Gemini and Keck directly image planetary system

Posted November 13, 2008 by glen1davidson
Categories: News

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I hope to post more on topic soon.  I haven’t been able to recently due to various commitments.

This just seemed so cool, though, that I thought it was worth a short post, and more importantly, a link.

According Dr. Marois, this discovery is the first time we have directly imaged a family of planets around a normal star outside of our solar system. Team member Bruce Macintosh of the Lawrence Livermore National Laboratories adds, “Until now, when astronomers discover new planets around a star,

all we see are wiggly lines on a graph of the star’s velocity or brightness. Now we have an actual picture showing the planets themselves, and that makes things very interesting.” The discovery article is published in the November 13, 2008, issue of Science Express, an international weekly science journal.

The host star (a young, massive star called HR 8799) is about 130 light years away from Earth. Comparison of multi-epoch data show that the three planets are all moving with, and orbiting around, the star, proving that they are associated with it rather than just being unrelated background objects coincidentally aligned in the image. HR 8799 is faintly visible to the naked eye, but only to those who live well away from bright city lights or have a small telescope or even binoculars, see online finder charts here.

The planets, which formed about sixty million years ago, are young enough that they are still glowing from heat released as they contracted. Analysis of the brightness and colors of the objects (at multiple wavelengths) shows that these objects are about seven and ten times the mass of Jupiter. As in our solar system, these giant planets orbit in the outer regions of this system – at roughly 25, 40, and 70 times the Earth-Sun separation. The furthest planet orbits just inside a disk of dusty debris, similar to that produced by the comets of the Kuiper Belt objects of our solar system (just beyond the orbit of Neptune at 30 times the Earth-Sun distance). In some ways, this planetary system seems to be a scaled-up version of our solar system orbiting a larger and brighter star.  First Direct Images Of A Planetary Family Around A Normal Star

While this is a fairly special case, which won’t be often replicated in other stellar systems with the present telescopes, we’re getting a lot closer to actually studying extra-solar planets.  Which does, of course, have a lot to do with the evolution of life.

We really need the space-based interferometers and other instruments to study extra-solar planets, and possibly to find out something about the origin and evolution of life on other planets.

Just the usual censorship of the anti-science faction

Posted November 5, 2008 by glen1davidson
Categories: News

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This is what showed up after I posted at Expelled‘s blog:

Glen Davidson Says: Your comment is awaiting moderation.

November 3rd, 2008 at 12:41 pm
If a theory claims to be able to explain some phenomenon but does not generate even an attempt at an explanation, then it should be banished. Despite comparing sequences, molecular evolution has never addressed the question of how complex structures came to be. In effect, the theory of Darwinian molecular evolution has not published, and so it should perish.

Yes, it’s the prominent IDist Behe who wants to banish evolution.

Of course he’s wrong about evolution’s explanatory ability, while ID has none whatsoever. By Behe’s standard, ID definitely deserves banishment, although I would not go that far.

To be sure, an idea like ID that never has–and never could–address the origin of complex structures has no business being called science.

Glen D

At the time of this writing, a much later comment than mine has appeared, while mine is nowhere to be seen.

They’ve never really caught onto the irony of expelling comments for their stated views, although they are not as quick to do so as Dembski’s blog, Uncommon Descent, is. 

Now it is not certain that they will not at some point publish my comment.  Even if they do, though, it’s still suppression, since people tend to read the most recent comments, and not to see comments which have magically appeared among the “older comments.”  They have played that game with past comments of mine.

At this moment, the comments on that blogpost are heavily in favor of Expelled, a fact that may owe much to rank censorship and hypocrisy on their part.  The people behind Expelled have always had the faults that they project onto science and science supporters, and this is just one more example of same.

It is lamentable that the too-frequent lack of openness in science is not discussed in various venues, and is instead trivialized by these liars and hypocrites.  There are problems with “authorities” in science (perhaps none that are not inevitable–humans have limits) dominating the conversation.  Naturally, this has nothing to do with the fact that IDists are called the pseudoscientists and would-be censors of science that they in fact are.

ID’s volte-face on the importance of meaning and evidence, since the time of Paley

Posted November 4, 2008 by glen1davidson
Categories: Darwin's Black Box

Tags: , , ,

IDists like to claim that they have a “new theory” that is being suppressed.  Needless to say, they don’t.  However, when one reads Paley and compares him to the current sorry crop of apologists, one realizes that Paley was genuinely (if not very successfully) trying to explain many aspects of organisms according to a “design” which was close to our actual understanding of what design is, and appears to see the very real flaws in some of the non-creation, including evolutionary, theories of his day.  The lack of supporting evidence for Buffon’s “theory of forms” to explain life, and of what are now called “Lamarckian” theories of evolution came under attack by Paley.

I have discussed the differences significantly in the past, like in this recent post.  However, I would like to quote extensively from Paley’s discussions of the failings of both Buffon’s conception of how life appeared, and the prominent evolutionary idea of his day, to show how he uses fairly competent criticisms, and how he contrasts those to design in life that he really thought was like our own, and thus considered to provide meaningful evidence.  For, altogether, Paley manages to attack pseudoscientific ideas for being meaningless and for being lacking in evidence, while holding ID to the standards of both meaning and evidence like a genuine scientist would do. 

Paley is hardly the person to which a person should turn to understand science.  He calls his output “natural theology,” not to distinguish it from science, but to suggest that science and theology may in fact be the same thing.  I can hardly applaud something like that, nor his many factual errors.  Nevertheless, he is a beacon of science and of good sense compared with the current bunch of IDists, and  I wish to demonstrate this fact through a passage of some of his best thought.  Today’s ID simply withers when one applies Paley’s standards, which should be obvious in the following piece.  The passage begins with Paley criticizing Buffon’s concept of “internal molds” producing life:

Lastly; these wonder-working instruments, these “internal moulds,” what are they after all? what, when examined, but a name without signification; unintelligible, if not self-contradictory; at best, differing in nothing from the “essential forms” of the Greek philosophy?  One short sentence of Buffon’s work exhibits his scheme as follows:  “When this nutritious and prolific matter, which is diffused throughout all nature, passes through the internal mould of an animal or vegetable, and finds a proper matrix, or receptacle, it gives rise to an animal or vegetable of the same species.”  Does any reader annex a meaning to the expression, “internal mould,” in this sentence?  Ought it then to be said that though we have little notion of an internal mould, we have not much more of a designing mind:  The very contrary of this assertion is the truth.  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.

Another system, which has lately been brought foraward, and with much ingenuity, is that of appetencies.  The principle, and the short account of the theory, is this:  Pieces of soft, ductile matter, being endued with propensities or appetencies for particular actions, would, by continual endeavours, carried on through a long series of generations, work themselves gradually into suitable forms; and at length acquire, though perhaps by obscure and almost imperceptible improvements, an organization fitted to the action which their respective propensities led them to exert.  A piece of animated matter, for example, that was endued with a propensity to fly, though ever so shapeless, though no other we will suppose than a round ball, to begin with, would, in a course of ages, if not in a million of years, perhaps in a hundred millions of years, (for our theorists, having eternity to dispose of, are never sparing in time,) acquire wings.  The same tendency to locomotion in an aquatic animal, or rather in an animated lump which might happen to be surrounded by water, would end in the production of fins; in a living substance, confined to the solid earth, would put out legs and feet; or, if it took a different turn, would break the body into ringlets, and conclude by crawling upon the ground.

Although I have introduced the mention of this theory into this place, I am unwilling to give to it the name of an atheistic scheme, for two reasons:  first, because, so far as I am able to understand it, the original propensities, and the numberless varieties of them (so different, in this respect, from the laws of mechanical nature, which are few and simple,) are, in the plan itself, attributed to the ordination and appointment of an intelligent and designing Creator; secondly, because, likewise, that large postulatum, which is all along assumed and presupposed, the faculty in living bodies of producing other bodies organized like themselves, seems to be referred to the same cause; at least is not attempted to be accounted for by any other.  In one important respect, however, the theory before us coincides with atheistic systems, viz. in that, in the formation of plants and animals, in the structure and use of their parts, it does away final causes.  Instead of the parts of a plant or animal, or the particular structure and use of the parts, having been intended for the action or the use to which we see them applied, according to this theory, they have themselves grown out of that action, sprung from that use.  The theory therefore dispenses with that which we insist upon, the necessity, in each particular case, of an intelligent, designing mind, for the contriving and determining of the forms which organized bodies bear.  Give our philospoher these appetencies; give him a portion of living irritable matter (a nerve, or the clipping of a nerve) to work upon; give also to his incipient or progressive forms, the power, in every stage of their alteration, of propagating their like; and, if he is to be believed, he could replenish the world with all the vegetable and animal productions which we at present see in it.

The scheme under consideration is open to the same objection with other conjectures of a similar tendency, viz. a total defect of evidence.  No changes, like those which the theory requires, have ever been observed.  All the changes in Ovid’s Metamorphoses might have been effected by these appetencies, if the theory were true; yet not an example, nor the pretence of an example, is offered of a single change being known to have taken place.  Nor is the order of generation obedient to the principle upon which this theory is built.  The mammae of the male have not vanished by inusitatem; nec curtorum, per multa saecula, Judaeorum propagini deest praeputium.  It is easy to say, and it has been said, that the alternative process is too slow to be percieved; that it has been carried on through tracts of immeasurable time; and that the present order of things is the result of a gradation, of which no human records can trace the steps.  It is easy to say this; and yet it is still true, that the hypothesis remains destitute of evidence. Natural Theology

One might first ask why ID should be privileged over evolution via appetencies, or Buffon’s “theory of forms,” at least if these were updated to avoid the problems that these ideas had (aside from no evidence).  The flying spaghetti monster is one thing, for even if it has provided a good deal of fun at the expense of IDists, it appears to be yet another “intelligent designer,” thus not an actual competitor with ID.  The ideas that Paley criticizes, on the other hand, were serious ideas a couple of centuries ago (the lack of evidence was not an immediate problem, since no well-evidenced theory–including design–existed at the time, and future evidence might have conceivably supported them).  And if they are seriously devoid of explanatory ability and evidence, so is today’s ID.

Secondly, how could Paley’s complaint about the meaninglessness of “internal moulds” not apply equally to present-day notions of ID?  They do not tell us what “design” means (except by illegitimately conflating what we know, that life is complex, with “design”), nor what “intelligence” is supposed to produce, rather they try their very best to avoid predicting known design principles behind organisms’ forms:

Another problem with the argument from imperfection is that it critically depends on a psychoanalysis of the unidentified designer.  Yet the reasons that a designer would or would not do anything are virtually impossible to know unless the designer tells you specifically what those reasons are.  One only has to go into a modern art gallery to come across designed objects for which the purposes are completely obscure (to me at least).  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

I have quoted this previously, but it is a frequent–if intellectually-unsound–excuse trundled out nearly every time we ask for evidence of design.  That it goes against other claims of Behe to find “purpose” in life should go without saying–for anyone who has read his books, that is (he claims that design is visible as the purposeful arrangement of parts–until he denies that we should be able to find purpose, as in the above passage).  But it also goes against a far more honest version of ID, that of Paley, who contrasted the pseudosciences of his day with an ID that appealed to observation and experience:  “When we speak of an artificer or an architect, we talk of what is comprehensible to our understanding, and familiar to our experience” (Paley, long quote above).  Well, Behe most certainly does not, for he is not trying to explain anything, except how it is that he is not required to produce evidence for his statements.

There is not much sense in belaboring these points.  Suffice it to say that, unlike Paley, Behe and the rest of the “DI fellows” do not mean anything more with terms like “purpose,” “Intelligence,” and “design,” than Buffon’s “internal moulds” had meaning (indeed, they really mean less, because Buffon’s terms still have a kind of abstract meaning, while the IDists use terms that do not comport even with abstract meanings of their words), and they are completely uninterested in providing evidence in favor of ID.  They wish to claim that scientific evolution is “insufficient” and to suppose that “design” (of indeterminate meaning) is the only alternative, even though at least several ideas at least as explanatory (that is to say, little if any) and with equal evidence (that is, little to none) have previously been broached.  That an IDist like Paley found fault with the alternatives, often on the exact same grounds with which we fault today’s meaningless and unevidenced ID, is either lost on today’s sorry apologists, or they ignore the fact as asiduously as they ignore virtually all empirical matters.

I would like to point out that both before and after the long Paley quote, the over-reliance upon analogy found in these alternative concepts came under Paley’s fire–just one more case where the old ID would be forced to condemn the new ID, if it were consistent anyhow (I do not say that Paley would denounce today’s ID if he encountered it, or that he would not.  That would be idle speculation).    The issue was too much to discuss here, other than this mention, since Paley’s criticisms of both the meaninglessness and the lack of evidence of pseudosciences (at least later they would be understood as such) of his day were far more important and meaningful.

ID has not always been a vapid attempt to avoid the meanings of terms and of the evidence.  It is not fair to Paley’s legacy for today’s ID to make the “design hypothesis” appear as though it was always a pseudoscience intent on destroying the standard’s of science so that even the most worthless ideas could be given the label of “science.”

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.

Logan Gage (DI) analogizes DNA with our evolved, undesigned, natural languages

Posted October 31, 2008 by glen1davidson
Categories: News

On the DI’s weblog, Logan Gage quotes a Dr. Story (from Christianity Today), then proceeds to rapidly get matters quite wrong:

Rana, like Behe before him, may be commended for providing a layman’s description of a number of astonishingly intricate cellular processes. But his portraits of cellular workings will fail to convince most mainstream scientists for the same reason that Behe’s book has been roundly dismissed: The analogy between manmade machines and cells is a poor one at best. Cellular components, although machine-like in some respects, do not behave like manmade machines. They self-assemble and self-manufacture, and they are able to transform available energy sources such as light to fuel metabolic activity.

Now what’s wrong with this reply? Didn’t we all learn from Hume that arguments from analogy are inherently weak? 

….  How anyone who has seen a bacterial flagellum could think there is not a strong resemblance to an outboard motor in both appearance and function is, I admit, beyond me. Behe’s Critics Fail to Understand Analogies and Design Detection

Actually, while Dr. Story is right enough in what he does mention, there are much better reasons not to accept Behe’s “arguments,” such as the fact that Behe manages to explain nothing about the lack of “common authorship,” after lines have diverged, of the various vertebrate wings, and of the two adaptive immune systems.  But the poor analogy of life’s machinery with designed machinery is certainly not a negligible argument, particularly because of the self-assembly that does not exist in human-made productions (one could argue that we now have harnessed self-assembly somewhat.  That it is nothing like life’s self-assembly is certain, however).

Moving to Gage’s response, I have never once understood the claim that there is a strong resemblance of the bacterial flagellum to an outboard motor.  The latter is made of metal, and is a heat engine (except for electrics, which also fail to work like a flagellum does).  The former’s materials are constrained by evolution, as is its chemical fuel.  And the parts do not look much the same at all, except in the rather misleading very mechanistic-looking illustrations that IDists are fond of using (there is nothing misleading about the figure to which he linked in normal science instruction, but it is misleading where one is claiming a strong resemblance between outboard motors and flagella).  Aside from rotary motion, I know of nothing closely or moderately analogous between an outboard motor and a flagellum, and that rotary motion is produced in a very different manner, while also propelling a very different sort of rotor.

Here, at figure 2, is an actual photomicrograph of a bacterial flagellum. It is somewhat machine-looking, all right (it is considered to be a machine, by today’s definition), but it looks far less like one of our mechanisms than the illustration to which Gage linked.

Gage moves on to the fact that self-assembly is disanalogous, but claims analogy all the same, because reproduction of bacteria means that their machinery is “MORE complex” than our own. Which suggests that he is playing fast and loose with words and definitions.  See for yourself:

According to Story, “Cellular components, although machine-like in some respects, do not behave like manmade machines. They self-assemble and self-manufacture, and they are able to transform available energy sources such as light to fuel metabolic activity. The cell can also replicate itself and copies of its parts, given energy and simple raw materials.”

But what does this show? Only that while cellular components are similar in many ways, they are also different in that…cells are actually much MORE complex than human-made machines! And therefore, it is likely that the process by which the cells originated is at least as complex as the process by which human-made machines appear (which we know involves intelligent design). What, after all, would we conclude if we stumbled upon a factory where machines not only worked with amazing efficiency but, before wearing out, actually reproduced themselves with astounding accuracy and converted energy from their environment into usable fuel so that they never needed electricity or gas?

In sum, if Rana is indeed making an argument from analogy, I think he escapes Story’s criticism unscathed.  Behe’s Critics Fail to Understand Analogies and Design Detection

Gage is apparently confused by Behe’s “complexity argument,” thereby being unable to notice that reproduction is hardly analogous with our non-reproductive machines, and indeed, reproducing robots and factories of our design are expected to have to reproduce very differently from how bacteria do.

Paley also made this argument, that reproduction of his example, the watch, would imply even greater intelligence behind it.  Which might be reasonable for Paley, because he did not recognize the reproduction is exactly what evolution needs, and, one might argue, even “predicts.”  Moreover, the reproductive methods of both eukaryotes (often with eukaryotic flagella getting the sperm to the egg) and of prokaryotes only make sense in evolutionary context, for IDists have never come up with a “design explanation” for the existence of sex and of bacterial conjugation.  The fact is that clades distribute according to clonal (with conjugation) patterns, and to sexual patterns, quite as one would expect from evolutionary predictions, and do not exhibit intervention by any “designer.”

Gage failed to support the analogy, and to show that reproduction is anything but a source of evidence that evolution occurred without any reason to suppose that any intelligence intervened.

Gage again:

What is worse for Dr. Story is that Behe does NOT make an argument from analogy, anyway. The arguments proffered by both Behe and other design theorists like Dembski and Meyer focus on the properties humanly designed objects and biological objects actually share, not properties that have some analogous resemblance.  Ibid.

Actually, Behe rests almost all of his “arguments” on faulty analogies, although he does base his “irreducibly complex argument” on faulty assumptions–these assumptions being both the “purpose” for which he never provides evidence, and the silly notion that complexity sans the design characteristic of rationality is evidence of intelligent intervention.

I wrote the post linked here before the present one, so that I could refer back to it.  Behe’s acceptance of the molecular clock as a viable possibility, and the evidence of common descent–which likewise depends upon non-intervention by a designer–demonstrate that Behe is not resting his “argument” upon similarities with human designs, he is trying to claim that non-teleological evolutionary expectations are the result of a designer.  It was Paley who argued that life really was made like an architect or artificer would produce, while Behe refuses all tests of design, mainly because he has no evidence for design.

Those who worry about “interference” should relax.  The purposeful design of life to any degree is easily compatible with the idea that, after its initiation, the universe unfolded exclusively by the intended playing out of laws.  Michael Behe  The Edge of Evolution, 232

This is Behe with his get-out-of-jail-free card.  In the end, his ID predicts absolutely nothing (though in other places he claims otherwise), including intervention (which contrasts with his interventionist view of the “Cambrian Explosion” in DBB).  This is completely contrary to what Gage said above, although it is also completely contrary to most of what Behe wrote in his books as well.  Yet in this place, he is (if he understands the implications of this statement) pointedly denying the “shared properties” of human and biological entities, for clearly, shared properties would require intervention by a designer that made objects akin to our own.

This was Gage’s supporting “argument” for the idea that Behe is discussing “shared properties” of human-made and biological entities:

For instance, these theorists often point to what is at the heart of all biological life, namely DNA. They then point out that this biological information has the SAME semantic properties that human written or spoken language has. They are not making an analogy at all.  Behe’s Critics Fail to Understand Analogies and Design Detection

I do not recall Behe making such an argument, although I would not be surprised if he has done so.  But there are two large problems for such an argument:  The first is that human languages also were not “designed,” with semantic structure apparently evolving at least part of the way prior to language, and evolving since humans began to truly speak.  It is begging the question to assume that human language was somehow “designed” apart from evolution, when all of the evidence indicates that, like nucleic codes, human language evolved.  The second problem pales by comparison, but of course the semantic structure of DNA is not that of a “natural language” at all.

I suppose that Gage is trying to claim that because human language (which he assumes, against the evidence, was “designed” or some such thing) has semantics, and the genetic code can be understood to have semantics, that the two have the same properties.  Since the DNA code, and what is encoded by it, is not like a “natural language” used by humanity, it is the same old argument by “analogy” that is presented by Gage–at least as weak as all of the other “analogies.” 

And, as I stated above, if we actually follow the analogy we’ll end by recognizing that human language semantics evolved without guidance (save our own evolving guidance), and so did DNA with its “semantics”.  So they can have that analogy, if they want to have it, and we will understand that DNA must have evolved, instead of being intelligently designed.

How could the molecular clock work with design happening?

Posted October 30, 2008 by glen1davidson
Categories: Darwin's Black Box

Tags: , ,

The molecular clock has been vigorously debated since it was proposed, and many issues surrounding it are still contended.  Overall, however, it remains a viable possibility.  Michael Behe, DBB, 174

He is right both about questions remaining, and that it is a viable possibility.

But how could it be, if ID were correct?  From Aristotle, down to Paley and the creationists, τεχνη or design has always been marked off from “nature” (nature in the exclusive sense) or “physis”.  Indeed, Behe and most of the other prominent IDists like to suggest that the “Cambrian Explosion” is an obvious time when “design” was effected (DBB 27-28).  And yet the molecular clocks (mostly DNA, now) tick through the “Cambrian Explosion” without marking any break from the usual processes, even though it is possible that more refined methods could yet capture an uptick in change (not the break that most would expect from a designer intervening, however).

For so long the various sorts of creationists have tried to argue that intervention by God would be obvious.  Since it never has been, however, Behe increasingly writes as though no intervention can ever be observed, from any sort of mark of design, to any break in the molecular clocks.

This criticism has nothing to do with the accuracy of molecular clocks, which may in fact not be as reliable as some have claimed.  It is that Behe never expects any of the effects of intervention to be visible in life (if these were found, you can be sure that most IDists, probably including Behe, would quickly adopt them, though).  This, perhaps, is the most important change that ID has produced, since the older IDist Paley, and traditional creationists, always expected design to be observable–and generally not by christening complexity as “evidence for design,” like Behe illegitimately does.

As it happens, we could easily apply Paley’s criticisms of the evolutionary concepts of his day (before Darwin came up with a scientific theory) to Behe’s evidence-free designer/evolution-tweaking God, because a major argument of Paley’s book was precisely that design has positive evidence in its favor (arguable then, but not now), while evolutionary ideas were lacking in evidence (not entirely true, since common ancestry did comport well with evolution).  Really, anyone who wanted to show conclusively how ID avoids all legitimate tests (falsification being the best rule-of-thumb) would do so by comparing Paley’s attempts to show that design is falsifiable, with Behe’s never-ending attempts to avoid all reasonable tests of ID.

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.

What is ID’s efficient cause?

Posted October 29, 2008 by glen1davidson
Categories: Darwin's Black Box, The Edge of Evolution

Tags: , ,

IDists are keen to return Aristotle’s “final cause” to the sciences, or at least to biology (see Dembski, for example).  Which is rather sad, because they can give us no evidence for the purpose of organisms, instead they wish to insist that life “had to be designed” and thus has purpose.  One has to wonder what good that would be to know, since we would still need to be able to discover purpose for it to impact us, and ID has never been able to demonstrate any purpose (to be sure, nearly all IDists have sacred writings in mind to provide specific purpose, but will not admit it in their supposed science).

So OK, they want final causes (aside from those of animals such as humans), and perhaps formal and material causes as well, but where is their “efficient cause”?  That is the closest that Aristotle’s “causes” (aitia, which probably would translate better as “reasons” than “causes”) come to fitting with scientific causation in the classical realm, they do not deny the importance of efficient causes, and yet they have none whatsoever.

It should be noted that Aristotle was not one who simply called “intelligence” or “design” the cause or the reason (not of a manufactured item, that is), the aition, because intelligence is just a faculty, and design is merely a category of actions or “causes”.  Thought using intelligence might be a cause, and design may be part of a specific process, but simply invoking intelligence, thought, or design would explain nothing by themselves.  There is an apparent exception to Aristotle’s “efficient cause” as a specific cause or set of causes, which is God the unmoved mover–a very indefinite “cause”–but even IDists don’t appeal to such ancient fictions, partly because it would too readily reveal the religious motivation behind ID.

Aristotle has these things to say of the “efficient cause”:

Again (3) the primary source of the change or coming to rest; e.g. the man who gave advice is a cause, the father is cause of the child, and generally what makes of what is made and what causes change of what is changed.

e.g. both the art of the sculptor and the bronze are causes of the statue. These are causes of the statue qua statue, not in virtue of anything else that it may be-only not in the same way, the one being the material cause, the other the cause whence the motion comes.

All causes, both proper and incidental, may be spoken of either as potential or as actual; e.g. the cause of a house being built is either ‘house-builder’ or ‘house-builder building’.

In investigating the cause of each thing it is always necessary to seek what is most precise (as also in other things): thus man builds because he is a builder, and a builder builds in virtue of his art of building. This last cause then is prior: and so generally.

Further, generic effects should be assigned to generic causes, particular effects to particular causes, e.g. statue to sculptor, this statue to this sculptor; and powers are relative to possible effects, actually operating causes to things which are actually being effected.  Aristotle’s Physics

In a scientific sense, this is all rather imprecise.  But even Aristotle’s generic causes, such as “the art of building,” is far more precise and meaningful than anything we have gotten out of ID as an efficient cause.  Dembski even makes “efficient cause” more precise than Aristotle does:

The efficient cause is the immediate activity that produced the statue–Michelangelo’s actual chipping away at a marble slab with hammer and chisel.  Dembski

Dembski’s example of an efficient cause moves us closer to scientific causation, and is a typical example used by those who are explaining Aristotle’s “four causes”.  Despite the fact that he waffles on mechanism in that article–and attacks the strawman of design being “barred from the content of science” (has any archaeologist tried to explain pottery without intelligent agents involved somehow?)–he is still hardly consistent when he makes statements such as this one:

You’re asking me to play a game: “Provide as much detail in terms of possible causal mechanisms for your ID position as I do for my Darwinian position.” ID is not a mechanistic theory, and it’s not ID’s task to match your pathetic level of detail in telling mechanistic stories. Notorious Dembski comment

Ah yes, Dembski has neither evidence for a final cause, nor for an efficient cause.  Likewise with Behe, who pretends to take a more scientific approach than Dembski, he will not even commit to the specificity that an ancient thinker like Aristotle would:

Another problem with the argument from imperfection is that it critically depends on a psychoanalysis of the unidentified designer.  Yet the reasons that a designer would or would not do anything are virtually impossible to know unless the designer tells you specifically what those reasons are.  One only has to go into a modern art gallery to come across designed objects for which the purposes are completely obscure (to me at least).  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

What, people refuse to call something like that science?  Notice how desperate he is to claim no distinguishing marks of design (since he knows that these are lacking from life that we have not engineered) that he goes to deliberately obscure art as his “example.” 

Yet in the first and second Dembski links (to the same source), it is argued, against a strawman, that design is readily detectable.  To be sure, he misunderstands his own sci-fi analogy as the search for “complex specified information,” when in fact it was rationality behind the signal that indicated intelligence.  Dembski explaining what was detected in the movie Contact:

In this sequence of 1126 bits, 1’s correspond to beats and 0’s to pauses. This sequence represents the prime numbers from 2 to 101, where a given prime number is represented by the corresponding number of beats (i.e., 1’s), and the individual prime numbers are separated by pauses i.e., 0’s).  Dembski

Yes, that’s right, it isn’t complexity that is discovered (Dembski calls unlikely simplicity by the name “complexity,” a distortion even of the meaning of the term), it is rationality.  Even Behe gets it slightly, and ludicrously brings up rational agents:

Rational agents can coordinate pieces into a larger system (like the ship) to accomplish a purpose.  Edge of Evolution, 168

Yes, and the context from which that comes has any number of rationally-devised artifacts being discovered.  Nevertheless, note how carefully he words it, to avoid the implication that life ought to appear rationally designed if it was intelligently designed.  He’s still relying on evident “purpose,” which he deliberately tried to avoid as a test of “design” in the previous quote.  There, too, he wrote of “reasons” for design, as he denied their visibility, suggesting that he knew very well that he was denying that purpose is evident in life, while in this later quote he is trying to suggest that rationality is found exactly through evident purpose (as he had also done in DBB, prior to denying it in order to avoid predicting evident purpose in life–in response to those who noted exactly the lack of purpose in so many aspects of life).

The fact of the matter is that both Dembski and Behe do not wish “design” to be tested by evidence of purpose, for they know that, for instance, malaria pathogens do not seem to fit any kind of evident purpose.  They bring up purpose in order to ignore efficient causation and the rationality typically evident behind such causation (even if some art is hard to figure out, the rationality of the frames betrays intelligence via rational efficient causation).  Likewise, they totally avoid efficient causation, for as I previously argued, they have no causes at all, only unconstrained accident (or whim).

Evolution is also fraught with accident (see link above), but these are “lawful accidents,” of the kind that are permitted and even (probabilistically) predicted.  We have “efficient causation,” or more exactly, scientific causation.  And what is interesting to note is that while Dembski and Behe contradict themselves and each other with their “arguments,” primarily because they can show no “intelligent design” causation whatsoever, earlier ID really did mean to find the marks of intelligence and rationality in life:

…We allege, that the same principle of intelligence, design, and mechanical contrivance, was exerted in the formation of natural bodies, as we employ in making of the various instruments by which our purposes are served […]. William Paley

Paley was looking for efficient cause (see also pp. 8 & 233 of the above link for his criticisms of explanations lacking in efficient causes), and for observable purpose.  Behe and Dembski contradict themselves on these matters, while generally trying to smuggle “purpose” in via “complexity.” 

Paley’s ID was tolerably close to a scientific hypothesis–which Darwin took seriously.  By avoiding all causes (even the ones they bring up, like “purpose”–Aristotle’s “final cause”), the current crop of IDists cannot even match Paley’s now-failed “science,” nor even keep from contradicting themselves as they both claim that purpose and rationality are evident, and that they are not.

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.

Evolutionary history of tuberculosis deciphered

Posted October 28, 2008 by glen1davidson
Categories: Darwin's Black Box, News, The Edge of Evolution

Tags: , ,

Or more exactly, the evolutionary history of Mycobacterium tuberculosis complex has been deciphered, indicating that there are two clades:

ScienceDaily (Oct. 22, 2008) — The evolutionary timing and spread of the Mycobacterium tuberculosis complex (MTBC), one of the most successful groups of bacterial pathogens, remains largely unknown. Here, using mycobacterial tandem repeat sequences as genetic markers, we show that the MTBC consists of two independent clades, one composed exclusively of M. tuberculosis lineages from humans and the other composed of both animal and human isolates.

The latter also likely derived from a human pathogenic lineage, supporting the hypothesis of an original human host. Using Bayesian statistics and experimental data on the variability of the mycobacterial markers in infected patients, we estimated the age of the MTBC at 40,000 years, coinciding with the expansion of “modern” human populations out of Africa. Moreover, the diversification of the oldest EAI and LAM populations took place during plant and animal domestication. Science Daily

It’s a somewhat interesting story, particularly due to its relevance to understanding tuberculosis as a disease.

One just has to wonder, in addition, how IDists propose to decide that this branch indicates normal processes of evolution (as at least most self-identified “IDists” would), while another branching happens to be due to design, despite the fact that it reveals no substantially different patterns.  Of course I have brought this up several times already, however it’s worth bringing up yet again, because it is important to understanding diseases like malaria (how adaptable are pathogens?), and because this aspect puts IDists squarely in the camp of creationists and their inability to tell “design” apart from “Darwinism.”

To put it more starkly than I have previously–the methods used for determining clades do not differ substantially across the taxa.  Some of the details change, of course, but the principles, the standards, are the same going back to the Cambrian and beforehand.  Furthermore, they do not differ meaningfully for “suddenly evolving” immunity genes like TCR and BCR (at least parts of which exist in the agnathans–hagfish and lampreys, but are much more diversified and important to jawed vertebrates–the gnathostomes–which use them in their adaptive immune systems, unlike agnathans with their adaptive immune systems), or the apparently far more sedately-changing Toll and Toll-like receptor genes.

Surely it is (in any “design” sense) a mystery of how malaria, tuberculosis, and humans, along with their ancestors, can be phylogenetically analyzed in essentially the same manner no matter whether we study their “designed” parts or their “evolved” parts.  Meaning that there is no obvious difference in causation of evolution across the taxonomic groups (and there is no definite way to assign the taxonomic categories, other than species, although the cladistic branches are not at all arbitrary), and no reason at all to think that design makes any difference to understanding the relationships of pathogens and hosts.  This is important to recognize when analyzing disease and our immune system, as well as when we recognize that Plasmodium spp. are vulnerable to certain drugs precisely because of their very different “lawfully accidental” evolutionary history–which means that drugs targeting the Plasmodium apicoplast have a good chance of being non-toxic to humans.

Then again, in a sense it’s somewhat silly to be discussing the IDist inability to distinguish “design” from “normal evolution” when they have no ability even to show that resistance to chloroquine (which Behe goes on about) actually evolved, rather than be the result of a miracle, or a series of miracles.  The fact is that the IDists attempt to empty science of any and all of the meaning that science gains by matching up cause and effect, and by understanding that similar effects have similar causes (unless, of course, another identifiable cause producing similar effects has been found–IDists only claim that it has, by refusing to differentiate the effects of “design” from those of evolution).

So it’s fail all the way, actually.  Of course they can’t say how “designed clades” differ from “evolved clades,” because they can’t ever rule out “design” with their (lack of) standards.