Posted tagged ‘Epistemics’

Causation without “naturalism” or “materialism”

November 14, 2008

Paley, of course, is to blame for not framing his arguments more tightly.  DBB, 213

Uh, yeah, Behe, then why have you backed away from all of the positive evidence that Paley adduced as being the effect of a mind similar to our own? That Paley lacked tightness of argumentation and exactness of fit between cause and effect I do not doubt, but it is the fact that Paley posited meaningful causation (that is, a mind similar to our own), which Behe completely fails to do, just as the “theories of origin” that Paley rightly criticized failed to do.  The reason glares out at us, of course, which is that evolution explains what we see in life, and design has nothing to explain the slavish copying evident in life, except that, wherever lineages break from each other, there is no commonality of “authorship” in any of the subsequent modifications.  The patterns are evolutionary, and unlike any design causation that we have ever observed.

The childishness, as well as the vacuousness, of ID is transparent whenever they whine about science’s devotion to “naturalism” or to “materialism”.  For, the fact of the matter is that mental causation was understood well before any “naturalistic” or “material” causes were known, and yet we still understand mental causes more commonly according to “non-natural” and “non-material” models than we do according to physics.  Most of the science-oriented types do not doubt that the brain operates according to physics, of course–and for very good reasons, especially the conservation laws, and small-scale cause and effect observations.  Yet we do not hesitate to understand causation outside of precise scientific understandings of the processes underlying our “theories of mind.”

This is all that we demand, all that we have ever demanded.  Let’s let Paley say so once again:

When we speak of an artificer or an architect, we talk of what is comprehensible to our understanding, and familiar to our experience.  We use no other terms, than what refer us for their meaning to our consciousness and observation; what express the constant objects of both; whereas names, like that we have mentioned, refer us to nothing; excite no idea; convey a sound to the ear, but I think do no more.  Natural Theology

How “design” means anything in the passage below I cannot say:

Features that strike us as odd in a design might have been placed there by the designer for a reason–for artistic reasons, for variety, to show off, for some as-yet-undetected practical purpose, or for some unguessable reason–or they might not.  DBB, 223

Yes, that’s why it’s called “design,” not “art.”  Paley was serious about design, which is why he discussed artificers and architects.  Darwin was also serious about design, which is why he noted that life does not look like anything we get from artificers and architects, but rather more like something that reproduced, faithfully for the most part, but with variations which were selected.

Partly I have been recapitulating the earlier, linked post.  But now it is for the additional reason that neither Darwin, nor most other competent scientists, ever hung the arguments regarding design vs. evolution on “naturalism” or “materialism”.  What is more, Darwin himself didn’t have a “natural” or “material” cause of the variations which “nature” selected, instead he was concerned about empirically-known causes matching up with empirically-discovered facts.  The gene fairy might have been responsible for inheritance and variation, for all he knew (by his time such fanciful “causes” were no longer taken seriously, however), but “survival of the fittest” explains (many of) the cumulative effects that we see.

And although he did not use this term, Paley hypothesized “rational choice” as being responsible for the “design” of organisms, exactly what we would expect of an artificer or architect.  His point was certainly not that the “designer” had to be “natural” or “material,” rather that it would be rational, and purposeful. And ultimately, Behe denies everything that we would expect of a designing mind, both purpose and rationality.

We just need causation of any hypothesized design, or in other words, we need to know the limits and peculiarities of a designer if we are ever to be able to identify such a cause.  That is all that Paley demanded of competing origination theories, and he rightly determined that they fell flat when they failed to explain anything by matching up cause and effect.  It hardly needs pointing out that Paley failed to explain much that he claimed to explain, let alone all that ignored.  Yet he at least claimed identifiable causation (or at least he analogized to identifiable causes–depending on what makes of God as a Cause) producing identifiable effects.  As loose as his argumentation was, it was indeed tight enough to be subjected to falsification tests, and thus it failed when organic articulations were shown to be explainable via natural selection, along with a host of data that design never could touch (although Paley tried get his readers to accept morphological similarities as produced by the “designer”).

No more of that from Behe, certainly.  He’s flailing away so badly that he’s bringing up art that is deliberately obscure, in order to avoid the fact that all of his “design” is lacking any of the expected marks of design–particularly rationality and purpose.  He knows that some of Paley’s arguments were poor, indeed, but he will not admit that his principal problem with Paley is that the latter invoked empirically-known causation which was falsifiable and falsified.  Worse, evolution is falsifiable, and has not been falsified, and it explains what his “design” deliberately avoids addressing–such as the aforementioned slavish copying along lines of vertical transmission, and no “common authorship” of modifications in lines which permanently broke away from each other.

We have only demanded that causes should actually produce their expected effects, from Paley, through Darwin, and down to the present day.  The utter lack of rationality and purpose behind organisms is enough to invalidate any “designing mind” worthy of the name (actual reference, as Paley demanded), quite apart from the evolutionary evidence. 

What is more, evolutionary theory has no dependence on the dearth of evidence for “design,” rather it is the match of cause and effect in the patterns of life (“slavish copying along lines of vertical transmission, and no “common authorship” of modifications in lines which permanently broke away from each other”), wherein causes with deep “memory” and no “knowledge of what is happening in unrelated lines” produce just the effects expected (predicted) by those causes.

This is part of a series of posts that I am combining into one long post, which may be found at Darwin’s Black Box.

Horizontal transmission of a transposon in animal species

October 22, 2008

Here is the core of the article, in my opinion:

The fact that invasive DNA was seen in a bush baby but not in any other primates, and in a tenrec but not in elephants, hints that something more exotic than standard inheritance is going on.

However, this patchy distribution by itself does not rule out the traditional method, as some of the species could have lost the transposon DNA throughout evolutionary history.

So the team looked at the position of the hAT transposon – if it had been inherited from a common ancestor it would have been found in the same position, with respect to other genes, in each species. But they could not find a single case of this.

Since first entering the genome, the hAT has been able to reproduce dramatically – in the tenrec, 99,000 copies were found, making up a significant chunk of its DNA. Feschotte speculates that this must have had a dramatic effect on its evolutionary development.

“It’s like a bombardment”, he says. “It must have been evolutionarily significant because the transposon generated a huge amount of DNA after the initial transfer.”

Feschotte says he expects many more reports of horizontal gene jumping. “We’re talking about a paradigm shift because, until now, horizontal transfer has been seen as very rare in animal species. It’s actually a lot more common than we think.”  New Scientist

“More” is probably a good bet, all right, but horizontal transmission of genes is still not all that common in animals, so far as we can tell.  Still, 99,000 copies is bound to have made a difference in the evolution of the tenrec.

I thought the story itself was interesting, but it also has elements in its discovery that demonstrate how out-of-the-ordinary animal genetics can be and is discovered.  IDists sometimes like to point to the fact that this or that scientist agrees that design could be detected. 

But that’s their entire problem, it could be detected and it never is.  Meanwhile, science continues to find “non-canonical” changes and evolutionary patterns, such as this gene being laterally transferred into animal genomes.  It is entirely a matter of what has evidence and what does not.  Vertical transmission is by far the dominant form of gene transmission in, say, vertebrate species, as indicated by both conserved genes and by the lack of commonality after taxa diverge.  Horizontal transmission occurs, and is identifiable by its “lawfully accidental” appearance in unrelated species, as well as by the fact that the gene is not found in the same places in the genomes of the animals having a particular gene.

Now if we could ever find the commonality of authorship in any evolutionary development, such as older IDists predicted, ID would at last have some evidence in favor of it.

Common descent is demonstrable only when causes are known

September 24, 2008

Bear in mind, throughout, that common descent is a distinct concept from the mechanism of natural selection acting on random variation.  Edge of Evolution, 64

In the abstract, the quote above is true.  It is in reality that Behe’s constant resort to the contingencies of “naturalistic” heredity, while denying “naturalistic” contingencies in adapatation, fails utterly and completely, both on the ground of consistency and because he is unable to differentiate between the causes of various effects.  If he is unable to constrain “design,” as he most certainly is not able to do (indeed, he takes pains to try make his claims of design unfalsifiable), then he cannot constrain anything else in the history of life.  If “…anything might have been designed” (DBB, 193)–including mutations which are directed (a favorite claim in EoE)–then we have no reason to believe that the evidence of common descent was not also designed, and produced by miracle.

Yet he does believe observable causes are responsible for similarities:

Like the sequence analysts, I believe the evidence strongly supports common descent.  DBB, 176

Unsurprisingly, where the actual “naturalistic” causes are unknown, whether in “design models” or in “atheistic models,” such certainties have not been obvious or accepted.  A philosopher such as Buffon could propose that life arose to fit “internal molds,” which shaped organisms into set patterns.  Paley states that “This similitude, surely, bespeaks the same creation and the same Creator” (Natural Theology, chap. 25).

One might suppose that Behe has more cause to believe in common descent than Paley did, however.  Well, yes, that is true, both in the huge amount of evidence which indicates what is expected of common descent, and at least as importantly, because we understand the mechanisms of both conservation and of non-conservation of genetic information in organisms.  The processes of preservation and of change are inextricably tied together within biology, never mind the fact that the concepts are different (the processes themselves are occasionally separable, such as during the early part of abiogenesis).  That is, we understand how genetic information is preserved both by reproduction and by natural selection, and we know that because we understand the limits of change imposed by (roughly) the neo-Darwinian model of evolution.

Paley credited God for similarity because he could not conceive of how morphology (which is about the only type of evidence that he had) could be preserved as a “general plan,” yet so thoroughly modified.  Darwin explained this, which is why he and most modern biologists have understood the evidence of common descent to implicitly support the known causes of organism modification.  For, if there is nothing that accounts for the differences between frogs and humans, how are the similarities going to be accounted for via common descent?  We have to understand similarities and differences under the same model, and we do so by understanding them all to be due to common descent as modified by mutation plus natural selection (plus other known processes).

Once one believes that an unobservable and unpredictable (in the probabilistic sense of the word) process, or processes, is responsible for the “design” of organisms, how can one possibly determine which aspects of organisms were not poofed into existence?  A rat might as easily be descended from, or designed from the template of, an octopus or a petunia, if we are not paying attention to the actual mechanisms of stability and of change.  The only apparent reason why Behe accepts the accidents of heredity, and not the evidence of accident in adaptation, is because he wishes his god to be responsible for the latter and not for the former.  This goes back to the fact that Behe has absolutely no means of independently observing design in life in an entailed manner, discussed here.

The evidence that life evolved in a process involving natural selection is precisely the evidence of accident and contingency found in life.  Two such crucial contingencies are the accidents of heredity and of mutation, and, aside from effects of the filter of natural selection, that is largely what we see in life (I write “largely” because causal regularities exist apart from natural selection and descent).  The accidents of heredity are accepted by Behe as causal, even though any accepted meaning of the term “intelligent design” implies that such accidents would not predominate in life as they do–we filter out many undesirable accidents whenever we adapt designs.  Then he wants “design” to hide underneath the accidents of mutation, and to be indistinguishable from them, except probabilistically.

Such a position must be called “incoherent,” at least if we are being charitable.  The filter of intelligence involves rationality, planning, and the correction of defective accidental characteristics, wherever these occur.  We accept that a filter quite different (if with some similarity in output) from intelligence produced life precisely because neither accidents of heredity nor of mutation characterize intelligent activity to any great degree, while they are unquestionably predicated of any unguided natural selectionist evolution involving the sorts of organisms we recognize.

I am writing this now because just one day previously I wrote a post about all of the evidence of evolution in the eukaryote flagellum, one of Behe’s “examples” of “irreducibly complex” systems. I noted there that Behe would accept the evidence of common descent, but would deny that it indicates that it evolved by the mechanisms by which we say it evolved, rather claiming that it had to be designed. That, however, is an absurd notion on his part, for the terms “intelligence,” “design,” and “intelligent design” do not even refer to processes adopting the contingencies of heredity and mutation that we observe in life. “Evolution,” and “evolution by natural selection,” by contrast, do refer to processes including such observed accidents and limitations.   We simply match up cause to effect to conclude that eukaryotes’ flagella evolved (with no poofs).

So of course it is true that “common descent” and “natural selection” are separate (at least separable) concepts. In science, though, we do what Behe and other IDists do not, which is to combine the two concepts in order to constrain these concepts as they actually (empirically) do pertain to life.

Because Behe does not follow science at all in the area of origins, we are at a loss to understand how his god of the miracle mutations is in any way preferable to, or more scientific than, the belief that some god simply spoke all of life into existence a few thousand years ago, complete with the evidence predicted for organisms that have evolved without any guidance of intelligence.

This is part of a series of posts that I am combining into one long post, which may be found at Darwin’s Black Box.

Only if it is found can the edge of evolution be calculated

September 17, 2008

NOTE: This was first published here on 8.25.08, and is simply being re-published as a separate post now.

No person–Darwinist, design proponent, or other–who wants to make a rational argument can seriously entertain an idea that pulls the rug out from under reason. Edge of Evolution, 226

No matter that Behe pulled the rug out from under reason at the beginning of the book.

There is a plethora of problems with Edge of Evolution, many of which I hope to address in the future. But the really big problem is something I want to address now, before I resume posting about DBB. The impossible problem for Behe is that he never once was able to show that evolution is responsible for some organic change, and that design is responsible for other organic change. Crucially, this is true for P. falciparum’s evolution of chloroquine resistance. Since under his own assumptions he cannot show that Plasmodium falciparum was not designed, either in the past (front-loading of the universe or of the genome) or in an ongoing intervention by the Creator, to develop resistance–and he merely assumes that such resistance evolved–from the very beginning his calculations have absolutely no basis at all.

Don’t suppose for a second that there aren’t many other problems with his calculations, which include the fact that he has no understanding of or regard for the population dynamics of malaria, knowledge of the selectional pressures for and against the mutations that give P. falciparum its resistance to chloroquine, nor even how many mutations are needed to confer positive selection. My present point is that from the very beginning he has no criterion for deciding what is designed and what is not, but he comes up with calculations based upon his mere belief that malaria evolved chloroquine resistance, rather than that resistance being designed.

The trouble is that the instant he decided that the supernatural designs organisms via evolution, and without any of the normally-recognized design characteristics being involved (like rationality, evident purpose), finding out what was caused by evolution and what was caused by “design” became completely and utterly impossible. Apparently the “designer” simply adds in mutations which cannot be expected to occur by chance, and (apparently) natural selection does the rest. And there is no qualitatively or quantitatively noticeable break between this “design process” and evolution. So how can this doofus ever presume to find out what evolved and what had to be designed, when he has nothing by which to decide what was designed and what was not?

What real science does is to understand cause and effect relationships first, and then to show reliably how one cause produces discernable effects, and to distinguish these effects from those caused by other processes, as best as can be done (and it is not possible to always distinguish effects). You already know what is design and what is not.

Behe’s way of determining what is designed and what is completely circular, save his initial assumption that what is happening today is not caused by non-human design. Because he simply believes that what is happening today is evolution and not design, he takes the mutations in humans and in P. falciparum to have evolved, and then makes illegitimate extrapolations from the already bogus figures that he got from that. Only if he already knew how to distinguish between design and evolution based on cause-and-effect criteria would he be able to show that chloroquine resistance is not the result of design, however, and he has no criteria which indicate that chloroquine resistance is not designed by his shadowy supernatural designer (or a designer indistinguishable from a supernatural one).

So he “found the edge of evolution” by merely assuming the edge of evolution–through his fully unsupported belief that design is not responsible for what is happening today. Even if he had begun this quest in all intellectual honesty (there is little indication of intellectual honesty in Behe’s writings), he would, as he himself noted, have to reevaluate what might have been designed in light of his “conclusion” that life was designed (see EoE 168), and would have to question his previous assumption that malaria has simply evolved. He does not do so, and if he had he would have had to face up to the fact that, lacking anything that distinguishes “design in life” from what has evolved, he simply cannot distinguish between the “two processes” at all.

He has pulled the rug out from any ability to reason in the empirical sciences, mainly because he’s strained so hard to claim that what evidently evolved was designed. By asserting that “looks designed” and “looks evolved” mean the same things, he has no basis whatsoever to come up with qualitative or quantitative criteria for determining design. This is another place where I made similar points.

The man seems to have no self-awareness, nor any capacity for thinking through his “scientific claims”. It appears that he is a hedgehog, plodding along with his one idea, and oblivious to the fact that he undermines his own claims during the course of his “argumentation.

This is part of a series of posts that I am combining into one long post, which may be found at The Edge of Evolution

Design in life is easy to detect–look for breaks in evolution

September 17, 2008

NOTE: This was first published here on 8.21.08, and is simply being re-published as a separate post now.

Since Dawkins agrees that biochemical systems can be designed, and that people who did not see or hear about the designing can nonetheless detect it, then the question of whether a given biochemical system was designed boils down to simply adducing evidence to support design. DBB, 203

Behe gets that much right. But how do you adduce evidence to support design? Well, a rationally thought out system would indicate design, and so would some actual purpose in living organisms, to bring up two important criteria. Less precisely, “conceptual precursors” instead of “physical precursors,” would fit the bill, as Behe pointed out, and as I discussed previously. Or another way of putting that fairly inchoate (but usable) conception–and extending it somewhat–would be that we would look for arrangements that do not fit evolutionary patterns.

In other words, probably one of the best ways of looking for design candidates would be to find something that does not fit with evolutionary predictions. After all, what would be a better potential marker for intelligent design than something that wouldn’t occur via natural processes (now using the definition “natural” which means “not caused by humans”)? One would probably still have to check to see if rational thought was used, and if the putative “design” serves a likely purpose, but merely breaking the mold of evolutionary expectations would tend to suggest that something has intervened in the natural processes of evolution.

Behe himself brings up the subject, writing, “…The work does show that an intelligent agent can design a system exhibiting biochemical-like properties without using the biochemicals known to occur in living systems.” DBB 202.

Yes, finding something like that would indeed be a pretty good first indication of design. For instance, find an malaria strain that has a completely new protein, which also has novel amino acids in it. But we wouldn’t have to be that exacting in our demands, a completely new protein would certainly flag researchers that this strain of P. falciparum likely was engineered.

By the way, I used Plasmodium falciparum for an example quite on purpose, since it does not normally share genes with other organisms (not so far as I know, anyway), like anthrax does. Since sharing genes is “natural” for anthrax, and not for malaria, a new protein in the latter would break the evolutionary expectations rather better than a new (or unknown) protein in anthrax would.

There are less clear examples of design, those which simply take a gene from one organism and insert it into a very distantly related organism. Interestingly, these also are relatively easy to find, at least so long as we have their genetically unmodified relatives around. I really do not think that aliens that came to earth would have any difficulty discovering that many of our food crops have been genetically modified by injecting the Bt gene (which produces an insect-killing protein) into these crops, even though the Bt gene has evolved naturally.

Aliens could discover design of Bt crops because, of course, Bt in corn breaks the evolutionary patterns of inheritance and change. Corn, like P. falciparum, does not typically receive genes from other species, while intelligent humans know how to insert Bt genes into the corn genome. To be sure, there are other tell-tale marks of genetic engineering, although many of these are also taken from nature and placed in “unnatural” contexts (like viral promoters are). Nevertheless, even if the genes were entirely “natural,” the fact that evolution would not be expected to produce corn plants with Bt toxin (and liverworts are not) would tend to give the game away. The other “unnatural” components only enhance the notion that Bt genes and other deliberately introduced genes were “designed” to at least a degree.

So why doesn’t Behe drive home the point that he delicately prompts, namely the easy manner in which human designs in nature could be detected (though generally they are detected by looking for known specific patterns of “engineered” genes), by recognizing their breaks from the evolutionary patterns? There is only one reason, this being the fact that he can produce nothing that does not fit the expected evolutionary patterns (aside from our own interventions). He wants to suggest in DBB that there is really no problem with deciding that life was designed because we can do it, while he pointedly ignores the fact that our interventions do not follow the (evolutionarily-produced) taxonomic patterns of nature, and also need not rely upon physical precursors (although we often do–yet we produce unnatural patterns even then).

The fact is that, in both of Behe’s books, he avoids integrating knowledge. That is unsurprising, since said lack would be expected in a creationist. He’ll happily bring up human modification of life as an analogy, but he will not discuss the fact that quite obviously our designs purposefully break the evolutionary patterns, unlike what we see in wild-type organisms. He insists that design can be detected in life (which almost all of us have agreed was possible from the beginning), but he avoids the fact that design would not follow evolutionary patterns, nor would it rely upon physical precursors, as empirically-known evolution does.

The one thing that we would expect almost any kind of biological design to do–step in where evolutionary limits prevent a desired capability–is absent from biology. And even more absurdly, Behe insists that evolution cannot produce complex biology–which conforms to evolutionary limitations–but he insists that design nudged evolution along without producing any of the evidence of genetic modification that even humans have done with their decidedly limited late 20th and early 21st century capabilities. Intelligent intervention is supposed to have occurred, and yet that intelligence didn’t dare to break the rules of evolution, or to deviate from evolutionary patterns.

Instead of breaking the evolutionary patterns, as we would expect of design, Behe insists that design is responsible for complex evolutionary patterns. Has any other crank scientist ever worked so hard to avoid the meaningful tests of his claims as Behe has with his “intelligent design”?

This is part of a series of posts that I am combining into one long post, which may be found at Darwin’s Black Box.