Molecular "Machines"

(from NCSE's critique of Explore Evolution) The chapter in EE called "Molecular Machines" (pp. 115-125) presents a rehash of standard claims made by "intelligent design" promoters, especially Michael Behe. These claims were examined and rejected by expert scientists well before EE's publication. The chapter simply ignores the published scientific literature which refutes its central claims. Unlike a genuine science book, EE makes no effort to correct mistakes made in earlier writings, but simply repeats yet again erroneous statements about the bacterial flagellum. The central claims in this chapter were heard in United States Federal court in the Kitzmiller v. Dover "intelligent design" trial and were decisively rejected there, too.

The chapter fails to make clear that it is essentially promoting intelligent design creationism. While avoiding the phrase "intelligent design," the chapter relies heavily on the work of Michael Behe who is simply called "a biochemist from Lehigh University." The chapter neglects to mention that Behe is a leading intelligent design proponent and testified in favor of teaching ID in the public schools in the Kitzmiller v. Dover case. The chapter also avoids mentioning the significant point that Behe's arguments have been rejected by scientists and also were famously debunked during cross-examination and rejected by the court in the Kitzmiller v Dover trial Bacteria with flagella The "intelligent design" movement presents the bacterial flagellum as a structure that supposedly could not have evolved, and therefore indicates the intervention of an "intelligent designer." Discovery Institute Fellow Michael Behe has been one of the most active promoters of erroneous claims about the bacterial flagellum.

The bacterial flagellum is a complex molecular structure, typically made of about 30 different proteins. Ten more proteins are involved in building it.

The ID/creationist movement claims that the structure requires all of its protein parts to function, and therefore could not have evolved in a stepwise manner, and therefore an "Intelligent Designer" must have been required.

The bacterial flagellum in young earth creationist literature

Before the flagellum was adopted by the ID movment, it was already common in arguments of "creation scientists" (Battson 1986, Anonymous 1992, Anonymous 1994, Lumsden 1994). As Henry Morris, the founder of "scientific creationism," wrote in 2005:

These well-meaning folks [ID advocates] did not really invent the idea of intelligent design, of course. Dembski often refers, for example, to the bacterial flagellum as a strong evidence for design (and indeed it is); but one of our ICR scientists (the late Dr. Dick Bliss) was using this example in his talks on creation a generation ago.

see "The Design Revelation" by Henry M. Morris (2005)

A connection between EE and earlier creationist and ID literature are apparent in the graphical depictions of the bacterial flagellum. The graphics are identical to, or closely resemble, images from previous "ID" works. For example, Figure 8.1 on page 117 (and on pages 115 and 116) is the same graphic used for the cover of DI fellow William Dembski's 2002 ID book No Free Lunch, and in the Discovery Institute's "ID" video Unlocking the Mystery of Life.

Claims about complexity of cells

This chapter attempts to argue that structures like the bacterial flagellum can not evolve through natural evolutionary mechanisms.

EE's Claim: Some scientists claim that features "that could not have been formed by the natural selection/mutation process have been found." (p.116)

Problems with claim: This claim is wrong and/or deceptive in 3 ways. First, no structures have been found in living things that cannot in principle be explained by evolutionary processes. Ongoing research in evolutionary biology is continuing to develop our understanding of the evolution of cell structures. Second, modern evolutionary theory encompasses much more than just mutation and natural selection. Evolutionists have made this point numerous times, but ID promoters and other creationists continue to ignore that fact. Third, EE uses the phrase "some scientists" in a misleading manner. The only scientists who doubt evolution are members of a fringe group of intelligent-design promoters and other creationists who reject evolution.

EE's claim: Molecular biology has shown that cells contain "machines" which can't be explained by evolution. (p. )

Problems with claim: EE highlights a quotation from the distinguished biological scientist Bruce Alberts in which he refers to "protein machines" and "assemblies with highly coordinated moving parts" inside cells (quoted on p. 116). EE uses this quote to imply that cell structures are just like human-made machines which break down if a part is taken out or broken. EE's use of the quote also suggests that Alberts shares ID-creationist doubts about evolution. What does Albert's really think about evolution? In a letter to the New York Times, Alberts objected to the way ID-promoters quote him, writing:

...the majestic chemistry of life should be astounding to everyone. But these facts should not be misrepresented as support for the idea that life's molecular complexity is a result of "intelligent design." To the contrary, modern scientific views of the molecular organization of life are entirely consistent with spontaneous variation and natural selection driving a powerful evolutionary process. In evolution, as in all areas of science, our knowledge is incomplete. But the entire success of the scientific enterprise has depended on an insistence that these gaps be filled by natural explanations, logically derived from confirmable evidence. Because "intelligent design" theories are based on supernatural explanations, they can have nothing to do with science. Bruce Alberts Letter to the New York Times, February 12, 2005

EE's claim: The flagellum is irreducibly complex. It requires 40 proteins -- 30 structural, 10 regulation. "[A]ll 30 parts have to be present together" to function

This claim is factually incorrect. The latest published review, apparently ignored by the authors of EE, showed that only 23 of the 42 proteins found in the bacterium E. coli are universally required in the flagella of all bacteria. This error has occurred repeatedly in ID literature.

Research has shown that the motor only functions after all 30 of the motor's protein parts are in place. All 30 are required for motor function. When experimenters in the laboratory take away even one part of the motor, it stops working. (EE, p. 118, italics original)

Unfortunately, the authors of Explore Evolution do not acknowledge a directly relevant paper by Pallen and Matzke (2006), which specifically debunked this point and was published online in September 2006. The paper debunked directly the ID movement's claims about the bacterial flagellum, for example as made by ''EE'' author Scott Minnich during his testimony on behalf of ID in the Kitzmiller v. Dover case.

Table 1 of Pallen & Matzke (2006) gave a systematic review of the literature on each protein of the bacterial flagellum, examining whether or not the protein was universally required in all functional flagella. The analysis showed that of the 42 flagellar proteins in the standard lab strains E. coli and Salmonella typhimurium only 23 (55%) were actually universally required in all functional flagella. Some proteins can be removed experimentally without removing flagellar function, and other proteins simply aren't found in all flagellated bacteria.

References

W. Ford Doolittle, Olga Zhaxybayeva, Evolution: Reducible Complexity -- The Case for Bacterial Flagella, Current BiologyVolume 17, Issue 13, , 3 July 2007, Pages R510-R512. (http://www.sciencedirect.com/science/article/B6VRT-4P3MFYD-G/2/7acab14271d539cac30d01d5e567a77d)

Pallen MJ, Matzke NJ. (2006). “From The Origin of Species to the origin of bacterial flagella.” Nature Reviews Microbiology, 4(10), 784-790. October 2006. Advanced Online Publication on September 5, 2006

Claims about "cooption"

EE's claim: Evolution via cooption can't really work.

Problems with claim:

EE almost acknowledges that "cooption" is a powerful evolutionary process. Cooption occurs when a given gene (or trait) acquires a new function, different from its original one. Genes can acquire new functions in several ways. Extra copies of genes are sometimes produced by DNA copying errors. These extra copies are free to mutate without disrupting the function of the original gene. Or, sometimes a mutation in a part of a gene can lead to the evolution of a new function in addition to the original one.¹ (True JR, Carroll SB, 2003)

EE attempts to cast doubt on the power of cooption by making comments like this:

For one thing, the co-option hypothesis underestimates the problem of coordinating the necessary transformations. How does an undirected process incorporate the "borrowed" parts to form a new system -- without disrupting the old system? What natural process ensures that previously unrelated parts fit together well enough to form a new, functioning system? (EE p. 121)

The old system is not disrupted because a duplicate is modified, not the original. Gene duplication has been a standard part of evolutionary theory for decades.

EE's Claim: The scientist H. Allen Orr thinks cooption doesn't work.

Critics, including many neo-Darwinian biologists, contend that these questions remain unanswered, and are skeptical of the co-option hypothesis. As H. Allen Orr has said, "You may as well hope that half your car's transmission will suddenly help out in the airbag department."

What does Orr think about Behe's argument?

The first thing you need to understand about Behe's argument is that it's just plain wrong. It's not that he botched some stray fact about evolution, or that he doesn't know his biochemistry, but that his argument—as an argument—is fatally flawed.>

1 True JR, Carroll SB. Gene co-option in physiological and morphological evolution. Annu Rev Cell Dev Biol 2002;18:53–80.

Claims about evolution of flagella

Claim: "[T]he proteins in the motor are older than those in the pump"

Explore Evolution again misleads readers. This issue is currently debated within the community of flagellum researchers (reviewed briefly in Pallen & Matzke 2006), and about half the papers go each way. The definitive study has not yet been done. Even if it turns out that the type 3 secretion system is derived from the flagellum, it will still prove that (a) Behe was wrong that reduced subsets of "irreducibly complex" systems "are by definition not functional", and (b) that a subset of flagellum parts has a plausible function different from motility. Furthermore, only the ID advocates think that the type 3 secretion system is the only known relative of the flagellum: the actual scientific community, in contrast, knows of several others.

Claim: The pump only accounts for 10 of the 30 proteins

Furthermore, critics of co-option point out that the bacterial motor is a machine with about 30 structural parts. While roughly 10 of these protein parts are found in the needle-nose pump, the other 20 are found in no other known bacteria or organism. They are unique. So, where are you going to 'borrow' them from? they ask.¹⁰

This is yet another claim copied straight from the ID literature. Here are several previous examples:

It follows that the TTSS does not explain the evolution of the flagellum (despite the handwaving of Aizawa 2001). Nor, for that matter, does the bacterial flagellum explain in any meaningful sense the evolution of the TTSS. The TTSS is after all much simpler than the flagellum. The TTSS contains ten or so proteins that are homologous to proteins in the flagellum. The flagellum requires an additional thirty or forty proteins, which are unique.
William A. Dembski (2003). "Still Spinning Just Fine: A Response to Ken Miller." DesignInference.com. February 17, 2003.

With the bacterial flagellum, you're talking about a machine that's got 40 structural parts. Yes, we find 10 of them are involved in another molecular machine, but the other 30 are unique! So where are you going to borrow them from? Eventually you're going to have to account for the function of every single part as originally having some other purpose. So you can only follow that argument so far until you run into the problem of you're borrowing parts from nothing.
Scott Minnich (2003), in the video Unlocking the Mystery of Life, online at The Apologia Project.

Miller's scenario faces at least key three difficulties. First, the other thirty or so proteins in the flagellar motor are unique to it and are not found in any other living system. From where, then, were these protein parts co-opted?
Stephen C. Meyer (2004). "Verdict on the Bacterial Flagellum Premature: A Response to Begley's ‘Evolution Critics Come Under Fire…' in the Wall Street Journal." Discovery Institute website, February 19, 2004.

Additionally, the other thirty proteins in the flagellar motor (that are not present in the TTSS) are unique to the motor and are not found in any other living system. From whence, then, were these protein parts co-opted?
Minnich (2005) expert report, March 31, 2005 / Scott A. Minnich & Stephen C. Meyer (2004). "Genetic Analysis of Coordinate Flagellar and Type III Regulatory Circuits in Pathogenic Bacteria." Second International Conference on Design & Nature, Rhodes Greece. Wessex Institute of Technology, September 1, 2004.

With regards to the flagellum at least 2/3 of the parts are not known to be shared with any other structure therefore might not be even a sub-part of another system at all.
Casey Luskin (2006). "Do Car Engines Run on Lugnuts? A Response to Ken Miller & Judge Jones's Straw Tests of Irreducible Complexity for the Bacterial Flagellum." Evolution News & Views. April 19, 2006.

In the Unlocking video, Scott Minnich stands in his microbiology lab and quietly assesses the Darwinian TTSS scenario. Yes, he says, it is remotely possible that the TTSS injector came first, and he affirms that its ten proteins do seem to parallel or match the core proteins of the flagellum. But that's where you bump into a huge problem. Where did the cell find the other thirty or so proteins to build incrementally from the TTSS all the way to a rotary-motor flagellum? You come to the point where you are borrowing from nothing, and the plausibility of the scenario fades quickly.
[...]
Many observers watching the shifting battles over Behe's theory feel that Kenneth Miller was premature in loudly declaring victory, insisting that the flagellum could possibly have evolved from the TTSS, when the evidence indicates that the TTSS was the fruit of reverse-evolution. Miller's exercise in hand-waving (arguing that the TTSS led right on to the flagellum) has always depended upon the other thirty proteins – floating in from the cellular environment. But what's the source? Are they just easily bubbling up from day-to-day cellular processes, in wondrous variety, ready to be recruited to build from ten TTSS proteins up to the flagellum's set of forty?here
Thomas Woodward (2006). Darwin Strikes Back: Defending the Science of Intelligent Design. Grand Rapids, Michigan: Baker Books, p. 80. Italics original.

The ID proponents are all telling the exact same story as Explore Evolution. (The difference between 20 or 30 unique proteins depends on whether or not regulatory proteins are included.) And they seem terribly confident that they know what they are talking about. After all, the flagellum is the "icon of ID," the ID movement's flagship example of something that could not have evolved, and must have been intelligently designed instead. Explore Evolution repeats the talking points almost word-for-word, with the only difference being that the "intelligent design" conclusion is tactically left out. Scott Minnich seems to be the original authority for the claim, and he is a published researcher on type 3 secretion systems. Furthermore, Minnich made the same claim in his expert report for the Kitzmiller case. As a named coauthor of Explore Evolution, he presumably checked or edited this section of the textbook, if he made any substantial contribution to the book at all.

Apart from dishonestly pretending that Explore Evolution is not making an ID argument here, the only problem with the "20+ proteins are unique to the flagellum, where did they come from?" argument is that it is wildly, hopelessly, false, and is obviously so to anyone familiar with the actual scientific literature and data on the subject. Pallen & Matzke (2006) reviewed the evidence on this specific point and published a table listing all 42 "standard" flagellar proteins (structural and regulatory) in the most-studied lab strains of E. coli and Salmonella typhimurium.

Here is a summary of the table published in Pallen & Matzke (2006) (the table is freely available online here):

Total number of proteins listed: 42
(this table excludes the chemotaxis proteins; there are ~10 chemotaxis proteins in standard E. coli, but the number can range from 0 to 10+ in various bacteria)
Total number thought to be indispensable in modern flagella: 23 (55%)
Total number "unique" (no known homologs): 15 (36%)
Total number of indispensable proteins that are also "unique": 2 (5%)

Claim about protein synthesis

Claim: Plus, you'd have to explain the origin of protein synthesis too

Summary of problems with claim:

This is a case of "shifting the goal posts," much as we saw in the chapter on fossils. The fact that we do not fully understand everything is not a problem for science. An inquiry-based textbook would not hold these lacunae in our knowledge out as problems, it would hold them out as exciting opportunities for students to explore.

Full discussion:

Explore Evolution, having presented a misleading and even erroneous case against the evolution of one particular structure, responds to the evidence showing that the structure would not be impossible to evolve by simply choosing a new target for their anti-intellectual pseudo-criticism":

In other words, even assuming the presence of all the necessary genes and protein parts, the only way co-option can explain the origin of one irreducibly complex system (the bacterial motor) is by assuming the pre-existence of another irreducibly complex system (the system of protein machines that reads and processes genetic information). Critics of co-option say this is rather like explaining the origin of machines by saying that a machine that makes machines makes them.
Explore Evolution , p. 122

Actually, it is like responding to a question about where heavy elements come from and being told that they are produced from reactions between lighter elements inside of suns. Explore Evolution's "critics of co-option" are doing the equivalent of demanding to know where suns come from before they will accept that nuclear fusion can occur. When three-year-olds ask "why?" until their parents can't (or decide not to) answer, it is cute. It is less cute when grown men attempt the same game.

As shown above, the flagellum is not actually irreducibly complex — it could have been assembled through a stepwise evolutionary process. Research into the evolution of protein synthesis is an ongoing area of research, and progress is indeed being made. If there were a model for that process, the authors of Explore Evolution would undoubtedly inquire about areas where our knowledge was less complete, and present those blank spots as if they were evidence that no knowledge of those subjects was even possible. In doing so, they follow their intellectual godfather, Philip Johnson, who once wondered "why the scientists won't admit that there are mysteries beyond our comprehension," and that phenomena like the origins of protein synthesis, the bacterial flagellum, or the origins of complex multicellular organisms might be among those mysteries (Philip Johnson, 1990. "Evolution as Dogma: The Establishment of Naturalism," First Things 6:15-22, reprinted in Robert Pennock, ed. 2001. Intelligent Design Creationism and its Critics, The MIT Press, Cambridge, MA, ch. 2).

Scientists do not work by that process. Scientists employ a process for asking questions and testing the answers to those questions which is comfortable with uncertainty and does not require that the currently unknown be branded as eternally unknowable. As discussed elsewhere (for instance, Chapter 3), areas once presented as insurmountable problems for evolutionary theory are now well-understood examples of evolution at work. The model of science that the authors endorse here (and elsewhere) is hopeless — and hopelessly wrong.

The idea of inquiry-based learning is to encourage scientific exploration. By getting students to propose their own experiments to test the hypotheses they develop about the world around them, they learn not just the facts of science (e.g., how protein synthesis works), but the process scientists employ (e.g., how scientists test hypotheses about the evolution of protein synthesis). The approach Explore Evolution adopts does not describe that scientific process, and in passages like this, it actively discourages students from those scientific pursuits. This inquiry-averse approach to science is inaccurate and inappropriate.