Darwinian apologists well behind on their homework

This is embarrassing: “Darwin’s Doubt” debunker is 14 years behind the times
Posted by vjtorley under Intelligent Design

Over at The Skeptical Zone, Mikkel “Rumraket” Rasmussen has written a post critical of Dr. Stephen Meyer, titled, Beating a dead horse (Darwin’s Doubt), which is basically a rehash of comments he made on a thread on Larry Moran’s Sandwalk blog last year. The author’s aim is to expose Dr. Stephen Meyer’s “extremely shoddy scholarship,” but as we’ll see, Rasmussen’s own research skills leave a lot to be desired.

Did Dr. Meyer fail to document his sources?

Rasmussen focuses his attack on chapter 10 of Dr. Meyer’s book, “Darwin’s Doubt.” He writes:

Having read the book, a recurring phenomenon is that Meyer time and again makes claims without providing any references for them. Take for instance the claim that the Cambrian explosion requires lots of new protein folds, from Chapter 10 The Origin of Genes and Proteins:

(Rasmussen proceeds to quote from Meyer’s book, on which he comments below – VJT.)

In the whole section Meyer dedicates to the origin of novel folds, he makes zero references that actually substantiate [his assertion] that the [C]ambrian diversification, or indeed any kind of speciation, or the [appearance of] new cells types or organs, require[d] new protein folds. ZERO. Not one single reference that supports these claims. At first it reads like what I quote[d] above, lots of claims, no references. Later on he eventually cites the work of Douglas Axe that atte[m]pts to address how hard it is to evolve new folds (and that work has its own set of problems, but never mind that). Axe makes the same claim in his ID-journal Bio-complexity papers (which eventually Meyers cites), but in Axe’s papers, that claim is not supported by any reference either. It’s simply asserted as fact. In other words, Meyer makes a claim, then cites Axe making the same claim. Neither of them give a reference.

(N.B. For ease of readability, I have used square brackets to correct Rasmussen’s spelling and punctuation errors, and I have also inserted four extra words, without which his meaning would have been obscure to readers, in the preceding paragraph – VJT.)

Rasmussen repeats his accusation that Dr. Meyer frequently makes claims in his book without providing any references for them, at the very end of his post:

Later Meyer gets a ID-complexitygasm when he asserts, again without any support, that:

“The Cambrian animals exhibit structures that would have required many new types of cells, each requiring many novel proteins to perform their specialized functions. But new cell types require not just one or two new proteins, but coordinated systems of proteins to perform their distinctive cellular functions.”

Where does he get this? His ass, that’s where.

Do new cell types require new kinds of proteins?

I find it quite astonishing that Rasmussen would require documentation for Dr. Meyer’s claim that new cell types would require new types of proteins, for three reasons. First, it’s a well-known fact that each different cell type has different cluster of differentiation proteins. Bojidar Kojouharov, a Ph.D. Student in Cancer Immunology, describes these proteins as follows:

Clusters of Differentiation (CD) are cell surface proteins used to differentiate one cell type from another. Each CD marker is a different surface protein from the others. As such, it will likely have different functions and may be expressed on different cells. Technically, different CD markers don’t really have to have anything in common, other than the fact that they are on the cell’s surface. Usually, it’s safe to assume any Clusters of Differentiation is a protein.

Second, it is widely admitted by authors in the field that the complex organisms which appeared in the Cambrian would have required a host of new cell types. Here, for instance, is what P. V. Sukumaran, of the Geological Society of India, says in his paper, Cambrian Explosion of Life: the Big Bang in Metazoan Evolution (RESONANCE, September 2004, pp. 38-50):

Yet another feature of the Cambrian explosion is the quantum jump in biological complexity. The early Cambrian animals had roughly 50 cell types while the sponges that appeared a little earlier had only 5… (p. 44, sidebar)

Unicellular life is relatively simple; there is little division of labour and the single cell performs all functions of life. Obviously the genetic information content of unicellular organisms is relatively meagre. Multicellular life, on the other hand, requires more genetic information to carry out myriads of cellular functions as their cells are differentiated into different cell types, tissues and organs. But new cell types themselves require specialised proteins, and novel proteins arise from novel gene sequences, that is new genetic information. As the organisms that appeared in the Cambrian explosion had many more novel and specialised cell types than their prokaryotic ancestors, the amount of new genetic information that arose in the Cambrian explosion represents a large increase in biological information. (p. 47)

Third, it turns out that Dr. Meyer provided the very references that Rasmussen chides him for failing to supply, over 14 years ago, in his 2001 paper, The Cambrian Explosion: Biology’s Big Bang, which he co-authored with Paul Nelson and Paul Chien, which is listed on page 471 of the bibliography of Dr. Meyer’s book, Darwin’s Doubt. (Actually, the bibliography cites a later and slightly more polished 2003 version of the same paper.) Allow me to quote from pages 32-33 of the 2001 paper (emphases mine – VJT):

As noted, the new animals of the Cambrian explosion would have required many new cell types and, with them, many new types of proteins acting in close coordination. It follows, therefore, that if the neo-Darwinian mechanism cannot explain the origin of new cell types (and the systems of proteins they require), it cannot explain the origin of the Cambrian animals. Yet given the number of novel proteins required by even the most basic evolutionary transformations, this now seems to be precisely the case.

Consider, for example, the transition from a prokaryotic cell to a eukaryotic cell. This transition would have produced the first appearance of a novel cell type in the history of life. Compared to prokaryotes, eukaryotes have a more complex structure including a nucleus, a nuclear membrane, organelles (such as mitocondria, the endoplasmic recticulum, and the golgi apparatus), a complex cytoskeloton (with microtubulues, actin microfilaments117 and intermediate filaments) and motor molecules.118 Each of these features requires new proteins to build or service, and thus, as a consequence, more genetic information. (For example, the spooled chromosome in a modern eukaryotic yeast [Saccharomyces] cell has about 12.5 million base pairs, compared to about 580,000 base pairs in the prokaryote Mycoplasma.)119 The need for more genetic information in eukaryotic cells in turn requires a more efficient means of storing genetic information. Thus, unlike prokaryotic cells which store their genetic information on relatively simple circular chromosomes, the much more complex eukaryotic cells store information via a sophisticated spooling mechanism.120 Yet this single requirement — the need for a more efficient means of storing information — necessitates a host of other functional changes each of which requires new specialized proteins (and yet more genetic information) to maintain the integrity of the eukaryotic cellular system.

For example, nucleosome spooling requires a complex of specialized histones proteins (with multiple recognition and initiation factors) to form the spool around which the double stranded DNA can wind.121 Spooled eukaryotic DNA in turn uses “intron spacers,” (dedicated sections of non-coding DNA), in part to ensure a tight electrostatic fit between the nucleosome spool and the cords of DNA.122 This different means of storing DNA in turn requires a new type of DNA polymerase to help access, “read,” and copy genetic information during DNA replication. (Indeed, recent sequence comparisons show that prokaryotic and eukaryotic polymerases exhibit stark differences).123 Further, eukaryotes also require a different type of RNA polymerase to facilitate transcription. They also require a massive complex of five jointly necessary enzymes to facilitate recognition of the promoter sequence on the spooled DNA molecule.124 The presence of intron spacers in turn requires editing enzymes (including endonucleases, exonucleases and splicesomes) to remove the non-coding sections of the genetic text and to reconnect coding regions during gene expression.125 Spooling also requires a special method of capping or extending the end of the DNA text in order to prevent degradation of the text on linear (non-circular) eukaryotic chromosomes.126 The system used by eukaryotes to accomplish this end also requires a complex and uniquely specialized enzyme called a telomerase.127

Thus, one of the “simplest” evolutionary transitions, that from one type of single-celled organism to another, requires the origin of many tens of specialized novel proteins, many of which (such as the polymerases) alone represent massively complex, and improbably specified molecules.128 Moreover, many, if not most, of these novel proteins play functionally necessary roles in the eukaryotic system as a whole. Without specialized polymerases cell division and protein synthesis will shut down. Yet polymerases have many protein subunits containing many thousands of precisely sequenced amino acids. Without editing enzymes, the cell would produce many nonfunctional polypeptides, wasting vital ATP energy and clogging the tight spaces within the cytoplasm with many large useless molecules. Without tubulin and actin the eukaryotic cytoskeloton would collapse (or would never have formed). Indeed, without the cytoskeleton the eukaryotic cell can not maintain its shape, divide, or transport vital materials (such as enzymes, nutrients, signal molecules, or structural proteins).129 Without telomerases the genetic text on a linear spooled chromosome would degrade, again, preventing accurate DNA replication and eventually causing the parent cell to die.130

Even a rudimentary analysis of eukaryotic cells suggests the need for, not just one, but many novel proteins acting in close coordination to maintain (or establish) the functional integrity of the eukaryotic system. Indeed, the most basic structural changes necessary to a eukaryotic cell produce a kind of cascade of functional necessity entailing many other innovations of design, each of which necessitates specialized proteins. Yet the functional integration of the proteins parts in the eukaryotic cell poses a severe set of probabilistic obstacles to the neo-Darwinian mechanism, since the suite of proteins necessary to eukaryotic function must, by definition, arise before natural selection can act to select them.

References:

117 Russell F. Doolittle, “The Origins and Evolution of Eukaryotic Proteins,” Philosophical Transactions of the Royal Society of London B 349 (1995): 235-40.

118 Stephen L. Wolfe, Molecular and Cellular Biology (Belmont, CA: Wadsworth, 1993), pp. 3, 6-19.

119 Rebecca A. Clayton, Owen White, Karen A. Ketchum, and J. Craig Ventner, “The First Genome from the Third Domain of Life,” Nature 387 (1997): 4459-62.

120 Stephen L. Wolfe, Molecular and Cellular Biology, pp. 546-50.

121 Ibid.

122 H. Lodish, D. Baltimore, et. al., Molecular Cell Biology (New York: W.H. Freeman, 1994), pp. 347-48. Stephen L. Wolfe, Molecular and Cellular Biology, pp. 546-47.

123 Edgell and Russell Doolittle, “Archaebacterial genomics: the complete genome sequence of Methanococcus jannaschii,” BioEssays 19 (no. 1, 1997): 1-4. Michael Y. Galperin, D. Roland Walker, and Eugene V. Coonin, “Analogous Enzymes: Independent Inventions in Enzyme Evolution,” Genome Research 8 (1998): 779-90.

124 Stephen L. Wolfe, Molecular and Cellular Biology, pp. 580-81, 597.

125 Ibid., pp. 581-82, 598-600, 894-96.

126 Ibid., p. 975.

127 Ibid., pp. 955-975.

128 Ibid., p. 580.

129 Ibid., pp. 17-19.

130 Ibid., pp. 955-975.

And here’s a highly pertinent quote from pages 5-6 of the paper:

Each new cell type requires many new and specialized proteins. New proteins in turn require new genetic information encoded in DNA. Thus, an increase in the number of cell types implies (at a minimum) a considerable increase in the amount of specified genetic information. For example, molecular biologists have recently estimated that a minimally complex cell would require between 318 to 562 kilobase pairs of DNA to produce the proteins necessary to maintain life.20 Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite would require an amount of DNA greater by several orders of magnitude (e.g., the genome size of the worm Caenorhabditis elegans is approximately 97 million base pairs21 while that of the fly Drosophila melanogaster (an arthropod), is approximately 120 million base pairs.22 For this reason, transitions from a single cell to colonies of cells to complex animals represent significant (and in principle measurable) increases in complexity and information content. Even C. elegans, a tiny worm about one millimeter long, comprises several highly specialized cells organized into unique tissues and organs with functions as diverse as gathering, processing and digesting food, eliminating waste, external protection, internal absorption and integration, circulation of fluids, perception, locomotion and reproduction. The functions corresponding to these specialized cells in turn require many specialized proteins, genes and cellular regulatory systems, representing an enormous increase in specified biological complexity. Figure 5 shows the complexity increase involved as one moves upward from cellular grade to tissue grade to organ grade life forms. Note the jump in complexity required to build complex Cambrian animals starting from, say, sponges in the late Precambrian. As Figure 5 shows Cambrian animals required 50 or more different cell types to function, whereas sponges required only 5 cell types.

(Note: Figure 5 can be viewed in this later version of the paper, where it is labeled as Figure 10 – VJT.)

References:

20 Mitsuhiro Itaya, “An estimation of the minimal genome size required for life,” FEBS Letters 362

(1995): 257-60. Claire Fraser, Jeannine D. Gocayne, Owen White, et. al., “The Minimal Gene Complement of Mycoplasma genitalium,” Science 270 (1995): 397-403. Arcady R. Mushegian and Eugene V. Koonin, “A minimal gene set for cellular life derived by comparison of complete bacterial genomes,” Proceedings of the National Academy of Sciences USA 93 (1996): 10268-73.

21 The C. elegans Sequencing Consortium, “Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology,” Science 282 (1998): 2012-18.

22 John Gerhart and Marc Kirschner, Cells, Embryos, and Evolution (London: Blackwell Science, 1997), p.

121

Did Dr. Meyer distort the words of geneticist Susumu Ohno?

Rasmussen also accuses Dr. Meyer of distorting the words of Susumu Ohno, a geneticist and evolutionary biologist whose work he discussed in chapter 10 of his book, Darwin’s Doubt:

It gets much worse, turns out Meyer is making assertions diametrically opposite to what his very very few references say. Remember what Meyer wrote above?

“The late geneticist and evolutionary biologist Susumu Ohno noted that Cambrian animals required complex new proteins such as, for example, lysyl oxidase in order to support their stout body structures.”

Well, much later in the same chapter, Meyer finally references Ohno:

“Third, building new animal forms requires generating far more than just one protein of modest length. New Cambrian animals would have required proteins much longer than 150 amino acids to perform necessary, specialized functions.21″

What is reference 21? It’s “21. Ohno, “The Notion of the Cambrian Pananimalia Genome.””

What does that reference say? Let’s look:

“Reasons for Invoking the Presence of the Cambrian Pananimalia Genome.

Assuming the spontaneous mutation rate to be generous 10^-9 per base pair per year and also assuming no negative interference by natural selection, it still takes 10 million years to undergo 1% change in DNA base sequences. It follows that 6-10 million years in the evolutionary time scale is but a blink of an eye. The Cambrian explosion denoting the almost simultaneous emergence of nearly all the extant phyla of the kingdom Animalia within the time span of 6-10 million years can’t possibly be explained by mutational divergence of individual gene functions. Rather, it is more likely that all the animals involved in the Cambrian explosion were endowed with nearly the identical genome, with enormous morphological diversities displayed by multitudes of animal phyla being due to differential usages of the identical set of genes. This is the very reason for my proposal of the Cambrian pananimalia genome. This genome must have necessarily been related to those of Ediacarian predecessors, representing the phyla Porifera and Coelenterata, and possibly Annelida. Being related to the genome – possessed by the first set of multicellular organisms to emerge on this earth, it had to be rather modest in size. It should be recalled that the genome of modern day tunicates, representing subphylum Urochordata, is made of 1.8 x 10^8 DNA base pairs, which amounts to only 6% of the mammalian genome (9). The following are the more pertinent of the genes that were certain to have been included in the Cambrian pananimalia genome.”

The bold is my emphasis. I trust you can see the problem here. So, Meyer makes a single goddamn reference to support the claim that the Cambrian explosion required a lot of innovation of new proteins, folds, cell-types and so on. What do we find in that references? That Ohno is suggesting the direct opposite, that he is in fact supporting the standard evo-devo view that few regulatory changes were what happened, that the genes and proteins were already present and had long preceding evolutionary histories.

Once again, Rasmussen hasn’t done his homework. A little digging on my part revealed that Dr. Meyer had previously discussed the Dr. Ohno’s claims at considerable length and responded to those claims, in his 2001 paper, The Cambrian Explosion: Biology’s Big Bang, which he co-authored with Paul Nelson and Paul Chien (bolding mine – VJT):

Ironically, even attempts to avoid the difficulty posed by the Cambrian explosion often presuppose the need for such foresight. As noted, Susumo Uno, the originator of the hypothesis of macroevolution by gene duplication, has argued that mutation rates of extant genes are not sufficiently rapid to account for the amount of genetic information that arose suddenly in the Cambrian.114 Hence he posits the existence of a prior “pananimalian genome” that would have contained all the genetic information necessary to build every protein needed to build the Cambrian animals. His hypothesis envisions this genome arising in a hypothetical common ancestor well before the Cambrian explosion began. On this hypothesis, the differing expression of separate genes on the same master genome would explain the great variety of new animal forms found in the Cambrian strata.

While Ohno’s hypothesis does preserve the core evolutionary commitment to common descent (or monophyly), it nevertheless has a curious feature from the standpoint of neo-Darwinism. In particular, it envisions the pananimalian genome arising well before its expression in individual animals.115 Specific genes would have arisen well before they were used, needed or functionally advantageous. Hence, the individual genes within the pananimalian genome would have arisen in a way that, again, would have made them imperceptible to natural selection. This not only creates a problem for the neo-Darwinian mechanism, but it also seems to suggest, as Simon Conway Morris has recently intimated,116 the need for foresight or teleology to explain the Cambrian explosion. Indeed, the origin of a massive, unexpressed pre-Cambrian genome containing all the information necessary to build the proteins required by not-yet-existent Cambrian animals, would strongly suggest intelligent foresight or design at work in whatever process gave rise to the pananimalian genome. (pp. 31-32)

In short: Dr. Meyer was not only aware that Dr. Ohno had proposed the existence of a pananimalian genome; he also explicitly referred to it in his 2001 paper, in order to demonstrate that Intelligent Design would be the best explanation of such a genome.

I’ll leave it to my readers to decide whether it is Dr. Meyer or Rasmussen who is guilty of “extremely shoddy scholarship.” Let me conclude by recalling an old saying: “People who live in glass houses shouldn’t throw stones.”

On Higher education V

On the firstfruits :The Watchtower Society's commentary.

FIRSTFRUITS

The earliest fruits of a season; the first results or products of anything. The Hebrew word reʼ·shithʹ (from a root meaning “head”) is used in the sense of first part, point of departure, or “beginning” (De 11:12; Ge 1:1; 10:10); the “best” (Ex 23:19, ftn); and “firstfruits” (Le 2:12). “First ripe fruits” is rendered from the Hebrew bik·ku·rimʹ, which is used especially with regard to grain and fruit. (Na 3:12) The Greek term for firstfruits (a·par·kheʹ) comes from a root having the basic meaning “primacy.”

Jehovah required of the nation of Israel that the firstfruits be offered to him, whether it be of man, animal, or the fruitage of the ground. (Ex 22:29, 30; 23:19; Pr 3:9) Devoting the firstfruits to Jehovah would be an evidence of the Israelites’ appreciation for Jehovah’s blessing and for their land and its harvest. It would be an expression of thankfulness to the Giver of “every good gift.”—De 8:6-10; Jas 1:17.

Jehovah commanded the nation, representatively, to offer firstfruits to him, especially at the time of the Festival of Unfermented Cakes. Then, on Nisan 16, at the sanctuary the high priest waved before Jehovah some of the firstfruits of the grain harvest, a sheaf of barley, which was the first crop of the year based on the sacred calendar. (Le 23:5-12) Again, at Pentecost, on the 50th day after the sheaf of barley was waved, the firstfruits of the wheat harvest in the form of two leavened loaves made of fine flour were presented as a wave offering.—Le 23:15-17; see FESTIVAL.

Besides these grain offerings by the high priest on behalf of the nation, the Israelites were required to bring the firstfruits of all their produce as offerings. Every firstborn male of man and beast was sanctified to Jehovah, being either offered or redeemed. (See FIRSTBORN, FIRSTLING.) The firstfruits of coarse meal were to be offered in the form of ring-shaped cakes. (Nu 15:20, 21) Fruitage of the soil was also put in baskets and taken by the Israelites to the sanctuary (De 26:1, 2), where they then recited certain words recorded at Deuteronomy 26:3-10. The words were actually an outline of the nation’s history from their entering into Egypt to their deliverance and their being brought into the Promised Land.

It is said that the custom arose whereby each locality would send a representative with the firstfruits contributed by the inhabitants of the district in order that not all would have to undergo the inconvenience of going up to Jerusalem each time that the firstfruits were ripe. The quantity of these firstfruits to be offered was not fixed by the Law; it apparently was left to the generosity and appreciative spirit of the giver. However, the choicest portions, the best of the firstfruits, were to be offered.—Nu 18:12; Ex 23:19; 34:26.

In the case of a newly planted tree, for the first three years it was considered impure as though uncircumcised. In the fourth year all its fruit became holy to Jehovah. Then, in the fifth year, the owner could gather in its fruit for himself.—Le 19:23-25.

Contributions of firstfruits to Jehovah by the 12 non-Levitical tribes of Israel were used by the priests and Levites, since they received no inheritance in the land. (Nu 18:8-13) The faithful offering of the firstfruits brought pleasure to Jehovah and a blessing to all parties involved. (Eze 44:30) A failure to bring them would be counted by God as robbing him of his due and would bring his displeasure. (Mal 3:8) In Israel’s history at times this practice was neglected, being restored in certain periods by rulers zealous for true worship. In King Hezekiah’s reformation work, he held an extended celebration of the Festival of the Unfermented Cakes, and on this occasion Hezekiah instructed the people to fulfill their duty with respect to the contribution of firstfruits and tithes. Cheerfully the people responded by bringing in great quantities of the firstfruits of the grain, new wine, oil, honey, and all the produce of the field, from the third month to the seventh. (2Ch 30:21, 23; 31:4-7) After the restoration from Babylon, Nehemiah led the people in taking an oath to walk in Jehovah’s law, including the bringing to him of firstfruits of every sort.—Ne 10:29, 34-37; see OFFERINGS.

Figurative and Symbolic Use. Jesus Christ was spiritually begotten at the time of his baptism and was resurrected from the dead to life in the spirit on Nisan 16, 33 C.E., the day of the year on which the firstfruits of the first grain crop were presented before Jehovah at the sanctuary. He is, therefore, called the firstfruits, being actually the first firstfruits to God. (1Co 15:20, 23; 1Pe 3:18) The faithful followers of Jesus Christ, his spiritual brothers, are also a firstfruits to God, but not the primary firstfruits, being similar to the second grain crop, the wheat, which was presented to Jehovah on the day of Pentecost. They number 144,000 and are called the ones “bought from among mankind as firstfruits to God and to the Lamb” and “certain firstfruits of his creatures.”—Re 14:1-4; Jas 1:18.

The apostle Paul also speaks of the faithful Jewish remnant who became the first Christians as being “firstfruits.” (Ro 11:16) The Christian Epaenetus is called “a firstfruits of Asia for Christ” (Ro 16:5), and the household of Stephanas “the firstfruits of Achaia.”—1Co 16:15.

Since the anointed Christians are begotten by the spirit as sons of God with the hope of resurrection to immortality in the heavens, they are said during their lifetime on earth to “have the firstfruits, namely, the spirit . . . while we are earnestly waiting for adoption as sons, the release from our bodies by ransom.” (Ro 8:23, 24) Paul says that he and fellow Christians with hopes of life in the spirit have “the token of what is to come, that is, the spirit,” which he also says is “a token in advance of our inheritance.”—2Co 5:5; Eph 1:13, 14.

Darwinists still don't (won't?)get it.

Methinks This Robot Has Been, Like, Weaseled into a Darwinian Tale

Evolution News &Views 

It's been 29 years since Richard Dawkins committed the Weasel Blunder and 25 years since Tim Berra committed Berra's Blunder, but some evolutionists still don't get it. You can't design something for a purpose and call it Darwinism. Even if some randomness is thrown in, once a goal is specified in advance, that's not evolution; it's intelligent design.

The latest example comes from PLOS One: "Morphological Evolution of Physical Robots through Model-Free Phenotype Development," by Brodbeck, Hauser, and Iida. Look for the evidence of guidance by the investigators:

Artificial evolution of physical systems is a stochastic optimization method in which physical machines are iteratively adapted to a target function. The key for a meaningful design optimization is the capability to build variations of physical machines through the course of the evolutionary process. Theoptimization in turn no longer relies on complex physics models that are prone to the reality gap, a mismatch between simulated and real-world behavior. We report model-free development and evaluation of phenotypes in the artificial evolution of physical systems, in which a mother robot autonomously designs and assembles locomotion agents. The locomotion agents are automatically placed in the testing environment and their locomotion behavior is analyzed in the real world. This feedbackis used for the design of the next iteration. Through experiments with a total of 500 autonomously built locomotion agents, this article shows diversification of morphology and behavior of physical robots for the improvement of functionality with limited resources. [Emphasis added.]

These researchers from Switzerland carefully crafted a "mother robot" that could assemble pre-fab parts into blocks that could perform some simplified locomotion. The algorithm was set to reward "offspring" that performed faster. Despite employing Darwinian words like "fitness" and "selection," their work has "design" stamped all over it. Reporters, though, went ape attributing this to Darwinian evolution.

At PhysOrg, Sarah Collins titled her report, "On the origin of (robot) species" in tribute to the Great Bearded Guru. She's like a viewer of a magic show unaware of how the trick is done:

For each robot child, there is a unique 'genome' made up of a combination of between one and five different genes, which contains all of the information about the child's shape, construction and motor commands. As in nature, evolution in robots takes place through 'mutation', where components of one gene are modified or single genes are added or deleted, and'crossover', where a new genome is formed by merging genes from two individuals.

In order for the mother to determine which children were thefittest, each child was tested on how far it travelled from its starting position in a given amount of time. The most successfulindividuals in each generation remained unchanged in the next generation in order to preserve their abilities, while mutation and crossover were introduced in the less successful children.

In all fairness, Collins points out some differences between robots and natural organisms. Still, nowhere does she explain how the experiment clearly requires design instead of natural selection. She thinks the "mother" robot did the designing. And she takes on faith the opinion of one of the authors that they were watching Darwinian evolution happen before their eyes:

"Natural selection is basically reproduction, assessment, reproduction, assessment and so on," said lead researcher Dr Fumiya Iida of Cambridge's Department of Engineering, who worked in collaboration with researchers at ETH Zurich. "That's essentially what this robot is doing -- we can actually watch the improvement and diversification of the species."

At the BBC News, evolution reporter Pallab Ghosh titled his coverage, "Robots learn to evolve and improve." It's not clear how one could "learn to evolve" if evolution is an unguided natural process, but that's not the only conundrum in his article. Like Collins, he fails to make any distinction between intelligently designed robots and natural processes.

Engineers have developed a robotic system that can evolve and improve its performance.

A robot arm builds "babies" that get progressively better at moving without any human intervention.

The ultimate aim of the research project is to develop robots that adapt to their surroundings.

There's a second conundrum: if human minds are developing robots that evolve, isn't Ghosh making a case for intelligent design?

What the designers and reporters all seem to be missing is the fact that goals were determined from the outset. "Improvement" was defined as the ability to move faster. Yet in nature, not every successful animal is the speediest (consider the sloth, or the fabled tortoise and hare). Darwinian evolution cannot work toward a distant target. As Paul Nelson remarks in the film Living Waters, "Any evolutionary process you consider, any materialistic process you can consider has no foresight. It can't see five years, five seconds, five milliseconds into the future. For that, you need a mind."

The paper actually makes a powerful if unintended case for intelligent design when you think about it. Ghosh reports that Dr. Iida got into robotics because the ones he saw in real life were not as good as the ones he enjoyed in movies like Star Trek and Star Wars. "His aim was to change that," Ghosh says, "and his approach was to draw lessons from the natural world to improve the efficiency and flexibility of traditional robotic systems." He had an aim. He had an approach. He wanted to gain knowledge, or information. So he looked at the efficiency and flexibility of natural solutions, where he found efficient designs worth copying. In other words, he was motivated by biomimicry -- an approach saturated with design thinking.

But he used an evolutionary algorithm, someone might complain. True, but it wasn't evolutionary in the Darwinian sense. There's no such thing as a Darwinian "algorithm" despite the use of familiar lingo like mutation, selectionand fitness in the paper. Algorithms are intelligently designed for function. Once an algorithm is defined, a mindless mechanism like a computer program or robot can use it, applying inputs and monitoring outputs, as in this case. But those mechanisms were also predesigned to implement the predetermined goal.

Animal and plant breeders use "evolutionary algorithms" of a sort; they know what they want; they use algorithms of sexual reproduction, and they monitor the output to decide what offspring get to breed in the next iteration. All this is under the guiding hand of the intelligent agent (the breeder). Artificial selection is intelligent design, not Darwinism.

If the authors and reporters really wanted to see materialistic Darwinian processes in action, they should have taken their hands off the equipment, shut the door, and let nature take its course. Most likely, nothing more interesting would happen than rust.

Dawkins set a goal of generating Shakespeare's phrase "Methinks it is like a weasel." Berra watched cars "evolve" but missed the role of designers. The designers of these robots (and their Darwin-friendly reporters) committed both blunders. They had a target, designed a way to reach it, yet presumed after the fact that their carefully engineered "mother robot" resembled a mindless, material entity working by Darwinian natural selection. We can at least thank them for providing another opportunity to show why they really made the case for design.

With apologies to Johnny cash.

Being Hated by the Right People

Jonathan Wells 

As Johnny Cash reputedly once said, "It's good to know who hates you, and it's good to be hated by the right people."

Darwinist bloggers P. Z. Myers and Ian Musgrave hate me. In fact, Myers writes, "My animus for Jonathan Wells knows no bounds." Well, at least he (unlike Musgrave) spells my name right.

The most recent outbursts by Myers and Musgrave were provoked bymy February 29 blog on Evolution News & Views, in which I predicted that Darwinists would try to take credit for a recent French discovery regarding antibiotic resistance. And indeed they did.

In the course of claiming credit for Darwinism, Musgrave claims that I completely misrepresent evolution, molecular biology, genetics and history. Wow. At least I get points for comprehensiveness. As proof of my misrepresentations, Musgrave cites Wikipedia, which everyone involved in this controversy knows is about as balanced and reliable on this issue as P.Z. Myers's Pharyngula or The National Center for Science Miseducation's Panda's Thumb.

The main points in my original blog post were these:

I. Darwinism provides no explanation for the origin of complex enzymes (such as the one described in the French study) except to invoke "imaginary mutations over unimaginable time scales." Musgrave counters that the enzyme in the French study "isn't particularly complex, it's a simple 201 amino acid long protein." Of course, it doesn't take much of a skeptic to doubt that a 201 amino acid enzyme could originate by random mutation and natural selection. But instead of tackling that problem Musgrave simply describes how single mutations have been demonstrated to alter the properties of existing enzymes.

Fine. Except that the issue is not how existing enzymes can be altered, but how they originated in the first place. As in the case of whole organisms, mutation and selection can explain minor changes in existing species, but not the origin of species. Yet that's what Darwin's theory was supposedly about.

II. Darwinism played no role in the current research. The principal researcher in the French study disagrees, and >wrote to Musgrave's blog that "we did indeed use Darwinian evolution within this work (something unusual in structural biology). In order to obtain an enzyme with increased stability (a critical point for structural studies), we used selective pressure to obtain mutants of the enzyme."

So the researchers used artificial selection to good advantage. But artificial selection is not Darwinism. People were using artificial selection for centuries before Darwin came along, and they didn't need Darwin to explain it to them. Darwin argued that an analogous process also operates in natural populations -- and so it does. But he and his devoted followers went much further and claimed that it also explains the origin of new species, organs and body plans, which it doesn't.

The question remains whether our understanding of antibiotic resistance would owe anything to Darwinian theory even in the limited (and true) sense that selection operates in natural populations. I don't think so. Antibiotic resistance arises in clinical situations that are anything but natural. In 1956 Selman Waksman, the discoverer of streptomycin, pointed out that the isolation, purification and clinical application of antibiotics is highly artificial and has no counterpart in nature. According to Waksman, the application of Darwinian theory to antibiotics in nature was "totally unjustified." (Waksman, "The Role of Antibiotics in Natural Processes," Giornale di Microbiologia 2 (1956): 1-14.)

So I repeat the question with which I concluded my original blog post: "How, exactly, is Darwinian evolution essential to understanding and overcoming antibiotic resistance -- as the Darwinists claim it is?"

On Quirinius :The Watchtower Society's commentary.

QUIRINIUS

Roman governor of Syria at the time of the “registration” ordered by Caesar Augustus that resulted in Jesus’ birth taking place in Bethlehem. (Lu 2:1, 2) His full name was Publius Sulpicius Quirinius.

In the Chronographus Anni CCCLIIII, a list of Roman consuls, the name of Quirinius appears in 12 B.C.E. along with that of Messala. (Chronica Minora, edited by T. Mommsen, Munich, 1981, Vol. I, p. 56) Roman historian Tacitus briefly recounts Quirinius’ history, saying: “[He] sprang from the municipality of Lanuvium—had no connection; but as an intrepid soldier and an active servant he won a consulate under the deified Augustus, and, a little later, by capturing the Homonadensian strongholds beyond the Cilician frontier, earned the insignia of triumph . . . , adviser to Gaius Caesar during his command in Armenia.” (The Annals, III, XLVIII) His death took place in 21 C.E.

Not mentioned by Tacitus is Quirinius’ relationship to Syria. Jewish historian Josephus relates Quirinius’ assignment to Syria as governor in connection with the simultaneous assignment of Coponius as the Roman ruler of Judea. He states: “Quirinius, a Roman senator who had proceeded through all the magistracies to the consulship and a man who was extremely distinguished in other respects, arrived in Syria, dispatched by Caesar to be governor of the nation and to make an assessment of their property. Coponius, a man of equestrian rank, was sent along with him to rule over the Jews with full authority.” Josephus goes on to relate that Quirinius came into Judea, to which his authority was extended, and ordered a taxation there. This brought much resentment and an unsuccessful attempt at revolt, led by “Judas, a Gaulanite.” (Jewish Antiquities, XVIII, 1, 2, 3, 4 [i, 1]) This is evidently the revolt referred to by Luke at Acts 5:37. According to Josephus’ account it took place in “the thirty-seventh year after Caesar’s defeat of Antony at Actium.” (Jewish Antiquities, XVIII, 26 [ii, 1]) That would indicate that Quirinius was governor of Syria in 6 C.E.

For a long time this was the only governorship of Syria by Quirinius for which secular history supplied confirmation. However, in the year 1764 an inscription known as the Lapis Tiburtinus was found in Rome, which, though not giving the name, contains information that most scholars acknowledge could apply only to Quirinius. (Corpus Inscriptionum Latinarum, edited by H. Dessau, Berlin, 1887, Vol. 14, p. 397, No. 3613) It contains the statement that on going to Syria he became governor (or, legate) for ‘the second time.’ On the basis of inscriptions found in Antioch containing Quirinius’ name, many historians acknowledge that Quirinius was also governor of Syria in the B.C.E. period.

There is uncertainty on their part, however, as to where Quirinius fits among the secularly recorded governors of Syria. Josephus lists Quintilius Varus as governor of Syria at the time of, and subsequent to, the death of Herod the Great. (Jewish Antiquities, XVII, 89 [v, 2]; XVII, 221 [ix, 3]) Tacitus also refers to Varus as being governor at the time of Herod’s death. (The Histories, V, IX) Josephus states that Varus’ predecessor was Saturninus (C. Sentius Saturninus).

Many scholars, in view of the evidence of an earlier governorship by Quirinius, suggest the years 3-2 B.C.E. for his governorship. While these dates would harmonize satisfactorily with the Biblical record, the basis on which these scholars select them is in error. That is, they list Quirinius as governor during those years because they place his rule after that of Varus and hence after the death of Herod the Great, for which they use the popular but erroneous date of 4 B.C.E. (See CHRONOLOGY; HEROD No. 1 [Date of His Death].) (For the same reason, that is, their use of the unproved date 4 B.C.E. for Herod’s death, they give Varus’ governorship as from 6 to 4 B.C.E.; the length of his rule, however, is conjectural, for Josephus does not specify the date of its beginning or of its end.) The best evidence points to 2 B.C.E. for the birth of Jesus. Hence Quirinius’ governorship must have included this year or part thereof.

Some scholars call attention to the fact that the term used by Luke, and usually translated “governor,” is he·ge·monʹ. This Greek term is used to describe Roman legates, procurators, and proconsuls, and it means, basically, a “leader” or “high executive officer.” Some, therefore, suggest that, at the time of what Luke refers to as the “first registration,” Quirinius served in Syria in the capacity of a special legate of the emperor exercising extraordinary powers. A factor that may also aid in understanding the matter is Josephus’ clear reference to a dual rulership of Syria, since in his account he speaks of two persons, Saturninus and Volumnius, serving simultaneously as “governors of Syria.” (Jewish Antiquities, XVI, 277, 280 [ix, 1]; XVI, 344 [x, 8]) Thus, if Josephus is correct in his listing of Saturninus and Varus as successive presidents of Syria, it is possible that Quirinius served simultaneously either with Saturninus (as Volumnius had done) or with Varus prior to Herod’s death (which likely occurred in 1 B.C.E.). The New Schaff-Herzog Encyclopedia of Religious Knowledge presents this view: “Quirinius stood in exactly the same relation to Varus, the governor of Syria, as at a later time Vespasian did to Mucianus. Vespasian conducted the war in Palestine while Mucianus was governor of Syria; and Vespasian was legatus Augusti, holding precisely the same title and technical rank as Mucianus.”—1957, Vol. IX, pp. 375, 376.

An inscription found in Venice (Lapis Venetus) refers to a census conducted by Quirinius in Syria. However, it provides no means for determining whether this was in his earlier or his later governorship.—Corpus Inscriptionum Latinarum, edited by T. Mommsen, O. Hirschfeld, and A. Domaszewski, 1902, Vol. 3, p. 1222, No. 6687.


Luke’s proved accuracy in historical matters gives sound reason for accepting as factual his reference to Quirinius as governor of Syria around the time of Jesus’ birth. It may be remembered that Josephus, virtually the only other source of information, was not born until 37 C.E., hence nearly four decades after Jesus’ birth. Luke, on the other hand, was already a physician traveling with the apostle Paul by about 49 C.E. when Josephus was but a boy of 12. Of the two, Luke, even on ordinary grounds, is the more likely source for reliable information on the matter of the Syrian governorship just prior to Jesus’ birth. Justin Martyr, a Palestinian of the second century C.E., cited the Roman records as proof of Luke’s accuracy as regards Quirinius’ governorship at the time of Jesus’ birth. (A Catholic Commentary on Holy Scripture, edited by B. Orchard, 1953, p. 943) There is no evidence that Luke’s account was ever challenged by early historians, even by early critics such as Celsus.

On Wikipedia's wizards of ID

Meet the Cast of Characters Who Edit Wikipedia’s Page on Intelligent Design

David Klinghoffer | @d_klinghoffer

In the few weeks since the fate of paleontologist Günter Bechly at the hands of Wikipedia editors came to light, we’ve been reminded of an important truth: the world is far too dependent on the well-known online encyclopedia. Its treatment of intelligent design and ID scientists, like the now-erased Dr. Bechly or the disemboweled Dr. Walter Bradley, is a case in point.

Here are links to recent posts:

• “Wikipedia Erases Paleontologist Günter Bechly”
• “How “Notable” Do You Really Have to Be to Merit a Wikipedia Entry?”
• “You’ve Been Edited — Another ID Scholar, Walter Bradley, Gets the WikipediaTreatment”
• “If Trolls Wrote and Edited an Influential Online Encyclopedia”
• “Scientist Protests Wikipedia’s Mob Rule; Gets a Form Letter in Response”
• “In Challenging Wikipedia‘s Masked Mob, It’s Not Just Intelligent Design Proponents”

We so long ago gave up on the main entry on ID itself that I’ve hardly mentioned it. But the first sentence is a distortion or a lie, depending on how charitable you feel about it.

Intelligent design (ID) is a religious argument for the existence of God.

ID is neither of those things. Nor is it, as they go on, “pseudoscience,” a “form of creationism,” “lack[ing] empirical support and offer[ing] no testable or tenable hypotheses .” These are all complaints we’ve addressed   many times over.

What readers most need to understand about Wikipedia is that the editors are almost all pseudonyms of volunteer non-authorities. Many have an axe to grind. They wield power over mass opinion not because they’re objective or knowledgeable but simply by virtue of being dedicated to Wikipedia, on call at a moment’s notice to “fix” any correction they don’t like. The sociological profile there, someone with that kind of free time on his hands, guarantees that the page will attract people unfriendly to an idea like the design hypothesis.

Who’s been editing the ID entry lately? Check out the Revision history. The participants’ User pages can be interesting to read. The editors include, most recently, PaleoNeonate, claiming expertise in Computer Science, “a male born in the seventies in Canada. I am not notable.” He says, under Interests, that he is “an agnostic with naturalist pantheistic tendencies, who has long ceased to believe in the supernatural.”

One week ago, someone cut the word “religious” in the description of ID as a “religious argument.” That was on October 27 at 6:41 pm. At 6:43 pm, PaleoNeonate was on the scene, putting “religious” back in. Two minutes later! These people can wear anyone out.

PaleoNeonate is not a rarity. MrBill3, another editor, is “a skeptic who works as a nurse in the Intensive Care Unit.” Pepperbeast is “from Earth,” “interested in New Zealand,” “interested in religion as an anthropological and historical phenomenon,” a “freethinker,” a “skeptic,” and a “foodie.” MPants at Work is “a (male) skeptical liberal atheist feminist American gun nut SJW.” He lets loose with a paragraph of insults and profanities if you care to check it out.

Some editors sound like normal people. Others appear random. Roxy the dog is a dog owner who just discovered that his pet has lymphoma, which is sad to hear. The only other information about Roxy is that he “resists the POV pushing of lunatic charlatans.” Others give neither a real name nor any other information at all to go on.

Someone called “dave souza” sounds like that could be his actual name. In a short autobiography on his page, written in the third person, he is frank about his bias against ID:

Irritated by something in the Charles Darwin article which didn’t fit with his memory of a library book, he borrowed the book and was soon involved in extensive revisions of the page and adding related articles. Nine months later he was still renewing the book and distilling its goodness into offshoots like the “the Devil’s Chaplain” while frantically editing related texts like Radicalism. He strayed into the history of creationismm [sic] leading to an unhealthy fascination with the great intelligent design con. Soon he was spending sunny days when he should have been out mowing the lawn hunched over his laptop, as each edit spawned innumerable corrections to other articles or new red links demanding to be fed. [Emphasis added.]

Now pull back and consider. ID poses an ultimate question that should be of interest to all thoughtful people. It’s a scientific argument, not a religious one. It’s not an argument for God’s existence, though it’s compatible with theism. The latter prompts us to expect evidence of purpose in nature.

Looking up ID on Google is very often the beginning and end of people’s investigation of the design question. Directed immediately to Wikipedia, the reader will find an article that starts out with a distortion, edited by this cast of pseudonymous characters. Few visitors to the page will think to wonder where the information came from, or who maintains or edits it. It’s like something out of a very weird and bad dream.

On Adam,Eve and Darwin.

Is a First Human Pair Possible or Impossible?
Ann Gauger


Sometimes the claims that scientists make go beyond what can be definitively established. They may overestimate the sensitivity of their analytical methods, or engage in somewhat circular reasoning. These kinds of things are hard for laypeople to detect; even scientists trained in a different field may not recognize there is a problem. That’s why it is enormously useful to have important claims evaluated by someone who is knowledgeable in the particular subject under dispute, especially if the dispute matters to a great many people.

Richard Buggs, Reader at Queen Mary University of London, is a well-respected geneticist, with numerous papers published in molecular ecology, genomics, and molecular evolution. He knows something about population genetics. In a post on October 28 on the Nature Ecology and Evolution community website, Buggs questioned assertions made by Professor Dennis Venema (Trinity Western University) in his book Adam and the Genome, concerning the possibility of a first human pair. He begins thusly:


Does genomic evidence make it scientifically impossible that the human lineage could have ever passed through a population bottleneck of just two individuals? This is a question I am asked semi-frequently by religious friends….

The issue is this. Believers in Abrahamic religions who accept evolution often combine it with belief that all humans have descended from a single couple. Until now, many have assumed that this belief is compatible with evolution and mainstream science.

This needs to change, according Christian biologist Dennis Venema writing in the 2017 book Adam and the Genome. Chapter 3 of this book claims that three population genetic studies give independent estimates that the population size of humans has never dropped below around 10,000 individuals. Venema declares that a bottleneck of two is impossible, and this is a fact of comparable scientific certainty to heliocentrism. He gives his Christian readers a stark choice between embracing mainstream science, or sticking with untenable beliefs about an ancestral couple.

Buggs finds himself unable to agree with such a dogmatic statement.

This is fine, so long as mainstream science really is showing that a single-pair bottleneck somewhere in the history of humankind is an absolute impossibility. But having looked at the evidence that Venema describes and cites, I am not yet convinced. I can’t echo him and say to someone who believes in an extreme human population bottleneck that they are against science.

His article goes through the arguments that Venema addresses in his book, and shows for each why it is impossible to rule out the possibility of a first pair as the origin of humanity.

Reduction in Genetic Diversity

Venema argues that having a single pair as the starting point for humanity would cause an extreme bottleneck, leading to an extreme loss in genetic diversity. (He assumes humanity is descended from ape-like ancestors that are the source of that diversity.) On the face of it, it seems reasonable that such a bottleneck in the human lineage would cause an extreme reduction in genetic diversity. But not all bottlenecks are the same. Bottlenecks that last a long time do eliminate diversity, but short sharp ones may not, such as would be the case for a single pair at the start of humanity.


[P]opulation geneticists (M. Nei, T. Maruyama and R. Chakraborty 1975 Evolution, 29(1):1-10) showed that even a bottleneck of a single pair would not lead to massive decreases in genetic diversity, if followed by rapid population growth. When two individuals are taken at random from an existing large population, they will on average carry 75% of its heterozygosity (M. Slatkin and L. Excoffier 2012 Genetics 191:171–181). From a bottleneck of a single fertilised female, if population size doubles every generation, after many generations the population will have over half of the heterozygosity of the population before the bottleneck (Barton and Charlesworth 1984, Ann. Rev. Ecol. Syst. 15:133-64). If population growth is faster than this, the proportion of heterozygosity maintained will be higher.

Buggs then goes on to address a related subject called allelic richness, or how many variants of each gene there are. Venema states the problem as follows:

Taking into account the human mutation rate, and the mathematical probability of new mutations spreading in a population or being lost, these methods indicate an ancestral population size for humans right around that 10,000 figure. In fact, to generate the number of alleles we see in the present day from a starting point of just two individuals, one would have to postulate mutation rates far in excess of what we observe for any animal.

How does Buggs respond?

We need to bear in mind that explosive population growth in humans has allowed many new mutations to rapidly accumulate in human populations (A. Keinan and A. G. Clark (2012) Science 336: 740-743). Hyper-variable loci like MHC genes or microsatellites have so many alleles that they seem to defy the idea of a single couple bottleneck until we consider that they have very rapid rates of evolution, and could have evolved very many alleles since a bottleneck.

Linkage Disequilibrium Within Populations

Linkage disequilibrium (LD) is a measure of how much recombination has occurred between sites on a chromosome, and because of mathematical relationships between LD and population size, can be used to estimate the size of a population at a particular time. Venema chose to use an LD study (Tenesa et al. “Recent Human Effective Population Size Estimated from Linkage Disequilibrium,” Genome Research 17: 520–26) to argue that we could never have come from just two. As Venema says:

The researchers found that, during this period [200,000 years ago], humans living in sub-Saharan Africa maintained a minimum population of about 7,000 individuals, and that the ancestors of all other humans maintained a minimum population of about 3,000 — once again, adding up to the same value other methods arrive at.

Buggs responds:

This is a rather inaccurate presentation of the paper. The paper’s discussion starts with the sentence: “Overall, the estimates of Ne [effective population size] appear to be much lower than the usually quoted value of 10,000”. It seems to me that the paper gives no warrant for Venema’s addition of effective population sizes above and below the Sahara, as it explains that the non-sub-Saharan populations contain a “subset of the amount of genetic variation present in the African population” due to an out-of-Africa expansion. It is the ancestral sub-Saharan estimate that therefore is of main interest to us. The mean estimated Ne for this population among chromosomes is 6286, with a standard deviation of 1357.

This study depends critically on knowing the recombination rate of the populations. Recombination rate is used both to calculate effective population size (from LD) and to estimate the time point that this is being measured for (from distance between loci). But the main method used to estimate the recombination rate by the authors is patterns of LD. Linkage disequilibrium patterns are also being used to calculate the effective population sizes given a known recombination rate. A degree of circular reasoning seems to be inevitable here. When the authors use a slightly different method to estimate recombination rate (which also relies upon measures of LD), all their estimates of Ne dropped by a mean of 27%. Thus, with the best will in the world, all we have here are ballpark figures for past effective population sizes. I am sure the authors of the study would not view their results as being of equivalent certainty to heliocentrism.

Obviously, however, the paper at no point gives an effective population size estimate as low as two individuals. Does this therefore disprove the hypothesis of a bottleneck of two? I don’t think so, because such a scenario is simply not on the radar of the methods employed. The methods assume that the populations at any given time point are at equilibrium and not expanding exponentially (the authors deliberately exclude the last 10,000 years from this analysis as they know that exponential population growth has occurred in this timeframe). It is hard to see how they could pick up on a short, sharp bottleneck even if one had happened. It would be nice to see this modelled, just to check.


Even if the results of this study are entirely correct, the authors do not make any statements about population size more than 200,000 years ago. This would appear to leave open the possibility of a bottleneck in the previous 5.8 million years.

PSMC Method

The pairwise sequentially Markovian coalescent model (PSMC) is used to analyze single genomes to infer past effective population sizes from patterns of heterozygosity. The first paper to do so was Li and Durbin 2011 (“Inference of Human Population History from Individual Whole-Genome Sequences” Nature 475: 493– 96). Buggs explains:


When run on human genomes, these analyses did not drop below an Ne [effective population size] of 5,700 for African individuals. Does this prove that a sudden, short bottleneck never happened? I don’t think so. Because a single couple can carry with them 0.75 of the heterozygosity of their ancestral population, we would not expect an extreme number of coalescence events at the bottleneck. Furthermore, those that are there were would be smeared out over a long period of time around the bottleneck.

Li and Durbin themselves acknowledge that their technique cannot detect short sharp bottlenecks.


…simulations did, however, reveal a limitation of PSMC in recovering sudden changes in effective population size. For example, the instantaneous reduction from 12,000 to 1,200 at 100 kyr ago in the simulation was spread over several preceding tens of thousands of years in the PSMC reconstruction.

Buggs concludes:

Thus I cannot see that PSMC analyses (many more of which have been done on human genomes since the original paper by Li and Durbin) can be cited as rigorously disproving a short, sharp bottleneck.

Incomplete Lineage Sorting

Short and sweet: incomplete lineage sorting doesn’t matter because it all happened before the human lineage was established.

Venema makes an argument based on incomplete lineage sorting among humans, apes and gorillas, which gives a large estimated effective population size. This argument is not relevant if we are only interested in the human lineage (the occurrence of ILS does not require maintenance of large populations sizes in every lineage after speciation and so does not exclude a bottleneck in the exclusively human lineage).

Conclusion

None of the methods that Venema cites are able to address the problem of the existence of a first pair. Either they are insensitive to short sharp bottlenecks (reduction in genetic diversity, PMSC) or they are not designed to ask the questions at hand, and even engage in somewhat circular reasoning (linkage disequilibrium, incomplete lineage sorting), or they neglect the fact of explosive population growth and high rates of mutation accumulation (allelic richness). It is not to say that these papers are bad, rather they do not address the possibility of a short sharp bottleneck. For that a new approach is needed.


In closing it is best to let Buggs speak for himself:

The question asked by my religious friends is different to the questions being asked in the studies discussed above. My religious friends are not asking me if it is probable that humans have ever passed through a bottleneck of two; they are asking me if it is possible. None of the studies above set out to explicitly test the hypothesis that humans could have passed through a single-couple bottleneck. This is what we need to nail this issue down.

I would very much appreciate feedback from scientific readers of this blog. I have dealt with arguments made in a single book chapter, that has addressed this issue more directly than any other source I have come across. The author, Dennis Venema, is the go to expert on this issue within the organisation BioLogos, set up by Francis Collins (now director of NIH) to explore science-faith issues, so he ought to know what he is talking about. However, there may well be other, perhaps better, arguments that Venema has not made and I have therefore not interacted with.


If I am missing something, then I would very much like to know. Whilst this issue may seem trivial to many readers, for large numbers of religious believers in the world, this is a critical issue. Do they really face a binary choice between accepting mainstream science and believing that humans have, at some point in their history, all descended from a single couple? I am open to the possibility that they do face this dilemma, but I need more evidence before I am persuaded.