@Brad: If I can find a property of genomes that …

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

@Brad:

If I can find a property of genomes that I can convince you is:

1. Highly likely to be non-functional; and
2. Sufficient to ground phylogenetic inference.

Will you accept that the design hypothesis you favour predicts that the phylogenetic inference is no more likely than chance to agree with an inference made on the basis of all other available data?

In other words, given the hypothetical that you can find a NHP in clearly non-functional DNA that matches the overall NHP of the ToL, would such a pattern suggest common evolutionary ancestry via some mindless natural mechanism over intelligent design? Is that your question?

If so, this is a fair and reasonable question, in my opinion. NHPs can be and are produced all the time by mindless random mutations in neutral or near-neutral DNA. While this does not mean that all NHPs are therefore clearly the result of mindless natural mechanisms, a match to another NHP that is associated with features that are proposed to require the input of ID would certainly be a curious finding. Why would a NHP of features where none of the features seem to require the input of ID match a NHP of features where at least some of the features do seem to require the input of ID?

Given such a phenomenon, what are the possible explanations? One possibility is that the neutral sequences aren’t really neutral, and have yet undiscovered functionality. Another is that the neutral sequences really are neutral but were recently created along with the functional sequences for some as yet unknown reason – to include the reason for their appearance in a very similar NHP to the functional sequences. Another option is that the neutral sequences were produced via mutations from previously functional sequences that have since lost their functionality over time via detrimental mutations or copy-n-paste mutations with subsequent loss of functionality (duplications with subsequent loss of functionality due to smaller point or short indel-type mutations).

There are many possibilities for such an observation which both do and do not clearly favor mindless natural mechanisms. Regardless, such a finding would certainly not favor mindless mechanisms to explain all of the features of the ToL. The requirement for ID to explain certain features of certain NHPs within the ToL remains unchallenged by your argument and trumps those features that may be, in isolation, explained by mindless mechanisms…

Once again arguments for common origin of certain features within the ToL are not arguments against the hypothesis that ID and only ID can explain certain aspects of the ToL.

You know what might help me out here? – illustrating your theory using a different medium besides DNA. Why not use my example of NHPs within geometric granite forms? – as in highly symmetrical polished granite cubes, quadrangles, etc., within a NHP of granite forms. What would the NHP of such forms indicate regarding their most likely origin? Mindless or intelligent? Is your theory of mindless natural production for all NHPs universally applicable regardless of the material or medium in question? What’s so special about DNA?

I’ll tell you that my basis for detecting the requirement for the input of ID is universally applicable…

Sean Pitman
www.DetectingDesign.com

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 cell’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 yawn…

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. It’s been there a long time…

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 “inverse gambler’s fallacy” 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 “fair” dice that haven’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 Paley’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


Recent Comments by Sean Pitman

Pacific Union College Encouraging Homosexual Marriage?

“Essentially all the administrators, staff and faculty on our campus, including the pastors on our campus already know where I stand. I have never kept any secrets. I have to laugh when I see you say that I am upset because you ‘blew my cover.’ There was no cover to blow.” – Bryan Ness

You’re not the main problem here. I’d have no problem with you personally and what you personally believe at all except that you are a professor in an Adventist school – Pacific Union College.

It’s this school who presents itself as being in line with the primary goals and ideals of the Adventist Church, when it really isn’t. I have friends of mine who have gone to PUC and talked to the leadership about sending their children to PUC. They’ve specifically asked about the situation at La Sierra University and asked the PUC leadership and heads of departments what their position is on teaching the theory of evolution as “the truth” – and if the teachers at PUC support the SDA position on origins and other issues? They were told that PUC does not condone what happened at LSU and that the professors at PUC are fully in line with the SDA position on origins and all of the other fundamental positions of the church.

Of course, you know and I know that this just isn’t true. You, for one, publically speak and teach against the church’s position on origins as well as human sexuality. This reality is not being presented by the leadership of PUC to the parents of potential PUC students. This reality simply isn’t being advertised to the general church membership at all. What PUC should be advertizing to parents and the church membership at large is,

    “Yes, we do maintain professors who teach our students that the church’s position on various fundamental doctrinal issues is in fact wrong and should be changed to reflect the more popular secular position on these topics.”

That’s what it should be telling everyone, but this just isn’t what is being done.

I am attacking no one… Since when is a difference of views an attack on the church?

Since it was placed as one of the church’s “fundamental beliefs” by the church (Link). When you publically publish an article stating that the Church’s position is clearly mistaken and should be changed, that’s an attack on the church’s position.

And of all the issues facing the church, same-sex marriage hardly rises to the level of a “primary goal and ideal.”

The SDA Church has chosen to describe the definition of marriage as being between one man and one woman as one of the “fundamental” messages to spread to the world – as one of the fundamental reasons for its very existence…

Now, you call what you’re doing, not an “attack”, but a “plea for compassion”. However, your plea for compassion is presented as a clear statement that the church’s position is absolutely mistaken – that the church’s position is not at all “compassionate” or even biblical. Now, you may be very honest and sincere in your views here, but that doesn’t mean that you’re not attacking the church’s position in a very real and fundamental way. The fact is that you are making a very clear attack on the church’s position while accepting money from the church as a representative who is supposed to be supporting the church as a paid employee.

Why do you want to cause such people so much pain?

That’s not my goal. However, if a person wants to know what the Bible has to say about what they are doing, I’m not going to pretend that the Bible has nothing to say when the Bible does in fact have something to say. If what the Bible says “causes pain” to a person living in what the Bible says is a “sinful” lifestyle, that’s between them and God. The very same thing is true of me and my own sinful tendencies. If what the Bible says about what I’m doing causes me pain, I can either respond to that by ignoring what the Bible has to say, or I can ask God for help in changing my ways.

Jesus himself said that He did not come to bring peace to those who are living in rebellion against God’s ideals for humanity, but a “sword” (Matthew 10:34). The denial of self and what we naturally want to do given our fallen condition, in order to follow God and what He calls us to do, is often quite painful indeed. That doesn’t mean it’s not the best path to follow. There simply can be no peace between God and those who wish to hang onto what God has said to give up. God does not condemn the sinner for being born broken, but He does warn those who refuse to accept His offer of help to escape their broken condition that, eventually, such refusals of help will not end well for those who are determined to follow their own way.


Pacific Union College Encouraging Homosexual Marriage?
Response from Bryan Ness:

Yet, these professors get very upset when their actions are made public – when they can no longer hide what they are doing from the church at large. – Sean Pitman

Uh, I have never hidden my support and affirmation for LGBTQ+ individuals, and any parent who wanted to know my views on the subject could easily look up what I’ve written, or they could just plain ask me. I openly acknowledge where I stand on these issues on social media too. Essentially all the administrators, staff and faculty on our campus, including the pastors on our campus already know where I stand. I have never kept any secrets. I have to laugh when I see you say that I am upset because you “blew my cover.” There was no cover to blow.

You have not simply let people know what I advocate, you have attacked me personally and impugned my motives and personal spiritual path. You are causing pain not just to me, but to the very people I am trying to comfort and encourage. Your words are not just being seen by the legalistic and judgmental people like yourself, but by parents of LGBTQ+ children and those LGBTQ+ individuals themselves, many of whom are likely already heavily weighed down with self revulsion and depression. And you are doing this for who’s good?

And you wonder why I might be angry and upset? As hard as it is for me to do, I have daily decided to pray for you and those like you that God would soften your heart and show you the grave wounds you are inflicting on God’s beloved. I pray God will help you find compassion and clearer spiritual insight.

Do you really think it’s a “little thing” when our own professors are attacking the primary goals and ideals of the church from the inside? – Sean Pitman

I am attacking no one. You act as if you have not even read my article. I did suggest in there that I think it is time for the church to change and affirm same-sex marriage, but that is not an attack, that is a plea for compassion, a plea that the church return and study this topic again, and I laid out the reasons I think it is fully warranted that we do so. Since when is a difference of views an attack on the church? And of all the issues facing the church, same-sex marriage hardly rises to the level of a “primary goal and ideal.” You are inflating the importance of this topic. the only place where same-sex marriage really rises to a high level of importance is when you are an LGBTQ+ person contemplating marriage, or are the parent, relative or friend of an LGBTQ+ person. Why do you want to cause such people so much pain?


Pacific Union College Encouraging Homosexual Marriage?
Posted by ArkDrey:

The purpose of the H.E. is not to wall people off by modifying curriculum of every subject to fit dogma. The dogma itself has to be enhanced with broader understanding of how to relate various perspectives to these fields of human enterprise.

Certainly, Adventist schools should by no means isolate students from popular ideas that are prevalent within secular culture. If anything, students educated in our schools should have a much better understanding of ideas like neoDarwinism or homosexuality than students educated in secular institutions. However, the education of students within Adventist schools shouldn’t stop here. Adventist education should also give students a reasonable explanation as to why the Adventist perspective on these ideas is actually supported by the Church – by professors who actually personally hold to the Church’s positions on these topics (like the topics of origins or homosexuality, etc).

Again, it is simply counterproductive to have a church school if professors in that school teach that the church’s position is not only wrong, but downright ludicrous, outdated, and completely opposed to the overwhelming weight of “scientific evidence”. Such teaching, by professors that are respected by the students, will strongly influence most students to be naturally opposed to the church’s position on these topics. Clearly then, this would not be in the church’s best interest. It would be far better, from the church’s perspective, not to form church schools at all than to have professors within their own schools attack the church organization from the inside.

But there is world of difference between presenting it as fact that the teacher believes, and a theory with problems. – @ajshep (Allen Shepherd)

I’m in total agreement here. Again, it is one thing to teach about a particular concept that opposes the teachings of the church. It is a far far different thing to then support this particular concept as “true” as compared to showing the students why you, as their teacher, don’t find it convincing.

That is why a teacher, employed by the church, is actually stealing from the church when they attack the church’s position on a given topic from within their own classroom or via a public forum. Such activity simply goes against what a teacher is being paid to do by his/her employer.


Pacific Union College Encouraging Homosexual Marriage?
From David1:

Your presumption and hubris are exactly what Jesus pointed out to those who brought the women caught in adultery. Have you learned nothing from the examples of what it means to be a Christian that you would indulge in such harshness and judgemental words and pronouncements.

Consider that while Jesus most certainly was very kind and gentle and forgiving to the woman caught in adultery (certainly one of the most beautiful stories in the Bible), that He did in fact tell her to “go and sin no more”.

I would say that the very same action and recommendation should be given to all who find themselves part of the LBGTQ+ community. God loves sinners and came to save all of us who find ourselves caught in the web of fallen and sinful lives. He doesn’t condemn us for being broken, but He does offer us a way out and tells us to “go and sin no more”.

In light of this, my problem with the efforts of Dr. Ness is that he is making the claim that there is no brokenness or moral problem with committed monogamous homosexual lifestyles – that the Bible says absolutely nothing in this regard and therefore there is nothing for God to forgive here. There is simply no need to say, “I love you, now go and sin no more”.

I’m also not quite sure why Dr. Ness draws the line with monogamy since he doesn’t accept the Biblical statements, often within the same passages as those discussing monogamy, that speak against homosexual activities? This seems inconsistent to me since it seems quite reasonable, given the arguments presented by Dr. Ness, that polygamy could also be argued as being even more consistent with God’s will and natural genetic mutations that God Himself designed. Upon what “scientific” or “religious” or “philosophical” basis does Dr. Ness draw the line at monogamy as being the clear Biblical standard where God draws the line? – when many have very strong and very “natural” polygamous tendencies?

Of course, I also have a problem with a paid representative of the Seventh-day Adventist Church, who is responsible for teaching our youth in support of the primary goals and ideals of the Church, publicly arguing that these goals and ideals are completely wrong – on the church’s dime. Such activity, even if one is totally convinced as to the error of one’s employer, is unethical since it is a form of stealing from one’s employer.

At the very least, parents who are paying a great deal of money to send their children to one of our church schools should be very well informed as to what they can expect their children to be taught at our schools and what positions the teachers at the school are publicly promoting. Providing this information to such parents is my primary purpose in responding to Dr. Ness’s publicly published article in public forum.


Pacific Union College Encouraging Homosexual Marriage?
Response from Dr. Ness:

Do you not understand what it is like in academia? Differences of opinion among scholars is not only tolerated, it is valued. I have nothing more to say concerning your accusations. Our church has no “official” stand on this issue, if by that you mean I am disavowing my membership in the church by simply believing that gays should allow ro get married to one another. That is not even how our church operates. I can point to many other church employees who openly disagree about certain issues of belief, including this one, and congregations that are fully affirming of same-sex marriage. They are a part of the SDA church just as I am.

My concern still is more about the tone and stance of your attacks. You are attacking fellow SDAs, some of them being the most vulnerable members of our church, and you seem to have no sense of the damage you are potentially doing to these individuals. By attacking me in the fashion you are you are also attacking all those for whom I am standing up. You may want to take Jesus’ words to heart:

But whoso shall cause one of these little ones that believe on me to stumble, it is profitable for him that a great millstone should be hanged about his neck, and that he should be sunk in the depth of the sea. Matt. 18:6

I know very well what it’s like to be involved in leadership positions within the church and within academia. My own father is a retired pastor and teacher. It’s one thing to publicly present and even promote various opinions that do not directly undermine the church or school one is working for. However, it is another thing entirely to directly attack the fundamental positions of the church while being a paid representative of the church. Such activity is not at all encouraged and is, in fact, unethical – a form of theft from your employer. Sure, there are many pastors and teachers who think to do such things anyway. That doesn’t make such activities morally right. It’s still wrong to do what you are doing.