Friday, 30 June 2023
On the anti-Darwinian bias of the natural law.
Intelligence Is Unnatural, and Why That Matters
One of the advantages we have in our study of nature is our ability to observe an entire “unpolluted” universe. By “unpolluted” I mean that as we look out from Earth, we observe an almost unlimited theater of the natural. And what do we observe? Mostly empty space, visibly interspersed with galaxies composed of stars and nebulae. The regularities of the laws of nature also reveal unseen actors such as dark matter and energy, planets, and even black holes.
Speaking of the laws of nature, the heavenly stage extends so far away that light’s finite speed shows us scenes that happened in the past — from about one and one fourth seconds in the past, when we look at the moon, to more than 13 billion years ago in recent images of distant galaxies revealed by the James Webb Space Telescope. The physical universe provides astronomers with a time machine for viewing nature throughout the history of the cosmos. And what we see confirms the unchanging nature of the laws of physics.
What Spectroscopy Reveals
Using spectroscopy, astronomers not only observe the large-scale features of the universe, but through analysis of the specific wavelengths of electromagnetic radiation received, details of the atomic components of stars and gas clouds also are revealed. In the past as well as in the present, both near to home in our solar system and out to the most distant reaches of the visible universe, the same atomic characters fill the arena of the universe. Throughout the entire long history of the universe and in every direction we look, nature has only managed to produce a very limited playlist of elements — 92 different elements, from hydrogen with one proton as its nucleus to uranium with 92 protons.1
The reason I emphasize the limited number of types of elements in the entire universe is to suggest that one of the characteristics of nature is its “sameness” or redundancy. Now, there’s a reason for this: natural outcomes are governed by natural law. Only four fundamental forces of nature exist. Gravity pulls masses together; the electromagnetic force has twice the fun and can both push and pull masses that possess electric charge. The strong nuclear force also pulls,2 but with restrictions. It only acts on nucleons (protons and neutrons, but not electrons), and it has an extremely short range of about one fermi (10-15 m). The weak force neither pushes nor pulls, but is responsible for certain decay processes of elementary particles.
An example of the sameness of the cosmos is seen in the limited range of star masses. From at least a billion trillion stars in the universe, we find that their masses vary only over a range of about 1800, from 8 percent of the sun’s mass up to about 150 times the sun’s mass. These mass limits are not accidental; they are fixed by the laws of physics.
Seemingly Endless Variations
But what about the seemingly endless variations in the palette of sunset colors and patterns in the western sky? Doesn’t that run counter to the concept of limited diversity of natural phenomena? Certainly, we all appreciate the beauty of the rosy colorations of clouds illuminated by the rays of the setting sun. However, if we spent a thousand evenings watching the sun set, the sky would simply depict variations on a theme, with amorphous shapes of clouds shaded with gradations of color. Air, clouds, and light all respond according to the laws of nature, limiting their arrangements to forms devoid of specific complexity. Sameness prevails.
Turning our gaze away from sky and stars to the biosphere of Earth, we are struck by diversity unlimited. First, consider the unbelievable range of sizes and forms and behaviors of the millions of species of creatures that have lived on Earth. From tiny diatoms to enormous dinosaurs, from worms to eagles, and ants to people, the variety of living forms on Earth is astonishing compared to the overall sameness of the entire non-living universe.
The stark contrast between our life-filled planet and the rest of the cosmos sharpens further when we take into account all of the things produced by humans throughout our relatively short history on the stage of existence. Clocks, cars, computers, castles, clothing, and can openers. Besides physical creations, humans have produced a fantastic variety of musical and literary forms and coding for computer programs. Our prolific creativity seems limitless, and the scope of what we make spans an enormously broad spectrum with a variety that’s anything but “more of the same.”
The contrast between variety in living forms on just one planet, compared to the vast sameness of the non-living universe suggests a clear-cut distinction between even the simplest living organisms and non-living arrangements of matter. An objective consideration of the flourishing creativity of human endeavors compared to the routine instinctual behaviors of other creatures further suggests a categorical difference between human beings and other creatures.
A Physics Point of View
The exceptionalism manifested by humans, when compared to the predictably limited outcomes of non-living matter, is evidence that the choices and actions of intelligent beings are not governed by the laws of physics. My body is affected by gravity, but the force of gravity doesn’t determine what I eat for lunch. My cellular biochemistry is affected by the electromagnetic force, but my decision about what topic to address in my next article is not. The strong force holds the nuclei of my carbon atoms together, but it in no way determines what color my wife will choose to paint the living room.
How did we become so unnaturally creative? The Judeo-Christian tradition offers one possible answer. The belief that human beings are made in the image of God resonates with the unique creativity expressed by humanity throughout history. The more closely related the created is to the Creator, the more attributes of the one are to be expected in the other.
With our intelligent and creative minds, we can bring together the raw materials of the natural universe into an unlimited variety of forms that are both functional and purposive. Human expression manifests the unnatural attributes of creating art, literature, and technology — outcomes that would never arise by the influence of natural processes alone. Freedom and creativity complement one another; neither will flourish under controlling forces. If the forces of nature governed our thoughts and actions, would we see the vast panoply of creative human expression displayed throughout the history of civilization? It seems not.
Notes
A few more (or fewer) natural elements could be considered, depending on whether one includes those that are extremely rare or have a very short half-life.
The strong force becomes repulsive for inter-nucleon distances less than about 0.5 fermi.
Thursday, 29 June 2023
Missing links aplenty?
Long Necks in Sauropod Dinosaurs — By Neo-Darwinism or Intelligent Design?
Editor’s note: We are delighted to direct readers to a new paper by geneticist Wolf-Ekkehard Lönnig, “A Brief Note on the Multiple Independent Origins of the Long Necks in Sauropod Dinosaurs: Neo-Darwinism or Intelligent Design?” What follows is the paper’s abstract:
Convergence is a deeply intriguing mystery, given how complex some of the structures are. Some scientists are skeptical that an undirected process like natural selection and mutation would have stumbled upon the same complex structure many different times.
MEYER, MINNICH, MONEYMAKER, NELSON, SEELKE1
Now it is precisely the phenomenon of convergence that poses further major problems for neo-Darwinism. For if the one-time emergence of completely “adapted” organs or characteristics through selection of random mutations can hardly be explained, the multiple formation of similar organs elutes the neo-Darwinian interpretation even further.
HENNING KAHLE2
Abstract
The phenomenon of complex convergences by selection of random mutations is “a deeply intriguing mystery” and “poses further major problems for neo-Darwinism,” because “if it is highly improbable for a complex solution to evolve once, ‘convergent evolution’ only exacerbates the improbability.” In contrast, “what we do know […] is that intelligence can take a solution to a problem and apply it in different circumstances over and over again” (see references in the text). I have chosen 20 examples (of at least 36 according to D’Emic 2023) of such long-necked sauropod dinosaurs and shown and discussed them in the article below.
Chronological occurrence of the 20 genera distributed in 9 families of the sauropod dinosaurs mentioned and shown in the present article. Note please that 5 and 4 of the genera arose almost simultaneously. And “nearly all did arise independently” (D’Emic, mail 26 June 2023 to W.-E. L.). Figure by Roland Slowik (Dietzenbach, Germany) for the present article (20 June 2023).
Now, the origin of the ingeniously intricate long necks (and their correspondingly fine-tuned body anatomy) in sauropod dinosaurs has been postulated to have arisen more than 35 times independently of each other by selection of random mutations. The improbability that such transformations having happened by natural selection of random or accidental or haphazard DNA mutations is again being multiplied almost unimaginably. The improbability of neo-Darwinian evolution thus becomes virtually immeasurable. How do our Darwinian friends react to such objections?
Well, they presuppose their evolutionary worldview as sacrosanct, unassailable, and irrefutable. They then argue that the origin of such sophisticated features must be so very easy, so utterly simple, that they can evolve even many dozens of times independently of each other almost everywhere in the realm of living beings.3 I met that “explanation” first in an article by Mayr and Salvini-Plawen. My comment: Hats off for such naïvety.
Comparing ID with Neo-Darwinism
Applying Dembski’s Explanatory Filter to this question, we get the following answers:
Law: There is no law that produces long necks inevitably under any defined ecological conditions.
Vast improbability: Fulfilled — chance to be excluded.
Specification: Fulfilled.
In comparing neo-Darwinism with the theory of intelligent design, we find the latter to be definitely the superior explanation.
Read the rest at, “A Brief Note on the Multiple Independent Origins of the Long Necks in Sauropod Dinosaurs: Neo-Darwinism or Intelligent Design?”
Wednesday, 28 June 2023
Correcting professor Dave on "Darwin devolves"
Answering Farina on Behe’s Work: Darwin Devolves
In three previous articles (here, here, andhere ), I began a series of four responses to You-Tuber “Professor Dave” Farina’s video review of Michael Behe’s three books. In this final post, I will turn my attention to Farina’s comments regarding Darwin Devolves.
Hemoglobin and C-Harlem
In Darwin Devolves, Behe contends that the majority of helpful mutations are deleterious rather than constructive, since there are far more ways to gain an advantage by breaking than by building something. Says the Farina video:
If Behe had bothered to look at some of the most well-documented examples of evolutionary change, he’d know that this isn’t the case. In fact, he should know this is nonsense based on examples he himself described in his other works. For example, in Edge of Evolution, Behe describes a hemoglobin allele called HbC-Harlem, which, similar to the allele that causes sickle-cell disease, confers resistance to malaria, with, as Behe describes, “the advantages but not the drawbacks of sickle.”
But this “example of evolutionary change” shows precisely the opposite of what Farina wants. As Behe explains in The Edge of Evolution, “Hereditary persistence of fetal hemoglobin (HPFH) is already widespread in Africa, ameliorating the problems of the sickle gene.”1 Surprisingly, however, “the C-Harlem gene, which builds directly on the foundation of the sickle gene and would entirely eliminate the drawbacks of the sickle mutation, has not yet turned up in Africa, where it would do the most good.”2 The reason for this is that the move from regular hemoglobin to C-Harlem would require two co-dependent mutations, whereas the sickle-cell trait requires only one. The probability of getting the sickle-celled trait in any individual is about one in a hundred million. Assuming a population size of a million people, it should thus be expected to arise spontaneously approximately every hundred generations, which is within the reach of evolutionary processes. For the two necessary mutations needed for hemoglobin C-Harlem to occur at the same time, the probability is a hundred million multiplied by a hundred million, which is 1016. As Behe summarizes, “With a generation time of ten years and an average population size of a million people, on average it should take about a hundred billion years for that particular mutation to arise — more than the age of the universe.”3Nonetheless, hemoglobin C-Harlem has arisen, and was first documented relatively recently in New York City.4 But this is because the initial sickle-cell trait was already adaptive, since it conferred resistance to the malarial parasite. Thus, natural selection can preserve the sickle-celled trait (requiring only a single mutation) first and then acquire the second mutation (building on the first), thereby giving rise to the C-Harlem trait, which confers an even greater advantage. It looks like Mr. Farina did not review this example very carefully.
Cit+ in E. coli
As Farina’s second example, he notes,
[Dr. Behe] also describes the aforementioned Cit+ trait in the E. coli of the LTEE [Richard Lenski’s long-term evolution experiment], which has a new metabolic option, without compromising any existing pathways, literally debunking himself yet refusing to acknowledge it.
I have already addressed this example (see here), so I will not belabor the point further. Suffice it to say that Behe discusses Lenski’s work at length in Chapter 7 of Darwin Devolves, and Farina fails to engage with anything Behe writes concerning the long-term evolution experiment.
De Novo Gene Birth
Another complaint in the Farina video is that,
As you are likely beginning to see, creationists [sic] have a sadistic obsession with painting evolution as some kind of destructive force, but to do so they have to ignore a long and expanding list of completely new genes rapidly evolving everywhere we look. There are many papers like this one examining the concept of de novo genes. These are new genes that originate when previously non-expressed DNA becomes protein-coding and preserved via natural selection due to promoters arising near previously non-coding sections of DNA. So, we have a section of DNA that was not a gene, which is now a gene. New genes. We used to think this was rare, but once we figured out how to look for them, by identifying protein-coding sequences that aren’t protein coding in all the most closely related species, we started finding them all over the place.
The review paper Farina cites, by Stephen Branden Van Oss and Anne-Ruxandra Carvunis, notes (as is common in review papers dealing with this subject) that, for a long time, “the consensus view was that virtually all genes were derived from ancestral genes, with Francois Jacob famously remarking in a 1977 essay that ‘the probability that a functional protein would appear de novo by random association of amino acids is practically zero’.”5 But “though de novo gene birth was once viewed as a highly unlikely occurrence, there are now several unequivocal examples of the phenomenon that have been described.”6 In other words, though it was once thought that the origins of fundamentally new genes from non-coding sequences was essentially impossible, the fact that we observe a plethora of taxonomically-restricted genes, rather than being taken as a disconfirmed prediction of evolution, is taken to show that de novo genes can be birthed by evolution quite readily after all. Evolutionary theory, remarkably, is taken to be completely insensitive to disconfirming evidence.
Moreover, though some examples of taxonomically restricted genes bear some resemblance to non-coding stretches of DNA in related species, this is not so with the majority of cases. Furthermore, there is no convincing mechanistic scenario by which non-coding DNA may be transformed into genes coding for proteins that are ready to fulfil a functional role.
Polar Bears
According to Farina,
Perhaps the best evidence that Darwin Devolves is nonsense is that Behe had to flat out lie to defend it. In a discussion of Behe’s treatment of documented adaptations in polar bears, Dr. Nathan Lents pointed out that Behe did not accurately represent the findings of a paper he cited, when he claimed that virtually all adaptations that polar bears have to their arctic climate are actually damaging in some way. In response, Behe provided a table from that paper, showing that all the documented mutations are either “possibly damaging” or “probably damaging.” But he must have thought nobody would check up on him, since Dr. Lents showed that Behe sneakily omitted two columns and many rows, and the omitted data, unsurprisingly, tell a very different story… Apart from the two restored columns, look at all those rows that say “benign,” meaning not harmful in effect. You know, the exact opposite of what Behe is claiming?
This claim has been rebutted thoroughly elsewhere (such as here). In brief, Behe nowhere denies that non-adaptive neutral mutations are common in evolution. Rather, his thesis is that the vast majority of positively selectedmutations are damaging, since there are far more ways for an organism to acquire an advantage by breaking something than there are ways to gain an advantage by building something new. In Darwin Devolves, Behe contended that “65 to 83 percent of helpful, positively selected genes are estimated to have suffered at least one damaging mutation.”7 Given that the entire chart from the Liu et al. paper, cited by Behe, is some 47 rows long and 8 columns wide, it made more sense to reproduce only the portion of the chart that was relevant to supporting his point. There is nothing duplicitous here. Behe omitted from the chart the data from the HVar algorithm (instead showing only the results of the HDiv algorithm) and also left out instances where the HDiv algorithm predicted that a mutation was benign. This served Behe’s purpose of confirming for his readers that up to 14 of the 17 genes examined (i.e., 83 percent) were probably or possibly damaging. The instances where a mutation was not predicted to be damaging (i.e., those listed as benign) do not contradict Behe’s thesis, since Behe never denied that many mutations are benign. Indeed, a significant majority of mutations are benign (e.g., the third codon position may be substituted without altering the amino acid sequence). But Behe’s thesis is that the vast majority of adaptive mutations (which make up a minority of mutations overall) are destructive rather than constructive. There is nothing in the chart that invalidates or undermines this thesis.
Conclusion
Farina’s video rebuttal directed at Behe’s work misrepresents Behe at multiple points. Moreover, Farina misreads several papers that he cites in his video, failing to understand how they intersect with Behe’s critiques of evolutionary theory. There is also little that is new to see in his video. Many of his criticisms of Behe have been made before by others and addressed in detail elsewhere. In short, despite Mr. Farina’s smug condescension and patronizing demeanor, he fails to mount a credible critique of Dr. Behe’s thesis.
Notes
Behe MJ, The Edge of Evolution: The Search for the Limits of Darwinism (Free Press, 2007), 29.
Ibid.
Ibid., 110.
Bookchin RM, Nagel RL, and Ranney HM. Structure and properties of hemoglobin C-Harlem, a human hemoglobin variant with amino acid substitutions in 2 residues of the beta-polypeptide chain. Journal of Biological Chemistry 1967; 242:248-255.
Van Oss SB, Carvunis AR. De novo gene birth. PLoS Genet. 2019 May 23;15(5):e1008160.
Ibid.
Behe MJ, Darwin Devolves: The New Science About DNA That Challenges Evolution (HarperOne, 2020), 17.
Correcting professor Dave on the "edge of evolution"
Answering Farina on Behe’s Work: The Edge of Evolution
In two previous articles (here and here), I began a series of responses to YouTuber “Professor Dave” Farina’s video about Michael Behe’s three books. In this essay, I turn my attention to Mr. Farina’s comments regarding The Edge of Evolution.
Malaria
In the video, Farina claims that “[Dr. Behe] seems to think that for any given biochemical trait, like drug resistance or disease immunity, there is one way, and only one way, to accomplish that job, despite he himself describing the biochemical details of more than one form of malaria resistance found in humans.” Actually, in The Edge of Evolution, Behe discusses the biochemical details of malarial resistance to two different drugs, namely, atovaquone and chloroquine. In regard to chloroquine resistance, Behe described the Plasmodium falciparum chloroquine resistance transporter, coded by the pfcrt gene, which is recognized to be of primary importance in conferring chloroquine resistance.1 This pump naturally functions as a peptide transporter. Mutations that enable the transporter to pump chloroquine impair its ability to pump peptides and actually entail a significant fitness cost to the parasite.2 As Behe explains in The Edge of Evolution, at least two co-dependent amino acid substitutions are necessary for this chloroquine resistance phenotype3 — and public health data suggests that it occurs approximately once in every 1020 cells.4 From this, it may be predicted that an adaptation requiring four co-dependent substitutions would arise in every 1040 malarial cells. Given that less than 1040 organisms have likely ever existed on earth5, this number is quite prohibitive. The challenge is even more acute when we are dealing with complex animals such as mammals, which have far, far fewer individuals. Until relatively recently, the effective population size of hominids, for instance, was only in the range of 10,000-20,000 individuals. If it is challenging for complex traits to evolve in single-celled organisms, it is much, much more difficult for them to evolve in more complex organisms. For a more detailed treatment of this subject, I refer readers to this article by Casey Luskin.
Farina contends that,
Behe butchers the concept of fitness landscapes in a way that is both extremely basic and completely undermines his argument…In one time or place, a particular genotype might be extremely fit, but in a different time or place, it might have low fitness. Behe completely misses this trivial detail. He argues that crossing “valleys” is impossible via evolutionary processes, since any intermediate between two peaks or two high-fitness genotypes will be low fitness, and selected against. In making this argument, he assumes that fitness landscapes are constant, and genotypes have fixed fitness values, regardless of environmental or ecological conditions.
But for many complex adaptations, such as those described in Behe’s books, a fitness benefit is not realized until multiple co-dependent mutations have arisen. A protein that stably folds, in order to mutate into a fundamentally different fold, will have to pass through a fitness valley where it does not stably fold and no longer performs its role. Such a protein will not be selected for under an alternative set of environmental conditions. It seems that, again, Farina fails to understand Behe’s argument.
Bizarrely, Farina asserts that “it’s quite amusing to note that if Behe considers [antimalarial] drug resistance to be impossible to evolve, it means that he believes in a god who deliberately bestowed plasmodia with resistance to our drugs in order to ensure that we continue to contract malaria. Gee, what a swell guy.” But this, too, betrays a misunderstanding of what Behe argues in The Edge of Evolution. He does not deny that malarial parasites have acquired resistance to chloroquine and other antimalarial drugs. Quite the contrary. Rather, as discussed above, he notes that malarial resistance to chloroquine has arisen and that it occurs approximately once in every 1020 cells. He then uses this data to extrapolate to a case requiring twice as many co-dependent changes to bring about, and he points out that this problem is far more acute in the case of more complex organisms like large mammals, with much smaller population sizes, longer generation turn-over times, and lower mutation rates.
Interestingly, this same misrepresentation of The Edge of Evolution was made by Nathen Lents in his review of Darwin Devolves (discussed by Casey Luskin here). This makes me wonder whether Farina has in fact read Behe’s book for himself, or whether he is relying upon others, such as Lents, for his information about what is in the book.
HIV
In his video, Farina takes issue with Behe’s claims concerning HIV that “there have been no significant basic biological changes in the virus at all” and “There have been no reports of new viral protein-protein interactions developing in an infected cell due to mutations in HIV proteins.”6 He cites the Vpu example discussed in part one. However, as Behe acknowledged years ago, this was one example he had overlooked in The Edge of Evolution. Nonetheless, it does not significantly impact the thesis of the book, since the statement may be modified to assert that “There have been hardly any reports of new viral protein-protein interactions developing in an infected cell due to mutations in HIV proteins,” despite the fact that “HIV has almost certainly altered its proteins at one point or another in the past few decades enough to cover all of shape space.”7 Behe does not deny that new protein-protein binding sites have arisen by mutations in HIV. In fact, he explicitly states that its mutated proteins must have bound many molecules, though “none seem to have helped it” such that they were preserved by selection.8 The reason for this is what Behe dubs the problem of restricted choice — “That is, not only do new protein interactions have to develop, there has to be some protein available that would actually do some good.”9 Vpu is one exception where it did apparently help. But given how much better an evolver HIV is relative to essentially any other organism (with its 109-1010 individual viruses per infected person and its mutation rate of 10-4, meaning that all possible double point mutations will arise in each virus in one individual every single day), the problem is certainly much more acute for other life forms.
Notes
Sidhu AB, Verdier-Pinard D, Fidock DA. Chloroquine resistance in Plasmodium falciparum malaria parasites conferred by pfcrt mutations. Science. 2002;298(5591):210-3.
Felger I, Beck HP. Fitness costs of resistance to antimalarial drugs. Trends Parasitol. 2008;24(8):331-3.
Summers RL, Dave A, Dolstra TJ, Bellanca S, Marchetti RV, Nash MN, Richards SN, Goh V, Schenk RL, Stein WD, Kirk K, Sanchez CP, Lanzer M, Martin RE. Diverse mutational pathways converge on saturable chloroquine transport via the malaria parasite’s chloroquine resistance transporter. Proc Natl Acad Sci USA.2014;111(17):E1759-67.
White NJ. Antimalarial drug resistance. J Clin Invest. 2004; 113(8):1084-92.
Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A. 1998; 95(12):6578-83.
Behe MJ, The Edge of Evolution: The Search for the Limits of Darwinism (Free Press, 2007), 139.
Ibid., 157-158.
Ibid.
Ibid., 157.
Nothing simple about these beginnings.
Gifted Microbes Elevate the Case for Intelligent Design to the Entire Biosphere
Far from being humble, primitive steppingstones to higher life, microbes display superpowers that so-called “higher” forms of life depend on. Here are some recent examples.
Never Say Forever
So-called “forever chemicals” known as PFAS (poly-fluoroalkyl substances) have been in the news as a pollution concern because they resist breakdown for decades in the soil and water. UC Riverside says that our lust for industrial applications comes at a price:
Chlorinated PFAS are a large group in the forever chemical family of thousands of compounds. They include a variety of non-flammable hydraulic fluids used in industry and compounds used to make chemically stable films that serve as moisture barriers in various industrial, packaging, and electronic applications.
The “unusually strong carbon-to-fluorine bonds” in these compounds make them resistant to natural decomposition. Yujie Men’s team at UCR recently found two species of bacteria, Desulfovibrio aminophilus and Sporomusa sphaeroides, that know how to break those bonds.
“What we discovered is that bacteria can do carbon-chlorine bond cleavage first, generating unstable intermediates,” Men said.
“And then those unstable intermediates undergo spontaneous defluorination, which is the cleavage of the carbon-fluorine bond.”
The team believes that providing these naturally occurring bacteria with nutrients like methanol in groundwater could increase their numbers. If they are not present, contaminated water could be inoculated with the bacteria. Why try to imitate their chemistry prowess when they are already at work doing what is needed? Just pamper them and PFAS can disappear.
The UCR team published their award-winning findings in Nature Water, but the bacteria are the deserving ones for a prize. This discovery adds to other abilities of bacteria to degrade pollution:
Microbes have long been used for biological cleanup of oil spills and other industrial pollutants, including the industrial solvent trichloroethylene or TCE, which Men has studied.
But what’s known about using microorganisms to clean up PFAS is still in its infancy, Men said. Her discovery shows great promise because biological treatments, if effective pollutant-eating microbes are available, are generally less costly and more environmentally friendly than chemical treatments. Pollutant-eating microbes can also be injected into difficult-to-reach locations underground.
While not an excuse to pollute, the findings give hope for cleaning our messes with gifted microbes.
Proficient Sorters
Some of the rare earth elements (REE) that are high in demand these days are difficult to separate. Again, a gifted bacterium is able to sort them better than humans can, announced researchers at Penn State. A protein in a bacterium may help pave the way for “green tech” with less cost.
Rare earth elements, like neodymium and dysprosium, are a critical component to almost all modern technologies, from smartphones to hard drives, but they are notoriously hard to separate from the Earth’s crust and from one another.
Penn State scientists have discovered a new mechanism by which bacteria can select between different rare earth elements, using the ability of a bacterial protein to bind to another unit of itself, or “dimerize,” when it is bound to certain rare earths, but prefer to remain a single unit, or “monomer,” when bound to others.
Instead of requiring toxic chemicals to do the separation, bacteria equipped with the LanM protein may be able to do it cleanly and quickly. The news item says that this bacterium lives on buds of English oak trees. Its ability to discriminate similar elements is very precise:
“This was surprising because these metals are very similar in size,” Cotruvo said. “This protein has the ability to differentiate at a scale that is unimaginable to most of us — a few trillionths of a meter, a difference that is less than a tenth of the diameter of an atom.”
Nature has reported on Penn State’s welcome discovery.
Mercury Impacts Earth
Concerned about mercury in your tuna and other seafood? Bacteria are coming to the rescue here, too. Scientists at Oak Ridge National Laboratory warn of the dangers of methylated mercury:
Methylmercury is a neurotoxin that forms in nature when mercury interacts with certain microbes living in soil and waterways. It accumulates at varying levels in all fish — particularly large predatory fish such as tuna and swordfish — and, when consumed in large quantities, can potentially cause neurological damage and developmental disorders, especially in children.
While microbes are involved in the formation of the toxin, scientists at Oak Ridge have discovered two species of methanotrophic bacteria that can degrade it.
Bacteria called methanotrophs feed off methane gas and can either take up or break down methylmercury, or both. Methanotrophs are widespread in nature and exist near methane and air interfaces, and both methane and methylmercury are usually formed in similar anoxic, or oxygen-deficient, environments.
To single out how and which methanotrophs perform demethylation, the ORNL-led team — along with methanotroph experts from the University of Michigan and Iowa State University — investigated the behavior of many different methanotrophs and used sophisticated mass spectrometry to analyze methylmercury uptake and decomposition by these bacteria. They discovered that methanotrophs such as Methlyosinus trichosporium OB3b can take up and break down methylmercury, while others such as Methylococcus capsulatus Bath only take up methylmercury.
In either case, the bacteria’s interactions can lower mercury toxicity levels in water.
The work is published in the open-access journal Science Advances by the AAAS. Perhaps safe tuna sandwiches are in our future, thanks to microbes.
Gut Helpers
A health partner inside our GI tract that many of us never heard of is named Akkermansia muciniphila. After enjoying a tuna sandwich, we depend on this little bacterium that lives inside us to avoid metabolid disorders. Here’s what it does for us, according to Phys.org’s report on findings at Duke University:
A. muciniphila can make up as much as 3 to 5% of the biota found in stool. It is present in wild animals, and its abundance in humans seems critical for healthy physiological functions, as abnormal levels are associated with immune disorders, pregnancy complications, cancer, neurological disorders and every kind of metabolic disease.
This gut germ helps regulate lipid biosynthesis and cholesterol levels. Would evolution generate as many redundant machines as this bacterium possesses?
A. muciniphila is known to use mucins as its preferred nutrient source. Mucins are large, highly glycosylated proteins that comprise the bulk of the intestinal mucus lining. The study found that, despite having the capability to produce a wide range of glycoside hydrolase enzymes, estimated to be around 60, only a few are needed to degrade intestinal mucins. This redundancy means that even if there were a mutation in one or most of these genes, the organism would still have the ability to survive.
Learn more about this essential microbe in Nature Microbiology.
Ocean Fertilizer
Another microbe — this one a cyanobacterium — performs a vital function for life in the seas. New Scientist describes how it changes its behavior depending on light levels.
These bacteria don’t just provide food for other organisms, they also turn nitrogen from the atmosphere into chemicals that other photosynthetic organisms can use. They fertilise vast areas of the ocean that would otherwise be too poor in nutrients for anything to grow, says [Ulrike] Pfreundt.
“It’s the living fertiliser for the oceans, essentially,” she says. “They provide a very large part of the nitrogen that is fixed in the ocean, and a whole lot of other organisms that sequester CO2 depend on this nitrogen.”
Our world could not function without microbes such as these, and uncountable numbers of additional species remain to be discovered. They are far from being mere primitive steppingstones to complex life. Without their engineering prowess to degrade harmful substances and provide nutrients for others, large organisms — animals and plants — could not exist. This elevates the evidence for intelligent design beyond cells and individuals to the entire biosphere.
Tuesday, 27 June 2023
John Money:a brief history.
John Money
John William Money (8 July 1921 – 7 July 2006) was a New Zealand American psychologist, sexologist and professor at Johns Hopkins University known for his research on human sexual behavior and gender.
Working with endocrinologist Claude Migeon, Money established the Johns Hopkins Gender Identity Clinic, the first clinic in the United States to perform sexual reassignment surgeries.[1] Money advanced the use of more accurate terminology in sex research, coining the terms gender role and sexual orientation.[2][3] Despite widespread popular belief, Money did not coin 'gender identity'.[4] Money pioneered drug treatment for sex offenders in order to extinguish their sex drives.[5] He began testing anti-androgen medications on offenders as early as 1966, which yielded successful results.[6]
Starting in the 1990s, the work and research conducted by Money has been subjected to significant academic and public scrutiny. A 1997 academic study criticised Money's work in many respects, particularly in regard to the involuntary sex-reassignment of the child David Reimer, and Money's sexual abuse of Reimer and his brother when they were children.[7][8] Some of Money's sessions involved Money forcing the two children to perform sexual activities with each other, which Money then photographed.[9][10] David Reimer lived a troubled life, eventually committing suicide at 38; his brother died of an overdose at age 36.[11][12]
Money's writing has been translated into many languages and includes around 2,000 articles, books, chapters and reviews. He received around 65 honours, awards and degrees in his lifetime.[2]
File under "well said" XCIV
"We have just enough religion to make us hate, but not enough to make us love one another."
Jonathan Swift
The Hindu/Muslim rivalry:a brief history.
Hindu–Islamic relations
Interactions between the followers of Islam and Hinduism began in the 7th century, after the advent of the latter in the Arabian Peninsula. These interactions were mainly by trade throughout the Indian Ocean. Historically, these interactions formed contrasting patterns in northern and southern India. In the north, there is a long-standing historical influence from Muslim rulers and Christian rulers dating back to the Delhi Sultanate of the 13th century. The patterns of relationship between Hindus and Muslims have been different between north and south India. While there is a history of conquest and domination in the north, Hindu-Muslim relations in Kerala and Tamil Nadu have been peaceful.[1] However, historical evidence has shown that violence had existed by the year 1700 A.D.[2]
In the 16th century, the Mughal Empire was established. Under the Mughals, India experienced a period of relative stability and prosperity.[3] The Mughals were known for their religious tolerance, and they actively patronized the arts and literature. During the Mughal era, Indian art and culture thrived, with the construction of grand monuments such as the Taj Mahal and the Red Fort. While the Mughals fostered religious harmony and cultural advancements and nurtured Hindu scholars, poets, and artists, facilitating a dynamic cultural interchange that enriched both Islamic and Hindu traditions, there were instances of religious conflicts between the Mughals and the Rajput over control of territories. Aurangzeb was criticized for his policies of religious intolerance towards Hindus.[4][5]
During the 17th to 19th centuries, India was ruled by the British, who introduced a policy of divide and rule to maintain their control over the country.[6][7][8] The British also introduced a system of separate electorates, which further exacerbated the divide between the Hindu and Muslim communities.[9][10] The Indian Rebellion of 1857, also known as the First War of Independence, was a major uprising against British rule in India. The rebellion was fueled by a range of grievances, including economic exploitation, social and religious discrimination, and political oppression.[11][12][13] While the rebellion was not solely based on religious tensions between Hindus and Muslims, these tensions did play a role in fueling the conflict. During the rebellion, there were instances of both Muslim and Hindu soldiers and civilians fighting together against the British, as well as instances of conflict between the two communities.[14][15][16]
Islam and Hinduism share some ritual practices, such as fasting and pilgrimage, but their views differ on various aspects. There are also hundreds of shared ritual spaces, called dargahs (literally, “doorway” or “threshold”), for Hindus and Muslims. These mark shrines for revered Muslim (frequently Sufi) leaders and are visited by both Muslims and Hindus. Their interaction has witnessed periods of cooperation and syncretism, and periods of religious discrimination, intolerance, and violence. As a religious minority in India, Muslims are part of the Indian culture and have lived with Hindus for over 13 centuries. Despite the longtime assertion that the origins of Muslim-Hindu tensions were greatly attributed to 19th Century British colonial rule in India, it has been argued that Britain had little influence on constructing the religious identities of Islam and Hinduism in the region and that divisions existed beforehand as well.[17] For example, 18th-century Mughal–Maratha Wars. Ajay Verghese argues that the Hindu-Muslim conflict in India can be better understood by analyzing the historical relationship between the two communities. He contends that precolonial India was marked by a fluidity of religious identity and that religious boundaries were not always clear-cut. This led to a degree of intermingling between Muslims and Hindus, but also created conditions for tension and conflict.[2]
Ps. What I would add is that most of these "religious" rivalries are really political rivalries masquerading as religious rivalries.
Darwinists' problem is not with design but the designer.
New Study Reveals How the Shape of My Nose Arose
It is ironic that Charles Lyell, whose seminal, if flawed, work in geology—the barrister is sometimes known as the father of modern geology—positively influenced Charles Darwin’s development of evolutionary theory—the young Darwin read Lyell’s book as he sailed around the world in the H.M.S. Beagle—and who helped to arrange for Darwin’s first formal, if awkward, presentation of his theory—an event precipitated by Wallace’s Ternate letter—was one of the last of the intelligentsia to accept Darwin’s new formulation of Epicureanism, known as evolution.
At one point an exasperated Darwin asked Lyell—it always comes down to metaphysics—if he believed “the shape of my nose was designed?” If Lyell did think so then, Darwin added, “I have nothing more to say.” The infra-dignitatem, or infra-dig for the irreverent, argument, which insisted that it was beneath the dignity of the Creator to stoop so low as to dwell in the details of the world, had been promoted by no less than the father of natural theology John Ray and Platonist Ralph Cudworth, and in Darwin’s day was in full swing. Its influence on the young Darwin was clear in the naturalist’s early notebooks, and here in his appeal to Lyell. One look at one’s nose is all one needs to know about origins. Obviously we evolved. Now, a century and a half later, science finally has its say in the matter.
A new Study out of, appropriately enough, England, now reveals the underlying genetic details that influence the shape of our noses. It seems there are four genes that influence the width and length of our olfactory device and, as the press release informs us, “The new information adds to our understanding of how the human face evolved.”
We are free to acknowledge free moral agency
Free Will: What Are the Reasons to Believe in It?
University of Missouri psychology professor Kennon Sheldon’s message is neatly summed up in an opening statement: “Regardless of whether humans do or don’t have free will, psychological research shows it’s beneficial to act as if you do.”
The author of Freely Determined: What the New Psychology of the Self Teaches Us About How to Live (Basic Books, 2022) responds to philosophers who say that we do not have free will:
All my life, I’ve struggled with the question of whether humans have ‘free will’. It catalysed my decision to become a psychologist and continues to inspire my research to this day, especially as it relates to the kinds of goals people set for themselves, and the effects of goal-striving on people’s happiness and wellbeing.
I’ve come to the conclusion that people really do have free will, at least when it is defined as the ability to make reasoned choices among action possibilities that we ourselves think up…
Regardless of who is correct in this debate, my work has led me to a second conclusion that I consider even more important than whether we have free will or not. It’s that a belief in our own capacity to make choices is critical for our mental health. At the very least, this belief lets us function ‘as if’ we have free will, which greatly benefits us.
KENNON SHELDON, “THE THREE REASONS WHY IT’S GOOD FOR YOU TO BELIEVE IN FREE WILL,” PSYCHE, JUNE 15, 2023
An Obvious Problem
Now, the obvious problem with his approach is that if we believe in free will simply because that belief is supposed to be good for our mental health, then we really don’t believe in it.
A simple example suffices: We sometimes hear that being optimistic is also better for mental health. In one sense, that’s true. If we focus on the positive things, our lives feel more pleasant and that is bound to be better for mental health. But what if we have no good reason for optimism? What if we live under an active volcano that shows signs of erupting? Optimism (“it probably won’t really happen this year”) could delay evacuation past the point of no return.
So let’s look back at free will in this light: If we believe that we have it — and that belief is true — we are empowered to deal with temptations and addictions, firm in the knowledge that we really can cast the deciding vote for our best possible outcome. But if free will is not true, we are setting ourselves up for delusion if we succeed and needless disappointment and misery if we fail. Not only that but we are participating in an unfair system where people are judged and punished for unwise or bad behavior that they cannot really help. So functioning “as if” we have free will turns out not to be very good at all.
“A Better Person”?
Sheldon goes on to say,
The second reason why I consider belief in free will to be beneficial is that it makes you a better person. Studies in social psychology show clearly that, if people become convinced that they have no free will, there can be negative effects on their ethical behaviour.
SHELDON, PSYCHE, 2023
Perhaps that’s true but it amounts to saying that perhaps we should be deluded for our own good. Even though delusions are said to be bad for us… Is there any light at the end of this tunnel?
Sheldon offers a reason why some thinkers deny free will:
You might wonder why anyone would choose to believe in determinism, given the clear negative effects of this belief? There are several possible reasons. Some people might think that determinism is the most scientific and intellectually sophisticated position to take, and they like feeling smarter than others.
SHELDON, PSYCHE, 2023
Well, if science matters, the good news is that neuroscience provides sound reasons to believe in free will. As Stony Brook neurosurgeon Michael Egnor has pointed out, the work of neuroscience pioneer Benjamin Libet established that we certainly have “free won’t” — the ability to choose not to do something:
[W]hat he found was, when you made a decision to push the button [in a psychological experiment], you still had the brain wave that preceded the decision by half a second. But when you decided to veto pushing the button, there was no new brain wave at all. It was silent in terms of brain waves. But you did make the decision to veto. So he said that it wasn’t so much that you have free will but you have free won’t. That is, you have the ability to decide whether or not you are going to comply with what your brain is urging you to do. And that compliance is not material. It’s not a brain wave. It’s immaterial.
MICHAEL EGNOR, “HOW A NEUROSCIENTIST IMAGED FREE WILL (AND “FREE WON’T”),” MIND MATTERS NEWS, MARCH 19, 2020
What Quantum Mechanics Shows
Physicist Marcelo Gleiser also notes that science does not really support the view that free will is an illusion: “[T]he mind is not a solar system with strict deterministic laws. We have no clue what kinds of laws it follows, apart from very simplistic empirical laws about nerve impulses and their propagation, which already reveal complex nonlinear dynamics.” In any event, quantum mechanics shows that nature is indeterminate at the fundamental level and that the observer’s decision of what to measure plays a role in what happens. One outcome is that a number of younger thinkers accept free will as consistent with the evidence.
In other words, we can accept free will based on the evidence. There is no particular need to think that it might be a possibly pleasant delusion.
A theory of devolution?
Is Adaptation Actually a Fight to Stay the Same?
On a new episode of ID the Future, host Casey Luskin talks with Eric Anderson on location at this year’s Conference on Engineering and Living Systems (CELS). The two discuss an intriguing new engineering-based model of bounded adaptation that could dramatically change how we view small-scale evolutionary changes within populations of organisms. In presenting his argument for natural selection, Charles Darwin pointed to small changes like finch beak size and peppered moth color as visible evidence of an unguided evolutionary process at work. Many have adopted this perspective, quick to grant the Darwinian mechanism credit for micro-, if not macro-, evolution. But Anderson and other attendees at the CELS conference are starting to promote a different view. “We need to stop saying organisms are partly designed,” says Anderson. “We need to view them as deeply designed and purposeful, active and engaged in their environments, and capable of adapting within their operating parameters.” To get a fascinating glimpse of this novel approach to biology, download the podcast or listen to it here .
Monday, 26 June 2023
On professor Dave and the bacterial flagellum
Answering Farina on Behe’s Work: Bacterial Flagella
In a previous article, I began a series of four responses to YouTuber Dave Farina (aka “Professor Dave”) about his video reviewing Dr. Michael Behe’s three books. Here I will turn my attention to Mr. Farina’s comments regarding bacterial flagella.
In relation to the flagellum, the video complains about Behe’s “dishonest usage of terminology pertaining to machinery,” including phrases such as “outboard motor,” “drive shaft,” “universal joint,” “bushings,” and “clutch and braking system.” In reality, this terminology is used widely in the scientific literature. It’s not unique to Behe. On the contrary, in reference to flagella, the literature is full of such terms including “motor”,1 “drive shaft,”2 “universal joint,”3“bushing,”4 and “clutch.”5 The word “machine” itself has a wide circulation.6 Is Farina going to charge the entire flagella research community with dishonesty as well?
Co-option Scenarios for the Origins of Bacterial Flagella
According to the video, “A flagellum that merely twitches instead of rotating smoothly would also produce motion and thus could be selected for.” But a type IV pilis, which enables twitching motility (a form of bacterial translocation over moist surfaces), is very different from a flagellum. Twitching motility occurs by extension, tethering, and retraction of the type IV pilus, which functions in a manner akin to a grappling hook. A flagellum, on the other hand, rotates as it is driven by a proton motive force across the cell membrane. The assembly mechanisms of pili and flagella are also quite different.
The video complains that Behe fails to acknowledge the existence of alternative flagellar systems that are simpler than the model system found in Salmonella species and Escherichia coli. However, the fact that an alternative system lacks a specific component that is essential in another system does not mean that the former lacks an alternative mechanism for achieving the same outcome. The most robust concept of irreducible complexity understands it as a property of a system that is contributed to by multiple subfunctions, the removal of one of which causes the overall system to effectively cease performing its job. Note that each individual subfunction could, in principle, be performed by multiple protein components. Likewise, a single protein component could perform more than one of those subfunctions. Furthermore, the identity of the specific components performing each respective subfunction could differ from one organism to the next. It is therefore not the identity of the structural parts that is important in an irreducibly complex system, but rather the essential functions that need to be performed in order for a higher-level objective to be realized.
Moreover, pointing to homologues of flagellar proteins does not undermine the argument from irreducible complexity, since co-opting those proteins to produce a flagellar system requires multiple co-incident changes in order for the new system to be realized. For example, flagellar-specific proteins would not confer a selective advantage until incorporated into the flagellar system. But the necessary proteins that serve roles in other systems will not become incorporated into the flagellar system before these flagellar-specific proteins arise. This is quite aside from the need to have complementary protein-protein binding interfaces, as well as a choreographed assembly system to ensure that the proteins are assembled in the appropriate order.
Resurrecting a Flagellum
In a 2016 article at Evolution News, Behe asks,
W]hy doesn’t [Kenneth Miller] just take an appropriate bacterial species, knock out the genes for its flagellum, place the bacterium under selective pressure (for mobility, say), and experimentally produce a flagellum — or any equally complex system — in the laboratory? (A flagellum, after all, has only 30-40 genes, not the hundreds Miller claims would be easy for natural selection to rapidly redesign.) If he did that, my claims would be utterly falsified. But he won’t even try it because he is grossly exaggerating the prospects of success.
The video by Farina comments,
hilariously, [Behe] is oblivious to the fact that this precise experiment was carried out the year before. Here’s the paper. Gene deletion produced two strains of bacteria with no flagellum. They then introduced selective pressure for motility by depleting the nutrients in the colony. Within 96 hours, both strains had regenerated flagellar motility by a pathway involving two successive point mutations in genes that served other purposes.
However, the paper that Farina cites7 does not do this at all. Not for the first time with this video, I wonder if he has in fact read the paper. All that the researchers deleted was the flagellar master switch protein, FleQ, in Pseudomonas fluorescens. After a few days of incubating the bacterial cells on Petri dishes, they reacquired their ability to grow flagella. The genetic basis for this reactivation of the flagella is that another master switch protein, NtrC, that is a structurally similar homolog of FleQ — responsible for turning on genes involved in nitrogen metabolism — already had the ability, to some extent, to cross-bind to the promoter usually bound by FleQ. When produced in excess, as a result of a broken regulator, NtrC was thus able to drive flagellar synthesis. As a consequence of this mutation, the bacterial cell lost its ability to regulate its nitrogen metabolism genes. An article in The Scientist describes this research:
But while the re-evolved flagella enabled the bacteria to access food supplies at the farthest reaches of the Petri dish, the ability came at a price. ‘The bacteria that became much better at swimming were much worse at nitrogen regulation,’ said Johnson. However, she added, ‘sometimes the advantage can be so great that it’s worth paying that cost because otherwise you die.’
Thus, contrary to the Farina video’s claims, this paper does not document the de novo evolutionary origins of a bacterial flagellum at all — far from it. In fact, Behe has already addressed the paper here.
The Waiting Times Problem
In 2004, Michael Behe and David Snoke published a paper in the journal, Protein Science.8 About this paper, Farina has three complaints. The first complaint is that, “Behe and Snoke found that the target sequence did actually evolve, in population sizes and timeframes that are entirely realistic, and if anything, quite small compared to real-world populations. The paper literally proves them wrong and they somehow count it as a win anyway.” Farina mentions Behe’s expert testimony at the 2005 Kitzmiller v. Dover trial:
When questioned about his 2004 paper, Behe tacitly acknowledged that the population size in their model was orders of magnitude smaller than real-world bacterial populations, which had the effect of vastly underestimating the rate at which such “irreducible” traits could evolve… In one striking exchange, Behe acknowledged a paper which indicated that there are more prokaryotes in a single ton of soil than in his model population, and that there is a lot more than one ton of soil on Earth.
However, this objection stems from Farina’s misreading of the paper. As Behe himself explains in the very transcript that Farina cites, “forming a new disulfide bond might require as few as two point mutations. But forming other multi-residue features such as protein-protein binding sites might require more.” The graph below (figure 6 of the paper) shows Behe and Snoke’s estimate of the time to fixation (along the y-axis) versus the number of substitutions needed for a new feature to evolve (along the x-axis). On the top axis, values for the needed population sizes are given. The point is that, as the number of needed co-dependent mutations increases, so too does the needed population size and waiting time to fixation.
As Behe and Snoke explain in the paper, in a scenario where three substitutions are required for a novel feature to arise, a population size of roughly 1011 individuals is necessary for it to become fixed over the course of 108 generations (108 generations is marked as a horizontal bar on the figure). If the complex trait in question requires even more substitutions, it would require considerably more time. If six mutations were needed, the average population size required for it to become fixed in 108 generations would be on the order of 1022 individuals. Given that 1030 is a plausible estimate of the number of microorganisms on the entire planet9, these numbers become prohibitive very quickly.
The second complaint is that, “In their model, Behe and Snoke permitted only single-base mutations and natural selection — no recombination, no duplications beyond the initial presumed one, no other evolutionary changes.” But the authors explicitly say that “Because the model presented here does not include recombination, the results can be considered to be most applicable to a haploid, asexual population.” Nonetheless, they do note in the conclusion to their paper that “the results also impinge on the evolution of diploid sexual organisms,” since large multicellular organisms have much, much smaller population sizes than bacteria. If the evolution of complex features is difficult for microorganisms (with their massive population sizes and short generation turnover times), how much more so for large animals? Though one might counter, in the case of diploid sexual species, that recombination allows for neutral mutations to occur separately in a population and to later combine by sexual recombination, Christiansen et al. have shown, in a paper published in Theoretical Population Biology, that “Recombination lowers the waiting time until a new genotypic combination first appears, but the effect is small compared to that of the mutation rate and population size” (emphasis added).10
Finally, Farina complains that “They also specified a pre-determined target sequence and only considered the simulation to have been ‘successful’ if that specific target evolved.” But this is incorrect. Rather, the paper provides estimates for how many organisms would be required, and over how long a time frame, for multiple co-dependent mutations (none of which by themselves confers an advantage) to become fixed in a population.
Notes
Minamino T, Imada K, Namba K. Molecular motors of the bacterial flagella. Curr Opin Struct Biol. 2008; 18(6):693-701.
Johnson S, Furlong EJ, Deme JC, Nord AL, Caesar JJE, Chevance FFV, Berry RM, Hughes KT, Lea SM. Molecular structure of the intact bacterial flagellar basal body. Nat Microbiol. 2021; 6(6):712-721.
Kitao A, Hata H. Molecular dynamics simulation of bacterial flagella. Biophys Rev. 2018; 10(2):617-629.
Yamaguchi T, Makino F, Miyata T, Minamino T, Kato T, Namba K. Structure of the molecular bushing of the bacterial flagellar motor. Nat Commun. 2021 Jul 22;12(1):4469.
Blair KM, Turner L, Winkelman JT, Berg HC, Kearns DB. A molecular clutch disables flagella in the Bacillus subtilis biofilm. Science. 2008;320(5883):1636-8.
Sowa Y, Berry RM. Bacterial flagellar motor. Q Rev Biophys. 2008 May;41(2):103-32.
Taylor TB, Mulley G, Dills AH, Alsohim AS, McGuffin LJ, Studholme DJ, Silby MW, Brockhurst MA, Johnson LJ, Jackson RW. Evolution. Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system. Science. 2015; 347(6225):1014-7.
Behe MJ, Snoke DW. Simulating evolution by gene duplication of protein features that require multiple amino acid residues. Protein Sci. 2004; 13(10):2651-64.
Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A. 1998; 95(12):6578-83.
Christiansen FB, Otto SP, Bergman A, Feldman MW. Waiting with and without recombination: the time to production of a double mutant. Theor Popul Biol.1998;53(3):199-215.
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