Saturday, August 13, 2005

Jason Pratt on ID

I got this note from Jason Pratt:

The question was recently asked, whether failures of Darwinism can be pointed to, similar to the crop failures resulting from trying to apply Lamarckism.In one sense, the obvious answer is that no such similar failure could_ever_ occur; because Lamarckism has a bit of leeway in its basis proposal which could allow the introduction of intentional development (e.g. a person _chooses_ to do this or that, and so passes on any physiological advantages thus gained genetically); whereas neo-Darwinian theory explicitly and exclusively proposes non-directed accidental effective mechanism. Consequently, any directed experiment (whether success orfailure) necessarily includes an element in its process and result which is supposed to be utterly foreign to the whole point of NDT process and result. Parts of the biological mechanism can be tested, and inferences can be drawn about how well the results fit into the basis theory; but the basis theory itself cannot (in this case) be validly tested.The results of testing parts of the mechanism can of course be combined with inferences grounded in systematic observations about actual real-world behavior; with these being compared to inferences grounded in what thebasis theory itself should be implying.So, for instance, if gradualistic NDT is correct, there should be asignificantly large number of 'link species' still in biological play.Mutant B from species A, isn't going to increase its numbers unless it canstill breed with species A. Ditto for Mutant C, D, etc. At some point (callit species X--the changes all being gradual, per gradualism), X shouldn'tbe able to breed with A anymore, and so an actually new species would be inexistence.(Taxonomically I suppose it wouldn't be called a species--a genus maybe? In popular pro-NDT arguments it's still called a new species, generalizing for the sake of simplicity--and I'm okay with that; the principles would be ineffect either way.) But even once X is in existence, there also ought to be a significant number of transitional species still around, able to interbreed with oneanother fairly successfully. (Even if, say, species F has gone extinct in the meanwhile, species K still ought to be able to breed fairlysuccessively with species D et al.) Humans, for instance, ought to be a rare exception--we can't breed with anything else, all our previous transitional species having gone extinct in the meanwhile (maybe because weintentionally killed them off?)In point of fact, however, we humans _aren't_ the rare exception. Cats, for instance, cannot breed with skunks, even though these are genetically very close to feline; just as we cannot breed with gorillas or chimpanzees. Thisis the very common norm. Whereas, even if X can no longer breed with A,there still should be x-number of genetically distinctive intermediary interbreeders between them, _all_ of which are capable of breeding with each other (except for X and A). It's also rather hard to see how multiple kinds of DNA configuration (different numbers of chromosomes, different amounts of DNA per chromosome,etc.) could effectively be transmitted once accidentally generated.A mutation to a gamete-producing cell, or a copy error from such a cell while producing a gamete, could theoretically generate a change of that sort (and it should be obvious that only cell mutations of this very limited sort would be in any position at all to generate mutants--heartcell mutations don't generate mutant offspring for instance). The question is whether the resulting mutant--assuming the mutation even succeeds in running the gamut of sheer luck against any particular gamete, up to thepoint of becoming a breedible entity that is actually performing nominal breeding operations (so to speak)--is carrying anything in his/her/its own gametes that could successfully pair up with non-mutated gametes (keeping in mind that only one pair of the mutant's chromosomes would be carrying the mutation in the first place at all--half the gametes being fired by the mutant will be altogether non-mutated, therefore not possibly sending along the mutation.) And this is only at the macrobiological level. The feasibility of the theory doesn't (currently) hold up very well at the microbiological level either.
Preliminary microbiological restrictions----------------------------------------
The key restriction that must be remembered, is this: **If a protein ismade from a random order of amino acids, chances are nearly certain the protein will do nothing at all.** Furthermore, in many (though not all) cases, something must already be in existence to be the _receiver_ of the protein behavior. Some proteins behave in ways that build such receiver-units, of course. The point is that even if a protein's order might do something, it usually needs a receptor already capable of receiving it to work. Otherwise it might as well be totally useless.Thus, (at least) five levels of protein functionality-composition: a.) the new protein is totally function less in any possible situation (within that organism); b.) the new protein would function if there was a receptor, but there isn't one; c.) a receptor exists which can receive the effect of the protein, but theuse is harmful or effectively neutral; d.) a receptor exists, which can _usefully_ use the protein;ande.) the protein builds a receptor. (It may be possible that this always results in a receptor which canusefully use a protein that does already exist; but I haven't yet heardthis for sure.) The complexity (and restrictions) intensify when we consider that sometimesa road (so to speak) must already exist to get the protein _to_ an alreadyexistant receptor.Aside from questions of original mutations _accidentally_ creating DNA sequences which generate proteins that build receptors and/or roads; anysubsequent random mutation in a DNA sequence becomes exponentially more improbable to generate useful (not even merely useable) proteins the more accidentally complex (so to speak) the organism _already_ is. Besides receptors, and roads (the chemical paths between receptors andDNA), the relevant reactions also require 'catalyst' chemicals. In many cases: no catalysts, no reactions at all. These protein catalysts are the'enzymes'. Enzymes are terribly important in another way, too. They not only helpcertain chemical reactions to work at all, they also help speed reactionsup to rates that are useful. All known enzymes speed up protein-receptor chemical reactions by a factor of at least a million. Factors of ten billion to a hundred trillion are not uncommon (i.e. a reaction that would normally take 3000 years happens in 1/1000th of a second.) One way or another (or sometimes both), enzymes are absolutely necessaryfor the other existant processes to work; thus adding yet another development-complexity factor--and adding yet another way in which an accidental copy error of the DNA in the chromosomes could (much morelikely) mess something up (rather than adding functionality). As I have been stressing, any addition to (existant) complexity not only adds development time constraints (especially when we consider that someextinct species _already_ had biological and genetic systems virtually as complex, at the microbiological level, as modern animals--subtractx-hundred million years for _their_ development time). It also adds increased liklihood that a random mutation will result in something that runs _against_ the existing system.Granted, a system could be complex enough, _in the correct ways_, to bemore tolerant to random copy errors. (Though mere toleration isn't the sameas positive increase of effective complexity.) But this level and (far moreimportantly) type of complexity cannot be legitimately posited to _already_exist to offset the problems which must be overcome _before_ such a system(on naturalistic evolutionary theories) _does_ exist.Also granted, any redundancy in DNA molecules might help overcome thedemerits of a bad copy error (mutation); but accounting for the developmentof those redundancies themselves introduces more complexity (and tightensthe time constrains for species development), even if it doesn't actually harm the organism. Which itself is somewhat questionable--a newly mutated creator-strand of protein 'x' will at least be taking up resources making that many more protein 'x's which could have been spent (with more overtprofit to the organism) elsewhere. Any excess of those proteins (i.e. produced by conveniently redundant protein generator sequences) might causeproblems elsewhere, too.In order to prevent runaway reactions of exactly this sort within a cell (or elsewhere outside the cell), a cell must be able to turn an enzyme group on or off. This adds _another_ level of complexity to the system. (A typical 'off' signal is generated by side-products of reactions, whichunder NDT must accidentally happen to inhibit further enzyme behavior.) More complex information can be carried by RNA strands than by simplerproteins (and their amino acids). RNA resembles DNA in structure: A,G and C nucleotides, plus a U which is a more unstable molecule than thymine butotherwise serves the same purpose, matching to any As. RNA functions a lot like portable DNA, but (because of the U) it isn't as stable. Also it doesn't have a double-helix structure like DNA. Evolutionists tend to think that RNA evolved first out of simpler proteins; and then DNA out of RNA--which again tightens the time constraints. A lot of the sequences in DNA strands don't seem to be contributing at allto the cellular reaction. Recently, biologists have proposed that this'junk DNA' may actually be equivalent to RNA, and perform much the samepurpose.The problem with this, is that the genetic sequences in question are _not_in fact RNA. It's attractive, but ultimately not very feasible (under thebasis NDT anyway), to propose that all such 'not-junk' sequences are the original RNA codes evolved into DNA upon which the rest of the DNA sequence then developed, perhaps melding various strands together. To whatever extent such sections of DNA do behave like RNA, though, more development-complexity with its inherent functionality-and-development-time restrictions must be allowed. This is why I suspect we'll be seeing a push back to 'junk DNA' eventually: it may require more complexity than 'mere'DNA, but requires _less_ complexity in development than RNA-equivalence strands. Though there's nothing saying that a DNA strand couldn't have someRNA-eq _and_ junk, of course. Ultimately, however, RNA-eq ability tends to lend weight against gradualistic neo-Darwin evolutionary theory, per se.These are some, by no means all, of the problems with the _basis_ theory(NDT). The problems are rising, because what we are learning doesn't square with the foundational theory being proposed. I think sooner or later, the basis theory itself will have to be significantly revised--which happened before, too: what we were discovering didn't mesh with the originalDarwinian theory (or its various alternatives, up to that point), so in1941 (notably at a meeting of the _Geological_ Society of America), a suggestion was made that geneticists should join hands with morphologists, taxonomists, zoologists and paleontologists to try to come up with a modernized version of Darwinian theory, rebuilding it from the most recent finds in their fields. (This mixture, happening where it did, gives evidence of all this being done in service to a strong and overarching ideological committment. Three guesses as to what _that_ might have been...) Together, over the next few years, these specialists created the modern synthetic theory of evolution, or as it came to be known' neo-Darwinian Theory' (or NDT). These new NDTheorists emphatically rejected the Lamarckian theory of acquired characteristics (e.g. a giraffe reaches for taller branches to eat, stretching his neck, and his descendents receive the advantages ofthis); and also rejected Darwin's suggestion of environmental induction ofheritable variations (which would work according to the same principles as Lamarckian theory but in reverse.) It seemed clear to them that neither environmental influences nor acquired characteristics could affect the germ cells (the gametes created by males and females, distinct from the somatic cells everywhere else); and heritable variation could only stem from changes in the germ cells.(Note: I don't know whether they recognized the existence of mutagenic environmental effects or not, but if they did they must have thought these were too few and too inherently harmful to contribute effectively to the number of positive mutations necessary for the theory to work.) Since they were unwilling to accept environmental influence as a cause of variation (probably because the natural evidence for it was lacking, but also possibly because it tasted too strongly of _directed_ evolution), they settled on sheer random copy-error as the source of the variations (a source Darwin had rejected).They agreed that the majority of these copy-errors (as experimentally demonstrated) would be detrimental to the organism's chances of surviving and/or breeding (which are two rather different processes--an improvement in one might be a detriment in the other); and much of the remaining possibilities would be effectively neutral. But, they figured that at leasta _few_ mutations might be beneficial in survival and/or breeding (without a sufficiently detrimental offsetting result in one compared to the other);and that the theory would work sufficiently well on these few positivemutations (plus perhaps the more common neutral mutations combined with eventual changes in environment, though only a fraction of a fraction ofthese would make those previously neutral changes positively beneficial), given the vast time frame available for the process to work.About a decade later, Watson and Crick discovered the DNA structure, and identified the heritable variation with random copy-errors in DNAreplication.This was, however, also the first in a series of dramatic scale-ups ofrecognized complexity in biological organisms. Notably, Crick decided that the vast complexity of DNA could not possibly have been created in the geological time-frame, given the process of random copy-errors plus naturalselection (which would almost always select _against_ the resulting mutant,if it did anything at all.) His solution was to propose that Terran DNA had been seeded on the planet millions of years ago by aliens. This was mocked by the establishment, partly because he was only putting the natural development of even _more-complex_ entities _further_ back in the cosmic time-scale (actually increasing the problem); and partly because it smacked too much of theism (i.e. the only reason Crick proposed naturally developed aliens was because he refused, as a dedicated atheist, to propose God.) Now, I have several problems with what the ID fellows are often doing. Butwhat they _are_ doing, isn't much different from what the NDT synthesisteam was doing back in the early 1940s. They're noting the basis theory isn't just failing to account cogently for operation in the real world, but actually runs _against_ the grain of significant parts of what we'refinding; so they're proposing revisions of the basis theory to try toaccount better for what we _are_ in fact discovering. It's a fact of history that the original NDT team members (along with many of their successors) weren't much (if any) less motivated than modern ID proponents, to be thereby attempting to defend and propogate an ideology (naturalistic atheism in their case, by and large); and it should be obvious that even if one of them (or someone supporting and agreeing with them) came up with crackpot theories (e.g. panspermia) to account for the data, this didn't obviate the other work he (or the others) had done.

13 comments:

Blue Devil Knight said...

I have been getting that junk at my chess blog. I delete it immediately. They are quite well-done spams, often starting with:

"Great blog. I've got it bookmarked!

Hey, if you want to know something about vacuum gaskets, check out my vacuum gasket site.

Have a good one, bud!"

The opening line is what does it, serving to make me happy that someone has actually bookmarked my blog. Wow, I must be important.

Then, 4 seconds later. HEY, wait a minute. I don't give a speck about heater gaskets! Dag.

It will be interesting to see how much more intelligent these spamtrolls get. They may even cut and paste topics, such as:

"Wow, great discussion of intelligent design and evolution! I've got you bookmarked and emailed Jurgen Habermas about it: I think he'll really like the blog!"

And so on....

Blue Devil Knight said...

Sorry for the previous deleted posts. One of the html links was not working, so I had to just paste the url, in lieu of the link, into the text
+++++++++++++++++++++++

As for the content of the original post, it is sometimes hard to discern given the unfortunately common rambling-manifesto style, but I can discuss a couple of points.

The claims about the frequency of beneficial mutations does point to an interesting scientific issue (this was a favorite of Gish and Morris in the 80s): that is, in nature, what types of mutations tend to happen, what is the phenotypic effect, and how does this affect fitness? This is addressed in the following excellent summary:
http://www.talkorigins.org/faqs/mutations.html

The above resource, itself incomplete, is a pretty good response, with a nice description of mechanisms of mutation. He has somewhat needlessly and conservatively limited himself to "beneficial" mutations observed in present-day conditions. Molecular systematics, which constructs phylogenetic trees based on comparison of DNA sequences (among other things) is filled with examples of simple phenotypic changes that could easily be driven by a series of point mutations (most of which are neutral).

For a great description of the genetic basis of evolution, see the recent book 'Endless forms most beautiful: the new science of evo devo.' What evolutionary developpmental biologists are starting to appreciate is that small changes in the genes that control developmental processes can have quite dramatic phenotypic effects, and we are finally starting to understand all this at a molecular level. Look up 'mutations' in the index.

The other major claim, that we should have missing links alive and interbreeding with the ancestor and descendent species, is a fun one. It is a great example of what I've been talking about: using your own ignorance as evidence for a designer. First, some relevant stuff is here:
http://taxonomy.zoology.gla.ac.uk/~rdmp1c/teaching/L1/Evolution/l5/what.html
or here:
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/Speciation.html
We do have cases where different species interbreed, but typically the offspring are infertile.

At any rate, rather than respond to this fun and interesting question by spending an hour writing out a worked out 'answer', I would first ask people reading this to put on their scientist cap, and think about what possible reproductive barriers exist in nature that would tend to stop similar species from interbreeding, even if both such species are NOT extinct. You might want to look at the above links for some ideas. Be creative, don't let your beliefs about gods and design stop you from freely thinking about possibilities in nature. That is the intellectual short-circuit of the ID folk I have discussed earlier. It will stop you from being a good scientist wrt the issue for which this short-circuit is activated.

Also, remember that we are discussing processes on time scales of hundreds of thousands to millions of years. A. afarensis, an early hominid species, is found in fossil strata over 3 million years old (scientists are as egotistical as your average person, if not more so, and hence the fossil and molecular evidence relevant for human evolution is correlatively well-developed, as can be seen here:

http://www.talkorigins.org/faqs/homs/


Can you think of possible reasons that A. afarensis isn't around to interbreed with humans? It is clearly an extinct species, and that is obviously the short and easy answer, but there are different ways to go extinct...Think about the possibilities...

It is easy for someone to come along and make a list of "problems" with evolution. If the ID creationists want to be taken seriously, they will need to act more like scientists. Overconfident, superficial remarks by people obviously ignorant of basic scientific results and methods will get brief and dismissive answers, especially when they are bringing up questions that have been thought about for decades by people doing the research (you will get a response similar to someone going to a technical forum and asking a stupid question, as is discussed in this wonderfully relevant article). You can imagine it gets pretty annoying: someone who is more humble and inquisitive, who has done their homework, and shows signs of actually listening to and understanding information, would get a VERY DIFFERENT response from any ethical scientist.

The other claims are not worth addressing (e.g., experiments on evolution involve experimenters, so we are surreptitiously adding a designer to the mix whenever we try to do evolutionary science).

As I've said previously, evolution is justifiably the default explanation for the origins of biological diversity. We do not, and should not, approach each species as if we had no pre-existing beliefs about this, as that would effectively set back research over a century and ignore all the empirical evidence that continues to support evolutionary theory (it is quite amazing that, even with new techniques such as those from molecular genetics, the expectations of the theory of evolution are born out: how many theories extend so gracefully to completely unexpected and unknown sources of data?). Too many ID folk act as if it is sufficient to convince someone who is completely ignorant of biology, as if that is the touchstone of having a viable alternate theory. Clearly, this is not the touchstone. The burden of proof is upon you to come up with something positive, strong, and sufficiently puzzling to evolutionary biology (in light of, not in ignorance of, its history) to really make us stop and think you have something worth listening to. Bohr and Einstein did it: you guys aren't even in the ballpark, I'm sorry to say. We'll welcome anyone who pulls it off (again, Bohr/Einstein). You have an even harder task, because it isn't "just another alternative" to evolutionary theory, but an alternative to the established methodological commitments that have become established in science over centuries. You will need more than the weak arguments of Behe, Dembski, and Johnson to make any headway.

I think, perhaps, you should consider that your criticisms of evolution are just off the mark, wholesale misguided ideas based on theology rather than consideration of data. Perhaps you should tweak your theology into thinking that evolution and Christianity are consistent, rather than trying to tweak science to force consistency with pre-existing religious biases.

Jason said...

BD (and hereafter): {{As for the content of the original post, it is sometimes hard to discern given the unfortunately common rambling-manifesto style, but I can discuss a couple of points.}}

Sorry--some of that derives from the lack of formatting. (I paragraph-break rather frequently, but that got lost somehow when Victor copy-pasted. So now it looks like one gigantic run-on sentence; with occasional blended words where line-breaks were added by various software codings. Oh well; it happens.)


{{experiments on evolution involve experimenters, so we are surreptitiously adding a designer to the mix whenever we try to do evolutionary science}}

That wasn't quite what I meant; but I'll blame it on the disappearance of the formatting.

What I actually wrote was: "Parts of the biological mechanism can be tested, and inferences can be drawn about how well the results fit into the basis theory; but the basis theory itself cannot (in this case) be validly tested.The results of testing parts of the mechanism can of course be combined with inferences grounded in systematic observations about actual real-world behavior; with these being compared to inferences grounded in what the basis theory itself should be implying."

I wasn't saying _anything_ against NDT here; it's just a technical limitation that ought to be kept in mind. I could have expanded it somewhat to give examples of other ways that inferences from scientific observations can be used to draw valid conclusions about the truth of the theory.

What I was pointing out, is that _opponents_ to NDT _shouldn't_ expect NDT to be validly testable in a _particular_ way that Lamarckism (as another basis theory) could be, and was, testable. That wouldn't be fair to the theory.


{{He has somewhat needlessly and conservatively limited himself to "beneficial" mutations observed in present-day conditions.}}

Instead of beneficial DNA mutations (point or otherwise) observed in... 19th century conditions?

Myself, I think it would be unfair to ask him to produce observations of such genetic mutations earlier than, say, the 1950s. Earlier mutations can't really be observed (per se), scientifically; their existence has to be inferred. Nor do I have any problem with that (in principle--whether the inferences are valid in practice is a further question, to be considered on a case-by-case basis.)

My point being that I wouldn't count it against him, or even call it needless. I have no problem believing he really does have good reasons for sticking with mutations observed in present-day conditions: e.g., those observations will be most likely to provide more accurate (in some cases even possible) results.

One result of which is to confirm that most such point mutations are neutral in effect.


{{Molecular systematics, which constructs phylogenetic trees based on comparison of DNA sequences (among other things) is filled with examples of simple phenotypic changes that could easily be driven by a series of point mutations (most of which are neutral).}}

Accepting for the moment that the point mutations are mostly neutral (or even harmful but not in such a way that the cell cannot easily work around it, therefore practically having no problematic effect)--neutralism still doesn't go very far in building up _effective_ complexity.

The results are passed on (maybe, assuming quite a few levels of odds still get favorably rolled past, so to speak) at no worse (or better) chances of survival in the gene pool; so, they _could_ admittedly still be around to suddenly come into play if a key positive mutation ever (accidentally) arrives to gell them all together.

At which point it's still a total toss-up whether the suddenly effectual mutation group gives a new effect that adds any survival-to-breedability benefit at all. Or, for that matter, whether roads and receptors are in place already for the newly generating proteins to make an effect. They might or might not be.

(All this assumes that the DNA proteins that got mutated weren't themselves important for survival, of course... which is a pretty big assumption to be making. Though a neutral point result might not hamper this, either, perhaps.)

Now, I _can_ see that there would be some survival value in mutations accidentally resulting in roads-and-receptors being more accepting of newly mutated proteins. (Assuming _those_ mutations survive the gene pool odds stacked hugely against any mutation from the get-go.)

On the other hand, such increased receptance to accidental results of protein copy-errors, would just as easily open up the cell to results that decrease efficiency, too; up to and including termination.

Even correcting 'most mutations are actually harmful' to 'most mutations are actually neutral in effect', it's still a lot easier to hurt a cell accidentally than to do something accidentally that helps it work better.


{{What evolutionary developmental biologists are starting to appreciate is that small changes in the genes that control developmental processes can have quite dramatic phenotypic effects}}

That stands to reason. (Just as, out of all the cell mutations that could possibly occur in a body, the only ones that count from the perspective of evolutionary development, are gamete-producing copy-errors. And only half of those--the other division from the original chromosome pairs will be normal. All evolutionary effects trace from that small source, too.)

Quite dramatic phenotypic effects are far from neutral, though; and it's a whole other question whether those effects will add survivability/breedability value to the developing organism (and if so how much--even a dramatic phenotype change might not add any appreciable survival value.)



{{The other major claim, that we should have missing links alive and interbreeding with the ancestor and descendent species, is a fun one. It is a great example of what I've been talking about: using your own ignorance as evidence for a designer.}}

Actually, I wasn't using that claim as evidence for a designer. I wasn't using it as evidence for anything; other than that the basis theory of NDT looks like it needs some fixing.

{{We do have cases where different species interbreed, but typically the offspring are infertile.}}

Didn't say the interbreeding species didn't exist. Just said, we find them to be a lot rarer than the basis theory would imply.

And in those rare cases, the offspring are, as you say, typically infertile.

So interbreeding species are (by all actual evidence) rare, and most of the rare instances are completely incapable of adding _anything_ to the species pool. This result is, to say the least, highly counterintuitive to NDT.

There _is_ an obvious and logical way to solve this problem, of course. (Sort of. {g})

And, that's what you try next:

{{I would first ask people reading this to put on their scientist cap, and think about what possible reproductive barriers exist in nature that would tend to stop similar species from interbreeding, even if both such species are NOT extinct.}}

That's quite true--indeed we hardly even need to go outside the species for such examples.

Problem is, those barriers (whether interspecies or intraspecies) also work against NDT as a basis theory.

If your defense to a problem with the theory is that _of course_ there are going to be even _more_ barriers to passing on mutant genes than we originally were supposing (not having put on our scientist caps first {g})... well, okay.

So, as I was saying: there are dozens of intrinsic barriers to passing on the mutations successfully--even more than I mentioned in my (relatively short) "manifesto". Even staunch proponents of the theory have no problem coming up with such barriers--especially when they think it's to their advantage to do so.


{{Be creative, don't let your beliefs about gods and design stop you from freely thinking about possibilities in nature.}}

Okey-doke. I freely think creatively, that tallying up _more_ barriers to successfully passing on mutations among a species' gene pool, kinda runs counter to what a particular theory needs in operation to work. {g}

Also, the whole point to _gradualism_ is that the changes (when they do occur) are so small that they'll hardly pose any problem in terms of being accepted and propogated in the gene pool (either at the micro- or macro-biological levels).

Given this, it seems a bit obtuse for me to be creatively free about coming up with all the various ways in which mutations would _hamper_ close-interspecies breeding. (At least if I was supposed to be defending the theory. {shrug})

If I was an atheist, I wouldn't let my atheism stop me from freely thinking that the math isn't adding up here. Neo-Darwinian gradualistic evolution theory _absolutely requires_ those mutations to be passed along at a sufficiently successful rate. You've basically just told me that NDT _does_ entail lots of transitional species as a natural result--and _also_ that, as a natural result, they aren't going to be interbreeding very effectively with each other. Well, yeah. Duh. {g}

I grant, this could easily mean that if the transitional species _are_ in fact around (somehow, _despite_ those interbreeding problems), we might have reasonable difficulty in detecting them--because they have significant problems ever successfully breeding.

It would also mean, however, that they're equally and proportionately impotent at doing what's necessary for NDT to work. (Not necessarily completely so, again I grant. But tallying up increases in mutant interbreeding difficulties, can only ramp up the implausibility of the theory, as it currently stands.)


{{Can you think of possible reasons that A. afarensis isn't around to interbreed with humans?}}

Sure. I even gave an example of one such reason myself. (Guess you lost it in the non-formatting.) But interbreedability problems between related species at highly distant ends of a species continuum (especially when one of those species is now extinct) _wasn't_ the problem I mentioned. Actually, I don't have _any_ problem with _that_. On the contrary, I included it as an expected NDT result (even if the species wasn't extinct.)


{{We do not, and should not, approach each species as if we had no pre-existing beliefs about this}}

Of course not. We should, however, add up the math concerning the implications and claims of the various beliefs.

And a lot of (even the current) b.e.t _does_ add up. Some of it still doesn't. I have no intention of ignoring either category.


{{The burden of proof is upon you to come up with something positive, strong, and sufficiently puzzling to evolutionary biology (in light of, not in ignorance of, its history) to really make us stop and think you have something worth listening to.}}

Surely. But different people are puzzled by different things. (Crick, as a matter of the history of evolutionary biology, was rather severely puzzled; as I pointed out. Nor did his goofy solution obviate the real work that he contributed.)

Obviously you aren't puzzled at all that you had to defend against one problem by ramping up another one. To me, this is a problem.

If a theologian tried to solve a problem _you_ brought up by proposing something that overtly and explicitly depended on increasing a related problem--would _you_ consider either problem therefore solved, and chalk up the appearance of a problem in one or both cases to your ignorance? Would _you_ accept a strong push by such a theologian to write you off as ignorant, overconfident, annoyingly manifesto-ish, etc., in such a case?

Admittedly, it _might_ only be a result of your ignorance. Or, it might not. Sometimes non-experts _do_ see real problems (even when they're atheists {g}).




Btw, as I wrote in my letter to Victor (and have written before in comments elsewhere): I don't put much stock yet in ID theory. I'm not an ID proponent (per se--in the sense of 'look!--this biological fact or problem is evidence of design, and so of a Designer'.) Frankly (as I've said before) I've found a significant amount of ID to rely on circular argumentation (for its positive claims anyway), and fwiw I'm not expecting this to ever improve dramatically. (Wouldn't mind if I was wrong about that, of course; but not expecting to be.)

In any case, it honestly wouldn't bother me at all for the current version of the b.e.t to pan out biologically. I'm pretty creative and free-thinking that way. {g}

(Actually, since I _am_ an AfR proponent, I have a _very_ high regard for that "free-thinking" part; and the various implications thereof. {g!})


Jason

Blue Devil Knight said...

Wow, those ads are getting way out of hand!

Jason, I started a post with specific responses to your claims. However, I realized it was going to be a waste of time if we didn't get some epistemological underbrush cleared, to see if it is even worth our time.

Let's assume that there were things that neo-darwinism can't explain (which there clearly are), what does that get you? It would buy the ID movement time to proudly march it about, trumpeting it as a nail in the coffin of naturalism. This, however, is as useless scientifically as it is unwarranted a conclusion. For some reason, IDers think that it is justified to go from "There is problem with scientific theory X" to "Naturalism if false" when it comes to species origins research but not other types of origins research: origins of stars, galaxies, AIDS, volcanoes, etc.. What if the investigators of AIDS, alzheimers, etc took this foolish approach, touting the death of naturalism wrt AIDS every time a problem was found with a theory? What if Einstein and Bohr had thought this way? "Wow, the precession of Mercury in its orbit proves that there is a god!" We would not have special/general relativity or quantum mechanics if every time a problem was found with a naturalistic theory, this was taken as evidence against naturalism.

In a sense, you are logically right, as since Duhem and Quine we know that a theories are tested in a bed of background assumptions. Probably the most central guiding epistemic principle is methodological naturalism. So, formally, you could say that any time any scientific (i.e., naturalistic) hypothesis is falsified, that could be just showing that naturalism is false. However, this anachronistic thought process was shown to be useless, as I have said an intellectual short-circuit that stunts creative scientific thinking. Methodological naturalism is so well-established, not by dogma but by its success, that the standards for taking it into question have correlatively increased. When my theory of the mechanisms of photosynthesis is not corroborated, why do you not say it is evidence for supernatural events?

I have repeatedly said that scientists are rebellious, that we love to overthrow sacred cows (Einstein and Bohr). For what kinds of evidence would a reasonable hypothesis be that there is something that transcends the physical?

One thing, really: unequivocal and massive miracles on a scale that would leave no room for reasonable doubt. For example, my deceased relatives rising from the earth, telling me of an afterlife. Previously cremated people rematerializing and chatting with me about our past together. While some naturalists could argue against me on this, I would be willing to say that if such grand violations of known physical law happened, we would only be reasonable to question the central guiding principle of methodological naturalism.

Blue Devil Knight said...

One note: in my previous message I was discussing methodological naturalism in science as a well-justified research strategy. I said nothing about being an atheist or naturalist generally. However, to the extent that I am not a naturalist about X, to that extent I will be a crappy scientist about X, and should probably pick a different topic if I want a career in science.

Ahab said...

I think you make an excellent point about scientists wanting to "overthrow the sacred cows." I would think any scientist who actually thought he had found a way to verify the existnece of some kind of supernatural being like god would be very excited - not try to cover up the evidence for such a being.

Jason said...

I wonder if Vic's picked up some kind of spyware on his computer, that's driving these things to his site?

(He could delete them, I guess, but then we'd be wondering why they were deleted.)

Now pondering on how to vaccinate the site...


Okay; Vic: odds are pretty good that the spam is showing up from a central routing location, which was given your address thanks to someone leaving your blog address somewhere else.

If you put in (or have already put in) a tracking device like Sitemeter (or Blogger's own proprietary system), you can find out where those posts are coming from, and block the router. I think. At the least, I _think_ you should be able to copy-paste the router's (or routers') address(es) thereby, and forward those on to Blogger's tech crew, so that _they_ can block the spamming from along those routes.

Blogger, Sitemeter, et al, make it pretty easy to add the relevant bits of code to your template, to activate the tracking. I'd go with Sitemeter, if you aren't already paying an upgrade fee to Blogger. It takes about 15 minutes to do.

(Other remarks elsewhere. {g})


Jason

Jason said...

BD (and hereafter): {{Let's assume that there were things that neo-darwinism can't explain (which there clearly are), what does that get you?}}

{shrug} Don't know that it gets me anything. I don't base my theism at all on design arguments; and I don't consider biological processes to be a primary ground for drawing metaphysical conclusions. Consequently, I don't consider neo-darwinism (considered as a biological theory) to be any kind of threat.

The _philosophical_ use of the theory (and related ones), attempted by a wide range of atheists, is a completely different issue; but I heartily insist that the two should _not_ be conflated by anyone (atheist, theist, whoever).

It happens to be a fact, that (as Richard Dawkins once said), Darwinism (and its variants such as NDT) helps people be intellectually satisfied atheists. I think that's a result of a common and easy (and quite forgiveable) category error; but it isn't my problem. It does mean, that if someone is grounding the (felt or apparent) strength of their worldview on NDT being viable, then there's going to be a strong temptation not to face any serious problems with the theory, if those problems show up. _But_ I also heartily agree that this is not an excuse for ID theorists, or anyone else, to promote problems with NDT as being equivalent to a refutation of either atheism or naturalism, much moreso as being therefore grounds for people to switch worldviews to theism.

I wrote the letter to Victor, because someone (Steve?--not you or Ahab iirc) had asked if anyone could point to any failures in NDT similar to (what amounted to) an experimental failure of Lamarckism. The first thing I did was point out that NDT would never be in any position of being validly disproven by _that_ kind of experiment. It _does_ however have some serious problems; and the problems are numerous and intrinsic enough to warrant (I think) a revision of the basis theory. Which, as I pointed out, has been done before; which is why we have NDT at all right now.

(Myself, I suspect we'll eventually be seeing a revision of the basis theory away from gradualism as more data continues to come in.)


Since I'm not an ID proponent, and I'm not trying to claim that the problems with NDT == a refutation of any philosophical position or as being positive grounds for a different philosophical position; I wish you would stop treating me as though this is what I am doing anyway.


{{Probably the most central guiding epistemic principle is methodological naturalism.}}

I think there are some more central guiding epistemic principles than this (e.g. the law of noncon.) Scientific principles are supposed to depend on philosophical ones, not supercede them.

So, for instance, if the only way to solve one problem with a theory involves increasing a related problem elsewhere, then it doesn't matter if you're using naturalism as a scientific methodology or not. Something's still wrong with the theory somewhere, as the theory currently stands (or is being presented, or whatever).


{{So, formally, you could say that any time any scientific (i.e., naturalistic) hypothesis is falsified, that could be just showing that naturalism is false.}}

Actually, no I wouldn't; partly because I don't conflate a hypothesis with a methodology, and partly because I don't accept the conflation of the philosophy of naturalism with a (much less _the_) scientific methodology.

(This is supposed to be reassuring. {g})


{{When my theory of the mechanisms of photosynthesis is not corroborated, why do you not say it is evidence for supernatural events?}}

I don't. You might try actually reading me, instead of making preliminary guesses about what I'm doing. I'm treating _you_ as a particular person, not as some hypostasized generalization of a group.

I know the regrettable disappearance of the formatting in my letter to Victor makes it difficult to follow; but you do have another letter now (with formatting intact) that you could have been easily reading.

However, I'm entirely willing to understand and accept that it's proper to clear out epistemological misunderstandings first.

Since I _don't_ in fact do what you're presupposing I'm doing--which I agree would make any discussion pretty much hopeless if I was--now you can go back and actually read something I actually wrote, and write comments and such; if you still care to.


{{For what kinds of evidence would a reasonable hypothesis be that there is something that transcends the physical? }}

I think your grammar is a bit swissed here, but based on your answer I'll suppose you are meaning: what kind of evidence would reasonably back a hypothesis that there is something that transcends the physical.


{{One thing, really: unequivocal and massive miracles on a scale that would leave no room for reasonable doubt.}}

Not at all--this would be circular argumentation, and I would reject it.

Feel better? {g}

Bunches and bunches of definite (unequivocal) supernatural events, requires that we can already tell (or are already presuming) they're supernatural events; so their existence _as_ such would be no good ground for _concluding_ thereby, that there must be such things as supernatural causes of effects.

Plus, the sort of conclusion you're talking about also depends heavily on the mere feeling of being overwhelmed by something. I don't recommend basing a conclusion on that. (It bespeaks a dangerous willingness to be impressed by the mere apparent size of something, rather than understanding and accepting or rejecting principles and principle application. Otherwise, you would have recognized that even _one_ confirmed miracle would work just as well--for this circular argumentation. {g})

Notice that I'm stressing this rejection, _despite_ the fact that the apparent conclusion would be nominally in favor of something _I'm_ actually in favor of believing (and do believe myself). But getting to it this way would be at least two combined mistakes (or even outright cheating).

(So, does that seem particularly manifesto-ish of me? {g})


{{For example, my deceased relatives rising from the earth, telling me of an afterlife.}}

I wouldn't consider that to be evidence (per se) for concluding there's something transcending the physical, even assuming it happened just like that. I might consider my experience of it evidence of my own delusion. {shrug}

Ditto with the previously cremated people.

Apparently my standards are more stringent than yours. {g}


{{I said nothing about being an atheist or naturalist generally.}}

Wasn't assuming you were. (I did make use of atheists as a typical example of opponents to theology, who might still be capable of seeing real problems with proposals of that discipline, even when they might not be experts.)

Based on your own testimony just now, however, I think I have grounds for concluding either that you are a philosophical naturalist; or else that you've experienced conversations about the afterlife or your past, with a bunch of people you knew very well who certainly died and were buried (or cremated), etc. {g}


Ahab: {{I think you [BDK] make an excellent point about scientists wanting to "overthrow the sacred cows."}}

Most people don't really get that excited about overthrowing the cows that _they_ are holding sacred, though.

I think the point has been recently made, that most ID proponents, for instance, _already_ were believers in a Designer, etc. They cow they're excited about overthrowing, is a secular one; not their own.

Why would you expect a scientist who starts with holding atheism (or even a biological theory like NDT) as a _sacred_ cow (so to speak), to be so positively excited about seeking to overthrow that?

People have to be _very_ much in love with truth, not just with an ideology, to have the strength to be willing to sacrifice their ideology (or even alter it in any major way). In my experience, that level of self-discipline is exceedingly rare, including among scientists.


We can't be positivists; but the positivists do (or did) have something close to being a good point. If we aren't willing, in principle, to ante up our own foundational beliefs and put them at risk of our really losing them, then we aren't primarily loving the _truth_--only our own beliefs _about_ the truth. That goes as much for me, as it does anyone (which is why I'm so intensely self-critical.)

Jason

Blue Devil Knight said...

Sorry, I am back at work so don't have time to respond, and it seems we don't disagree that much anyway when it comes to science and its methods. That was my main focus, not general metaphysics.

As I'm sure you know, the folks at talk.origins actually like to argue about this stuff.

Ahab said...

Jason wrote:
Most people don't really get that excited about overthrowing the cows that _they_ are holding sacred, though.


I'm not talking about 'most people' but rather most scientists. Guess we could go back and forth on whether its different among scientists.

I would agree with you to the degree that any scientist who develops an hypothesis or theory is going to fight tooth and nail to see it validated - that would be her sacred cow. But she would most likely be knocking some other sacred cow of science in the process.I don't see such motives for someone coming new into the field and wishing to discover something new. Seems to me that they have a rather good reason for overturning, or at least re-tuning, the current sacred cows of science.

I know that even though I'm an atheist, I would be delighted if I could find a way to scientifically verify the existence of a god. Of course, that may be because I'm not so much an atheist in the sense of ruling out all possible deities, but because my atheism is pretty much directed toward the Abrahamic versions of god.

Jason said...

Hey BD!

Yep; 'work' work is kinda encroaching here, too. {sigh} {g} (Payroll today for instance.)


Hey, Ahab!

{{Seems to me that they have a rather good reason for overturning, or at least re-tuning, the current sacred cows of science.}}

Eh; it's _a_ reason. Don't know that I would call it a good one, though.

If someone's trying to turn over someone else's sacred cow, for the sake of protecting one's ideology or for the sake of promoting one's own importance within a group--really, what difference does it make? Is either one of those really any kind of respect for truth? Is either one of those _intrinsically_ all that likely to discover anything better in regard to truth?

Doesn't seem so to me. {shrug}

I've known a lot of scientists and doctors. Most of them care primarily about following what light they _can_ see, and looking for more light thereby. Sometimes that means overturning what they come to believe is a _mistake_. But I think most of them would recognize the desire to do that for their own self-promotion to be a temptation--something to be resisted and avoided.

But maybe my sample is skewed. {shrug}{g} (I live in the South, and most of them either are various shades of Christian, or at least grew up that way. {s})

Jason

Jason said...

Oh--I meant to add a reassurance, too...

Ahab: {{Of course, that may be because I'm not so much an atheist in the sense of ruling out all possible deities, but because my atheism is pretty much directed toward the Abrahamic versions of god.}}

{shrug} If you decide that various "Abrahamic" notions of God are untrue, then of course you shouldn't believe them. I have no problem with that, in principle. I'd _rather_ you disbelieve what you think is untrue! {g}

This is despite the fact that you may (in some cases) be thereby disbelieving something that _I_ believe to be true. I care primarily about the truth; my own beliefs about what is true are only some handy tools I have, that help me understand truth. My beliefs, themselves, are not _the_ Truth.

(That doesn't mean I think my beliefs are unimportant. But they aren't _that_ important. {s!})


It is better to disbelieve, than to believe in a God unworthy of belief. _I_ think the Abrahamic notion of God (by and large) is true, and worthy of belief. I also reject what I believe is heretical.

So what? I would be a hypocrite, if I didn't agree that _you_ should _also_ reject what _you_ believe is heretical--even if that puts you in confliction with me.

We can dispute about what is true; or even about what is untrue. I have no intention at all of disputing, that you shouldn't believe what you think is untrue.

So, don't worry about that. {s}

Just be sure to walk according to what light you _do_ see, looking for more light thereby. I entirely trust God to take care of the rest--and indeed to be doing that for you already, whether _you're_ doing that or not. {g}

(the same as He does for me. {s})


Jason

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