. I don’t know what that pathway is. I don’t believe anyone else does at this stage but that doesn’t mean it was a miracle just because this is a big gap in our understanding”. Catalyst ABC 20/10/2005

Roger Penrose:
“.. On the other hand I cannot believe that the anthropic argument is the real reason (or the only reason) for the evolution of consciousness. There is enough evidence from other directions to convince me that consciousness is of powerful selective advantage, and I do not think that the anthropic argument is needed.” The emperors new mind pg 562

Arno Penzias;
(As a jew he clearly believes in God as the originator of the cosmos but there is a paucity of information on his beliefs on biological evolution). He does however appear to restrict science to things susceptible to naturalistic explanation. Like Gould he seems to favour NOMA.

“Most physicists would rather attempt to describe the universe in ways which require no explanation. And since science can’t *explain* anything – it can only *describe* things – that’s perfectly sensible.” quoted in http://www.the-atheist.com/theistic-education-course-day-2-again-with-the-irrelevant-quotes/

Freeman Dyson:

“Trouble arises when either science or religion claims universal jurisdiction, when either religious or scientific dogma claims to be infallible. Religious creationists and scientific materialists are equally dogmatic and insensitive. By their arrogance they bring both science and religion into disrepute. The media exaggerate their numbers and importance. The media rarely mention the fact that the great majority of religious people belong to moderate denominations that treat science with respect, or the fact that the great majority of scientists treat religion with respect so long as religion does not claim jurisdiction over scientific questions.” http://www.edge.org/documents/archive/edge68.html

“The argument from design…was at the heart of the battle between creationists and evolutionists in nineteenth-century biology. The evolutionists won the battle. Random genetic variations plus Darwinian selection were shown to be sufficient causes of biological evolution.”
Infinite in all directions

His book Origins of life should not at all give solace to the modern intelligent design community.

Charles Hard Townes: in an interview says

Q “Should intelligent design be taught alongside Darwinian evolution in schools as religious legislators have decided in Pennsylvania and Kansas?”

A “I think it’s very unfortunate that this kind of discussion has come up. People are misusing the term intelligent design to think that everything is frozen by that one act of creation and that there’s no evolution, no changes. It’s totally illogical in my view. Intelligent design, as one sees it from a scientific point of view, seems to be quite real. This is a very special universe: it’s remarkable that it came out just this way. If the laws of physics weren’t just the way they are, we couldn’t be here at all. …. The other possibility is that ours was planned, and that’s why it has come out so specially. Now, that design could include evolution perfectly well. It’s very clear that there is evolution, and it’s important. Evolution is here, and intelligent design is here, and they’re both consistent.”

Q “They don’t have to negate each other, you’re saying. God could have created the universe, set the parameters for the laws of physics and chemistry and biology, and set the evolutionary process in motion, But that’s not what the Christian fundamentalists are arguing should be taught in Kansas.”

A “People who want to exclude evolution on the basis of intelligent design, I guess they’re saying, “Everything is made at once and then nothing can change.” But there’s no reason the universe can’t allow for changes and plan for them, too. People who are anti-evolution are working very hard for some excuse to be against it. I think that whole argument is a stupid one. Maybe that’s a bad word to use in public, but it’s just a shame that the argument is coming up that way, because it’s very misleading.”
http://berkeley.edu/news/media/releases/2005/06/17_townes.shtml

Fred Hoyle: in “Cosmic Life-force” Chapter 10

“The alternative to assembly of life by random, mindless processes is assembly through the intervention of some type of cosmic intelligence. Such a concept would be rejected out of hand by most scientists, although there is no rational argument for such a rejection. With our present knowledge, chemists and biochemists could now perform what even ten years ago would have been thought impossible feats of genetic engineering. They could, for instance, splice bits of genes from one system to another, and work out, albeit in a limited way, the consequences of such splicings. It would not need too great a measure of extrapolation, or too great a license of imagination, to say that a cosmic intelligence that emerged naturally in the Universe may have designed and worked out all the logical consequences of our own living system. It is human arrogance and human arrogance alone that denies this logical possibility.”

Chandra Wickramasinghe: in; Darwinism, Design, and Public Education, John Angus Campbell and Stephen C. Meyer, eds http://www.panspermia.org/thirdalt.htm

“Besides the origin of life, there is equal trouble for Darwinian idea of evolution where the doubts are even older. Although sustained macroevolutionary progress, as evidenced in the geological record, must be accepted as an irrefutable fact, major questions remain in regard to the precise mechanisms by which evolutionary changes are wrought. ….. The fossil record, however was generated in an open system the biosphere. Here just as cells from elsewhere may have seeded life on Earth originally, the genes that bring the sustained macroevolutionary progress we observe may also come from elsewhere.”
……
“Science and religion are two great manifestations of the human spirit. Religious belief is essentially of a revelatory character, while scientific facts are the result of rigorous experiment and intellectual discipline. Scientific procedures are based on the assumption that no violations of physical law occur. When violations seem to occur, scientists may decide that the evidence was anomalous. Or perhaps the laws were not correctly understood and need to be amended. Of course, this process of amendment and reappraisal has not been completed. Today, Darwinian theory extends well beyond the evidence, as creationists rightly notice. In this case, the details of the theory, not the underlying principles of science, should he challenged. But Phillip Johnson’s attempt to overthrow “naturalism” does attack these very principles. As William Dembski complains, “For the sake of inquiry we are required to pretend that God does not exist.” Yes, that’s how science is done. One may object to this principle, but it is the essence of science. Even if it were true that God by a miracle, created life out of ordinary matter, it could not be established scientifically. Miracles are simply not amenable to scientific investigation, and scientists are right to dismiss them as unscientific.”

As a scientist who is want to look at the provenance of a statement or the basis for fact I really don’t understand why you cite these scientists in arguing the virtue of a God of the gaps? Is it simply that you need to garner support from wherever you can for your contention that the weight of scientific evidence supports your views. In doing so it seems you disregard context and the intention of the authors and expect that none will be interested enough in “truth” to investigate further? It seems clear to me that virtually all the practicing scientists who would accept the anthropic principle and Fred Hoyles original ideas of “intelligent design for the universe do not accept a God of the gaps or YEC.

I apologize in advance for my prolix contribution and accept with grace the attendant thrumbs down it will engender.

pauluc Also Commented

The God of the Gaps
@Sean Pitman:

I am astounded that you can without blushing confidently assert that intelligent design as a surrogate for literal creationism is scientific but the views of scientists based on observable data and routinely subject to hypothesis testing is not.

“My views are testable in a potentially falsifiable manner. Unfortunately, yours are not… ”

I am not sure which of my scientific ideas are not testable. Clearly I have religuous views which I accept by faith and which I would never claim to be amenable to hypothesis testing. I do not however accept that the process of science is in any way deceptive and accept that scientists almost without exception have a high regard for honesty and openness as evidence by the process of peer review and open publication and do science in good faith.

In contrast to my acceptance of complementary roles of science and religion and faith you have a view that denigrates blind faith as a path to understanding of the transcendent and claim you must only accept in religion what is supported by the predominance of scientific evidence.

One of the main problems we are confronting here is of definitions. I think you are concatenating 2 ideas about probabilities and design and using one legitimate scientific observation of unlikely contingencies in cosmology to lend validity to another; a rebadged literal creationism and a God of the gaps which I think denies legitimate scientific investigations in biology and not surprisingly is deprecated by most biologists.

There would be much more clarity if you kept these 2 ideas separate and were open about the history of the ideas. The anthropic principle although accepted by many physicist was almost uniquely described by Fred Hoyle in terms of intelligent design. Other physicists have continued to more accurately use the descriptive term “‘the anthropic principle”. Few if any physicists would accept Fred Hoyles idea of panspermia which not surprisingly he has linked back to his designation of the anthropic principle as intelligent design.

The Kitzmiller vs Dover court case has been over the issue of what is intelligent design and clearly established that the way you are using intelligent design is a cut and paste for “scientific” creationism.

I must be obtuse. I can see the tenuous logic but I still really cannot see where the intense fervour for intelligent design comes from. As a scientist reading DI writings is a painful process that seems like a desperate and last ditch attempt to cling to a failing world view that is contingent on a fundamentalist assumptions and understandings of revelation. I much prefer to accept the Grace of God as revealed in Jesus and communicated within his Church and let the science resolve itself.

Like the scientific creationism before it, I cannot see that ID really has any significant explanatory value in terms of generating hypotheses. I am however really pleased that you think that your ideas “are testable in a potentially falsifiable manner” I look forward to seeing them presented in the only forum in which science is conducted; the peer reviewed literature.


The God of the Gaps
@Sean Pitman:

At risk of being drawn further into the vortex that is dialogue on this site I would offer a final comment to once again try to counter the woolly thinking and confusion about science and religion that is all too prevalent here.

As I have said before the bottom line for me is that I am a disciple of Christ and accept the Pauline synthesis offered in 1 Cor 1 as the core of my religious belief.

20 Where is the wise man? Where is the scribe? Where is the debater of this age? Has not God made foolish the wisdom of the world? 21 For since in the wisdom of God the world through its wisdom did not come to know God, God was well-pleased through the foolishness of the message preached to save those who believe. 22 For indeed Jews ask for signs and Greeks search for wisdom; 23 but we preach Christ crucified, to Jews a stumbling block and to Gentiles foolishness, 24 but to those who are the called, both Jews and Greeks, Christ the power of God and the wisdom of God.

Like Bonhoeffer, Barth and more recently Alister McGrath I would see natural theology as a largely meaningless endeavor in terms of our knowledge of of God which only comes through his revelation in the life and death of the person Jesus.

We can argue ad infinitum as we have done before about how this knowledge can be imparted but I make no apology that it is not by the rational and logical process sought by Greeks and Sean.

In response to Peter’squestion I would say that we must accept we are ignorant on many things not least of which is the origin of life. There is no adequate explanation for the origin of the life but does that mean we then must say there is therefore no natural explanatory mechanisms and this is the locus of Gods activity. There is an anthropic universe which gives us some reason to say that the universe may be ordered and meaningful but it argues no more than that. As a Christian I can only say that the locus of Gods activity and revelation is in Christ who reveals the nature of God and the ethic of the kingdom.

As Sean has well indicated in his original blog at the head of this column, historically implicating God as the cause for the many unknowns is a losing strategy and will lead to an decreasing role for God as explanator.
I should not have to repeat the simple and obvious examples such as the new testaments attribution of mental illness and epilepsy to demons and the supernatural. I cannot see how rational therapies with anti-epileptic drugs and antidepressants that have cleared out our asylums and allowed people to live relatively normal lives would have developed if we had continued to accept these explanations rather than explored the possibility of natural mechanisms amenable to natural interventions.

I think it incontrovertible that accepting the meta-narrative of intelligent design as a theoretical basis for the natural world stops scientific research as can be easily verified by searching in the original published research in life sciences based on this premise. Intelligent design has a vested interest in not finding explanation for its strength lies in its explanation of the unknown or improbability based on the current known mechanisms. Sean is a prime example of an intelligent design. Excellent in the meta-analysis of the meta data but not in generation of original hypothesis driven research outputs. I would be happy to be corrected on this with reference to papers indexed on pubmed based explicitly on IDT.

In contrast biological science practiced as hypothesis testing based on the core premise of science; natural mechanisms and experimentation has produced 259,888 papers on aspects of evolutionary processes and mechanisms. In terms of abiogenesis there has been 721 original research publications including the work of nobel laureate Jack Szostak.

1. Trevino SG, Zhang N, Elenko MP, Lupták A, Szostak JW. Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity. Proc. Natl. Acad. Sci. U.S.A. 2011 Aug;108(33):13492–13497.
2. Schrum JP, Zhu TF, Szostak JW. The origins of cellular life. Cold Spring Harb Perspect Biol 2010 Sep;2(9):a002212.

You may dismiss these as simply basic data points only tangentially relevant to the big question but this is the nature of science. An original research paper is an incremental increase in knowledge never the definitive answer to a big question. Surely these nearly 250000 incremental increases in knowledge amount to something. At least to me it seems somewhat arrogant, when I have said I accept naturalism as the basis of scientific research on origins as evident in the peer reviewed literature, to dismiss this body of evidence with a statement like;

“If by “natural mechanisms” you mean mindless natural mechanisms, then how is this statement remotely scientific? It’s a sincere question on my part. I fail to see how you’ve presented any testable argument regarding your proposed mechanism for either the origin or diversity of life beyond very low levels of functional complexity? How is the hypothesis of a mindless mechanism, without any input from any intelligent source of any kind, testable? How is it scientific?”

I am not sanguine enough to expect that I will have had any effect on the thoughts of most commenters on this site but if I have been able to help even one observer see that the Grace God revealed in Jesus is not incompatible with full participation in the process of science I would be happy.


The God of the Gaps
Sean

You hopefully suggest

“The only real question that remains, then, is if there is a valid naturalistic explanation for living things and their diversity or not?”

There are many more questions than that.

What the writers you cite above realize is that in honestly following the scientific evidence there is 3 things that they must conclude.
1] There is an anthropic principle; the Goldilocks principle the world is just right for life and that this is a highly unlikely scenario and would require a multitude of universes not evident for this to be by chance.
2] The evidence for evolution of the complexity of life once established on earth is irrefutable. Darwinian mechanisms may or may not be sufficient but natural mechanisms are most likely
3] Intelligence and mind are natural consequences of a highly complex brain that arose by these natural mechanisms.

This is the scientific position. Whether God was working through these processes is a philosophical not a scientific question.
You enamoured as you are with statistical inference twist these arguments about to invoke some grand theory of intelligent design when none is required.

In terms of my 3 points of science you I think would agree with the anthropic principle
On point 2 all I have read from you says you dispute the evidence and argue that most scientists are honestly deceived. You do not agree on dating methods, ice cores, varves, volcanic ocean ridges, continental drift, fossil evidences and geological columns, relatedness of genomic sequences or phylogenies, history of insertions of repetitive elements; all evidences that most scientists including those above would accept in good faith as likely true.
On point 3 you have this idea of some overarching intelligence that is God like but may or may not be natural that is responsible for anything that is more complex than close to inanimate objects.

With such a gulf between what you will accept of reality it is not surprising there is little common ground between your views and conventional hypothesis driven science.


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.