Darwin, Wallace and class.

 Why Darwin Eclipsed Wallace: Darwin and the English Class System 

Neil Thomas 

The theory of natural selection was the co-discovery of two men, but by the mid 1860s one of its progenitors began to reject his own theory, scarcely more than a half decade after first announcing it to the world. Towards the end of his life Alfred Russel Wallace would resolve the conceptual confusion surrounding the curious “half-and-half” dualism which initially prompted him to claim that it was only mankind’s mental faculties which had been designed, natural selection having fashioned our bodies. That improbable thesis was later to be replaced by his contention that the totality of (wo)man — body and mind — had arisen from what today would be called intelligent design, and, moreover, that the same applied to the whole sentient universe. This was indeed a root-and-branch “apostasy” from his prior convictions.

Why have people not registered this rejection of the theory by its co-author more strongly? Why is it Charles Darwin’s view which has persisted while Wallace’s has been airbrushed out of history? Predictably, the quintessentially English subject of class has been invoked to answer this question. Sociologists of science often point to the fact that the progress of scientific ideas advances in part as a form of social process, and Darwin, unlike the impoverished and socially less well-placed Wallace, was fortunate to have an upper-middle-class support group to promulgate his ideas. 

How convincing is this thesis as an explanation for Darwin’s greater success? I have argued elsewhere that the major role in the acceptance of Darwinism depended not so much on social factors but on the truly seismic changes in attitudes to religion experienced by all classes of society by the middle of the 19th century. But this does not mean that social factors played no part at all. How might those factors be characterized?

With a Little Help from His Friends

There are indications that Darwin over time gained something of the de facto status of a cult leader (in an unexceptionably benign sense). There cannot be many natural scientists who have inspired a follower to write a fulsome, 50-page poem in their memory, but after Darwin’s death in 1882 this is precisely what occurred. A younger acolyte, the naturalist George Romanes (pictured above), venerated Darwin so greatly — “this side idolatry” seems the entirely appropriate phrase — that he chose this form of laudation for a commemorative poem titled with lapidary simplicity, “Charles Darwin: A Memorial Poem.”1 There is ample evidence in Darwin’s voluminous correspondence with both indigenous and overseas scholars —continued without interruption even when chronic illness kept him house-bound — and in the “pilgrimages” to Down House he inspired from his old boys’ network of former college friends and tutors, that he had an enviable gift for friendship, even to the point of being able to inspire forms of fraternal love.

Only on the assumption of such personal magnetism can we understand such things as his limitlessly supportive inner circle meeting regularly to discuss matters of personal and professional interest with him. The severe-looking photographs of the bearded patriarch that have come down to us clearly give few hints of the sheer charisma he must have projected to inspire such admiration and affection. Romanes’s poem, which set off the high honour already accorded to Darwin in his burial in the north aisle of the nave of Westminster Abbey, near to Sir Isaac Newton, might have suggested to some an aura close to sanctity or at the very least a symbolic assumption into a form of scientific empyrean. 

The Darwin Circle: A Small World

To those acquainted with modern Britain, a place which frowns on nepotism and cronyism (at least officially), and which has opened itself up to meritocratic selection procedures and the importation of foreign talent, it is rather surprising that the same cast of characters keep popping up again and again in the drama of Darwin’s life.2 Clergyman and botanist Professor John Stevens Henslow (1796-1861)3 would regularly hold soirées at his home, attended by Darwin and Darwin’s Cambridge tutors, William Whewell and Adam Sedgwick, the latter having been Darwin’s companion on a number of geological field trips when Darwin was younger and in better health. Henslow’s daughter was later to marry one of Darwin’s closest friends, the botanist Joseph Dalton Hooker. It was Henslow who recommended Darwin for the Beagle expedition in the early 1830s and again Henslow who chaired the famous Oxford debate in 1860 where Bishop Wilberforce squared off against Darwin’s “bulldog,” Thomas Henry Huxley. Despite his reservations about Darwin’s ideas, Henslow’s avuncular relationship with Darwin bade him always do his best to protect Darwin from harsh criticism.4 The same was the case with Adam Sedgwick. Sedgwick disagreed with Darwin’s ideas in the Origin so radically that, far more in sorrow than in anger, he once described Darwin’s ideas in a confidential letter to palaeontologist Richard Owen as being at one and the same time saddening and risible. For him, his erstwhile protégé was “a teacher of error instead of the apostle of truth.”5 Notwithstanding these reservations, he remained on commendably friendly terms with Darwin for the remainder of his life.The recipient of this amount of indulgence from his friends clearly had every reason to feel secure in the knowledge that he commanded a supportive in-group whose loyalty he could depend on absolutely. So it was that in 1856, at a hush-hush meeting at Down House convened by Darwin, he took soundings with Hooker and Huxley as to how best to proceed with his heretofore secret ideas concerning evolution. Huxley, despite the fact that he had condemned ideas similar to those of Darwin when they had been presented in Robert Chambers’s Vestiges of the Natural History of Creation (1844), and that he would never reconcile himself with Darwin’s special theory of natural selection, immediately volunteered to defend Darwin’s ideas, being more than willing to take Darwin’s corner against the high authority of Richard Owen. In the words of Iain McCalman, alluding to the fact that so many of Darwin’s intimates were part of an old sea-dog confraternity who had made voyages of scientific discovery of their own, Huxley had come aboard and “joined Darwin’s fleet.”6 Huxley might have been, in Peter Bowler’s phrase, a “pseudo-Darwinian” (that is, a believer in evolution but not natural selection), yet he would not hear a word said against Darwinism in any of its facets.There is no getting away from the socially parochial aspect of English life at this time. The same names recur in the Darwin story simply because debate about matters of high import at the time were debated and largely decided by an “upper crust” of ex “public”7 school boys and Oxbridge graduates. These persons would typically not even meet, let alone converse with members of “lower” social classes (except in trading transactions) because it was tacitly accepted that it was only the views of the social elite which counted.

Tomorrow, “Why Darwin Eclipsed Wallace: Darwin Comes to America. 

Ps. Ecclesiates9:16KJV"Then said I, Wisdom is better than strength: nevertheless the poor man's wisdom is despised, and his words are not heard."

Resistance is futile.

Ecclesiastes7:13KJV"Consider the work of God;

For who can make straight what He has made crooked?"

Here is the expositor's commentary on this passage: ); once let him see that the thing is crooked, and was meant to be crooked, and he will accept and adapt himself to it, instead of wearying himself in futile attempts to make, or to think, it straight.:  Now consider our Lord words at John17:9KJV"I pray for them: I pray NOT for the world, but for them which thou hast given me; for they are thine." And also Jeremiah7:16KJV"Therefore pray not thou for this people, neither lift up cry nor prayer for them, neither make intercession to me: for I will NOT hear thee."  It is waste of time and resources to attempt to save any nation or civilization rejected by The Lord JEHOVAH. Individuals who humble themselves and prove to be of a different spirit to their contemporaries may be shown mercy. But their is truly no straightening of what the Lord JEHOVAH has decreed crooked.

The prosecutor's fallacy: a brief history.

 Prosecutor's fallacy 

The prosecutor's fallacy is a fallacy of statistical reasoning involving a test for an occurrence, such as a DNA match. A positive result in the test may paradoxically be more likely to be an erroneous result than an actual occurrence, even if the test is very accurate. The fallacy is named because it is typically used by a prosecutor to exaggerate the probability of a criminal defendant's guilt. The fallacy can be used to support other claims as well – including the innocence of a defendant. 

A simple example illustrating the prosecutor's fallacy. (The hypothesis is the possibility that the defendant is guilty, whereas the evidence found refers to a positive test result, such as a DNA or blood type match.) Although the probability that evidence is found on the real culprit may be quite high (in this case, two-fifths, or 40%), the probability that a certain individual is guilty given that said evidence was found in him is unrelated to the former, and will often be much smaller (in this example, only two-eighths, or 25%). For instance, if a perpetrator were known to have the same blood type as a given defendant and 10% of the population to share that blood type, then one version of the prosecutor's fallacy would be to claim that, on that basis alone, the probability that the defendant is guilty is 90%. However, this conclusion is only close to correct if the defendant was selected as the main suspect based on robust evidence discovered prior to the blood test and unrelated to it (the blood match may then be an "unexpected coincidence"). Otherwise, the reasoning presented is flawed, as it overlooks the high prior probability (that is, prior to the blood test) that he is a random innocent person. Assume, for instance, that 1000 people live in the town where the murder occurred. This means that 100 people live there who have the perpetrator's blood type; therefore, the true probability that the defendant is guilty – based on the fact that his blood type matches that of the killer – is only 1%, far less than the 90% argued by the prosecutor. 

At its heart, therefore, the fallacy involves assuming that the prior probability of a random match is equal to the probability that the defendant is innocent. When using it, a prosecutor questioning an expert witness may ask: "The odds of finding this evidence on an innocent man are so small that the jury can safely disregard the possibility that this defendant is innocent, correct?"[1] The claim assumes that the probability that evidence is found on an innocent man is the same as the probability that a man is innocent given that evidence was found on him, which is not true. Whilst the former is usually small (approximately 10% in the previous example) due to good forensic evidence procedures, the latter (99% in that example) does not directly relate to it and will often be much higher, since, in fact, it depends on the likely quite high prior odds of the defendant being a random innocent person. 

Mathematically, the fallacy results from misunderstanding the concept of a conditional probability, which is defined as the probability that an event A occurs given that event B is known – or assumed – to have occurred, and it is written as P(A|B). The error is based on assuming that P(A|B) = P(B|A), where A represents the event of finding evidence on the defendant, and B the event that the defendant is innocent. But this equality is not true: in fact, although P(A|B) is usually very small, P(B|A) may still be much higher. 

 

And still yet more on why primeval tech is the bane of Darwinism.

 Yes, a “Host of Machines” Are at Work in the Cell 

David Coppedge 

Much as we love the old standbys (the flagellum, cilium, ATP synthase, etc.), we should never assume that the case for intelligent design is restricted to those iconic favorites. In 2002, Jed Macosko claimed in Unlocking the Mystery of Life that there are “a host of machines” at work in the cell — as many as there are functions that the body has to perform. Each machine is a marvel of engineering and precision. Let’s visit a few more of them.Another Topoisomerase

Discovery Institute’s recent animation of a Type 2 topoisomerase dazzled us with its ability to accurately cut DNA and stitch it back together to fix twisted loops that could send a genome into a tailspin. The family of topoisomerase machines, though, includes six types just as amazing. Topoisomerase 3β (abbreviated TOP3B) received an ovation this month from Yang et al. in Nature Communications. This one “regulates R-loop dynamics and mRNA translation, which are critical for genome stability, neurodevelopment and normal aging.” TOP3B is a Type 1 topoisomerase that repairs one strand of DNA (see below for a simple video demonstration). The details are more complex than shown, as this excerpt from the paper demonstrates:

As a Type IA topoisomerase, TOP3B acts by general acid-base catalysis to break and rejoin single-stranded DNA. Passage of a second DNA strand through the transient break permits dissipation of hypernegative DNA supercoiling and catenation/knotting. Additionally, hsTOP3B was recently demonstrated as the human RNA topoisomerase, required for normal neurodevelopment and proposed to be a potential anti-viral target upon RNA virus infection. Here we elucidate the biochemical mechanisms of human TOP3B. We delineate the roles of divalent metal ions, and of a conserved Lysine residue (K10) in the differential catalysis of DNA and RNA. We also demonstrate that three regulatory factors fine-tune the catalytic performance of TOP3B: the TOP3B C-terminal tail, its protein partner TDRD3, and the sequence of its DNA/RNA substrates.One other surprise is worth noting: the need for metal ions to cut the nucleic acids: “addition of Mg2+ and to a greater extent Mn2+ stimulated DNA binding and cleavage by TOP3B.” Is it fair to say that this machine has metal cutting blades?

Another Dart Gun 

We’ve learned about the Type 3 Secretion System and the Type 4 Secretion System in bacteria that shoot molecules outside their membranes, but there’s another we haven’t considered for a while: Type 6. An Evolution News article in 2015 discussed its firing mechanism. Now, Lin Lin and colleagues at the University of Basel, Switzerland, have published an open-access paper in the EMBO Journal describing T6SS assembly. The machine looks like a cannon or bazooka in the figures. Remarkably, this “large nanomachine that can deliver toxins directly across membranes of proximal target cells” appears to assemble rapidly on contact when the bacterium encounters a rival in “interbacterial competition.”We identified a class of diverse, previously uncharacterized, periplasmic proteins required for this dynamic localization of T6SS to cell–cell contact (TslA). This precise localization is also dependent on the outer membrane porin OmpA. Our analysis links transmembrane communication to accurate timing and localization of T6SS assembly as well as uncovers a pathway allowing bacterial cells to respond to cell–cell contact during interbacterial competition.

This implies that the components are stored locally throughout the inner membrane to avoid the cost of maintaining an arsenal all over the cell. It also implies contact sensors to activate the assembly — which the authors found.In this work, we reveal a mechanism of localization of a complex nanomachine in response to contact with another cell. Such precise positioning likely requires temporal and spatial coordination of many regulatory proteins at the membrane. Since many T6SS accessory proteins remain uncharacterized, we propose that some of these proteins might be required for spatiotemporal regulation of T6SS assembly. We expect that additional mechanisms of dynamic localization of T6SS will be identified in more bacteria and shown to play an important role in their pathogenesis or ecology.

The authors use strategic mission terms like “attack” in their belief that the T6SS “likely evolved to allow efficient killing of target cells.” But we shouldn’t take the warfare motif too seriously. They’re just bacteria. Maybe the colony is programmed to regulate its surroundings this way. They expect that higher resolution imaging will “unravel additional intricate mechanisms of T6SS targeting.”Nitrogenase Black Box

One of the most important enzymes in all nature, nitrogenase has defied analysis. This multi-part machine with metals in its core is the only enzyme that can split the tough triple bonds of atmospheric nitrogen. The enzyme is only found in bacteria that form symbiotic relationships with the roots of some plants. Biophysicists have tried for years to open the black box of nitrogenase, but its conformational changes are fleeting and difficult to capture. 

Reduced forms of nitrogen are essential for the biosynthesis of amino acids and nucleic acids as well as the production of fertilizers and many commodity chemicals. As the only enzyme capable of nitrogen fixation, nitrogenase catalyzes the eight-electron reduction of atmospheric nitrogen (N2) and protons (H+) into ammonia(NH3) and hydrogen (H2) (Fig. 1A). Nitrogenase is a two-component enzyme, which, in its most common form, consists of the iron protein FeP (a γ2 homodimer) and the molybdenum-iron protein MoFeP (an α2β2 heterotetramer) (Fig. 1B) (4, 5). Nitrogenase is distinct from most redox enzymes in its requirement for adenosine triphosphate (ATP) hydrolysis to enable the successive transfer of electrons and protons for substrate reduction. 

As stated, this machine can precisely break and re-join single strands of DNA to untie knots. Like its Type 2 counterpart that can cut and splice two strands at a time, TOP3B works in a “three-step strategy — DNA cleavage, strand passage, DNA rejoining.” It requires three fine-tuned regulatory cofactors to work. And it is required for normal neurodevelopment. Hannah L. Rutledge at UC San Diego (Science) used cryo-electron microscopy and abundant ATP to capture a few more frames in the “movie” of this remarkable and unique machine. Based on the states they were able to capture, they think they see how the game is being played:

Given the asymmetry between the FeMoco’s in the two αβ halves, it is tempting to propose a “ping-pong”–type mechanism in which the cofactors proceed through each of the eight catalytic steps in an alternating fashion. This scenario would assign a dual role to FeP: (i) to deliver an electron to one αβ subunit of MoFeP and (ii) to suppress FeP binding to the opposite αβ subunit while priming it for catalytic transformations through long-distance activation of electron, H+, and/or substrate access pathways to the distal FeMoco. Establishing whether such a mechanism is operative will require future studies, but our current work illustrates that it is possible to characterize nitrogenase under turnover conditions by cryo-EM at near-atomic resolution, representing a critical step toward understanding the mechanism of this enigmatic enzyme in full structural detail.

When that day comes, it could revolutionize agriculture. An article from Tsinghua University Press (Phys.org) says that “major breakthroughs are still badly needed” to replace the energy-intensive Haber-Bosch process which “is disrupting the planet’s nitrogen cycle, warming the globe, and potentially risking the health of millions.” Imitating the way cells do it might allow scientists to fix nitrogen at ambient temperatures. Nitrogenase is a molecular machine to watch! 

Rubisco Geometry

Another vital enzyme for the biosphere is Rubisco, which fixes carbon for conversion to sugars. Emily Reeves wrote about how it works last year, so readers are referred to that article for background. A new open-access paper in Nature Communications by Lauren Ann Metskas et al. adds some interesting details about its geometry: it forms a lattice inside tiny geometric domes. 

This arrangement preserves freedom of motion and accessibility around the Rubisco active site and the binding sites for two other carboxysome proteins, CsoSCA (a carbonic anhydrase) and the disordered CsoS2, even at Rubisco concentrations exceeding 800 μM. This characterization of Rubisco cargo inside the α-carboxysome provides insight into the balance between order and disorder in microcompartment organization.The research team points out that many prokaryotes segregate their machines into microcompartments like this, contrary to earlier assumptions that the enzymes just float around in the interior. Like the cell’s outer membrane, a proteinaceous shell “selectively restricts passage of key intermediates and improves on-target catalysis.” 

Interest in “microcompartment bioengineering” has grown in recent years, the authors say. The paper shows electron micrographs of some of these remarkable geometric compartments with the Rubisco enzymes neatly packed inside but “surprisingly” not in contact with the shell. “The six-fold lattice may therefore be a packing mechanism to preserve function at concentrations that could otherwise crystallize or sterically impede function.” That makes design sense.

Microcompartment bioengineering is a growing field, and this polymerization-based mechanism for efficient, functional, and controlled packing of enzymes may be useful for future discovery and designs in both CBs [carboxysomes] and other microcompartments.Once again, observation and expectation of design from an engineering perspective is proving fruitful in opening the black boxes of the cell and peering at the watch-like moving parts inside. The future looks bright for nanobiotechnology, and with it, increases in global human flourishing. Intelligent design is proving to be “useful for future discovery and designs.” 

Closer to a theory of devolution

 Michael Behe: Evolution, Devolution, Design 

Evolution News @DiscoveryCSc

A new ID the Future episode features three recent Evolution News essays by Lehigh University biology professor and Darwin Devolves author Michael Behe, as read by host Andrew McDiarmid. In the first, nothing shows the feebleness of Darwinism quite so much as breathless stories about new results that turn out to be much ado about nothing. In this case, it’s some recent speculation about the rise of “lactase persistence” in many human adults. Then it’s onto malaria, much beloved of evolutionists, not for its lethality but as a demonstration of evolution in action. But Behe dissects the latest news story on the topic to show that the touted malaria evolution is, once again, malaria gnawing off the proverbial leg to achieve a niche advantage — that is, mere devolution. It’s akin, Behe says, to the rise of tuskless elephants in Africa, where having the devolutionary mutation that leaves an elephant tuskless renders the creature of no interest to elephant-slaying ivory poachers, thereby improving its chances of survival. In the third essay Behe makes a case for his favorite way of concisely describing what we detect when we detect intelligent design in biology.Download the podcast or listen to it here.

Knowing the truth v. Possessing the truth /being possessed by the truth.

 Luke8:4-8NIV"4While a large crowd was gathering and people were coming to Jesus from town after town, he told this parable: 5“A farmer went out to sow his seed. As he was scattering the seed, some fell along the path; it was trampled on, and the birds ate it up. 6Some fell on rocky ground, and when it came up, the plants withered because they had no moisture. 7Other seed fell among thorns, which grew up with it and choked the plants. 8Still other seed fell on good soil. It came up and yielded a crop, a hundred times more than was sown.”

When he said this, he called out, “Whoever has ears to hear, let them hear.” 

Luke8:11-15NIV"11“This is the meaning of the parable: The seed is the word of God. 12Those along the path are the ones who hear, and then the devil comes and takes away the word from their hearts, so that they may not believe and be saved. 13Those on the rocky ground are the ones who receive the word with joy when they hear it, but they have no root. They believe for a while, but in the time of testing they fall away. 14The seed that fell among thorns stands for those who hear, but as they go on their way they are choked by life’s worries, riches and pleasures, and they do not mature. 15But the seed on good soil stands for those with a noble and good heart, who hear the word, retain it, and by persevering produce a crop."

The call of Christ is a call to arms.

Matthew 10:34NIV"Do not suppose that I have come to bring peace to the earth. I did not come to bring peace, but a sword."

But having made common cause with JEHOVAH and his Son how does one avoid becoming numbered among the casualties on this battlefield. Obviously knowing the truth or knowing JEHOVAH is not enough.

James2:19NIV"You believe that there is one God. Good! Even the demons believe that—and shudder."

So what then?

James4:8NIV"Come near to God and he will come near to you. Wash your hands, you sinners, and purify your hearts, you double-minded." 

The trouble is ,that like every other truly worthwhile achievement this kind of transformative intimacy with the Lord JEHOVAH requires disciplined effort. Note also that an outward change is not the primary objective ,for this change must affect the examiner of hearts himself.

1Thessalonians2:4NIV"On the contrary, we speak as those approved by God to be entrusted with the gospel. We are not trying to please people but God, who tests our hearts."

We leave off the transactional way of thinking that marked our initial relationship with JEHOVAH and with his unfailing help adopt a more devotional mindset. Our Lord has shown us the way to wage victorious spiritual warfare.

John16:33NIV"I have told you these things, so that in me you may have peace. In this world you will have trouble. But take heart! I have overcome the world.”" his intimate relationship with his God JEHOVAH is our model.

The Lord JEHOVAH and numbers.

 Deuteronomy7:7NIV"The LORD did not set his affection on you and choose you because you were more numerous than other peoples, for you were the fewest of all peoples."

Matthew22:14NIV"For many are invited, but few are chosen.”

Luke6:26NIV"Woe to you when everyone speaks well of you, for that is how their ancestors treated the false prophets."

Matthew7:14NIV"But small is the gate and narrow the road that leads to life, and only a few find it."

Matthew7:21-23NIV"“Not everyone who says to me, ‘Lord, Lord,’ will enter the kingdom of heaven, but only the one who does the will of my Father who is in heaven. 22Many will say to me on that day, ‘Lord, Lord, did we not prophesy in your name and in your name drive out demons and in your name perform many miracles?’ 23Then I will tell them plainly, ‘I never knew you. Away from me, you evildoers!’"

Matthew5-11,12NIV"“Blessed are you when people insult you, persecute you and falsely say all kinds of evil against you because of me. 12Rejoice and be glad, because great is your reward in heaven, for in the same way they persecuted the prophets who were before you."

Judges7:2NIV"2The LORD said to Gideon, “You have too many men. I cannot deliver Midian into their hands, or Israel would boast against me, ‘My own strength has saved me.’ "

The Lord JEHOVAH is a majority all by himself thus unsurprisingly his view of numbers is very different from that of mere men.

The Lord JEHOVAH vs. all flags.

Only when mankind is governed by a ruler who needs nothing from it (including it's consent) will there be liberty and justice for all.

 1JEHOVAH hath reigned, The earth is joyful, many isles rejoice.

2Cloud and darkness [are] round about Him, Righteousness and judgment the basis of His throne.

Charles Darwin and the tower of Babel.

 Language: Darwin’s Eternal Mystery

Neil Thomas. 

In a previous contribution I expressed regret that the modern age did not have an outstanding satirist willing to take on overblown scientific pretensions of the stature of the early 19th-century satirical novelist Thomas Love Peacock. I recalled the magnificent quatrain he chose as the preface for his first novel, Headlong Hall (1816), which, although it was meant to lampoon ideas like phrenology belonging to his own age, would seem to fit the post-Darwinian era all too well: 

All philosophers, who find

Some favourite system to their mind

In every point to make it fit,

Will force all nature to submit.1

One can only speculate what Peacock (1785-1866) in his prime might have made of Darwin. His second novel, Melincourt (1817), featured an ape standing for Parliament under the name of Sir Oran Haut-ton, a spoof on the 18th-century speculation of the Scottish jurist Lord Monboddo (James Burnet) on the simian ancestry of mankind. But since the eccentric Monboddo’s ideas were commonly taken to be an elaborate joke born of intellectual diablerie, Peacock could not advance far beyond the slapstick element of his conceit to explore the deeper, metaphysical implications of Monboddo’s idea.

Enter Tom Wolfe

When I lamented the absence of such a writer as Peacock in the 21st century it must have temporarily slipped my mind that we do have a writer of a standing fully equal to that of Peacock in the shape of Bonfire of the Vanities author Tom Wolfe. In Wolfe’s The Kingdom of Speech (2016),2 published just two years before the author’s death, Wolfe took time out from his creative writing to focus on the everlasting crux of the origin of the human speech facility. It is a mystery which has puzzled humanity at least since the time of Johann Gottfried Herder in the 18th century and, as Wolfe points out with some humorous relish,3 the roots of the language facility remain as unknown now as they did when Herder wrote his Ueber den Ursprung der Sprache (On the Origin of Language) in 1772.

Neither Herder nor later Darwin, as Wolfe points out, could find one shred of evidence that human speech had evolved from animals. This was particularly galling to Darwin since his whole life was essentially a quest for the secrets of creation or, as Wolfe phrases it in more mordant tones, “Darwin had fallen, without realizing it, into the trap of cosmogonism, the compulsion to find the ever-elusive Theory of Everything, an idea or narrative that reveals everything in the world to be part of a single and suddenly clear pattern.” (p. 20)

Western and Native American Cosmogonies

In reviewing that fruitless human quest for explanations about origins, Wolfe appends an overview of native American cosmogonies, finding the Apache version of the creation of the whole firmament by a scorpion to be but a more colorful and imaginative version of “the currently solemnly accepted — i.e., ‘scientific’ — Big Bang theory, which with a straight face tells us how something, i.e. the whole world, was created out of nothing.” (p. 22)

Wolfe surely has a point. The current understanding of the universe’s origin — subject of course to no other, more convincing theory being advanced in my or your lifetime — is that about 15 billion years ago all mass and energy were compacted together but (for reasons equally unknown and doubtless forever unknowable) simply proceeded to inflate. Cosmologists, who are remarkably honest about their inability to illuminate the sheer unintelligibility of the cosmos (sometimes, it strikes me, even taking a perverse, mock- masochistic delight in the way it seems to cast out curve-balls in the way of human understanding4), concede that this originary event occurred “just like that” ­— without discernible rhyme or reason (that we or they can know of).

It can scarcely be denied that the Big Bang theory, despite its widespread acceptance by the scientific community and by the public at large (albeit passively), remains irredeemably problematic in logical terms: how can something come from nothing? It seems that the primal ka-boom lies quite beyond our conceptual bounds. Or, with reference to the older steady-state theory, how could something always have been there? The human mind at this point inevitably experiences what Chomsky once called “cognitive closure” — complete bafflement. We are left in the unenviable position of neither alternative making sense to us, both Big Bang and Steady State paradigms being equally overweighted by logic-defying anomalies.

The Big Bang theory is perhaps the more problematic of the two. To accept the proposition that an unregulated, chance explosion/expansion produced our terrestrial order is rather like buying into that old canard that the multiple volumes of the Oxford English Dictionary could have been produced by an explosion in an ink shop. If on the other hand the explosion had been very precisely calibrated (somehow, by a higher power unknown) in order to deliberately retrieve order from seeming chaos, then that premeditated deliberation would in good logic demand a designing originator, and this would make the Big Bang a story of creation in the fullest sense.5 That conclusion of course would tip us into the theological realm of discourse in quest of a logical explanation to cover the totality of known facts. For the idea of the whole universe-in-embryo compressed into the space of a single subatomic particle would count in most people’s book as a full-on miracle, barely if at all distinguishable from the Bible’s creation ex nihilo, and it is little wonder that advances in modern science have sometimes been read as confirmation of the Biblical account contained in Genesis.6 They have at the very least done nothing to disprove the Biblical narrative.

Science and Educated Guesswork

What is striking about Wolfe’s analysis is the intellectual equivalence he perceives between such narratives as George Lemaître’s Big Bang, Darwin’s “abiogenetic” theory of life emerging from chemical reactions in a small warm pond, and what he sees as broadly corresponding native American versions. All such theories are “educated guesses,” with minor differences to be explained by the shibboleths of modern science vis-à-vis the more uninhibited speculations of native peoples. So for instance “in the Navajo cosmogony the agent of change was alive. It was the Locust. In Darwin’s cosmogony it had to be scientifically inanimate [to escape charges of animism]. Locust was renamed Evolution…. Like every other cosmogony, Darwin’s was a serious and sincere story meant to satisfy man’s endless curiosity about where he came from and how he came to be so different from the animals around him. But it was still a story. It was not evidence. In short, it was sincere, but sheer, literature.” (p. 27)

“Literature” then, not science, Wolfe concludes — all the more so since evolutionary theory flunks all five commonly acknowledged tests for a valid scientific hypothesis:

Observability

Ability to be replicated

Capacity for Popperian falsification

Can scientists make predictions from it?

Does it illuminate other puzzling areas of science?

Wolfe remarks apropos of those five criteria: “In the case of Evolution… well…no…no…no…no… and no. In other words, there was no scientific way to test it.” (p. 27)

Ape and (Wo)man

In fact, Wolfe suggests with devastating bathos that what moved Darwin to postulate ape ancestry for humankind had nothing to do with science, but rather his visit to London Zoo in 1838 and his observations there of the facial and postural movements of the female orangutan, “Jenny,” sometimes sentimentally decked out in women’s clothing by her keepers.  Such were the rather skewed perceptions which informed Darwin’s Descent of Man (1871) and which, Wolfe reasons, will have lain behind the accumulated excesses and improbabilities of that much later, Darwin-inspired discipline which took off in the 1970s, calling itself first sociobiology before tactically rebranding itself evolutionary psychology.7

With the benefit of hindsight, it appears that the morphological link between ape and (wo)man becomes on closer inspection much less straightforward than it might at first appear, as is shown pre-eminently in the different language competences of apes and humans. To establish a convincing evolution of ape to human it would be necessary to establish that simians could over time have increased their communicative vocabularies so as to transform inarticulate emotional cries into specific vocal symbols. But this in turn brings up the closely related problem of how to explain the rapid mentalprocessing on which articulate speech depends. Without the simultaneous co-adaptation of the simian brain, how could the facility of speech, which depends on the interdependent agency of the brain in tandem with the specialised organs of vocal articulation, have developed by the essentially aleatory processes of natural selection? In order to prove that connection, one would have to be able to point to a precise physiological/neurological pathway of development, which nobody has yet been able to establish.8

Driving Darwin Crazy

How humankind gained its monopoly on language was a puzzle apt to drive Darwin crazy, writes Wolfe, and his co-discover Alfred Russel Wallace to one of the biggest U-turns in recorded history when he came to renounce his own theory of natural selection tout court.  By contrast, notes Wolfe, “a cosmogonist like Darwin couldn’t let it go at that. Speech had to have some animal genealogy…had to fit into his Theory of Everything.” Hence there emerged, concludes Wolfe, “Darwin’s real tour de force of literary imagination, the Descent of Man.” (p. 65) Here he had the licence to develop his Kipling-esque just-so stories (this allegation was made by the late Stephen Jay Gould, to the predictable displeasure of many colleagues). Darwin’s imaginative forays certainly ran counter to the more sober professional counsels of the day. The Philological Society of London in 1872 imposed a form of moratorium on research into language’s origin in 1872 and had been preceded by the Linguistic Society of Paris which actually banned speculation on this subject in 1866.

Bringing the story up to date, Wolfe points out that Noam Chomsky, who for decades thought that he had cracked the language problem by his postulation of a language “organ” situated in the brain, finally threw in the towel and admitted defeat. And as Wolfe somewhat impishly points out, if Chomsky, who had never accepted the development of language by successive evolutionary adaptations, and was now recanting his “organ” theory, then this inevitably had large implications: “Chomsky made it clear he was elevating linguistics to the altitude of Plato’s transcendent eternal universals… He was relocating the field [of inquiry] to Olympus.” (p. 89)

This meant in plain English that he was all but conceding language might have been “God-given” which, in Richard Lewontin’s old phrase, could be construed as the heresy of “allowing a divine foot in the door.”

The Zero-Sum Game

As Wolfe documents, a whole host of “certified geniuses” have failed to crack the human language problem, and this must count as a blow to Darwinian ideas of evolution. For Darwin’s theory is essentially a zero-sum game — if it fails to explain one of its aspects, it flunks the lot. For instance, if you do not prove that life originated by the chemical fluke of abiogenesis, then you cannot coherently argue that “natural selection” went to work on a “creation,” which you have not even proved to have occurred in the way you describe. The well-known Miller-Urey experiment in 1953, designed to spark life in a test tube, was not ultimately successful. Its implicit promise was to be able to extend Darwin’s timeline back to the pre-organic formation of the first cell of life, and so establish the fundamental point of departure for the mechanism of natural selection to go to work on. This would also of course have delivered a stunning victory for the materialist position. In the event, though, it succeeded only in dealing a disabling body blow to materialist notions by its failure to discredit the theistic position.

Without a traceable abiogenetic moment, Darwin’s entire theory of evolution via natural selection fails: as matters stand, the bare emergence of living cells remains an unsolved mystery, let alone the claimed corollary of that mysterious and suspiciously unexplained cellular “complexification” said to follow from it and to have occasioned in future time the fabled development from microbes to (wo)man. In fact, the most significant finding of Miller and Urey appears to have been a presumptive indication of a supra-natural etiology for the cellular system — an inference to theistic creation or theistic evolution which was of course the very obverse of the result both scientists were seeking. 

Hence the attempt to discuss the subject of how the process of selection by Nature began to operate whilst not even broaching the question of how Nature itself arose in the first place must count as a major evasion and as a failure of Darwinian theory as a whole. Which is why Wolfe concludes his study with remarks which call into question the whole neo-Darwinian narrative: “To say that animals evolved into man is like saying that Carrara marble evolved into Michelangelo’s David.” (p. 169) We should be grateful to Wolfe for his single foray into the area of evolutionary speculation, deserving, I would add, of the kind of readership numbers which he was able to command for his creative works.

References

The Novels of Thomas Love Peacock, edited by J. B. Priestley (London: Pan, 1967), p. xvix.

Wolfe, The Kingdom of Speech (London: Jonathan Cape, 2016).

The 20th century’s premier linguist, Noam Chomsky, never backed the idea of language being an evolutionary “adaptation” and latterly even forsook his own theory of there being a language “organ” in the brain. In later years Chomsky retreated to a position of stoic bafflement in the face of the inexplicable. See Wolfe, pp. 3-6. 

I am thinking for instance of the television cosmologist Hakeem Oluseyi (distinguished research professor at the Florida Institute of Technology) whose TV persona contrives not to take either himself or the theories of sundry colleagues overly seriously.

And of course it does come perilously close to the Genesis account, because according to the originating father of the Big Bang theory, the Catholic priest Georges Lemaître, the present exponential expansion of the universe could, by our reversing the process, be traced all the way back to the putative cosmic microdot, the primeval atom. 

See Max Jammer, Einstein and Religion: Physics and Theology (Princeton: Princeton UP, 1999), pp. 253-257.

Wolfe refers to Darwin’s own words in the peroration to his Origin of Species as a kind of “smoking gun” linking Darwin with sociobiology: “In the distant future I  see open fields for far more important researches. Psychology will be securely based on a new foundation, that of the necessary acquirement of each mental power of gradation. Light will be thrown on the origin of man and his history.” (p. 44)

The explanation Darwin advanced in The Descent of Man for his alleged perfectly orchestrated co-adaptation was entirely speculative, as for instance when he muses on where we humans might have got our superior IQ and articulacy from: “The mental powers of some earlier progenitor of man must have been more highly developed than in any existing ape, before even the most imperfect form of speech could have come into use; but we may confidently believe  that the continued use and advancement of this power would have reacted on the mind itself, by enabling and encouraging it to carry on long trains of thought.”

NEIL THOMAS

Neil Thomas is a Reader Emeritus in the University of Durham, England and a longtime member of the British Rationalist Association. He studied Classical Studies and European Languages at the universities of Oxford, Munich and Cardiff before taking up his post in the German section of the School of European Languages and Literatures at Durham University in 1976. There his teaching involved a broad spectrum of specialisms including Germanic philology, medieval literature, the literature and philosophy of the Enlightenment and modern German history and literature. He also taught modules on the propagandist use of the German language used both by the Nazis and by the functionaries of the old German Democratic Republic. He published over 40 articles in a number of refereed journals and a half dozen single-authored books, the last of which were Reading the Nibelungenlied (1995), Diu Crone and the Medieval Arthurian Cycle (2002) and Wirnt von Gravenberg's 'Wigalois'. Intertextuality and Interpretation (2005). He also edited a number of volumes including Myth and its Legacy in European Literature (1996) and German Studies at the Millennium (1999). He was the British Brach President of the International Arthurian Society (2002-5) and remains a member of a number of learned societies.

College outdated?

Exiting the cave?

 Paul Nelson: Freeing Minds Trapped in a Naturalistic Parabola

Evolution News @DiscoveryCSC

On a classic episode of ID the Future, philosopher of biology Paul Nelson talks with host Andrew McDiarmid about pursuing intelligent design theory in a science culture committed to naturalism. As Nelson puts it here, it’s about trying to communicate with scientists who are trapped in a “naturalistic parabola.” That parabola sets the rule and defines the boundaries for science: naturalistic answers only. And it extends to infinity, so no finite number of objections or counter-examples can force naturalistic scientists out of it. Nelson, however, offers an alternative strategy for drawing them out of the parabola. Download the podcast or listen to it here.

The thumb print of JEHOVAH re: Earth's giants.

 Prior Fitness and Dinosaurs

David Coppedge

How big can animals get on a given planet? Michael Denton has made a compelling case that given a habitable planet the size of Earth, humans must be the right size to have the ability to use fire and create technology (The Miracle of Man, pp. 194-197). Humans appear to have the optimal size for these purposes, with arm lengths and hand shapes appropriate for swinging axes and hauling wood for the controlled use of fire. 

These optima have allowed humans to develop modern technology. Physical laws, he shows, rule out the possibility that we could do all we do if we were as small as ants or as tall as 60-foot giants. “We could be neither fire makers nor metallurgists if we were significantly smaller” than we are, he says.

On the other hand, it is fortunate that the ability to hew wood and mine for ores does not necessitate kinetic forces much greater than those that can be generated by organisms of our dimensions. While significantly larger android beings could exert greater kinetic forces, the design of a bipedal primate of, say, twice our height would be severely constrained by kinetic and gravitational forces and be structurally problematic.

Why? For one, and as discussed in Chapter 9, mass (and weight) increases by the length cubed (L3) while the strength of bone and the power of muscles increases only by the length squared (L2). [Emphasis added.]

If we were giants, we would be at daily risk of shattering our bones into pieces. And that’s not all that physics requires of us. In addition to the right body size and shape, Denton argues that we must live on the right size planet. If Earth were smaller, ants might do fine, but such a planet could not maintain a life-giving atmosphere. If Earth were larger, gravity would “exacerbate the dangers of tripping” for upright bipedal creatures like us. Higher gravity would impose “severe constraints on the capacity of muscles to empower movement and support an upright bipedal stance.” Undoubtedly those constraints would impose ripple effects on all our systems: circulatory, respiratory, metabolic, and everything else.

Design Inference from Bones

What about size limits on big animals, like the giant sauropods? Given Earth’s gravity, are there physical limits to their existence, too? 

We don’t expect to find sauropod technology, but the same physical laws (mass increase with height) apply to them. The giant sauropods like Titanosaurus, Ultrasaurus, and Seismosaurus may have lived close to the physical limits of size on an Earthlike planet. Blue whales grow even more massive but are buoyed by water. Extant whales and large land mammals allow us to test theories about design limitations. What about giant creatures that can only be known from their bones?

Denton says that large land animals reduce the risk of falling (and breaking their bones) by walking on all fours. Even so, falling endangers horses and cows. A two-meter tall man faces 20 to 100 times the force of a fall compared to a two-foot child, he notes. (p. 196) The larger the animal, the greater the danger. The fact that giraffes and elephants can survive to adulthood suggests that their large bodies are well engineered for stability. From reconstructions of dinosaurs, the bipedal ones (like theropods) appeared to have good balance because of their tails, and the quadrupeds also had long tails and big feet for stability. In every case, engineering for stability would require attention to bone density, muscle strength, and kinesthetic sense (e.g., inner ear balance organs). 

Biological Cushions

Scientists at the University of Queensland in Australia applied engineering design principles to the largest land animals that ever lived: the sauropods. They applied what is known about tissue anatomy and physiology of elephants and other extant large animals. Elephants, despite appearing to walk flat-footed, actually walk on their toes. Their heels are cushioned by soft tissue padding made of muscles, tendons, ligaments, cartilage, and sole skin. This padding is a design requirement due to the elephant’s high mass. The Australian team wondered if dinosaurs also required foot pads.

Without having living sauropods available to observe, physiologists can infer things from the data available. Knowing that mass increases by the cube of length, biophysicists can estimate requirements for bone density and muscle strength for the giant dinosaurs. The fossilized bones, though mineralized, provide cross-checks for those inferences to a certain extent. Trackways also inform the diameters and shapes of dinosaur feet. What can’t be checked is the soft tissue padding around the foot bones, which is not preserved in fossils.

The Queensland team, led by Andréas Jannel, inferred that a sauropod would have needed padding in its feet to survive. And since dinosaur foot bones are not homologous to elephant feet, the padding had to be designed differently than the padding observed in the hind foot (pes) of an elephant or rhino. Their open-access paper in Science Advances explains how they inferred foot padding as a requirement.

Our results show that, irrespective of skeletal pedal posture (Fig. 1), all sauropodomorph specimens examined (i.e., representatives of distinct clades and diverse body sizes) would have been unable to support their weight without a soft tissue pad in the pes (Figs. 2 and 3). All skeletal morphotypes without a soft tissue pad resulted in maximum von Mises stresses higher than 500 MPa [megapascals] for all pedal models (up to 5000 MPa as recorded in Rhoetosaurus brownei; Fig. 3). As expected, bone stress increased principally in the shafts of each metatarsal and the most proximal phalanges (Figs. 2 and 3), likely due to the pedal posture, boundary conditions, and the fact that the metatarsals are the longest bones in the sauropod pes. Mechanically, it is highly unlikely that sauropod pedal bones could have withstood bone stresses of this magnitude without failing. This is because sauropod bones have been shown to retain the general structural properties of Haversian bone tissue seen in modern birds and large mammals, indicating that they were most likely subjected to comparable mechanical constraints. In humans and bovids, cortical bone (e.g., such as in the femur) has been evaluated to withstand maximum stress < 150 to 200 MPa (44, 45). Hence, within the context of comparable loading regimes, the mechanical state of each sauropod model examined suggests that all skeletal pedal postures would most likely have resulted in mechanical failure (e.g., stress fractures). This state would have been intensified when subjected to repetitive heavy loadings, as would be expected during normal locomotion, ultimately resulting in fatigue fracture in all digits. Being unable to support or move properly, the high probability of mechanical failure would have had a substantial impact on the animal’s survival.

Thinking Like Engineers 

The team used this reasoning to construct models showing where soft tissue would have been needed for cushioning the foot bones of various sauropod species. That’s thinking like engineers. These scientists, being Darwinists, believe that the engineering was supplied by natural selection. But that’s a story for another time. 

The fact remains that they made a design inference based on physics, fossils, and comparisons with living animals. As Denton argues in his “Privileged Species” books and videos, physical laws constrain what beings are possible on a habitable planet. That humans and other living beings thrive so well, and have thrived through Earth’s history, suggests that prior fitness was designed in the fabric of the earth and the universe. And if that is the case, then it’s not a big leap to reason that the specific forms these organisms took were also crafted according to engineering principles — with some artistry thrown in, too.

Darwinism continues to devolve.

 Mammoth Support for Devolution

Michael Behe

The more science progresses, the more hapless Darwin seems.

In my 2019 book Darwin Devolves I showed that random mutation and natural selection are powerful de-volutionary forces. That is, they quickly lead to the loss of genetic information. The reason is that, in many environmental circumstances, a species’s lot can be improved most quickly by breaking or blunting pre-existing genes. To get the point across, I used an analogy to a quick way to improve a car’s gas mileage — remove the hood, throw out the doors, get rid of any excess weight. That will help the car go further, but it also reduces the number of features of the car. And it sure doesn’t explain how any of those now-jettisoned parts got there in the first place.

The Bottom Line

The same goes for biology. Helpful mutations that arrive most quickly are very much more likely to degrade genetic features than to construct new ones. The featured illustration in Darwin Devolves was the polar bear, which has accumulated a number of beneficial mutations since it branched off from the brown bear a few hundred thousand years ago. Yet the large majority of those beneficial mutations were degradative — they broke or damaged pre-existing genes. For example, a gene involved in fur pigmentation was damaged, rendering the beast white — that helped; another gene involved in fat metabolism was degraded, allowing the animal to consume lots of seal blubber, its main food in the Arctic — that helped, too. Those mutations were good for the species in the moment — they did improve its chances of survival. But degradative mutations don’t explain how the functioning genes got there in the first place. Even worse, the relentless burning of genetic information to adapt to a changing environment will make a species evolutionarily brittle and more prone to extinction. The bottom line: Although random mutation and natural selection help a species adapt, Darwinian processes can’t account for the origins of sophisticated biological systems.

In Darwin Devolves, I also mentioned work on DNA extracted from frozen woolly mammoth carcasses that showcased devolution: “26 genes were shown to be seriously degraded, many of which (as with polar bear) were involved in fat metabolism, critical in the extremely cold environments that the mammoth roamed.” It turns out that was an underestimate. A new paper1 that has sequenced DNA from several more woolly mammoth remains says the true number is more than triple that — 87 genes broken compared to their elephant relatives. The authors write of the advantages provided by destroyed genes (references omitted for readability):

Gene losses as a consequence of indels and deletions can be adaptive and multiple case studies investigating the fate of such variants have uncovered associations between gene loss and mammalian phenotypes under positive selection. In laboratory selection experiments, gene loss is a frequent cause of adaptations to various environmental conditions. Given that we focused on those indels and large deletions that are fixed among woolly mammoths, the majority of these protein-altering variants likely conveyed adaptive effects and may have been under positive selection at some point during mammoth evolution. We did not find specific biological functions overrepresented among these genes (see methods), but many of the affected genes are related to known mammoth-specific phenotypes, such as total body-fat and fat distribution (EPM2A, RDH16, and SEC31B), fur growth and hair follicle shape and size (CD34, DROSHA, and TP63), skeletal morphology (CD44, ANO5, and HSPG2), ear morphology (ILDR1 and CHRD), and body temperature (CES2). In addition, we find several genes associated with body size (ZBTB20, CIZ1, and TTN), which might have been involved in the decreasing size of woolly mammoths during the late Pleistocene.

There’s Lots More

The point is that these gene losses aren’t side shows — they are the events that transformed an elephant into a mammoth, that adapted the animal to its changing environment. A job well done, yes, but now those genes are gone forever, unavailable to help with the next change of environment. Perhaps that contributed to eventual mammoth extinction.

As quoted above, the mammoth authors note that gene losses can be adaptive, and they cited a paper that I hadn’t seen before. I checked it out and it’s a wonderful laboratory evolution study of yeast.2 Helsen et al. (2020) used a collection of yeast strains in which one of each different gene in the genome had been knocked out. They grew the knockout yeast in a stressful environment and watched to see how the microbes evolved to handle it. Many of the yeast strains, with different genes initially knocked out, recovered, and some even surpassed the fitness of wild-type yeast under the circumstances. The authors emphasized the fact of the evolutionary recovery. However, they also clearly stated (but don’t seem to have noticed the importance of the fact) that all of the strains rebounded by breaking other genes, ones that had been intact at the beginning of the experiment. None built anything new, all of them devolved.

Well, Duh

That’s hardly a surprise. At least in retrospect, it’s easy to see that devolution must happen — for the simple reason that helpful degradative mutations are more plentiful than helpful constructive ones and thus arrive more quickly for natural selection to multiply. The more recent results recounted here just pile more evidence onto that gathered in Darwin Devolves showing Darwin’s mechanism is powerfully devolutionary. That simple realization neatly explains results ranging from the evolutionary behavior of yeast in a comfy modern laboratory, to the speciation of megafauna in raw nature millions of years ago, and almost certainly to everything in between.

References

Van der Valk, Tom, et al. 2022. Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome. iScience 25, 104826.

Helsen, J. et al. 2020. Gene loss predictably drives evolutionary adaptation. Molecular Biology and Evolution 37, 2989–3002.

Common descent v. Common design again.

 Why Their Separate Ancestry Model Is “Wildly Unrealistic”

Emily Reeves

In my post yesterday I outlined how Erika, aka the popular evolution YouTuber “Gutsick Gibbon,” critiqued my earlier post, which commented on an important paper in the field of phylogenetics, Baum et al. (2016), which purported to test separate ancestry. Between 7:55 and 9:24 of her response video, Erika shows a diagram (above) to respond to my point that the Baum et al. (2016) paper tested a model of separate ancestry that is not endorsed by anyone in the ID community.

Here’s what Erika, aka Gutsick Gibbon, is saying. In the diagram, she has two different models of what creationists (left) and intelligent design (ID) proponents (right) might be saying. (Note that she disagrees with both; she’s just trying to describe what she thinks the groups are saying.) Each “finger” in the diagram is supposed to represent an instance where the designer acted to influence the course of biological history. The left tree is supposed to show what she thinks the creationist’s model is that was tested by Baum et al. (2016). She mistakenly thinks that ID proponents are angry because we’re really putting forth some model like the diagram on the right — where a designer creates a group but then allows evolutionary tinkering. So, she thinks we’re upset because Baum et al. (2016) didn’t include tinkering in their model. This is actually not the case.

When I argued that Baum et al. (2016) failed to properly test separate ancestry, that has nothing to do with a failure to incorporate “tinkering” into the model. Also, as a side note, ID proponents do not advocate a “tinkering” hypothesis. This is a common misconception about the ID view. Instead, the primary objection of ID proponents to the Baum et al. (2016) paper is due to how the separate ancestry and family ancestry models were created in the first place. In short, Baum et al. (2016) assumes that shuffling of the synapomorphies is an accurate model for separate ancestry. ID proponents and others who have a design-based perspective would heartily reject that, for reasons I will explain.

How They Chose Data for the Separate Ancestry Model

Baum et al. (2016) uses several different datasets to test separate ancestry. Their molecular dataset, our focus here, is from a 2011 paper by Perelman et al. where 54 genes were used to construct a molecular phylogeny of living primates. (We’ll call this the “Perelman dataset.”) Primates all have around 30,000 genes, so the first question is how the authors got from 30,000 genes to 54. Note the details given from Perelman et al. (2011):

A complete list of 54 primer sets used in this study is presented in Table S2. This list includes primers from earlier studies (Murphy et al. 2001), as well as those designed specifically for this study using a unique bioinformatics approach (Pontius, unpublished data). (Perelman et al. 2011)

If you look at Table S2 in you can see that the majority (38 of the 54 genes) came either from Murphy et al. (2001) (9 genes) or were specially designed for the study and no details are given (29 genes). For our purpose, let’s just look at the 9 taken from Murphy et al. (2001) which are described as being selected in the following way:

The GenBank and UniGene databases (NCBI) were searched for genes with exons of sufficient length (>200 bp) and variability (80±95% nucleotide identity between mouse and human), thereby providing adequate variation for the purpose of phylogenetic and somatic cell/ radiation hybrid mapping. (Murphy et al. 2001)

What’s Happening Here? 

Two types of selection or filtering are going on when they choose genes for their study. The first selection is to remove genes not present in all the species they were studying. In other words the genes had to be within the databases, be of sufficient size, and exist in all the species being considered. This rules out species-specific genes such as orphan genes. The second selection is that genes having the greatest number of phylogenetically informative sites or synapomorphies were chosen. (A synapomorphy is a variant/trait that is shared by at least two descendent taxa and thought to be inherited from a most recent common ancestor, where it evolved.) In order to win at this second selection, a gene should have the greatest number of variants which differ between at least two taxa, but in the same way (i.e., at site 1 two taxa have ‘A’s while the ancestral site was a ‘G’). A simpler way of putting this is they picked genes that varied the most between species, but in a likely functional way. If you look at Table 1 from Murphy et al (2001) you can see that the ADORA3 gene has 191 phylogenetically informative sites out of 330 base pairs. That means that at 191 positions it differs between at least two of the comparison taxa in a consistent way. To help better understand why these filters are stacking the deck from a design perspective, I want to give an analogy.

Let’s do a thought experiment where we want to create a distance tree demonstrating the evolution of household chairs. We choose five traits to compare. Those five traits must be exhibited by all the chairs and the five traits must vary between at least two chairs. This type of selection effectively eliminates unique properties of the chairs such as leather because not all chairs have this. Instead it prioritizes specific parts of chairs that were made intentionally different for functional or economic reasons. This type of selection on a designed object, such as a chair, will create an intuitive hierarchical tree even though the chairs are not actually related. How? Read on.

For example, screws, which hold chairs together, are likely to be a trait shared by all chairs (first criterion passed), but screws aren’t likely to vary a lot between chairs and therefore wouldn’t be selected as a trait. On the other hand, legs are a trait shared by all chairs and these are likely to vary quite a bit between different chairs based on the function of the chair. Children’s chairs will have shorter legs. Decorative chairs will have aesthetically pleasing legs. Folding chairs will have collapsible legs. Some chairs may have four legs while others five or even more. Seats are another example of a trait that will be common to all but differ a lot. Children’s seats on chairs will be smaller. Decorative chairs will have aesthetically pleasing seats. Collapsible chairs will have mobile seats. Thus, a selection for “differentness” with designed objects enriches for traits that cluster due to functional constraints or compatibility, not ancestry. If organisms are in fact designed, a very similar phenomena could be occurring in these phylogenetic comparisons.

Now let’s look at how this data set was used by Baum et al. (2016) in their separate ancestry model and what about the model is so problematic from an ID perspective.

They Used Synapomorphy Shuffling to Test Separate Ancestry

In describing the separate ancestry model Baum et al. (2016) says:

A key feature of the species SA [separate ancestry] model is that for each character [meaning genetic variants or fossil characters] the state drawn by each species is independent of that drawn by other species.

But what do they mean by saying that the state drawn by each species is “independent” of that drawn by another species? How are they actually creating their separate ancestry model? What I’ve gathered is this essentially means that in their “separate ancestry” model, the traits or synapomorphies were shuffled randomly to create a hypothetical model of what they think separate ancestry would be. I will illustrate with an example in Figure 1 adapted from the molecular Perelman dataset, where I took actual names of genes used by Baum et al. (2016), but then represented the different synapomorphies of those genes as spelling changes for the function of the gene.

To elaborate, in Figure 1 above are genes ABCA1, BNDF, AFF2, APP, and ATXN7. I have represented their DNA sequences simply as lowercase letters (transport, memory, splicing, migration, and cytoskeleton respectively) corresponding to their major functions. Then, to represent the synapomorphies between these organisms I’ve introduced some spelling errors. For example, in Figure 1A the ABCA1 gene in organism 1 is the sequence is transwort (lowercase) and BNDF is menory, AFF2 is splycing, APP is megration, and ATXN7 is cytosqeleton respectively. The pattern of changes within the gene (columns) are the same for all five genes in Figure 1A — notice how top to bottom the phylogenetic trees are the same. Thus, Figure 1A represents the data observed with one important caveat — I have artificially made the pattern of synapomorphies perfect (CI =1) just for clarity (not the case in the real data).

Now, the authors Baum et al. (2016) constructed their separate ancestry model by permuting (shuffling) the synapomorphies of these sequences (Figure 1B), in a random manner which assumed there would be no reason to find correlations of traits across different organisms. Here’s how they described their methods:

To evaluate whether the observed hierarchical signal is more than expected under species of family SA, we used the PTP test which uses a Monte Carlo approach to simulate data under the SA hypothesis. We implemented PTP tests using the permute function of PAUP* ver. 4.0a134-146 with parsimony as optimality criterion and hence tree length as a measure of tree-like structure.

In other words, Baum et al. (2016) gave the synapomorphy of the ABCA1 gene sequence of organism 2 to organism 4 and vice versa using a permute function (see Figure 1B). They did not just swap the whole genome sequence between two organisms but swapped individual characters — in this case base pairs — to remove the connection between them (notice how top to bottom the colors are scrambled). As expected, after random shuffling of the synapomorphies the tree length drastically increased — meaning more evolutionary events were required to explain the data, and the tree was not very parsimonious (see Table 1 from Baum et al. (2016)).

Following this they calculated the p-values (see Table 3 from Baum et al. (2016)). The p-values are outrageously low, dictating a strong rejection of the separate ancestry model tested. Erika interprets this here as indicating that at least this model of separate ancestry is a totally unreasonable hypothesis. Their method is given below:

For many of the tests the observed test statistic fell well outside the range of values obtained under the SA hypothesis. In such cases, we report the distance of the observed data from the mean of the SA distribution in units of the SD (the z-score) and also provide a P-value assuming a normal distribution. Although the latter is only an approximation, it will provide the reader with a sense of how improbable the data would be under SA. 

Of course, I reject this model of “separate ancestry” as well. This model, as they’ve developed it, is totally unrealistic for all kinds of reasons and therefore far less likely than the observed model. Now, anytime one observes this type of data in biology it should definitely make one question if not immediately reject the model. Erika also partially recognizes this because in reference to these zeros she also says “That’s insane! You don’t see that in regular science.” Basically, p-values this low typically indicate that there is something really wrong with one’s model. So, let’s talk about this, and what might be wrong with their model of separate ancestry.

Synapomorphy Shuffling is Not a Good Test of Separate Ancestry

The short(er) explanation for why synapomorphy shuffling is not a good model of separate ancestry is that synapomorphies or traits may cluster for designed systems based upon functional reasons like optimization, constraints, or compatibility. Recall that a synapomorphy is a trait or site uniquely shared by members of a group that helps to define that group. Under typical phylogenetic thinking, synapomorphies are thought to exist because they evolved in the common ancestor that gave rise to the group. But in an ID-based world, synapomorphies might exist because they represent a suite of traits required for a group of organisms to perform some important function related to their survival. 

In designed systems, traits don’t vary randomly, and often vary according to predictable patterns which may be related to functional needs. In biology, these functional needs could be related to an organism’s niche, lifestyle, locomotion, metabolism, diet, or other behaviors. In other words, organisms which live in similar niches and/or have similar lifestyles, modes of locomotion, metabolisms, diets, or other behaviors, may tend to have similar traits all related to functional constraints that are required for that organism to survive in its environment. Thus, in a designed biosphere, traits won’t vary randomly but will follow similar patterns, correlations, and relationships across organisms according to their various survival needs. To put it simply, organisms with similar lifestyles will show similar architecture. This will be true not because of common ancestry but because of design constraints which must be fulfilled for an organism to survive in its environment. 

Now, the Long(er) Answer… 

ID proponents have a problem with this model of separate ancestry because it does not account for anticipated taxa-specific design constraints (aka what I am calling “functional synapomorphies”). Most ID proponents would hold that only synapomorphies that are historical in nature could be shuffled in such a fashion. As a thought experiment, if one selected synapomorphic chair traits, a very nice nested hierarchical pattern will result. Collapsible chairs will cluster, desk chairs will cluster, armchairs will cluster, children’s chairs will cluster, and the universal common ancestor might be something like a stool. Thus, if a synapomorphy is functional (i.e., contributes to the function) and not historical, this random shuffling of synapomorphies would be analogous to taking chair-specific design differences (like a collapsible seat and short legs for a children’s chair), mixing them up, and then observing that collapsible chairs and children’s chairs no longer group together. When you shuffle functional traits of designed objects, you will get statistical zeros, because you have obliterated the design signal. Most likely you’d also get some quite weird designs that don’t work very well! Imagine outdoor patio furniture with traits of indoor office chairs. It wouldn’t work!

Given how the data were selected in the first place, it is very likely that many of these synapomorphies are functional.

The reason why functional synapomorphies cannot be used is because hierarchical clustering of functional synapomorphies or traits are abundant in scenarios that we know have not arisen due to a process of descent with modification. Don’t like my chair analogy? Take the distance tree, created by Doolittle and Bapteste 2007, of French departments based on the number of shared sur-names (See Figure 1b in the paper). This is a great example of how functional synapomorphies or traits can result in logical clustering of data when no descent with modification process has occurred. Baum et al. (2016)’s error is therefore as follows: They assume that design must produce random distributions of traits. However, all of our experience with sets of designed systems shows this is not the case. Erika doesn’t appreciate this point, and thus she misunderstands our critique of the Baum et al. paper.

What we know about design, from engineering and other life scenarios, is that design often creates a hierarchical similarity pattern centered around function that could look like ancestry if one forces it. Why do designers produce these hierarchical patterns? They aren’t trying to be deceptive, mimicking systems that look like they are the product of common ancestry. Rather, designers are simply applying logical design considerations like optimization, constraints, compatibility, dependencies, or reuse during the design process.

Thus, I hold that the model of separate ancestry rejected in the Baum et al. (2016) paper is not endorsed by most in the ID community because it does not account for the design expectation that functional synapomorphies or traits will cluster due to optimization, constraints, and a need for compatibility.

On Monday, I will look at the consistency of the phylogenetically informative sites for the Baum et al. (2016) paper. Spoiler alert: It looks like design.