@wesley kime: After scrathing in dust for a little while …

Comment on Believing the Disproven – An Adventure in Science by pauluc.

@wesley kime:

After scrathing in dust for a little while
He lifts his head with a bemused smile
Descends Olympus and joins the fray
With mortals there who wander and stray
As they circle and carp about things ethereal
Divining poor what’s substance not immaterial

The method they argue is the critical stance
Do you favour the gestalt, cause purely by chance
We arrive where we are by virtue of genes
A weltanschauung cast like minting machines
Groups and people defined by kith and kin
Apprehending vaguely any concept of sin

By culture and tribe we start where we are
But some hear the call of the hope from afar
And then where we are the divine intervenes
And asks us to think beyond such routines
To intuit a logic that is sensible too
To dream and imagine a place that’s true

Though seldom its found by the intellectual few
But by a leap of faith with danger, and risk too
For when you can’t compute the whole score
You’re left with no option but to try to explore
The will to power or faith in a spiritual realm
And follow the God we trust’s at the helm

But some need more substance, proof too
Empirical facts undeniable, abundant, not few
Hypothesis, experiment, results, to publish verboten
But to believe without proof that’s completely broken
Empiricism and science we need to maintain
that holy writ’s empirically real, straight and plain

We draw up a new thesis that helps us see
You can transfer the virtue to a claim you agree
Can’t be tested because its just intractable
As long as that claims empirical or actual
if it belongs to a group clustered by religious intent
Then testing one claim in the group gives assent
To the truth and verity of the group as a whole
’cause empirical proof’s needed to save our soul

To the claim this makes a fragile approach
a monolithic construction too difficult to broach
we’re proffered a defence that claims for its virtue
the alternatives lack sense are have no logic
wishful thinking, insubstantial and certainly toxic
For faith comes by knowledge that’s ever been clear
For only by logic can God’s spirit draw near.

And back and forth they go. Claiming text,
proofing same to make their point, perplexed,
And why indeed should not these mortals cite
Their holy texts and argue whose right
To believe without substance is irrational, obscene
To claim faith as the substance for thing not seen

But he shakes his head in sorrow and funk.
How wrong are these mortals to believe such bunk,
Words tapped by mortals, versions, ceaseless suppositions
Must divinity come and show their sacred propositions.
Cannot they see the words of the prophets spoken then
exist only as words serving the logos to come again.

pauluc Also Commented

Believing the Disproven – An Adventure in Science
@Sean Pitman:
Dont worry I as a scientist engaged in the process of scientific research have looked at the consequences of rigorous application of these same methods to all of life including the provenance of the Canon and of EG White. I accept the conclusions of the best biblical scholarship on the origins of the canonical text and of the writings of the Adventist pioneers.

By those methods I have arrived precisely at your “..If I ever…” dilemma and have concluded that fundamentalism and its assumptions are fatally flawed. I have concluded that there are evidences beyond the empiricism of the enlightenment that warrant belief in the divinity of Christ and the Way of the followers of Christ.


Believing the Disproven – An Adventure in Science

Sean&#032Pitman: St. Paul as somehow supporting your position when his sudden paradigm shift and the life-long basis of his Christian faith and hope was entirely the result of the empirical demonstration of the Risen Christ

Empirical demonstration?
Acts 9
3 And as he journeyed, he came near Damascus: and suddenly there shined round about him a light from heaven:
4 And he fell to the earth, and heard a voice saying unto him, Saul, Saul, why persecutest thou me?
6 And he trembling and astonished said, Lord, what wilt thou have me to do? And the Lord said unto him, Arise, and go into the city, and it shall be told thee what thou must do.
7 And the men which journeyed with him stood speechless, hearing a voice, but seeing no man.
8 And Saul arose from the earth; and when his eyes were opened, he saw no man: but they led him by the hand, and brought him into Damascus.

Acts 22
6 And it came to pass, that, as I made my journey, and was come nigh unto Damascus about noon, suddenly there shone from heaven a great light round about me.
7 And I fell unto the ground, and heard a voice saying unto me, Saul, Saul, why persecutest thou me?
8 And I answered, Who art thou, Lord? And he said unto me, I am Jesus of Nazareth, whom thou persecutest.
9 And they that were with me saw indeed the light, and were afraid; but they heard not the voice of him that spake to me.
Act 26
11 And I punished them oft in every synagogue, and compelled them to blaspheme; and being exceedingly mad against them, I persecuted them even unto strange cities.
12 Whereupon as I went to Damascus with authority and commission from the chief priests,
13 At midday, O king, I saw in the way a light from heaven, above the brightness of the sun, shining round about me and them which journeyed with me.
14 And when we were all fallen to the earth, I heard a voice speaking unto me, and saying in the Hebrew tongue, Saul, Saul, why persecutest thou me? it is hard for thee to kick against the pricks.
15 And I said, Who art thou, Lord? And he said, I am Jesus whom thou persecutest.
16 But rise, and stand upon thy feet: for I have appeared unto thee for this purpose, to make thee a minister and a witness both of these things which thou hast seen, and of those things in the which I will appear unto thee;
17 Delivering thee from the people, and from the Gentiles, unto whom now I send thee,
18 To open their eyes, and to turn them from darkness to light, and from the power of Satan unto God, that they may receive forgiveness of sins, and inheritance among them which are sanctified by faith that is in me.
19 Whereupon, O king Agrippa, I was not disobedient unto the heavenly vision:
20 But shewed first unto them of Damascus, and at Jerusalem, and throughout all the coasts of Judaea, and then to the Gentiles, that they should repent and turn to God, and do works meet for repentance.

Which account is true according to empirical evidence? Did Paul’s attendants see the light (Jesus face as Paul indicates in 1 Cor 9:1 and 1 Cor 15:8,9) or hear the voice or see or hear neither. Empirical evidence is all about what can be detected by the sense including sight and hearing. If there was concern about empirical evidence surely this would be very clear and explicit. Logically they can only be unconcerned about your obsession with physical evidence.
Other discrepancies are covered in this comment;
http://www.huffingtonpost.com/john-dominic-crossan/paul-and-damascus_b_1348778.html

To pretend to believe only those parts of the biblical account that can be verified by empirical evidence as usually understood is ridiculous and is not what you really do so why imagine that I am any different.


Believing the Disproven – An Adventure in Science
@Sean Pitman:

For someone so critical of anyone even minimally acknowledging expertise and authority you are astoundingly deferential to EGW and the estate. A scientist would properly look at what the critics say not just look to the choir.
David Depinho may be disaffected but I think he can critically appraise the data and what he says should be seriously considered.
http://www.formeradventist.com/studies/topical/shutdoorteaching.html
Even Olson’s argument that later visions corrected the misunderstanding of that given to her at 18 years of age tacitly admits that the “I was shown… was in fact incorrect.
http://www.whiteestate.org/issues/shutdoor.html


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.