@pauluc: 1] You will know from reading Cochrane reviews that

Comment on GC Votes to Revise SDA Fundamental #6 on Creation by Sean Pitman.

1] You will know from reading Cochrane reviews that there are levels of evidence. As my post-doctoral supervisor said it does not exist until it has been published in a peer review. I would add to this the online databases. I therefore am loath to take journalistic spin from 60 minutes as having any evidentiary value

I would think that you would consider the comments of Mary Schwitzer and Jack Horner on their own work at least of some relevance. They’ve also written papers specifically rebutting several of your arguments – such as your quoted biofilm argument which they convincingly falsified.

2] You are correct in that there is now sequence data that has been matched with hemoglobin but as a pathologist I would hope you recognize that the antibody binding data that Schweitzer presents in her science paper is suggestive but is not really compelling. Here in Australia adventist well remember Lindy Chamberlain who spent several years in jail on the basis of bogus immunochemical finding of large amounts of fetal haemoglobin in the car used by the Chamberlains.

Antibody binding evidence is very compelling when it comes to the specific argument that large sections of intact hemoglobin molecules were present in the dinosaur bones analyzed. Beyond this there is the electrophoresis evidence which shows a spectrum of hemoglobin molecular sizes from small to large fragments. The paper you cite below is also supportive of this conclusion. So, I really don’t understand your efforts to discredit the conclusion of Schwitzer and Horner in this regard.

3] The original mass spec data has been reanalysed independently and supports the original conclusion that there is sequence matching haemaglobin and collagen in the sample from bone and the surrounding soil. Bern M, Phinney BS, Goldberg D (2009) Reanalysis of Tyrannosaurus rex Mass Spectra. J. Proteome Res 8:4328-4332.

More supportive evidence of intact protein sequences…

4] What is the actual data on the sequences and what is the scientific argument from which you are deriving so much support for a 6000 year earth history?

My ideas for the age of life on Earth is not based on sequence data. In fact, I consider the molecular clock hypothesis to be fraught with so many problems as to be quite unreliable. The circularity of this hypothesis has also been demonstrated by showing that estimates based on evolutionary assumptions are off by 20 to 100 fold when compared to real time phylogenetic analysis of historically known family relationships.

Why all the XX s in the T rex and only a 36 aa fragment for the Brachylophosaurus canadensis sequence?

The scientific argument is whether or not the Trex and B Candensis should be all Xs which was the conventional understanding although the idea that protein can be present in fossils is not new ( see for example; Semal, P.; Orban, R. Collagen extraction from recent and fossil bones: quantitative and qualitative aspects. J. Archaeol. Sci. 1995, 22, 463â€“467.) and was the underlying premise of Peter Hares work of which you are so dismissive.

Peter Hare’s premise was that amino acid racemization rates could be used as an independent molecular clock. This view has been clearly falsified since his death. Even mainstream scientists no longer use AARD as an independent dating technique. At the very best it is only considered useful as a local dating technique once it has been calibrated against another dating method – like radiocarbon.

I think it is fair to say that the consensus is swinging to the view that Schweitzer and her colleauges are correct and that there is protein even in conventionally very old fossils.

If you knew that the consensus view now favored Schweitzer’s view, why did you attempt argue otherwise at first?

Does Schweitzer and others who do this work interpret this as suggesting that the earth is therfore 6000 years old?

No. They still believe in the mainstream chronology because of their confidence in other forms of radiometric dating. However, neither Schweitzer nor anyone else has been able to explain how molecules that were long thought to self-degrade in well less than 100,000 years could still be around 60-90 million years later. According to mainstream science this is still a seeming impossibility which Schweitzer herself admits. She doesn’t understand how it could possibly happen and nobody else does either.

If this was the only bit of evidence in line with young-life creationism, there might be more room for suggesting some unknown alternative to explain this evidence. However, there is a great deal more evidence favoring the young-life model of origins to the point where the great weight of evidence, scientific evidence, is actually strongly in favor of the young-life/catastrophic model of the origin of the geologic/fossil records.

If you accept the premise that Mastodon, T rex and b Canadensis are all less than 6000 years old then you still have to explain the differences in the frequency of Xs in the sequence data. The emerging scientific view is that these reflect difference in age of the material and a decay in protein with time.

Or it could represent differences in temperature exposure over time or local differences in acidity, etc. This is yet another problem with AARD that Hare didn’t seem to fully appreciate. Time isn’t the only factor that affects racemization or protein decay.

5] You have not addressed the point of my last post which was that it is illogical to assume that your position of 6000 years is correct simply because proteins persist longer than has been conventionally thought.

Again, this is by no means the only evidence for a young age of life on Earth. There is a great deal more evidence. It is just interesting that this particular piece of evidence is so strikingly contrary to everything that mainstream scientists had observed and claimed about the rate of protein and DNA and soft tissue decay over time – by several orders of magnitude. It is so far off based of these claims as to be quite a mystery for mainstream science – as Schweitzer herself repeatedly points out in the 60 Minute interview as well as many other news interviews and various published articles and papers.

6] I do not leave the Adventist church probably for the same reason you do not leave the Adventist Church and go join Jerry Falwell and the Thomas Road Baptist Church where I am sure your views on literalism and biblical inerrancy would find ready acceptance and you would feel completely at home. Since I was baptized in an Adventist church as a teenager and joined the community of faith I have sought to uphold the principles of that community and to live honesty before my God. As a University student I had a crisis of faith when I realized that some of the things, such as a literal sanctuary in heaven, were not biblical. I was challenged by the message of salvation by faith as presented by people like Desmond Ford and confronted by the perfectionism of Robert Brinsmead that is finding re-expression in the last generation theology of today. I was appalled by the Churches actions in the 1980s when a large number of committed laypersons and ministers were rejected by the administration. I did not attend Adventist church for a time but with the arrival of children began to appreciate that belief in isolation missed an important part of being a Christian. The participation in the life of the church of God the body of Christ. It was the message of Grace and salvation and the presence of a community of believers that expresses the goodness of God in word and action that compels me to continue to seek to belong and to invite others to experience the Grace of God in community.

I believe the Adventist church is a movement that arose to call us to see within this world another dimension. To live within hope and to practice the principles of the Kingdom of God now as we wait for the coming when this carbon based life form will be changed and will put on immortality. Adventism has I believe more than other protestant groups stressed the significance of living a life in this body temple that is according to kingdom principles of peace compassion and Grace. I believe the writings of EG White have been of great value in this call to orthopraxy but I view her as lead by the same holy spirit which informs all men and was lead not inerrant. I believe that the last generation theology is an abberation to the spirit of this church as I believe your call for purging is an abberation to the story of the unfolding Grace of God I see in the Adventist tradition.

I write on this blog not because I wish to destroy the church but because I do not wish you to destroy the church with your platitudes of certainty and hostility to one of the least of these who wish to come to salvation through the God of Grace.

The early founders of the SDA Church, to include Mrs. White, proposed an interesting concept of “present truth”. I do not make claims of absolute certainty. In my view there is no such thing from the perspective of a subjective human being. What I do claim is to support what I consider to be “present truth” as best as I can understand “truth”.

I do not consider this knowledge or “truth” in and of itself “salvational”. In other words, I don’t believe that knowledge or the lack thereof is the basis of morality. Morality, in my opinion, is based only on motive – i.e., the presence or lack of love toward one’s neighbor. I believe that God will not base his judgment on what we knew, but on the Royal Law of Love alone. The only question He will ask is, “What did you do for the least of these my brothers and sisters?”

However, this does not mean that knowledge is pointless. If it was, God wouldn’t have given us such big brains with the ability to appreciate many aspects about Him and His nature as He reveals these to us. Knowledge has the power to provide a solid hope to those who would otherwise be hopeless in this world of sin, pain and suffering. Knowledge is the basis of a solid hope in the validity of the Gospel’s “Good News”. If the evidence behind this “Gospel” message is shown to be clearly in error in a fundamental degree, then the very basis of the Gospel’s hope is also called into question within the intelligent mind.

So, this is why I’m an Seventh-day Adventist. I think that the SDA message is a very hopeful message that is based on a great deal of very reliable scientific evidence. I believe that the organization of the Church, as inspired by God Himself, is more effective at spreading this message than any one person could be by his/her self.

In order to maintain the relevance and power of an organization, there must be rules that are internally maintained within the organization. No viable organization functions without rules of internal order and government. Your notion that the SDA Church, as an organized body, should financially support a person as a teacher or preacher regardless of his/her views on the clearly stated ideals and goals of the organization is a recipe for chaos, not a viable organization.

So, if you really do value the organized aspect of the SDA Church, and you are working to “preserve” and not destroy the Church as an organization, you should really join me and my efforts to maintain some sort of order within the Church based on the Church’s view, as a collective body of believers, of “present truth”.

If you as an individual have progressed significantly beyond the Church’s view, as a body, regarding its own clearly stated goals, ideals, and Pillars of Faith, then why do you support opposition to the Church on the Church’s dime? I think it is fine to oppose to SDA Church, but not while one is getting paid by the Church to do the Church’s work. In my book this is stealing of the Church’s time and money… a moral wrong in anyone’s book.

Anyway, I do thank you for your thoughts and your time. I simply think that you are promoting a position of anarchy which will eventually erode the very thing you think you are striving to protect…

Sean Pitman
www.DetectingDesign.com

Table of Contents

1 Sean Pitman Also Commented
- 1.1 Recent Comments by Sean Pitman
2 Related

Sean Pitman Also Commented

GC Votes to Revise SDA Fundamental #6 on Creation
@Brad:

I am probably going to write far too much but if you want the conclusion, it is that Sean Pitman is completely and utterly wrong in everything he says in his comments and displays a great ignorance of proteins and their structure and function.

And:

I hope the above short essay on protein structure and function is useful even to Sean Pitman who needs to stop being obsessed with computer-based numerology and do some reading and talk to some practical protein scientists.

From David Dryden of the University of Edinburgh. See: http://groups.google.com/group/talk.origins/msg/a7f670c859772a9b

Ah, so you’ve read Dryden’s arguments…

Where did Dryden point out my ignorance of protein structure and function? I am, after all, a pathologist with a subspecialty in hematopathology – a field of medicine that depends quite heavily on at least some understanding of protein structure and function. Yet Dryden says that I’m completely and utterly wrong in everything I say on this topic? Sounds just a bit overwrought – don’t you think?

In any case, where did Dryden substantively address my argument for an exponential decline of evolutionary potential with increasing minimum structural threshold requirements? Dryden himself only deals with very low level examples of evolution in action. He doesn’t even consider the concept of higher levels of functional complexity and the changes in the ratios of beneficial vs. non-beneficial sequences that would be realized in sequence space.

Dryden also completely misunderstands the challenge of the structural cutoff of systems that require a minimum of at least 1000 specifically arranged amino acid residues to work to do a particular function. He also flatly contradicts Axe’s work which suggests that it is not an easy thing to alter too many amino acid residue positions at the same time and still have the system in question work to do its original function. There is some flexibility to be sure, but there is a limit beyond which this flexibility cannot by crossed for protein-based systems. And, as this minimum limit increases for higher level systems, the ratio of beneficial vs. non-beneficial does in fact decrease exponentially. Dryden seems completely clueless on this particular all-important point.

This cluelessness is especially highlighted by Dryden’s comment that the bacterial rotary flagellum isn’t very complex at all:

These increasing degrees of functional complexity are a mirage.
Just because a flagellum spins and looks fancy does not mean it is
more complex than something smaller. The much smaller wonderful
machines involved in manipulating DNA, making cell walls or
cytoskeletons during the cellâ€™s lifecycle do far more complex and
varied things including switching between functions. Even a small
serine protease has a much harder job than the flagellum. The
flagellum just spins and spins and yawnâ€¦

I really couldn’t believe that Dryden actually said this when I first read it. Dryden actually suggests that a small serine protease is more functionally complex than a bacterial flagellum?! – just because it is used more commonly in various metabolic pathways? – or more interesting to Dryden? He completely misses the point that the bacterial flagellum requires, at minimum, a far far greater number of specifically arranged amino acid “parts” than does a serine protease – thousands more.

And Dryden is your “expert” regarding the potential of RM/NS to create protein-based systems beyond very low levels of functional complexity? Why not find somebody who actually seems to understand the basic concept?

Here’s another gem from Dryden. In response to my comment that, “The evidence shows that the distances [in sequence space] between
higher and higher level beneficial sequences with novel functions
increases in a linear manner.” Dryden wrote:

Reply: What evidence? And if importance of function scales with
sequence length and the scaling is linear then I am afraid that 20^100
is essentially identical to 2 x 20^100. Also a novel function is not a
new function but just one we stumble upon in doing the hard work in
the lab. Itâ€™s been there a long timeâ€¦

Dryden doesn’t grasp that in the debate over the creative potential of RM/NS that a novel functional system is one that the evolving population is looking for – not some lab scientists. It is only there in the potential of sequence space. It is not found until random mutations within the gene pool discover it by pure luck.

Dryden also doesn’t understand that this discussion isn’t over the “importance of function” but over levels of beneficial functionality – regardless of there “importance”. He also doesn’t understand that if a system requires a minimum sequence length or size (to include multiprotein systems) and a minimum degree of specific arrangement of amino acid residues within that minimum size, that a linear increase in this minimum structural threshold requirement does not result in a linear increase in average number of random mutations needed to achieve success. The linear increase in structural threshold results in an exponential decrease in the ratio of potentially beneficial vs. non-beneficial. This, obviously (to the candid mind anyway) will result in an exponential increase in the average number of random mutations needed to achieve success at the higher level.

Really, I would love to hear your take on Dryden’s paper in the light of a complete lack of evolution in action beyond very very low levels of functional complexity – i.e., minimum structural threshold requirements. I’m sure you could do a better job than he did…

Sean Pitman
www.DetectingDesign.com

GC Votes to Revise SDA Fundamental #6 on Creation
@Brad:

I’ll reply to your comments over on the special thread I created for this particular discussion regarding the anti-ID arguments of Elliot Sober:

http://www.educatetruth.com/la-sierra-evidence/elliot-sober-just-dont-call-the-designer-god/

Sean Pitman
www.DetectingDesign.com

GC Votes to Revise SDA Fundamental #6 on Creation
@Brad:

So, do you or do you not accept that, regarding this specific question, the design hypothesis predicts that we will not see congruence between the phylogenies (conditional on the two testable possibilities you provided having low probability)? If you do not, you owe us an explanation of why not, given your claim that the hypothesis is testable.

The “prediction” of ID is that only ID-driven mechanisms will be found to produce the phenomenon in question – that no non-intelligent mechanism will come remotely close to doing the job.

As I’ve mentioned to you before, you cannot “predict” any particular features of what a designer will do or would have done without direct knowledge of the designer in question. However, a lack of such direct knowledge does not remove the scientific ability to detect a true artifact when you see one with high predictive value.

This is the reason I’ve asked you to discuss the granite NHP problem I’ve presented. Instead, you’ve referred me, yet again, to the arguments of another without presenting any argument of your own or even commenting on those ideas that you consider to be most personally convincing to you.

My interest is in forcing you to make a prediction. You claimed you have one; we are all still waiting.

My claim was that evolutionists would have an easier time of things if functionality wasn’t involved in the ToL. The reason for this is that mindless mechanisms can produce NHPs – and do so all the time. However, mindless mechanisms are extremely unlikely to produce high levels of functional complexity in a reasonable amount of time and have never been observed to do so.

In short, some things you can’t predict; some things you can – – with regard to the ID-only hypothesis. You are asking me to predict those things that are not predictable from an ID perspective. You are then arguing that because such things are not predictable that ID cannot be scientifically detectable. This assumption of yours simply doesn’t follow for me…

Therefore, I’m interested in hearing you explain the logical basis behind various fields of science which invoke ID (such as anthropology, forensics, and SETI). What “predictions” are needed to support the ID hypothesis in those sciences? You don’t seem to want to personally address this question for some reason. Why not?

Regarding your reference to Elliot Sober, it would be more interesting for me if you would present your personal take on his arguments rather than simply referencing him without presenting any argument of your own.

But anyway, to get you started, I suggest that there are a number of logical flaws in Elliott Sober’s paper:

The anti-ID Arguments of Elliot Sober

http://philosophy.wisc.edu/sober/design%20argument%2011%202004.pdf

For example, Sober presents the â€œinverse gamblerâ€™s fallacyâ€ noting that it would be a logical error to assume that just because a pair of dice landed on double sixes the first few times that they were observed to be rolled does not mean that a roll of double sixes is more likely. After all, Sober argues, the odds of rolling double sixes are 1/36 regardless of how many times double sixes are initially observed to be rolled in a row. The problem here is that Sober assumes, a priori that the dice are actually â€œfairâ€ dice that havenâ€™t been loaded or biased in any way.

The problem here is that Sober assumes, a priori that the dice are actually “fair” dice that haven’t been loaded or biased in any way. The assumption of fair dice is a hypothesis that can be subject to testing and potential statistical falsification simply by observing the outcome of a number of rolls of the dice – without actually knowing, for sure, if the dice are or are not loaded. Based on the statistical pattern alone one can gain very high predictive value regarding the hypothesis that the dice are in fact loaded or biased vs. the alternate hypothesis that they are actually fair dice. Such observations have been very successfully used by carefully observant gamblers to exploit subtle biases in roulette wheels, dice, and other games of chance that are dependent upon apparent randomness or non-predictability of a biased pattern against the pattern that the house is betting on…

Can such biases be determined with absolute certainty? – based only on the patterns produced and nothing else? Of course not! But, science isn’t about perfection, but about determining useful degrees of predictive value that are always open to additional testing and potential falsification by future information.

This addresses yet another flaw in Sober’s paper. Sober accuses IDists of appealing to the concept of “modus tollens“, or the absolute perfection of the ID hypothesis. He uses the illustration of a million monkey’s randomly typing on typewriters producing all of the works of Shakespeare. He argues that while such a scenario is extremely unlikely, that it isn’t statistically impossible. There is still a finite probability of success.

While this is true, science doesn’t go with what is merely possible, but what is probable given the available evidence at hand. This is the reason why nobody reading a Shakespearean sonnet would think that it was the product of any kind of mindless random production. The same would be true if you were to walk out of your house and see that the pansies in your front yard had spelled out the phrase, “Good Morning. We hope you have a great day!”

Given such a situation you would never think that such a situation occurred by any non-deliberate mindless process of nature. You would automatically assume deliberate design. Why? Do you know?

Sober argues that if a known designer is not readily available to explain a given phenomenon, that the likelihood that a designer was responsible is just as remotely unlikely as is the notion that a mindless process was responsible for such an unlikely event. Therefore, there is essentially no rational basis to assume intelligent design. However, by the same argument, there would be no rational basis to assume non-intelligent design either.

The detail that Sober seems to selectively overlook is that if certain features fall within the known creative potential of known intelligent agents (i.e., humans) while being well outside of the realm of all known non-deliberate forces of nature, the most rational conclusion is that of ID.

Essentially, Sober does away with all bases for hypothesizing ID behind anything for which an intelligent agent is not directly known. This essentially includes all of modern science that deals with ID – to include anthropology, forensic science, and especially SETI. Yet, amazingly, he goes on to use this very same argument in support of the ID detecting abilities of the same.

In the end, it seems like Sober is more concerned about the specific identity of the designer not being “God” rather being concerned about the idea that the scientific inference of a need for some kind of intelligent designer to explain certain kinds of phenomena is in fact overwhelmingly reasonable – scientifically.

Ultimately, it seems to me like Sober’s arguments are really directed against the detection of God, not intelligent design…

In this line Sober writes:

The upshot of this point for Paleyâ€™s design argument is this: Design arguments for the existence of human (and human-like) watchmakers are often unproblematic; it is design arguments for the existence of God that leave us at sea.

– Elliot Sober

Of course, my ID-only hypothesis does not try to demonstrate the need for God. Rather it suggests that at least human-level intelligence had to have been involved to explain certain features of the universe and of life on this planet. It doesn’t attempt to argue that a God or God-like intelligence had to have been involved. If fact, it is impossible for the finite to prove the need for the infinite. However, one may argue that from a given finite perspective a particular phenomenon would require the input of a creative intelligence that would be indistinguishable from a God or God-like creative power.

At this point, a belief that such a God-like creator is in fact omnipotent is not unreasonable, but must be based, not on demonstration, but on trust in the testimony of this Creative Power. If a God-like creative power personally claims to be “The” God of all, Omnipotent in every way, it would be very hard for someone from my perspective to reasonably argue otherwise…

Anyway, your thoughts regarding what seems so convincing to you about Sober’s “arguments” would be most interesting – especially as they apply to granite NHPs or other such “artifacts”…

Sean Pitman
www.DetectingDesign.com