The Bacterial Flagellum Revisited: A Paradigm of Design

Going back to my undergraduate days, I have long been struck by the engineering elegance and intrinsic beauty of that familiar icon of intelligent design, the bacterial flagellar nano-motor. In tribute to this masterpiece of design, I have just published a detailed (31 pages, inclusive of references) literature review in which I describe the processes underlying its self-assembly and operations.

My essay also attempts to evaluate the plausibility of such a system having evolved by natural selection. Here’s a short excerpt to whet your appetite.

The bacterial flagellum is a reversible, self-assembling, rotary nano-motor associated with the majority of swimming bacteria. There exists a number of different models of this rotary motor (Pallen and Matzke, 2006; Soutourina and Bertin, 2003). Flagella are produced by a very tightly regulated assembly pathway (Chevance and Hughes, 2008; Macnab, 2003; Aldridge and Hughes, 2002), and the archetypical system for understanding flagellar assembly belongs to Salmonella enterica serovar Typhimurium, a rod-shaped gram negative bacterium of the family Enterobacteriaceae.

Flagella receive feedback from the environment by virtue of an elegant signal transduction circuit and can adjust their course in response to external stimuli by a mechanism known as chemotaxis (Baker et al., 2006 Bourret and Stock, 2002; Bren and Eisenbach, 2000). The most extensively studied chemotaxis system belongs to Escherichia coli.

By itself, the rotor is able to turn at a speed between 6,000 and 17,000 rotations per minute (rpm) but normally only achieves a speed of 200 to 1000 rpm when the flagellar filament (that is, the propeller) is attached. Its forward and reverse gears allow the motor to reverse direction within a quarter turn.

The bacterial flagellum, which has been described as a “nanotechnological marvel” (Berg, 2003), has long been championed as an icon of the modern intelligent design movement and the flagship example of “irreducible complexity” (Behe, 1996). But even biologists outside of this community have been struck by the motor’s engineering elegance and intrinsic beauty. As one writer put it, “Since the flagellum is so well designed and beautifully constructed by an ordered assembly pathway, even I, who am not a creationist, get an awe-inspiring feeling from its “divine’ beauty” (Aizawa, 2009).

The mechanistic basis of flagellar assembly is so breathtakingly elegant and mesmerizing that the sheer engineering brilliance of the flagellar motor — and, indeed, the magnitude of the challenge it addresses to Darwinism — cannot be properly appreciated without, at minimum, a cursory knowledge of its underlying operations. The purpose of this essay is to review these intricate processes, and evaluate the plausibility of such a system evolving by natural selection.

Click here to continue reading.

On the Origin of Protein Folds

A common objection to the theory of intelligent design is that it makes no testable predictions, and thus there is no basis for calling it science at all. While recognizing that testability may not be a sufficient or necessary resolution of the "Demarcation Problem," my article, which I invite you to download, will consider one prediction made by ID and discuss how this prediction has been confirmed.  

Click here to continue reading>>>

Latest ENCODE Research Validates ID Predictions On Non-Coding Repertoire

Readers will likely recall the ENCODE project, published in a series of papers in 2007, in which (among other interesting findings) it was discovered that, even though the vast majority of our DNA does not code for proteins, the human genome is nonetheless pervasively transcribed into mRNA. The science media and blogosphere is now abuzz with the latest published research from the ENCODE project, the most recent blow to the “junk DNA” paradigm. Since the majority of the genome being non-functional (as has been claimed by many, including notably Larry Moran, P.Z. Myers, Nick Matzke, Jerry Coyne, Kenneth Miller and Richard Dawkins) would be surprising given the hypothesis of design, ID proponents have long predicted that function will be identified for much of our DNA that was once considered to be useless. In a spectacular vindication of this hypothesis, six papers have been released in Nature, in addition to a further 24 papers in Genome Research and Genome Biology, plus six review articles in The Journal of Biological Chemistry.

The lead publication of the finding (“An Integrated Encyclopaedia of DNA Elements in the Human Genome“) was released in Nature. The abstract reports,

“The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.” [emphasis added]

They further report that,

“[E]ven using the most conservative estimates, the fraction of bases likely to be involved in direct gene regulation, even though incomplete, is significantly higher than that ascribed to protein- coding exons (1.2%), raising the possibility that more information in the human genome may be important for gene regulation than for biochemical function. Many of the regulatory elements are not constrained across mammalian evolution, which so far has been one of the most reliable indications of an important biochemical event for the organism. Thus, our data provide orthologous indicators for suggesting possible functional elements.”

As this Nature press release states,

“Collectively, the papers describe 1,640 data sets generated across 147 different cell types. Among the many important results there is one that stands out above them all: more than 80% of the human genome’s components have now been assigned at least one biochemical function.” [emphasis added]

The UK Guardian also covered the story, noting that

“For years, the vast stretches of DNA between our 20,000 or so protein-coding genes – more than 98% of the genetic sequence inside each of our cells – was written off as “junk” DNA. Already falling out of favour in recent years, this concept will now, with Encode’s work, be consigned to the history books.” [emphasis added]

This new research places a dagger through the heart of the junk DNA paradigm, and should give adherents to this out-dated assumption yet further cause for caution before they write off DNA, for which function has yet to be identified, as “junk”. Be sure to also check out Casey Luskin’s coverage of the findings at ENV.

Are these atheists and agnostics really covert creationists?

This article was originally published at Uncommon Descent.

We’ve all heard it before. Time and time again the somewhat tiresome and predictable Darwinian propagandists, in a fit of florid indignation, assert that intelligent design will be the death of science and the dawn of theocracy. The claim that ID is nothing more than warmed-over creationism is one that has been thoroughly addressed by ID proponents, yet, the vacuous claim continues to be thrown around.

Over at Evolution News And Views, John West recently highlighted the upcoming release of Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False (Oxford University Press, 2012), a new book by New York University’s atheist philosopher Thomas Nagel. Those immersed in the debate over ID and Darwinism will be familiar with Nagel’s open scepticism towards neo-Darwinian theory and his sympathetic attitude towards ID theory. Though Nagel does not accept ID, he goes as far as to say that it has much merit and that it is science. Good on him! Nagel’s views on this issue can be found in his 2008, Philosophy & Public Affairs article Public Education and Intelligent Design. It will be good to read more about his views as they are further expressed in his new book Mind and Cosmos. West includes a couple of delicious quotes from chapter 1 of Nagel’s book:

On the Evolution of the Mammalian Middle Ear

This article was originally published on Evolution News & Views.

A correspondent recently asked me about the evolution of the mammalian middle ear in relation to the fossil record. Based on data gathered from embryology, it is widely thought that the bones of the mammalian middle ear (the region just inside the eardrum) evolved from bones of the reptilian lower jaw joint. Besides the paleontological data, this hypothesis is based on the fact that, in mammals, Meckel's cartilage plays a role in forming the middle ear bones and mandible before subsequently disappearing. In reptiles, it ossifies to become part of the jaw.

Two of the three bones that comprise the mammalian middle ear are located in the lower jaw joint of reptiles. During the transition of mammals to reptiles, therefore, it is supposed that the quadrate and articular (as well as pre-articular) bones became separated from the posterior lower jaw and evolved into the incus and malleus, two of the bones associated with the mammalian ear.

Dolphins and Porpoises and...Bats? Oh My! Evolution's Convergence Problem

This article was originally published on Evolution News & Views.

I have recently been reading George McGhee's Convergent Evolution: Limited Forms Most Beautiful. McGhee's book is a gripping read, and it favorably cites the work of both Michael Denton and Douglas Axe, ID-friendly scientists well known to readers of ENV. The book documents a multitude of cases of convergent evolution (homoplasy), the phenomenon of repeated evolution. When similarity is thought to have arisen by means of common ancestry, the features in question are said to be "homologous." When similarity is thought to have arisen by means other than common ancestry, the features are said to be "analogous."

Those who subscribe to universal common ancestry interpret biological similarity of sequence, structure and anatomy as resulting from descent with modification from a common ancestral source. ID proponents who question common ancestry typically interpret biological similarity as resulting from a common blueprint. Is there a way to evaluate which of these two competing hypotheses better fits the evidence?

If you take such similarity as pointing to common descent, then you would expect to see it exhibiting a nested hierarchical distribution, the more seamless the better. In other words, the patterns of distribution of this similarity ought to mutually corroborate a single family tree. Sure, there might be occasional deviations from that tree, the results of phenomena such as incomplete lineage sorting. One would not expect to see the pervasive occurrence of a high degree of similarity -- what would normally be regarded as "homology" -- that decidedly cannot be accounted for within the framework of common descent. Yet that is in fact what we do observe.

In Explaining the Cambrian Explosion, Has the TalkOrigins Archive Resolved Darwin's Dilemma?

This article was originally published on Evolution News & Views.
A correspondent recently referred me to an article in the TalkOrigins Archive responding to the argument that "Complex life forms appear suddenly in the Cambrian explosion, with no ancestral fossils." TalkOrigins is a popular online resource that collects attempted answers to some often-heard challenges to Darwinian evolutionary theory. The article offers seven responses to the contention that the Cambrian explosion, which occurred some 530 million years ago, represents a significant difficulty for the neo-Darwinian view on how animal body plans evolved.

Since this subject comes up frequently in the evolution debate, as indeed the seeming dilemma posed by the Cambrian event troubled Darwin himself, I here offer a brief reply to TalkOrigins.

Nice Try! A Review of Alan Rogers's "The Evidence for Evolution"

 This article was originally published on Evolution News & Views.
I recently read The Evidence for Evolution by University of Utah professor of anthropology and biology Alan Rogers. The book is certainly concise, only 102 pages long. Christina Richards, of the University of South Florida, has praised it for presenting its arguments "in a respectful manner that is accessible to a broad audience without condescending language." Indeed, I was pleasantly surprised to find that the book lives up to this claim.

Unlike Richard Dawkins in The Greatest Show on Earth or Jerry Coyne in Why Evolution is True, Alan Rogers refrains from sneering condescension and seeks to engage with the dissenting position respectfully and gracefully. For this, he is to be commended. What about the arguments presented in the book? The author attempts to demonstrate scientific support for the notion of common ancestry -- drawing on several disciplines -- as well as the proposition that an entirely unguided process (involving such mechanisms as natural selection and random mutation) can plausibly be responsible for what we find in biology.

In this review, I want to select some of what I consider to be the strongest argumentation presented.

Centre for Intelligent Design Lecture 2011 by Stephen Meyer on 'Signature in the Cell'

The Nature of Human Beings and the Question of their Ultimate Origin: Richard Dawkins vs. Rowan Williams

One Long Bluff: A Review of Richard Dawkins' "The Greatest Show on Earth"

Richard Dawkins’ The Greatest Show on Earth hopes to convey and document some of the evidence which compels him to embrace a Darwinian perspective on origins. Dawkins is also author of The God Delusion and probably today’s best known Darwinian apologist. Dawkins, in his 2009 book, The Greatest Show on Earth, lives up to his legendary reputation of creative tale-telling.

Just how strong are Richard Dawkins’ arguments? Does he present anything new? Do his claims stand up when subjected to careful scrutiny? Richard Dawkins clearly thinks so. In chapter 1 of his book, entitled Only a theory? Dawkins remarks:

Evolution is a fact. Beyond reasonable doubt, beyond serious doubt, beyond sane, informed, intelligent doubt, beyond doubt evolution is a fact. The evidence for evolution is at least as strong as the evidence for the Holocaust, even allowing for eye witnesses to the Holocaust. It is the plain truth that we are cousins of chimpanzees, somewhat more distant cousins of monkeys, more distant cousins still of aardvarks and manatees, yet more distant cousins of bananas and turnips…continue the list as long as desired. That didn’t have to be true. It is not self-evidently, tautologically, obviously true, and there was a time when most people, even educated people, thought it wasn’t. It didn’t have to be true, but it is. We know this because a rising flood of evidence supports it. Evolution is a fact, and this book will demonstrate it. No reputable scientist disputes it, and no unbiased reader will close the book doubting it.

One wonders, of course, how many times Richard Dawkins believes that he has to rephrase the core contention of his book in order to legitimise it!

Richard Dawkins further remarks:

…Imagine you are a teacher of recent history, and your lessons on 20th century Europe are boycotted…by politically muscular groups of Holocaust deniers. The plight of many science teachers today is not less dire. When they attempt to expound the central principle of biology they are harried and stymied, hassled and bullied.

Such dogmatic rhetoric and ad-hominem name-calling is highly indicative of the level of Dawkins’ argumentation. Nonetheless, it should be noted that no critic of Darwinism seeks the outlawing of the concept of evolution — or even common descent — from the academic environment. Rather, most critics would argue that the significant criticisms of Darwinism — which are, as yet, without resolution — should be referenced such that Darwinism is not taught in an uncritical fashion. Richard Dawkins’ claim, then, that critics want to torpedo the public education system is a simple point of misrepresentation.

The GULO Pseudogene and Its Implications for Common Descent

L-gulonolactone oxidase (GULO), the final enzyme in the biosynthetic pathway of ascorbic acid (vitamin C), is a subject that comes up often in discussions of common ancestry. The functioning GULO gene allows most plants and many animals to produce vitamin C from glucose or galactose. In some taxa, however, the GULO gene does not function in this capacity and is given the "pseudogene" label. The GULO gene is thought to be broken in humans (Nishikimi and Yagi, 1991), primates and guinea pigs (Nishikimi et al., 1994; Nishikimi et al., 1988), as well as in bats of the genus Pteropus (Cui et al., 2011).

When scientists compared the human GULO pseudogene to its functional counterpart in the rat genome, they found that regions equivalent to exons I to VI, as well as exon XI, were absent (Inai et al., 2003). This means that the human GULO pseudogene has only five exons out of the twelve found in the functional rat GULO gene. Other features of note associated with the human GULO pseudogene included one single nucleotide insertion, two single nucleotide deletions, and one triple nucleotide deletion. Researchers also identified additional stop codons. Similar mutations have been identified in the genome of chimpanzees, orangutans and macaques (Ohta and Nishikimi, 1999).

On the Origin of Mitochondria: Reasons for Skepticism on the Endosymbiotic Story

I was saddened to learn of the recent passing of biologist Lynn Margulis. Margulis, a scientist whom I admired greatly, was never a stranger to controversy, going so far as to call neo-Darwinism "a complete funk" and asserting that "The critics, including the creationist critics, are right about their criticism. It's just that they've got nothing to offer by intelligent design or 'God did it.' They have no alternatives that are scientific." She was a scientist who wasn't afraid to think creatively, disregarding the scorn of her colleagues. According to the Telegraph, a response to one grant application she made said: "Your research is crap. Don't ever bother to apply again."

Lynn Margulis took a controversial view on how evolution works, stressing the importance of symbiotic and co-operative relationships over competition. This concept of evolution inspired what is now recognized as her most notable idea, the notion that the eukaryotic mitochondrion -- the power plant of the cell -- was acquired by virtue of an endosymbiotic event. Endosymbiotic theory essentially maintains that mitochondria arose by virtue of a symbiotic union of prokaryote cells. The nearest living relative to the mitochondrion is thought to be the alpha-proteobacteria Rickettsia (Emelyanov, 2000; Andersson et al., 1998). Chloroplasts are also thought to have arisen in a similar manner from the photosynthetic cyanobacteria.

In November 2010, I drew attention to a paper in Nature by Nick Lane and Bill Martin, who showed that the prokaryote-to-eukaryote transition was effectively impossible without the energy demands, pertinent to the biggest event of gene manufacture in the history of life on earth, being met by the mitochondrial processes of oxidative phosphorylation and the electron transport chain. The bacterial cell alone could not meet these energy demands.

The evidence that is typically offered for endosymbiotic theory includes the following:

1. Mitochondria possess a circular genome (lacking in introns and independent from the nuclear DNA) in which transcription is coupled to translation, characteristic of bacterial DNA. There are also some other notable similarities. For example, in both mitochondria and Mycoplasma, the codon UGA specifies the amino acid Tryptophan (Hayashi-Ishimaru et al., 1997; Martin et al., 1980; Inamine et al., 1990; Yamao, 1985), whereas in the conventional code it serves as a stop codon.


2. Mitochondria divide and replicate independently of host cell division and do so in a manner akin to binary fission, possessing homologues of the bacterial division protein FtsZ (Kiefel et al., 2004).


3. They are enclosed by a double-membrane.


4. Mitochondria and bacteria are of a similar size and shape.

Functional Proteins And Information For Body Plans: Stephen C. Meyer

Stephen Meyer - Functional Proteins And Information For Body Plans - More amazing videos are a click away

"Proselytizing for Darwin's God in the Classroom" (from 2008): John G. West

Front-Loading & Theistic Evolution: Stephen C. Meyer

Whale Evolution vs. Population Genetics: Richard Sternberg

Whale Evolution Vs. Population Genetics - Richard Sternberg PhD. in Evolutionary Biology - More bloopers are a click away

Metamorphosis: The Beauty and Design of Butterflies

Does the Chromosome 2 Fusion Evidence Prove Our Shared Ancestry With Chimpanzees?

Those of you who follow discussions surrounding evolution and intelligent design will doubtless have heard of the argument for human-chimp shared ancestry based on evidence for a fusion event with respect to chromosome 2. This argument is put forward quite famously by Brown University biologist Ken Miller in this video:

Briefly, the chromosomal fusion argument for human-chimp common descent begins with the observation that humans possess 23 pairs of chromosomes, whereas apes possess 24 pairs, thus allowing one to predict that -- evolution being true -- a chromosomal fusion must have taken place at some point in our lineage. And, indeed, this is what we observe. Chromosome 2 possesses two centromeres. It also possesses a section where there are two telomeres in the middle of the chromosome, which are oriented in such a way so as to suggest that the ends of the two chromosomes were fused together. Every telomere in human and great-ape chromosomes has the six base-pair sequence TTAGGG repeated over and over approximately fifty to one hundred times in tandem. Such telomeric repetitive units, when they are found not in the telomeres at the end of the chromosome, but rather in the middle of the chromosome (perhaps near the centromere), are referred to in the literature as "interstitial telomeric sequences" (or ITS's). At the supposed fusion site in chromosome 2, the sequence in the upper strand abruptly changes from TTAGGG repeats to CCCTAA repeats (the complementary sequence of the inversion). This is taken to indicate that the DNA in a telomere of one chromosome and the DNA in a telomere of the other chromosome broke and subsequently the two chromosomes fused at the broken ends. This site is referred to in the literature as 2q13 ("2" referring to the chromosome number, "q" referring to the long arm, and "13" referring to the position on the arm).

Furthermore, chromosomal centromeres possess a characteristic DNA called alpha satellite sequences. Secondary alpha satellite DNA (over and above that which is associated with the active centromere), which has been found in the case of chromosome 2 (see Avarello et al. 1992), is taken as further evidence for this fusion event.

But just how sound is this argument?

For one thing, there are, in fact, plausible alternative explanations for this observation. For example, envision a scenario where our genus Homo, originally possessing 48 chromosomes, underwent a chromosomal fusion event within its own independent lineage. Sure, the banding patterns of chromosome 2 are similar to two of the autosomes in the chimpanzee lineage. But then we are only coming back to the argument from similarity, which supports common descent no more than it suggests common design.

Secondly, some of the arguments for supposing that chromosome 2 did indeed arise from a fusion event have been significantly weakened in recent years. One very interesting peer-reviewed paper, appearing in the journal Cytogenetic and Genome Research in 2009, by Farre, Ponsa and Bosch, reported:

Although their function has not yet been clearly elucidated, interstitial telomeric sequences (ITSs) have been cytogenetically associated with chromosomal reorganizations, fragile sites, and recombination hotspots. In this paper, we show that ITSs are not located at the exact evolutionary breakpoints of the inversions between human and chimpanzee and between human and rhesus macaque chromosomes. We proved that ITSs are not signs of repair in the breakpoints of the chromosome reorganizations analyzed. We found ITSs in the region (0.7-2.7 Mb) flanking one of the two breakpoints in all the inversions assessed. The presence of ITSs in those locations is not by chance. They are short (up to 7.83 repeats) and almost perfect (82.5-97.1% matches). The ITSs are conserved in the species compared, showing that they were present before the reorganizations occurred.

So, what is the significance of the cited paper? Though there are many documented instances of these interstitial telomeric sequences in the genomes of humans and chimps, the 2q13 interstitial telomeric sequence is the only one that is able to be associated with an evolutionary breakage point or fusion. The other ones fail to line up with primate chromosomal breakpoints.

As the authors of the paper note,

The availability of complete genome sequences (Hubbard et al., 2007) offers the opportunity to characterize the regions flanking the breakpoints of chromosomal reorganizations at the molecular level. However, to our knowledge, only the head-to-head ITS located in the human 2q13 region, which is a relic of an ancient telomere-telomere fusion, is precisely associated with an evolutionary breakpoint (Ijdo et al., 1991). Here, we used bioinformatic tools to analyze, in the current genome releases, the presence of short ITSs in the chromosomal inversions that do not involve terminal regions and that occurred between human and chimpanzee and between human and rhesus macaque during evolution."

The pro-ID evolutionary biologist Richard Sternberg has also briefly weighed in on the paper here. Sternberg notes,

How, precisely, are miles and miles of TTAGGG of significance? From the standpoint of chromosome architecture, the repetitive elements en masse have the propensity to form complicated topologies such as quadruplex DNA. These sequences or, rather, topographies are also bound by a host of chromatin proteins and particular RNAs to generate a unique "suborganelle" -- for the lack of better term -- at each end. As a matter of fact, the chromatin organization of telomeres can silence genes and has been linked to epigenetic modes of inheritance in yeast and fruit flies. Furthermore, different classes of transcripts emanate from telomeres and their flanking repetitive DNA regions, which are involved in various and sundry cellular and developmental operations.

[...]

ITSs reflect sites where TTAGGG repeats have been added to chromosomes by telomerases, that these repeats are moreover engineered -- literally synthesized by the telomerase machinery, that ITSs have a telomere-like chromatin organization and are associated with distinct sets of proteins, and that many have been linked to roles such a recombination hotspots.

Thus, the take-home message is this: To make much of the 2q13 interstitial telomeric sequence and portray it as typical of what is observed in chimp and human genomes may be considered careful cherry-picking of data.

And what about the secondary alpha satellite sequences found in chromosome 2? Is that not best understood as a genetic residue from a previously functioning centromere on a separate chromosome? Perhaps. But the situation is not quite as clear as is often made out. Neo-centromeres, for example, are rare events which result in the formation of a new centromere (see, for example, Warburton 2004). One suggestion, however, that the additional centromere in chromosome 2 did not arise by this process is the fact that neo-centromeres are usually not associated with the characteristic centromeric repetitive alpha-satellite DNA. But these neo-centromeres are poorly understood, and it may come to pass that a mechanism is discovered that can make these neo-centromeres full of alpha-satellite DNA.

One particularly interesting study, from Baldini et al. (1993), reported the presence of secondary alpha satellite DNA on human chromosome 9! To further complicate matters, Luke and Verma (1995) subsequently reported on the occurrence of secondary alpha satellite DNA in all primates. In 1997, a research group published another interesting study (Samonte et al., 1997). These researchers hybridized twenty-one different chromosome-specific human alpha satellite DNA probes to the full complement of chromosomes from the chimpanzee, gorilla and the orangutan. They reported that most of the human probes failed to hybridize to the equivalent ape chromosome. Instead, they gave positive signals on non-corresponding chromosomes. Thus, they concluded, alpha satellite DNA sequences show little conservation in primate lineages.

In summary, the argument for human-chimp common ancestry, based on the chromosome 2 fusion evidence, is inconclusive. Given the sheer lack of a viable naturalistic mechanism to account for the evolution of life on earth, I am inclined to be rather skeptical of the claims of common descent -- particularly in its universal sense.

This article was excerpted from a longer article on Evolution News & Views.

Climbing Mount Improbable: What's the Problem?