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Tom
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   Posted 1/5/2010 5:50 AM (GMT -6)    Quote This PostAlert An Admin About This Post.
Jeff, Corey, D, and others interested in the ID/Science-Theology conversation.

Check it out: www.idnet.com.au/files/pdf/James%20Shapiro%20Boston%20Review.PDF

Very interesting.

Tom


"Man is a person not by nature but by spirit. By nature he is only an individual." Nicolas Berdyaev

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Tom
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   Posted 1/5/2010 5:54 AM (GMT -6)    Quote This PostAlert An Admin About This Post.
Don't know why the link doesn't work. If you copy and paste it into your line then hit enter, it'll put the article up. But if you just click on the link there, it won't. Hmmm.

Tom


"Man is a person not by nature but by spirit. By nature he is only an individual." Nicolas Berdyaev

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Corey
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   Posted 1/5/2010 12:36 PM (GMT -6)    Quote This PostAlert An Admin About This Post.

This board software is too smart by half. It's freaking out on the url because it has % signs in it. Whatever.

I made a TinyUrl for it: http://tinyurl.com/yeq4c7q

 

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Corey
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   Posted 1/5/2010 12:40 PM (GMT -6)    Quote This PostAlert An Admin About This Post.
The aspect of the article that I found most interesting was the tie-in to information science. But perhaps a more apt analogy would be to linguistics: we see that DNA has more than just letters, we see words, sentances, grammatical rules, etc.

Kind of interesting if you think about us as logoi.

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Tom
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   Posted 1/5/2010 12:50 PM (GMT -6)    Quote This PostAlert An Admin About This Post.
YES!


"Man is a person not by nature but by spirit. By nature he is only an individual." Nicolas Berdyaev

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Starkman
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   Posted 1/5/2010 3:02 PM (GMT -6)    Quote This PostAlert An Admin About This Post.
Corey said...
The aspect of the article that I found most interesting was the tie-in to information science. But perhaps a more apt analogy would be to linguistics: we see that DNA has more than just letters, we see words, sentances, grammatical rules, etc. [emphasis Starkman's]
Kind of interesting if you think about us as logoi.


Ah, so now I know why I'm so screwed up: never did fair well with grammar...apparently, as I now understand, because it's first screwed up inside me and then reveals just how fouled up things are every time I speak! (Oh, and if they find a mathematical link, that would really explain my ineptness in the rest of life's arena!)

So there it is. Most, of the mystery solved.

(Well, I can at least cook a killer steak, though!)

Starkman
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Similitude
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   Posted 1/5/2010 9:46 PM (GMT -6)    Quote This PostAlert An Admin About This Post.
I won't have time to check it out til tomorrow, at the earliest. But thanks for the link.
 

 


 

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Similitude
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   Posted 1/7/2010 7:23 AM (GMT -6)    Quote This PostAlert An Admin About This Post.

from the article:

How all of this modularity, complexity, and integration arose and

changed during the history of life on earth is a central

evolutionary question. Localized random mutation, selection

operating "one gene at a time" (John Maynard Smith's

formulation), and gradual modification of individual functions

are unable to provide satisfactory explanations for the molecular

data, no matter how much time for change is assumed. There are

simply too many potential degrees of freedom for random

variability and too many interconnections to account for.

This has been the standard criticism of the mathematically knaive view of random change ever since it was understood that DNA plays a profound role in phenotypic expression. He's writing as though new findings have brought this to light. On the contrary, new findings have shown that much functional/adaptive variation is NOT random. But that is just another way of saying that for all we know, such change is directed in the same way that what a robot does is directed. And that's just another way of saying that, for all we know, teleology applies to biological origins at some level. The burden of proof is on those making the grand claims about the potency of chance in limited time-frames. Teleologists don't have to claim macroevolution is impossible. They only need to argue that, insomuch as teleology is non-falsifiable, final causes can be held as tentative explanations for some of those aspects of our current understanding characterized by FINALITY. We're open to falsification of our ideas WHEN there are appropriate tests that DO falsify them. Until then, the difference of inference has to do with differences in metaphysics, not aposteriori science. Thus, even Greg's teleological views about angelic roles is on the inductive table until we have a bona-fide causal theory of macroevolution that is not mostly assumption.


 

Post Edited (Similtude) : 1/7/2010 6:48:37 AM (GMT-6)

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Tom
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   Posted 1/7/2010 8:27 AM (GMT -6)    Quote This PostAlert An Admin About This Post.
I'm missing something then. I thought he was AGREEING with what what you're saying, i.e., that much functional/adaptive variation is not random. It's behaves as if designed, or purposefully, i.e., teleologically. No?

Tom


"Man is a person not by nature but by spirit. By nature he is only an individual." Nicolas Berdyaev

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Tom
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   Posted 1/7/2010 8:47 AM (GMT -6)    Quote This PostAlert An Admin About This Post.
Steve, a friend and Fermilab insider, sent me the article. Super smart guy. Anyhow, Steve writes (nothing personal in the note):

Hi Tom,

Glad to hear that you found it interesting. I tend to agree with Shapiro in the second paragraph of his conclusion that (biblical) creationists are expected to be less fluid in their interpretations since we base our understanding at some level upon revelation made credible by the miraculous (however reading too much into the biblical accounts is sometimes a problem). But neo-Darwinism claims to be based entirely upon science and yet "our current knowledge of genetic change is fundamentally at variance with neo-Darwinist postulates" (section 3 last paragraph). Shapiro's comment at the end of section 2 that cells "have the capacity to set the level of background localized mutability by adjusting the activity of their repair systems" may reflect the biblical concept of reproduction limits within "kinds." In any case, the blind jump from mud to the ever more amazing cell seems further than ever, and as Shapiro notes at the beginning of his conclusion this new science may possibly open up new avenues of addressing the central issue of whether there is a guiding intelligence at work in the origin of the species.

Blessings, Steve


"Man is a person not by nature but by spirit. By nature he is only an individual." Nicolas Berdyaev

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Similitude
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   Posted 1/9/2010 4:44 PM (GMT -6)    Quote This PostAlert An Admin About This Post.
TOM: I'm missing something then. I thought he was AGREEING with what what you're saying, i.e., that much functional/adaptive variation is not random. It's behaves as if designed, or purposefully, i.e., teleologically. No?
 
JEFF: Yes, I think he was saying that. But he seems, both in his specific language and his discussion about the relevence of the analogue of computer processing, to be saying that the teleology is IN the cell. Hence the grounds of his distinguishing himself, as a scientist, from a creationist. I find in the literature that I'm aware of that creationism is referred to as the notion that teleology in nature is attributed to one or more creatORs. That's what he seems to have no sympathy with. I could be wrong, but that's just how it reads to me. He does take care to word the article in such a way that it is not offensive. But Shapiro is a well-known biologist that is respected in the biological community. It is quite doubtful to me that he is attempting to show sympathy to ID (capital "D", as in God) in any form or fashion. That would virtually be academic suicide in the present SOFA.
 
ID'ists tend to be clear to link their idea of design to libertarian free-will. As such, computer analogies have their relevance to cellular "processing," to be sure. But even apart from computers, all designoids that don't seem to be capable of forming independently of intelligence serve as analogues of configurations of matter that find their unique, directed functionality explicable ONLY in terms of intelligently DIRECTED causality. Cells and organisms SEEM like that, whether or not scientists will find that to be false, eventually.
 
But there is no doubt about it, the article shows that everything ID'ists have been saying is right on. There simply IS finality to what can causally be explained naturalistically, given our knowledge of genetics (as he admitted, we can't predict phenotypes at all, yet. And that would be the criteria of a truly causal account of macroevolution, as opposed to the ex post facto speculative approach that just assumes that macroevolution occurred for metaphysical reasons, however valid they may be). And that finality comes LONG before any explanation can get us to common descent all the way down to one or more single-celled organisms in the precambrian. If we ever get a causal account that gets us down that far, I'll concede it to them as the most parsimonious explanation and call it day. They're just not anywhere near that yet.
 
Thus, Greg's view is still on the table from an inductive perspective. And it has the added value of explaining how, for those uncomfortable with a more historical exegetical approach to Genesis, sin can still be that which is contrary to a competent God's benevolent intent and therefore NOT be inevitable. Because Greg's approach, like the historical approach to Genesis, implies that original design features have been misdirected by volitional agents other than God. And what follows therefrom is that even though NOW sin is inevitable, it is not necessarily because of HOW God designed the world. And this, to me, seems to be entailed in what is meant by a COMPETENT and BENEVOLENT creator.
 
Granted, it is consistent to say that all natural "evil" is necessary for the optimal becoming of eschatological beings. But that is a hard sell seeings how it is virtually impossible to imagine HOW that can be. Especially if that becoming is to be done AS a living human in THIS world. For it does seem inevitable, NOW, that all infants and fetuses just won't make it to the point of meaningful becoming in this world given the kinds of natural "evil" that exist.
 
And once we say that optimal becoming never was to be attained ONLY in this world, we've just made our case even more complicated. Because at that point, we're going beyond the universe itself and basically saying that benevolent theism is just unfalsifiable. And that is true. But that doesn't make other explanatory accounts of that fact less plausible by default. We have to explain WHY one view is more plausible than others. And that takes defining plausibility and then assessing the data in terms of that criteria.
 
Personally, I think Christ's statement that the devil came to rob, kill, etc. is indicative of the fact that something about human becoming has been rendered less than optimal in at least SOME aspects BECAUSE of Satan. So that much seems to me to be a given no matter which route we go. So to say that Satan just made sin MORE inevitable IN DEGREE ONLY than it already would have been due to God's design doesn't seem to really solve what we're trying to solve. We're not trying to argue that God is just MORE benevolent than Satan, but that He is ABSOLUTELY benevolent. And that's why I think Greg is right at that level of abstraction even though, for now, I disagree with him on the details.


 

Post Edited (Similtude) : 1/11/2010 6:23:22 AM (GMT-6)

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Similitude
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   Posted 1/9/2010 6:10 PM (GMT -6)    Quote This PostAlert An Admin About This Post.
Here are some more examples of what seem to be directedness in genetically-conditioned cellular activity (from http://www.answersingenesis.org/articles/arj/v2/n1/classification-of-mutations):
 
... our understanding of the genome and its intricacies has increased by leaps and bounds over the last few decades. While it was previously thought that only protein-coding genes would be relevant, it is now known that the regulation of protein-coding genes is just as important, if not more so. While it was previously thought to be intellectually irresponsible to consider a biological function for transposable elements, we are now understanding their ubiquity and importance in shaping the genome (Sternberg 2002).


... It is becoming increasingly apparent that the cell itself can induce mutational processes in the right genes to produce beneficial changes at appropriate times. The most well-studied of these systems is the somatic hypermutation (SMH) system in the vertebrate immune system. In order to increase the binding potential of immunoglobulins to antigens, the cells direct mutations to a specific region of a specific gene in order to produce immunoglobulins that have a higher affinity to the antigens (Papavasiliou and Schatz 2002).


This mutational process skips the region of the gene which attaches to the B-cell entirely, and focuses only on the region of the gene which binds to the antigen. It is not deterministic—that is, the specific changes which are made seem to be stochastic—but the changes are focused to the right gene in the right situation, bypassing well over 99.99% of the genome and focusing on the correct few hundred base pairs which would matter.


Some transposable elements are triggered in direct response to specific cell stressors. For instance, Hall (1999) showed that E. coli can use insertion sequences to activate the gene required to metabolize beta-glucoside sugars.


Simple sequence repeats (SSRs) have shown to mutate primarily in copy-number, acting as a genomic tuning knob or state switch. King, Trifonov, and Kashi (2006) enumerate several, including an AC repeat in a promoter which causes variation in body weight in Angus beef cattle, and an AC repeat in tilapia fish with similar effects. Bayless and Moxon (2006) report that a 4-nucleotide repeat (CAAC) can cause the lic2A gene of H. influenzae to switch between three states—off, low expression, and high expression—as it alters the reading frame on which the ATG start codon is found.


Semi-palindromic DNA often points to potentially beneficial areas where mutations might take place. For instance, one study of the genetic adaptation of E. coli to low glucose concentrations found identical modifications of the mgl operator sequence (mglO) in multiple populations (Notley-McRobb and Ferenci 1999). These were later found to be in loops that were near stem-loop structures in DNA, formed by semi-palindromic sequences (Wright 2004).


Caporale has synthesized this new research into what she terms an “implicit genome.” That is, a genome has an implicit range of mutations which are likely to occur, and these mutations are part of evolutionary “strategies” for organisms to survive changing environments (Caporale 1999; Caporale 2006).


SSRs are quite interesting subjects because, in general, they are both highly mutable as well as being easily reversible. Historically, they have been viewed as evolutionary byproducts, or junk DNA. However, current research is continually finding new ways in which SSRs allow for the genome to adapt to changing circumstances (Kashi and King 2006).

And from a very recent article (http://www.sciencedaily.com/releases/2009/10/091021133852.htm):
 
Bits of movable DNA called transposable elements or TEs fill up the genomes of plants and animals, but it has remained unclear how a genome can survive a rapid burst of hundreds, even thousands of new TE insertions.

... research led by plant biologists at the University of Georgia have documented the impact of such a burst in a rice strain that is accumulating more than 40 new TE insertions per plant per generation of an element called mPing.

The big surprise of their study is that the impact on the host seems to be modest. Not only that, the research shows that the genetic diversity created by massive and rapid TE insertions can actually benefit the plant in entirely unexpected ways.

..."We found that the TE we studied avoids insertion sites in exons [sequences of DNA that code information for protein synthesis that is transcribed to messenger RNA]. But even more important may be that this shows that for rice and other `selfing' plants [ones that essentially pollinate themselves], TE bursts may be one of the critical solutions to rapidly generate genetic diversity in the face of an ever-changing environment."

...the team demonstrated that a large subset of new alleles (different forms of a gene) that contain mPing "may actually benefit the host by creating potentially useful . . . and novel, stress-induced regulatory networks." The stresses tested that demonstrate this were drought and salt-tolerance.

"... being able to observe the effects of their rapid increase in a well-characterized genome like rice gives us tremendous insights into these critical early events and permits us to glimpse how they alter the host organism."

Demonstration that a rapid burst of TE insertions generate new regulatory networks is consistent with the ideas ... that they were tools of evolutionary change.

It appears, the team said, that the ability of mPing to target its insertion sites helps to mitigate the effects of sudden rapid bursts of large-scale TE insertions -- something one might think could be detrimental to the health of the host.


And from this new article (http://www.uncommondescent.com/evolution/the-next-revolution-in-biology-according-to-the-templeton-foundation/):
 
“In every field of science, when it’s successful, you think you understand all of it,” says Martin Nowak, professor of mathematics and biology at Harvard University. “In classical mechanics,” he explains, “there was a time when physicists thought, “‘Well, that’s all there is. If I know the place of the particles in the universe, I can predict the future.’ But then came quantum mechanics and relativity theory. There was a total revolution.” Nowak is hard at work trying to launch another revolution, this time in evolutionary biology. “Our understanding of evolution,” he says, “is very incomplete."

"... Some of the other questions to be addressed by the FQEB initiative include:

• What are the limits of evolvability, and how are these transcended?
• Why does evolution (sometimes) lead to increasing complexity?
• Are there different kinds of evolution, and is there evolution in the context of evolution itself?
• What are the natural laws of evolutionary change, and can we derive a complete mathematical theory of evolutionary laws?"

Note, to admit that it is a question as to whether there is "evolution in the context of evolution itself" is an admission that they can't explain the whole macroevolutionary hypothetical history with what is currently known about genetics. You have all these DNA-conditioned functions that have to be accounted for by chance mutations unless you just want to say these sequences which currently condition these functions just happily existed as soon as abiogenesis supposedly occurred (which is assuming what needs to be accounted for). Given the number of DNA sequence possibilities that exist at a given time, we can't even calculate the odds of such sequences coming about by chance. For all we know, it is prohibitively small. And there is no scientific reason to believe the odds is GOOD.

That's the problem. A-plausible claims that are untestable are not what we usually expect from scientific researchers. They are non-explanatory and are utterly void of utility. This is why even Karl Popper didn't think evolutionary research was scientific at first. According to Berlinski and others, he was pressured by his peers until he caved. Many macroevolutionists today don't even agree with the kinds of examples he finally imagined might falisfy the hypothesis.



 

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Similitude
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   Posted 1/12/2010 8:37 AM (GMT -6)    Quote This PostAlert An Admin About This Post.

I've been thinking more about the theodicy approach of Miller, Collins, Ayala, etc. They say God couldn't have intelligently designed critters because it implies that God is the author of natural evil in an intentional way. To get around this, Miller (I'm not sure how Collins, Ayala, etc. get around it) says there is true non-volitional contingency in the unfolding of cosmic history. Hence, the natural evils entailed in predator-prey relationships, e.g., are not intended by God.

The first obvious problem with that approach is that it doesn't really solve what most people are trying to solve in theodical thought. If God intentionally risked this natural evil Miller is so troubled by (not natural evil resulting from volitional abuse or negligence, but just raw indeterminism) it is not clear how God is not yet responsible for it in the first place. Regardless, He is, and has, clearly done nothing to alleviate the damage that resulted BECAUSE of that risk.

So in the first place, it's hard to see how this theodicy explains anything comforting. If I throw a rock randomly while blind-folded, not intending to knock anyone's eye out, but nevertheless with the knowledge that there is the possibility that I MIGHT knock someone's eye out, why am I benevolent MERELY because I didn't INTEND that SOFA? On the other hand, if I literally had NO idea what might happen, in which case the subsequent unforeseen SOFA's are not my intention in any sense, how is my refusal to intervene after the damage is done (or just prior to the worst of it) anything but a clear indication of a lack of sympathy on my part?

When we talk about the risk of sin, by definition, risk means that which is not inevitable. If it's inevitable, it wasn't a risk at all. But then if outcomes aren't due to God's causal activity, we at least know that sin, if it is indeed non-necessary, is due to volitional agents--agents that, per original design specifications at least, had or would have had the intellectual and volitional wherewithal to act NON-sinfully. But once we talk about risk in terms of INDETERMINISTIC (even to God) events that have nothing to do with intellectual/sentient conditions, we are talking about events for which we can not conceive ANY conditions for their occurrence, necessary or sufficient. But that is just to say that the event, per our understanding of it, is literally un-caused.

But if events can be uncaused, we don't need God to account for anything in the first place. It is the belief that events ARE caused that grounds the intelligible conception of a final causER we recognize as a deity/creator. IOW, if events can be uncaused, we need a more fundamental and intuitive criteria to know when an event is caused and when it is not, otherwise, we couldn't know what we or God is actually responsible for. I know of no one that has ever claimed there was such an intuitive criteria. And it seems logically impossible to generate one aposteriori. For all aposteriori arguments are discursive ways of moving from GROUNDS (which are species of causes) to INFERENCES (which are conditioned/caused by their grounds).

Thus, the whole non-causal indeterminism approach is, by definition, NON-explanatory, and therefore provides NO explanation for anything, theological or otherwise. Explanations just ARE causal accounts. So that's a second problem with that approach.

Third, once you say God risked all this undetermined but unchosen suffering that He Himself finds troubling supposedly, you are falling into to the same knowledge-problem that the atheist has that Plantinga has written about. IOW, the only reason why it is important to believe that we apprehend is because we can not conceive of how we could attain any sentient satisfaction or avoid sentient dissatisfaction UNLESS we apprehend. If we truly believed that by apprehending we would be miserable but by having illusions we would be blissed out, we would prefer the illusions every time.

But Miller doesn't think God is in the business of setting up an orderly, predictable world where sentient beings could, by original design specifications, competently avoid vain, unintended misery in the first place. So there is no reason to believe, given his views, that he can get around the very knowledge problem of the atheist. As Plantinga argues, God must be benevolent in such a way that we can intelligibly account for human knowledge. Which is to say, that to claim we are apprehending sufficiently well to make VALID and WARRANTED arguments about REALITY, God must be competent AND benevolent in such a way that our apprehensive capacities must have been INTENDED and intended precisely to attain sentient satisfaction. Otherwise, we have no way to account for whether we are apprehending at all.

In short, it seems to me that the Miller/Collins/Ayala theodicy buys us nothing worth having from a purely theodical point of view, it is non-explanatory to the extent that it involves causeless events, and it creates the very knowledge problem that atheists already have. In short, if there is a God, and that God is benevolent, that fact is not entailed in the metaphysics of Miller in any sense, because his metaphysic literally implies (assuming that he is at least right about the LNC) that his own categories and conceptions, including those about God, may have nothing to do with reality in the first place. Thus he is, as atheists say of all of us, believing in the existence of a God and specific attributes of a God for reasons that can not be accounted for by his own metaphysic (we call such beliefs superstition for a reason).

And yet, all that we say about God, thus, is intelligible EVEN to the atheists. Thus, the epistemological elements that render those conceptions intelligible must be somehow entailed in our categorical understanding of reality. Which is just to say that Miller etal seem to be making a category mistake. Any time we have to just assert a-plausible claims to render our view coherent, we have just said that we aren't GIVEN enough to get to where we need to get. But where nothing is given, nothing is required. And if a thing is not given/required, epistemologically, we couldn't possibly know it in the first place. This is why Lewis says if nothing is obvious, nothing can be proved. It is just to say that discursive reasoning is worthless unless the relations that ground it are, in some sense, obvious--i.e., GIVEN.

What this means is that there are no intelligible solutions to theological philosophy that imply similarly intelligible SCIENTIFIC solutions to all scientific questions. But that's OK. Having coherent theology that is grounded in intuitions that account for knowlege and HOPE for humanity is much more important than having solutions, or plausible ones, to all scientific questions. Science is tentative, and there is plenty about science we will die not knowing--it is a slow train of progress characterized by revolutions of thought, and many scientists want to explain too much before we have all the data to render explanations plausible in terms of true inductive thought. Answering all scientific questions plausibly is impossible, and therefore it is the least of our concerns to do so if, by knaively pretending we can, we get the philosophical underpinnings of the very inductive thought that conditions human, scientific progress doable wrong.


 

Post Edited (Similtude) : 1/12/2010 10:08:12 AM (GMT-6)

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