Archive for the ‘News’ category

David Klinghoffer thoroughly misunderstands science

November 25, 2008

One problem with theistic evolution is that natural laws are predictable whereas Darwinian evolution, according to its own theorists, is entirely unpredictable. Think of those laws that govern weather patterns or the formation of geological features. Not so with Darwinian evolution, which can take any of countless very different directions. How could such a purposeless process reflect divine purpose?  Jerusalem Post

The excerpt above is also at the DI’s blog, which is why I am commenting on it.  I had seen the article previous to their post.

The man clearly knows nothing about logic, or he is deliberately conflating two different issues.  For, all of the laws behind evolution are the same laws behind all of science, including geology and meteorology.  Like any other complex system, evolution cannot be predicted very far out, which is certainly true of meteorology, and even many geological events (predict the timing of the next large California earthquake).  That’s what is wonderful about evolution as science, it brought life into the same scientific sphere as meteorology, geology, and ballistics.

Klinghoffer is clearly equivocating regarding the laws behind weather, which are quite stable, and the fact that the complex process of evolution itself is unpredictable in many of its aspects.  Of course he is just plain wrong when he claims that evolution “is entirely unpredictable,” since it would be in the same meaningless pit of baseless assertion that ID is in if that were the case.  The cladistic branchings in evolution are a firm prediction for any evolution involving primarily vertical transmission of genetic information, and any deviation from that must have a good explanation compatible with nature’s laws (as is the case with retroelements in eukaryotic genomes which came from viruses).

Related to the above prediction, but getting into some of the specifics, there can be no “common authorship” of modifications between lineages which have split from each other in “Darwinian evolution,” and indeed that is the case.  Also, complex working “machinery” of the cells is not going to arise de novo, but must have precursors.  This is almost certainly the case even with biochemical pathways which may conceivably (according to some) have arisen through processes other than “Darwinian processes,” for even “self-organization,” or some such thing, can hardly begin without complex precursors.  And again, these are the sorts of things we see in life, notably in the evolution of the two types of adaptive immunity, for once the two lines of immune evolution had split off from each other, no “common authorship” is visible, and both lines have crucial precursors existing in related related organisms which are without adaptive immunity.

Klinghoffer has long been a critic of evolution, but apparently has not even learned the solid predictions of “Darwinian evolution.”  He instead favors a “design process” which is truly without any constraints of “natural law” or of probabilistic processes.  So he criticizes evolution for being like his own mindless and undetectable “process,” which isn’t at all what evolution is about, while preferring exactly such meaningless tripe over the evolutionary theory which in fact brought life under the same causal understanding as Newton’s physics.

This all reminds me of when Paul Nelson was at Panda’s Thumb, complaining that evolution wasn’t predictable while other scientifically-understood processes were. So I asked him to join me in a thunderstorm and to tell me then (not days beforehand) where the next lightning strike would take place. Well, of course Nelson didn’t answer me, nor does he ever engage honestly and forthrightly with the difficulties raised by any of us. 

And to be really equal, I probably should have asked him to predict where the next lightning strike would occur well before the thunderstorm took place, since they’re asking for completely ridiculous predictions and impossible (due to lack of full information) explanations regarding evolution.  But I didn’t need to do so, because it is well beyond our present powers to predict where the next lightning strike will take place even a minute ahead during a thunderstorm.

So as usual, they completely fail to understand science, evolution, to engage honestly with us the few times when they’ll even meet us on an uncensored (at least not much censored) forum, or to meet any of the demands that they try to impose upon our science.  Unfortunately, almost to a person, the proponents of this pseudoscience fail as much through a lack of morality as they do through their large lacunae in knowledge of science and of philosophy.

Grape-sized protists make tracks

November 20, 2008

 I think this is great, macroscopic single-celled organisms making tracks that can be confused with multicellular organisms:

DNA analysis confirmed that the giant protist found by Matz and his colleagues in the Bahamas is Gromia sphaerica, a species previously known only from the Arabian Sea.

They did not observe the giant protists in action, and Matz says they likely move very slowly. The sediments on the ocean floor at their particular location are very stable and there is no current—perfect conditions for the preservation of tracks.

Matz says the protists probably move by sending leg-like extensions, called pseudopodia, out of their cells in all directions. The pseudopodia then grab onto mud in one direction and the organism rolls that way, leaving a track.

He aims to return to the location in the future to observe their movement and investigate other tracks in the area.

Matz says the giant protists’ bubble-like body design is probably one of the planet’s oldest macroscopic body designs, which may have existed for 1.8 billion years.

“Our guys may be the ultimate living fossils of the macroscopic world,” he says.

Discovery Of Giant Roaming Deep Sea Protist Provides New Perspective On Animal Evolution

The above excerpt suggests that these organisms are not in fact entirely new, but I wasn’t aware of such huge protists before this. It does indicate that evolution has more than one way to make larger organisms, although it does not seem likely that they would ever evolve into the many forms that multi-celled animals have.

Other than that, it appears that at least many Precambrian tracks are put into doubt by this, since multicellular organisms aren’t necessary to leave tracks behind. What is confusing is that the article implies that there may have been no multicellularity, and then there was a “Cambrian explosion”–ignoring the fact that there was an “Ediacaran explosion” before the Cambrian began.

Still, it could mean that the Ediacaran (presumably) multicellular organisms have no known precursors, and it’s still a good question whether or not any Ediacaran organisms left descendents. The appearance of multicellular life is not as mysterious as the anti-evolutionists pretend, but it continues to leave a lot of questions to be answered.

Gemini and Keck directly image planetary system

November 13, 2008

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

November 5, 2008

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.

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

October 31, 2008

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.

Evolutionary history of tuberculosis deciphered

October 28, 2008

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.

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.