Mexican flu virus

Revere at Effect Measure has the first picture of the new flu virus, from the CDC. He remarks that it was probably grown in dog kidney cells, giving a classic virus shape. Apparently growing a virus in mammal cells is like growing a tree in an arboretum, with lots of space all round.

mexican-swine-flu_h1n1_virus

Trichoplax genome is sequenced

Over at Sandwalk, Larry Moran has reviewed the new information from this week’s publication of the Trichoplax genome. Trichoplax is a very simple metazoan. It is a very flat, slow-moving pancake. You’d probably think it was a mold colony or a splat of spilled glue. But it’s a multicelled creature with a definite top skin, bottom skin, and some tissue in between. Exactly where it fits in the base of the multicellular tree of life is debated. But go read about it: “Trichoplax genome.”

Like something turned on a lathe

I got my new eSkeptic magazine with a feature article by Mark Perakh. It bears a strong resemblance to my earlier blog article, “Who’s Zoomin’ Who?“.

One point that Mark fails to make is that the candelabrum-like image of a flagellum (3rd image) is not just superimposed images: it’s more than 100 images that are superimposed and then rotationally averaged. It can’t help but look like something turned on a lathe. Thus, the impression of artificiality was added by humans doing image processing.

Flagella Myths –by Mark Perakh

Figure 1: An artist’s rendition of a flagellum as it appears on William Dembski’s blog Uncommon Descent. A similar image appears on the dust cover of Dembski’s book No Free Lunch.

In 1996 a professor of biochemistry at Lehigh University named Michael Behe published Darwin’s Black Box1, in which he presented his concept of “irreducible complexity” (IC). Behe and his Intelligent Design (ID) colleagues claim that IC is strong evidence of “design” of biological systems, and ever since his book IC has acquired the status of one of the main pillars of the Intelligent Design platform.The concept of irreducible complexity was in fact known for many years before Behe’s book. The Nobel Prize winning biologist Hermann J. Müller had already discussed it (under the slightly different name of “interlocking complexity”) in 1918.2 Some 10 years before Behe’s book the same idea was explored by A. Graham Cairns-Smith.3 Unlike Behe, however, these pioneers did not claim that the concept in question was a great discovery on a par with those by “Newton and Einstein, Lavoisier and Schroedinger, Pasteur, and Darwin” (as Behe asserted in Darwin’s Black Box). Neither did they claim that “irreducible complexity” was a “marker” of a supernatural design. To the contrary, according to Müller, development of interlocking complexity in biological systems is to be expected from Darwinian evolution. Therefore the concept in question, as such, evoked no resistance from mainstream science.

As an example of an allegedly irreducibly complex system Behe suggested a mousetrap. Soon afterwards, in multiple publications by various Intelligent Design advocates, images of a mousetrap were endlessly reproduced. The mousetrap, however, was not accepted by the mainstream scientific community as a genuine example of IC. For example, professor of biology John McDonald suggested4 an animated illustration of how, starting with just a piece of a hook-shaped wire serving as a primitive mice-catching device, a full-fledged mousetrap can be gradually built up via two-part, then three-part, etc. contraptions, improving its mice-catching ability at each step in a Darwinian fashion.

Apparently finally realizing that a mousetrap was not a very successful choice for illustrating Behe’s IC concept, ID advocates switched to another example — a bacterial flagellum, a “device” used by bacteria for motility.5 By 2002, the image of a flagellum had become a ubiquitous accompaniment to ID advocates’ books, papers, lecture slides, etc. According to one of the main advocates of ID, William Dembski, the flagellum had become the “mascot” of ID. The image of the flagellum appeared on the cover of Dembski’s book No Free Lunch6, on creationist blogs, etc. Figure 1 (above article title) shows an image of a flagellum as it appears on Dembski’s blog named Uncommon Descent. Notice the smooth surface of the depicted contraption, its perfect symmetry, its tightly fitting components — features we usually see in man-made machinery. This image is a product of an artist’s imagination of how a flagellum “must” look. Does this image truthfully represent the real flagellum? No.

a schematic model of a flagellum

Figure 2: A schematic model of a flagellum. From Yonekura, K., S. Maki, D. G. Morgan, D. J. DeRosier, F.Vonderviszt, K.Imada, and K. Namba, 2000. “The Bacterial Flagellar Cap as the Rotary Promoter of Flagellin Self-Assembly”, Science 290: 2148–2152.

Flagella are tiny organelles that can’t be seen directly by the unaided human eye. Their dimensions are measured in nanometers (billionths of a meter). Modern versions of cryogenic electron microscopy and of X-ray techniques have, though, enabled scientists to form a pretty good understanding of flagellum’s structure and shape. Figure 2 shows a schematic model of a flagellum’s structure.7 This model (one of several published in scientific literature) is a theoretical interpretation of the data obtained via electron microscopy, and mainstream scientists construe it more as an idealized schematic than a true-to-life representation of a flagellum’s actual structure. ID advocates, however, happily treat such images as if they are real replicas of the tiny flagella, usually providing no disclaimers as to the degree of idealization inherent in such images.

a composite electron micrograph of flagella

Figure 3: A composite electron micrograph of flagella. It has been obtained by a superposition of multiple photographs shot from various angles, of a number of flagella. From Francis, N. R., Sosinsky, G. E., Thomas, D. and DeRosier, D. J., 1994. “Isolation, characterization and structure of bacterial flagellar motors containing the switch complex.” J Mol Biol. 235 (4), 1261–1270.

In 2004, when Dembski debated Professor Niall Shanks (at UCLA) he displayed8 a different image of a flagellum (Figure 3). Unlike Figures 1 and 2, Figure 3 is neither an artist’s rendition, nor a schematic theoretical model; it is a “real” electron-microscopic photographically obtained image. While produced by scientists, such images are often exploited by ID advocates who are fond of pointing out their striking similarity to man-made machines. However, such illustrations are misleading, picturing the flagellum in a geometrically perfect shape, fully symmetric and consisting of geometrically perfectly formed parts. The real flagellum is far from having such a perfect geometric shape. Unlike machines, which may be close replicas of each other (say, all Jeeps of the same year have almost exactly the same shape) the real flagella, first, have shapes with many deviations from a perfect geometric symmetry, and, second, there are no two flagella exactly identical. Individual flagella differ in various respects, just as biological organisms vary from individual to individual.

Likewise, when I debated Behe on February 15, 2008 on a Larry Kane’s TV show on the Comcast network, Behe supported his pro-ID thesis by displaying the same images of a flagellum as shown in Figures 1, 2 and 3. Behe’s argument essentially boiled down to the stale asseveration that can be succinctly summarized as follows: “You see — it looks like a man-made machine! If it looks like a duck, then it must be a duck! All machines we are familiar with have been designed. Therefore the flagellum must be a product of intelligent design!” Oddly, Behe and his ID friends seem not to realize that the “it must be a duck” argument is an obvious non-sequitur: there are numerous examples of objects whose appearance is deceptive. Just think of the mimicry, so common in nature. For example, look up the article on “Mimicry” in Wikipedia where examples are presented of animals looking like “twigs, bark, leaves, or flowers” etc., thus negating the “it must be a duck” conclusion.

the structure of the hook�a part of a flagellum

Figure 4: The structure of the hook—a part of a flagellum. From Samatey F.A., Matsunami, H., Imada, K., Nagashima, S., Shaikh, T.R., Thomas, D.R., Chen, J.Z., Derosier, D.J., Kitao, A., Namba, K. “Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism.” Nature. 2004, Oct 28;431(7012):1047. (In the online version the image is animated, illustrating the flagellar hook’s rotation, see this webpage. Reproduced in accordance with the blanket permission granted in the referenced website, stipulating that a reference to the above article as well as to proteinexplorer.org is provided.

In fact the images that Behe, Dembski, and their ID colleagues show are often not pictures of real flagella. Some of them are just products of an artist’s imagination (Figure 1); others are computer-generated images of imaginary machine-like contraptions. The schematics like that in Figure 2, while reflecting many actual features of flagella, are products of a modeling approximation which likewise can’t pretend to reflect adequately the actual structure of a tiny organelle. However, some other pictures of flagella may indeed be “real” photographically obtained images (Figure 3). Are the images in the latter category adequate representations of the flagella structure?

Look again at Figure 3. It is, at a glance, impressive. Indeed we see here a contraption which is symmetric, its structure machine-like, so it is easy to understand the satisfaction of Dembski and Behe at the sight of this contraption so neatly fitting in with their “design” hypothesis. There are, however, two important details that must be noted. The first detail is that the image in Figure 3 is a composite photo. It is the result of a superposition of many photos, of several flagella, made from various angles. This way the image in question is eliminating from view various imperfections which, unlike in man-made machinery, are inherent in every natural flagellum. Moreover, the procedure of superposition of a number of photos eliminates from view the inevitable individual differences between various flagella, which radically distinguish flagella from “designed” machinery.

The second detail is that the resolution of this picture is insufficient to see the flagellum’s intrinsic structure. To appreciate the significance of this, recall, by analogy, the “face on Mars,” or Lowell’s nonexisting Martian “canals.” When the resolution is insufficient, we “see” nonexisting structures, which on closer inspection look dissolve into natural patterns. This is equally true for the images of very small objects perused under insufficient magnification and/or resolution. The images of flagella obtained at higher resolution, and assisted by other modern sophisticated methods of investigation, reveal the actual configuration of flagella, demonstrating that the seeming machine-like appearance of the flagella in Figure 3 is deceptive.

the structure of the flagellar filament

Figure 5: The structure of the flagellar filament. Side views showing the inner side (left) and outer surface (right). The amino acid sequence of each flagellin subunit is color-coded. From Yonekura, K., Maki-Yonekura, S., Namba, K. “Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy.” Nature, 424: 643–650 (2003); See the online version.

It should be noted that scientists often use such terms as “machine” when describing various biological assemblies. This usage, however, unlike in case of ID advocates, is purely metaphorical, reflecting the superficial resemblance of certain biological structures to man-made machinery. Scientists normally do not imply that biological entities are intrinsically similar to man-made machinery. Perhaps such a usage by scientists is not very fortunate given ID advocates’ misuse of the superficial resemblance between the designed man-made objects and natural biological entities. We have to realize, though, that scientists by and large are not aware of ID advocates’ misuse of such terminology, as only a small minority of scientists pay any attention to ID advocates’ actions.

Let us look at a few selected illustrations of my thesis. The detailed images of the flagella structure obtained via cryogenic electron microscopy combined with sophisticated X-rays techniques are exemplified in Figures 4, 5, and 6. These images, showing the actual configuration of the flagellum, have been selected practically at random from numerous similar images available in the scientific literature. Instead of tightly-fit machine-like parts, we see in these pictures convoluted garlands of protein molecules. These structures look similar to typical bacteriophage viruses5, and have nothing in common with any man-made machine. They vividly illustrate that the image shown in Figure 3 is deceptive and owes its machine-like appearance to the insufficient resolution (not to mention the utter artificiality of the artist’s renditions of flagella, whose variations serve as “mascots” of ID).

partial structure of the flagellar filament's cross-section

Figure 6: Partial structure of the flagellar filament’s cross-section. By Keiichi Namba. See this webpage.

ID advocates often point to the allegedly fraudulent “icons of evolution” utilized by “Darwinists” for their nefarious purposes.9 One such “icon” are the illustrations of embryos made by the 19th-century German biologist Ernst Haeckel. In fact, the faults of Haeckel’s embryological illustrations (dated 1874) were revealed not by creationists but rather by the “Darwinists” themselves.10 On the other hand, creationists of various hues, including ID advocates such as Dembski and Behe, incessantly reproduce images of flagella that are often heavily doctored, without any disclaimers as to the great degree of idealization inherent in these images. Indeed, look again at the images of flagella’s actual molecular structure, as shown above in Figures 4, 5, and 6, and it becomes obvious that real natural flagella are far from looking like man-made machines.

An interesting question arises: Why ID advocates and other creationists, who so eagerly and persistently display pictures like those in Figures 1, 2, and 3, never deign to show much more realistic representations of flagella structure such as those shown in Figures 4, 5, and 6? If they are unaware of these better pictures, perhaps they should try to educate themselves regarding the entirety of the available information about flagella? If, though, they are familiar with the images such as those shown in Figures 4, 5, and 6 (which are freely available both in print and on the internet) could it then be that they are less interested in facts and truth and more focused on winning the “cultural war” by any means?

We must conclude that the argument in favor of “design” of biological entities based on their alleged similarity to man-made machinery is not supported by evidence.

Acknowledgment: My thanks to Matt Young, Paul R. Gross, and Nicholas Matzke for pithy advice.

References
  1. Behe, Michael, 1996. Darwin’s Black Box. New York: Free Press.
  2. Muller, Hermann J. 1918. “Genetic Variability, Twin Hybrids and Constant Hybrids, in a Case of Balanced Lethal Factors.” Genetics 3: 422–499.
  3. Cairns-Smith, A. Graham 1986. Seven Clues to the Origin of Life: A Scientific Detective Story. Cambridge University Press.
  4. MacDonald, John. Online: http://udel.edu/~mcdonald/mousetrap.html, last accessed on June 20, 2008.
  5. Luria, Salvador E., Stephen J. Gould, and Sam Singer. 1981. A View of Life. Menlo Park, CA: The Benjamin Cummings Publishing Co.
  6. Dembski, William A. 2002. No Free Lunch: Why Specified Complexity Cannot Be Purchased Without Intelligence. Lanham, MD: Rowman & Littlefield Publishers.
  7. Yonekura, K., S. Maki, D. G. Morgan, D. J. DeRosier, F. Vonderviszt, K. Imada, and K. Namba, 2000. “The Bacterial Flagellar Cap as the Rotary Promoter of Flagellin Self-Assembly.” Science 290: 2148–2152.
  8. Perakh, Mark. 2004. “Three SH’s and One D.” Online at Panda’s Thumb: http://pandasthumb.org/archives/2004/06/three-shs-and-o.html ; last accessed on June 20, 2008.
  9. Wells, Jonathan. 2002. Icons of Evolution: Science or Myth? Why Much of What We Teach About Evolution is Wrong. New York: Regnery.
  10. Nic Tamzek (Nicholas Matzke). “Icon of Obfuscation”. In Talk Reason: www.talkreason.org/articles/icon.cfm (last accessed on June 20, 2008).

Bacteria respond to stress with more mutation

I’d like to see Mike Behe and Bill Dembski explain this solid research finding.

Carl Zimmer’s new book, Microcosm, has a chapter on E. coli in hostile environments. The bacterium has a precise DNA-repair chemistry (enzyme?) that it uses in normal times. But when it suffers a lot of damage, a fast but sloppy chemistry takes over (different enzyme?). It makes more mistakes but it might keep more bacteria alive.

The result is that in a really hostile environment, e.g. flooded with antibiotics, the bacteria begin to mutate at a rate a hundred times faster than their usual rate. If I read your definition correctly, they increased their evolvability by the same factor. As a result, they evolve at startling rates. That’s probably what happened when bacteria were sent into space and came back with an unexpectedly high number of mutations to help them survive.

When the environment settles down, they go back to using the more precise repair chemistry and the mutation rate falls back to its usual level.

Simply put, it seems to be the bacterial equivalent of panic: When you’re going to die, do something – anything! Maybe it will work.

Currently reading: “Microcosm” by Carl Zimmer

Microcosm by Carl Zimmer

I’ve started to read Carl Zimmer’s latest book, Microcosm, and learned many fascinating facts about the bacterium. For the first few chapters, Zimmer is reviewing the history of research on bacteria and DNA. He mentioned that Oswald Avery, a microbiologist at the Rockefeller Institute, was the first to prove that DNA was the material of heredity and genes; that the food-poisoning bacterium Shigella is really just a strain of Escherichia coli; and that E. coli itself is more comples\x and individual than we dreamed of.

Historical contingency in evolution is demonstrated in the lab

It was S. J. Gould’s contention that evolution is a contingent process: its path is contingent on historical events, so that if you “re-wound the tape” of evolution and started it again from an earlier point, you would not get exactly the same results.

Well, historical contingency — and macroevolution — have both been demonstrated by Richard Lenski in a long-running laboratory experiment using the bacterium Escherichia coli. The results were published June 4th in PNAS. In addition, in case irreducible complexity needed another nail in its coffin, the experiments demonstrate the accumulation of mutations over years that result in a novel change requiring more than one step.

rod-shaped bacteria, possibly E. coliThe experiment started with one bacterium. Its daughters were divided into twelve populations. The bacteria were bred in containers with a small amount of glucose, which they could use for food, and a large amount of citrate, which they could not. The experiment ran for twenty years and more than 44,000 generations. Every 500 generations, the researchers removed a sample and froze it. These samples can be revived and allowed to multiply again.

First notable result: one population out of the twelve, after more than 31,000 generations, evolved the completely new ability to use citrate as food.

Second notable result: samples from that population, after 20,000 generations but not before 15,000 generations, are more likely to re-develop the ability to use citrate. None of the other populations have evolved that ability.

Conclusions: first, macroevolution has been observed again. This new ability makes the E. coli virtually a new species. Second, something happened between the generation 15,000 and generation 20,000 that made it easier for the bacteria to evolve the new ability. They were accumulating changes that pre-adapted them to the next step.

Read all about it on Pharyngula: Historical contingency in the evolution of E. coli and in Kasama: Evolution documented in the lab.

UPDATE from Carl Zimmer at The Loom: the scientists have posted it on their own web site (PDF link).

Geovandals target archean bacterial mats

Chris Rowan at Highly Allochthonous writes about archean bacterial mats that are important evidence of life 2.9 billion years ago. Unfortunately, someone is trespassing onto the site, which is private property, and stealing samples, presumably for sale: “Archean bacterial mats under the hammer.”

%d bloggers like this: