Thursday, 13 July 2023
James Tour vs. Dave Farina: the view from the centre
Origin of Life: Cambridge Astrochemist Paul Rimmer Analyzes the Tour-Farina Debate
Cambridge University astrochemist Paul Rimmer analyzed the debate between James Tour and Dave Farina on the Podcast Capturing Christianity. Rimmer has been recognized as a rising star in the study of the origin of life (OOL). In his charitable and thoughtful demeanor, he represents the antithesis of Farina. He also displays a commitment to describing the science with precision and nuance.
I have many positive thoughts about Rimmer, and I anticipate that many people who watch his post-debate analysis will rightfully come away with a positive view of him. However, the viewer should be aware of a critical caveat: Ultimately, Paul Rimmer is far too credulous about chemical explanations for the origin of life. His stance undoubtedly reflects his membership in the field of mainstream OOL research. To those outside that community, even the research Rimmer lauds as advancing the field only further confirms that life’s originating through natural processes is impossible on scientific grounds.
Analysis of the Debate
Rimmer begins with a helpful tutorial on research into life’s origin. He includes a diagram by John Sutherland on the presumed stages leading to the first self-replicating cell and the current state of the field. Rimmer summarizes the journey toward life as a continuous series of stable systems gradually increasing in complexity until one emerges capable of Darwinian evolution.
Rimmer then expands on specific topics raised by Tour and Farina. He elucidates the research cited by Farina in response to Tour’s question about how the amino acids Asp and Lys could have linked together on the early Earth. Rimmer acknowledges that the articles Farina cited do not directly address Tour’s questions, but he claims they still provide clues as to how amino acid chains could have emerged. He describes how Leman, Orgel, and Ghadiri (2004) linked the amino acids Ala, Phe, Leu, Ser, and Try together with the assistance of carbonyl sulfide. He then describes how Singh et al. (2022) linked aminonitriles (precursors to amino acids) to amino acids by employing catalysts such as thiols.
Rimmer continues by explaining the research referenced by Farina related to the origin of RNA. During the debate, Tour described how nucleotides often join a growing chain with 2’-5’ linkages instead of the standard 3’-5’ linkages — nucleotides connect at the wrong carbon on the ribose molecule. Farina responded to this hurdle by citing Engelhart et al. (2013) who validated that a nucleotide chain known as a hammerhead ribozyme (RNA enzyme) could still break apart an RNA molecule even if the ribozyme possessed some 2’-5’ linkages.
Rimmer states that RNA with the wrong linkages could not have been reliably copied, posing a major hurdle to further progress toward life. A single RNA molecule would almost always break apart before it could migrate to the right local environment where it could facilitate a life-relevant reaction. It would have to be copied numerous times before it could play any role in life’s origin.
Yet Rimmer argues that this challenge is not necessarily insurmountable since Mariani and Sutherland (2017)demonstrated a chemical pathway that replaces 2’-5’ linkages with the correct 3’-5’ linkages. Rimmer acknowledges that this study does not fully solve the problem of building RNA since the correction process is not highly efficient or reliable, but he claims such research provides a “clue” as to how RNA molecules could have emerged. There are additional problems with this research that I will describe below.
Differing Assumptions
The differing perspectives of Tour and Rimmer result from the differences in their starting assumptions. Rimmer’s scientific education trained him to only consider the possibility that life originated from natural processes. Rimmer tacitly acknowledges this fact in his response to a question about the appearance of design in life. He essentially argues that the origin of life requires “mind” only insofar as chemistry or biology or anything else that happens in nature requires mind. This is consistent with what he has written elsewhere predicting that we will one day find a “complete biological explanation … for the question of how life first originated on Earth.” He states that he does not wish to examine the evidence for design beyond the apparent design behind the laws of physics that allow for life to exist. Consequently, he is not concerned if experiments perfectly match what could have occurred on the early Earth or even if the chemistry is prebiotically plausible.He considers progress as simply finding clues as to what might have occurred.
In contrast, Tour considers progress in understanding life’s origin as demonstrating a chemical process that could have occurred naturally and could have produced molecules in sufficient abundance and purity to drive the next step toward life. Tour has convincingly argued that no such research exists (see for example here or here).
From Tour’s perspective, a careful analysis of the procedures used in the research Rimmer references (here and here, ) reveals that the studies only moved chemical systems toward life by starting with carefully chosen molecules in concentrations and purities that could never have arisen naturally. The experiments also employed meticulously designed experimental protocols with only marginal similarity to what could have transpired on the ancient Earth.
If the experiments used more realistic chemical mixtures and environmental conditions, they would not have produced anything biologically relevant. In addition, if the resulting products were deposited in any ancient environment, they would have simply degraded into biologically useless asphalts. Steven Benner describes this tendency as the Asphalt paradox. In other words, this research, while interesting, does not mimic a realistic natural environment, nor does it produce chemical mixtures that could eventually produce life.
Probability Paradox
The hammerhead ribozyme study cited by Farina and Rimmer poses an additional seemingly insurmountable hurdle to the RNA world hypothesis. Ribozymes with 2’-5’ bonds have primarily been shown to break apart RNA, leading to what Benner refers to as the Probability paradox , which he describes as follows:
Experiments show that RNA molecules that catalyze the destruction of RNA are more likely to arise in a pool of random (with respect to fitness) sequences than RNA molecules that catalyze the replication of RNA, with or without imperfections.
If a system of randomly sequenced RNA had emerged on the early Earth, biologically useful ribozymes would have quickly vanished as the system degraded into simpler molecules.
Future Presentations
As I noted, Paul Rimmer is thoughtful, civil, and his voice should be heard. He said nothing wrong in his presentation since he was asked to analyze the debate from the perspective of a scientist working in the field of OOL research. But those not working in the field can find many reasons why the research he cites is not persuasive that the chemical origin of life is possible. Perhaps in future discussions, Rimmer could explore how his philosophical framework shapes his interpretation of the results of OOL studies. Ideally, he would also explain why scientists not operating within the same framework assess the state of the field very differently.
As someone who has also engaged in thoughtful dialogue with OOL researchers, I would be very happy to be part of such a conversation. But I do not want to put Paul Rimmer’s career in any jeopardy: Those working in the field of OOL research would be ill-advised to publicly speak with too much candor about fundamental weaknesses in that field since doing so might jeopardize their career.
Nebuchadnezzar : the Watchtower Society's Commentary.
NEBUCHADNEZZAR
(Neb·u·chad·nezʹzar), Nebuchadrezzar (Neb·u·chad·rezʹzar) [from Akkadian, meaning “O Nebo, Protect the Heir!”].
Second ruler of the Neo-Babylonian Empire; son of Nabopolassar and father of Awil-Marduk (Evil-merodach), who succeeded him to the throne. Nebuchadnezzar ruled as king for 43 years (624-582 B.C.E.), this period including the “seven times” during which he ate vegetation like a bull. (Da 4:31-33) To distinguish this monarch from the Babylonian ruler by the same name but of a much earlier period (the Isin dynasty), historians refer to him as Nebuchadnezzar II.
Historical notices in cuneiform inscriptions presently available about Nebuchadnezzar somewhat supplement the Bible record. They state that it was in the 19th year of Nabopolassar’s reign that he assembled his army, as did his son Nebuchadnezzar, then crown prince. Both armies evidently functioned independently, and after Nabopolassar went back to Babylon within a month’s time, Nebuchadnezzar successfully warred in mountainous territory, later returning to Babylon with much spoil. During the 21st year of Nabopolassar’s reign, Nebuchadnezzar marched with the Babylonian army to Carchemish, there to fight against the Egyptians. He led his forces to victory. This took place in the fourth year of Judean King Jehoiakim (625 B.C.E.).—Jer 46:2.
The inscriptions further show that news of his father’s death brought Nebuchadnezzar back to Babylon, and on the first of Elul (August-September), he ascended the throne. In this his accession year he returned to Hattu, and “in the month Shebat [January-February, 624 B.C.E.] he took the vast booty of Hattu to Babylon.” (Assyrian and Babylonian Chronicles, by A. K. Grayson, 1975, p. 100) In 624 B.C.E., in the first official year of his kingship, Nebuchadnezzar again led his forces through Hattu; he captured and sacked the Philistine city of Ashkelon. (See ASHKELON.) During his second, third, and fourth years as king he conducted additional campaigns in Hattu, and evidently in the fourth year he made Judean King Jehoiakim his vassal. (2Ki 24:1) Also, in the fourth year Nebuchadnezzar led his forces to Egypt, and in the ensuing conflict both sides sustained heavy losses.
Conquest of Jerusalem. Later, the rebellion of Judean King Jehoiakim against Nebuchadnezzar evidently resulted in a siege being laid against Jerusalem by the Babylonians. It appears that during this siege Jehoiakim died and his son Jehoiachin ascended the throne of Judah. But a mere three months and ten days thereafter the reign of the new king ended when Jehoiachin surrendered to Nebuchadnezzar (in the month of Adar [February-March] during Nebuchadnezzar’s seventh regnal year [ending in Nisan 617 B.C.E.], according to the Babylonian Chronicles). A cuneiform inscription (British Museum 21946) states: “The seventh year: In the month Kislev the king of Akkad mustered his army and marched to Hattu. He encamped against the city of Judah and on the second day of the month Adar he captured the city (and) seized (its) king [Jehoiachin]. A king of his own choice [Zedekiah] he appointed in the city (and) taking the vast tribute he brought it into Babylon.” (Assyrian and Babylonian Chronicles, by A. K. Grayson, 1975, p. 102; PICTURE, Vol. 2, p. 326) Along with Jehoiachin, Nebuchadnezzar took other members of the royal household, court officials, craftsmen, and warriors into Babylonian exile. It was Jehoiachin’s uncle Mattaniah that Nebuchadnezzar made king of Judah, and he changed Mattaniah’s name to Zedekiah.—2Ki 24:11-17; 2Ch 36:5-10; see CHRONOLOGY; JEHOIACHIN; JEHOIAKIM.
Sometime later Zedekiah rebelled against Nebuchadnezzar, allying himself with Egypt for military protection. (Eze 17:15; compare Jer 27:11-14.) This brought the Babylonians back to Jerusalem, and on Tebeth (December-January) 10 in the ninth year of Zedekiah’s reign, Nebuchadnezzar besieged Jerusalem. (2Ki 24:20; 25:1; 2Ch 36:13) However, news that a military force of Pharaoh was coming out of Egypt caused the Babylonians to lift the siege temporarily. (Jer 37:5) Subsequently Pharaoh’s troops were forced to go back to Egypt, and the Babylonians resumed the siege against Jerusalem. (Jer 37:7-10) Finally, in 607 B.C.E., on Tammuz (June-July) 9 in the 11th year of Zedekiah’s reign (Nebuchadnezzar’s 19th year if counting from his accession year or his 18th regnal year), a breach was made in Jerusalem’s wall. Zedekiah and his men fled but were overtaken in the desert plains of Jericho. Since Nebuchadnezzar had retired to Riblah “in the land of Hamath,” Zedekiah was brought before him there. Nebuchadnezzar had all of Zedekiah’s sons slaughtered, and then he blinded and bound Zedekiah in order to take him as a prisoner to Babylon. The postconquest details, including the burning of the temple and the houses of Jerusalem, the disposition of temple utensils, and the taking of captives, were handled by Nebuzaradan the chief of the bodyguard. Over those not taken captive, Gedaliah, an appointee of Nebuchadnezzar, served as governor.—2Ki 25:1-22; 2Ch 36:17-20; Jer 52:1-27, 29.
His Dream of an Immense Image. The book of Daniel states that it was in “the second year” of Nebuchadnezzar’s kingship (probably counting from the destruction of Jerusalem in 607 B.C.E. and therefore actually referring to his 20th regnal year) that Nebuchadnezzar had the dream about the golden-headed image. (Da 2:1) Although the magic-practicing priests, conjurers, and Chaldeans were unable to interpret this dream, the Jewish prophet Daniel did so. This moved Nebuchadnezzar to acknowledge Daniel’s God as “a God of gods and a Lord of kings and a Revealer of secrets.” He then constituted Daniel “ruler over all the jurisdictional district of Babylon and the chief prefect over all the wise men of Babylon.” Nebuchadnezzar also appointed Daniel’s three companions, Shadrach, Meshach, and Abednego, to administrative posts.—Da 2.
Later Exiles of Jews. About three years later, in the 23rd year of Nebuchadnezzar’s reign, more Jews were taken into exile. (Jer 52:30) This exile probably involved Jews who had fled to lands that were later conquered by the Babylonians. Lending support to this conclusion is the statement of the historian Josephus: “In the fifth year after the sacking of Jerusalem, which was the twenty-third year of the reign of Nebuchadnezzar, Nebuchadnezzar marched against Coele-Syria and, after occupying it, made war both on the Moabites and the Ammanites. Then, after making these nations subject to him, he invaded Egypt in order to subdue it, and, having killed the king who was then reigning and appointed another, he again took captive the Jews who were in the country and carried them to Babylon.”—Jewish Antiquities, X, 181, 182 (ix, 7).
Takes Tyre. It was also sometime after the fall of Jerusalem in 607 B.C.E. that Nebuchadnezzar began the siege against Tyre. During this siege the heads of his soldiers were “made bald” from the chafing of the helmets and their shoulders were “rubbed bare” from carrying materials used in the construction of siegeworks. As Nebuchadnezzar received no “wages” for serving as Jehovah’s instrument in executing judgment upon Tyre, He promised to give him the wealth of Egypt. (Eze 26:7-11; 29:17-20; see TYRE.) One fragmentary Babylonian text, dated to Nebuchadnezzar’s 37th year (588 B.C.E.), does, in fact, mention a campaign against Egypt. (Ancient Near Eastern Texts, edited by J. Pritchard, 1974, p. 308) But it cannot be established whether it relates to the original conquest or a later military action.
Building Projects. Besides attaining numerous military victories and expanding the Babylonian Empire in fulfillment of prophecy (compare Jer 47-49), Nebuchadnezzar engaged in considerable building activity. To satisfy the homesick longings of his Median queen, Nebuchadnezzar reportedly built the Hanging Gardens, rated as one of the seven wonders of the ancient world. Many of the extant cuneiform inscriptions of Nebuchadnezzar tell of his building projects, including his erection of temples, palaces, and walls. An excerpt from one of these inscriptions reads:
“Nebuchadrezzar, King of Babylon, the restorer of Esagila and Ezida, son of Nabopolassar am I. As a protection to Esagila, that no powerful enemy and destroyer might take Babylon, that the line of battle might not approach Imgur-Bel, the wall of Babylon, that which no former king had done [I did]; at the enclosure of Babylon I made an enclosure of a strong wall on the east side. I dug a moat, I reached the level of the water. I then saw that the wall which my father had prepared was too small in its construction. I built with bitumen and brick a mighty wall which, like a mountain, could not be moved and connected it with the wall of my father; I laid its foundations on the breast of the under-world; its top I raised up like a mountain. Along this wall to strengthen it I constructed a third and as the base of a protecting wall I laid a foundation of bricks and built it on the breast of the under-world and laid its foundation. The fortifications of Esagila and Babylon I strengthened and established the name of my reign forever.”—Archaeology and the Bible, by G. Barton, 1949, pp. 478, 479.
The foregoing harmonizes with Nebuchadnezzar’s boast made just before he lost his sanity: “Is not this Babylon the Great, that I myself have built for the royal house with the strength of my might and for the dignity of my majesty?” (Da 4:30) But when, in fulfillment of his divinely sent dream about the chopped-down tree, his reasoning powers were restored, Nebuchadnezzar had to acknowledge that Jehovah is able to humiliate those walking in pride.—Da 4:37; see MADNESS.
Very Religious. The indications are that Nebuchadnezzar was extremely religious, building and beautifying the temples of numerous Babylonian deities. Particularly was he devoted to the worship of Marduk, the chief god of Babylon. To him Nebuchadnezzar gave credit for his military victories. Trophies of war, including the sacred vessels of Jehovah’s temple, appear to have been deposited in the temple of Marduk (Merodach). (Ezr 1:7; 5:14) Says an inscription of Nebuchadnezzar: “For thy glory, O exalted MERODACH a house have I made. . . . May it receive within itself the abundant tribute of the Kings of nations and of all peoples!”—Records of the Past: Assyrian and Egyptian Monuments, London, 1875, Vol. V, p. 135.
The image of gold set up by Nebuchadnezzar in the Plain of Dura was perhaps dedicated to Marduk and designed to promote religious unity in the empire. Enraged over the refusal of Shadrach, Meshach, and Abednego to worship this image even after being given a second opportunity, Nebuchadnezzar commanded that they be thrown into a fiery furnace heated seven times hotter than usual. However, when these three Hebrews were delivered by Jehovah’s angel, Nebuchadnezzar was forced to say that “there does not exist another god that is able to deliver like this one.”—Da 3.
Nebuchadnezzar also appears to have relied heavily on divination in planning his military moves. Ezekiel’s prophecy, for example, depicts the king of Babylon as employing divination in deciding whether to go against Rabbah of Ammon or against Jerusalem.—Eze 21:18-23.
From following the science to leading the science?
Is There a Boom in Research Dishonesty?
What to make of this news stream?
Distinguished Professor Francesca Gino of Harvard Business School was recently accused by other academics of falsifying data in a number of studies, including one on dishonesty, where she was a co-author:
Professors Joseph Simmons, Uri Simonsohn and Leif Nelson of University of Pennsylvania, Escade Business School in Spain, and University of California, Berkeley, respectively, accused Gino of the fraud on their blog Data Colada.
“Specifically, we wrote a report about four studies for which we accumulated the strongest evidence of fraud,” they wrote, stating they shared their concerns with Harvard Business School.
THERESE JOFFRE, “HARVARD ETHICS PROFESSOR ALLEGEDLY FABRICATED MULTIPLE BEHAVIORAL SCIENCE STUDIES” AT THE COLLEGE FIX, JUNE 28, 2023
Breaking Rules
Gino, currently on administrative leave, is also the author of Rebel Talent: Why It Pays to Break the Rules at Work and in Life (2018). From the blurb: “Award-winning Harvard Business School professor Francesca Gino shows us why the most successful among us break the rules, and how rebellion brings joy and meaning into our lives.” Here are the details at Data Colada.
Another of the authors of the dishonesty paper, the well-known Dan Ariely of Duke University, author of The Honest Truth About Dishonesty: How We Lie to Everyone — Especially Ourselves (Harper 2012), has also been accused by the other authors of Providing fraudulent data:
Behavioral scientists Leif Nelson and Joseph Simmons, who exposed the apparent fraud via their blog Data Colada together with their colleague Uri Simonsohn, say a thorough, transparent investigation is needed. But given other universities’ past reluctance to investigate their own researchers, they are skeptical that Duke will conduct one. That may leave Ariely’s supporters insisting he is innocent and detractors assuming he is guilty, Nelson says. “No one knows. And that’s terrible.”
CATHLEEN O’GRADY, “FRAUDULENT DATA RAISE QUESTIONS ABOUT SUPERSTAR HONESTY RESEARCHER” AT SCIENCE (AUGUST 24, 2021)
Come to think of it, a similar situation arose over a decade ago. Harvard’s Marc Hauser, a principal investigator at the Cognitive Evolution Laboratory, was famous and popular for his research claims that “the foundations of language and morality are hardwired into the brains of humans and our kin.” But he found himself in hot water in 2010 because “lab workers observed huge discrepancies between his descriptions of monkey behavior and the experimental results captured on Video.”
On Aug. 10, the Boston Globe reported the psychology professor was taking a one-year leave of absence after a three-year internal investigation found evidence of scientific misconduct in his lab. Days later, Faculty of Arts and Sciences Dean Michael D. Smith confirmed that a committee found Hauser “solely responsible” for eight instances of misconduct — three of which were published studies that needed to be retracted or corrected to remove unsupported findings.
ERIC P. NEWCOMER AND ELYSSA A. L. SPITZER, “MARC HAUSER’S FALL FROM GRACE” AT THE HARVARD CRIMSON (SEPTEMBER 4, 2010)
Hauser resigned from Harvard in 2011 in the wake.
Dumped by Viking
As it happens, he was working on a book as the story broke: Evilicious. Apparently the book was originally to be published by Viking, with the subtitle Why We Evolved a Taste for Being Bad, but Viking dumped it, post-scandal, in 2012. Hauser later self-published it as Evilicious: Cruelty = Desire + Denial (CreateSpace, 2013). It was endorsed by (among others) some oft-quoted science celebs:
Dumbfounded Harvardites
Many Harvardites found the accusations against Hauser hard to believe:
As Hauser faces federal inquiry, many of his former co-authors, graduate students, and undergraduate advisees struggle to comprehend how the man they knew as a prolific researcher, skilled communicator, and heavyweight in the field of cognitive psychology became enmeshed in scandal.
ERIC P. NEWCOMER AND ELYSSA A. L. SPITZER, “MARC HAUSER’S FALL FROM GRACE” AT THE HARVARD CRIMSON (SEPTEMBER 4, 2010)
But perhaps Ariely and at least some of his colleagues would take a more ambivalent view than theirs, if we are to judge by the abstract of a recent paper:
People like to think of themselves as honest. However, dishonesty pays — and it often pays well. How do people resolve this tension? This research shows that people behave dishonestly enough to profit but honestly enough to delude themselves of their own integrity. A little bit of dishonesty gives a taste of profit without spoiling a positive self-view. Two mechanisms allow for such self-concept maintenance: inattention to moral standards and categorization malleability. Six experiments support the authors’ theory of self-concept maintenance and offer practical applications for curbing dishonesty in everyday life.
MAZAR, N., AMIR, O., & ARIELY, D. (2008). THE DISHONESTY OF HONEST PEOPLE: A THEORY OF SELF-CONCEPT MAINTENANCE. JOURNAL OF MARKETING RESEARCH, 45(6), 633-644
Here’s a Thought
Could seeing morality in purely materialist or naturalist terms, as above, makes it all seem like a game? Then, when dishonesty (or whatever) blows a hole in the system, the researcher finds that colleagues, unlike those human- or monkey-study subjects, are very old-fashioned about cheating… A Bible Belt without the Bible could be a really scary place.
Wednesday, 12 July 2023
Deconstructing David Hume.
Reconsidering David Hume’s Critique of Design Thinking
Recently, one of my philosophy colleagues, upon learning of my interest in intelligent design, asked me what I thought about the criticisms leveled at design thinking by 18th-century Scottish philosopher David Hume. According to my colleague, many think Hume destroyed once and for all the intellectual coherence of design theories. Therefore, he assumed I would have an opinion on the matter. I am not trained as a philosopher, and I had to confess that I had little knowledge regarding Hume’s arguments against design. But this question sent me scurrying to the library for some unplanned research. And I’m glad for this, for after engaging with Hume’s work, I came to the unexpected and somewhat ironic conclusion that while Hume’s arguments might have had some currency in their 18th-century context, the findings of modern science have actually rendered them much less convincing.
Hume’s anti-design arguments are found in his Dialogues Concerning Natural Religion. Here, he uses the character Cleanthes as the spokesperson for design, with Philo being the one to convey Hume’s own critical thoughts. A major part of Hume’s critique revolves around what he sees as the great dissimilarity between the world of nature and the world of human artifice. All knowledge, he says, comes through experience and we experience humans designing things all the time. But nature is unique and completely unlike the world of human contrivance, leaving us devoid of experience to draw on. We can thus draw no analogy between the work of human designers (of which we have much experience) and a designer of nature (which is singular and unlike anything produced by humans).
The Argument for Design
In one passage, Hume has Cleanthes clearly state the argument from design:
Look around the world: Contemplate the whole and every part of it: You will find it to be nothing but one great machine, subdivided into an infinite number of lesser machines….The curious adapting of means to ends, throughout all nature, resembles exactly, though it much exceeds, the production of human contrivance….Since therefore the effects resemble each other, we are led to infer, by all the rules of analogy, that the causes also resemble; and that the Author of nature is somewhat similar to the mind of man; though possessed of much larger faculties, proportioned to the grandeur of the work which he has executed.
But Hume does not buy Cleanthes’s analogy:
If experience and observation and analogy be, indeed, the only guides which we can reasonably follow in inferences of this nature; both the effect and cause must bear a similarity and resemblance to other effects and causes, which we know, and which we have found, in many instances, to be conjoined with each other.
Since nature, in Hume’s view, is unique and unlike anything we can ascribe to human contrivance, we have no experience of nature being designed and cannot analogize it to human artifice, of which we have much experience.
What the Future Held
Little could Hume know what the future would hold — the discovery that at the cellular level, all organisms are driven by molecular machinery that looks and acts uncannily like the machines produced by humans, but far more sophisticated. Whether it be the bacterial flagellum with its rotor, stator, clamps, and bushings, the efficient whirring of the ATP synthase, or the mechanical movements of the kinesin walking protein (see below), every cell is a vast factory of biochemical processes and information processing being carried out by a nano-technology of unbelievable complexity and sophistication, but a technology nonetheless. Hume’s argument for the dissimilarity between natural and human-designed entities begins to melt away. If living organisms are indeed built on a nano-technology that mimics human-designed technology, and if similar effects do have similar causes, then molecular machines must be intelligently designed just like human machines. Cleanthes’s analogy seems to hold in a way that Hume could never have foreseen.
William Paley may be hinting at Hume’s critique in the following passage from Natural Theology:
I have sometimes wondered why we are not struck with mechanism in animal bodies as readily and as strongly as we are struck with it, at first sight, in a watch or a mill. One reason of the difference may be, that animal bodies are, in a great measure, made up of soft flabby substances, such as muscles and membranes; whereas we have been accustomed to trace mechanism in sharp lines, in the configuration of hard materials, in the moulding, chiselling, and filling into shapes of such articles as metal or wood. There is something, therefore, of habit in the case; but it is sufficiently evident that there can be no proper reason for any distinction of the sort. Mechanism may be displayed in the one kind of substance as well as in the other.
Hume wanted to maintain the distinction between nature and human artifice as the heart of his argument against design. But modern science sides with Paley. Below the level of flabby muscles and membranes, organisms do indeed display the sharp lines of mechanism.
Mind and Matter
In a second criticism of Cleanthes, Hume has Philo say to his friend:
Let us once more put the argument from design to trial. In all instances which we have ever seen, ideas are copied from real objects, and are ectypal, not archetypal….You reverse this order, and give thought the precedence. In all instances which we have ever seen, thought has no influence upon matter, except where that matter is so conjoined with it, as to have an equal reciprocal influence upon it.
In other words, minds can only influence matter making up the body to which the mind is attached. Here again, modern science undermines Hume’s point. We now know about quantum theory and the collapsing of the wave function of an elementary particle when it is observed and measured. Minds profoundly influence matter at the most fundamental level, not to mention research showing the possible influence of mind on random number generators or even in intercessory prayer. And certainly, the world of human culture and technology powerfully testifies to the power of mind to force matter into configurations that would never occur if left to natural laws (as I type this on a plastic keyboard). Hume’s criticism falls flat. Minds have transformed the world of matter.
In a somewhat humorous tip of the cap to irreducible complexity, Paley noted how a structure like the epiglottis could not have evolved gradually from a simpler form, because with only half an epiglottis, we would all choke to death! Paley comes off to me as a far keener observer of nature than Hume. And now from the vantage point of 21st-century science, we can see even more clearly the bankruptcy of Hume’s skepticism. There is no sense in which we can say that Hume destroyed the intellectual coherence of design thinking. Paley could already see this in 1802. How much more clearly can we see it today in the light of modern scientific advancement?
Man as natural element?
Complementary Design: Nature and Gardens
We are familiar with the compelling design features of planet Earth as a place for life and the abundance of evidence for design seen in the human body. But we may be less familiar with the complementary design of nature, the physical realm accessible to humans, and what I’ll call gardens.
The latter of these terms denotes human stewardship of Earth. It is not my invention. The Genesis narrative, while proclaiming Earth “good” and human beings as having been formed with intention, uses “garden” as an epitome of their mutually beneficial interactions.
Consider some ways that humans have complemented the natural features of Earth to their mutual benefit. Complementary features speak of intelligent design in multitudes of different scenarios. For example, a key that opens a lock is almost always a result of intentional design. A radio receiver that can pick up a local broadcast signal as I drive my car across town involves multiple layers of design. Finding at a department store shoes and clothing that fit comfortably (although a somewhat rare experience) could hardly happen without intentional design.
Our Desperate Needs
One of the overarching themes of the garden is need. Humans as physical beings are desperately needy. Air, water, food, and shelter represent our basic survival needs, and the global features of our planet have answered these needs for billions of people throughout human history.
The concept of a garden also embodies mutual flourishing. A vegetable garden can produce edible food, but we will flourish more if we learn how to nourish the soil to enhance the yield and nutritional content of the plants. Clearing weeds, mulching, watering, and warding off pests are all familiar activities to gardeners. Is the Earth healthier when well-tended? I visited a small-scale organic farm recently — just a few acres — and the variety of vegetables and flowers in all stages of growth was a thing of beauty. If land could express satisfaction at flourishing to its full potential, this small farm exemplified the mutual benefit of a tended garden.
Less Is More
Evidence of intelligent design shines forth when we consider how the complementarity of human need and tended earth enhances the well-being of both. But design is seen not only in the traditional sense of garden as a plot of vegetables. One of my favorite recreations when I was younger was visiting national parks and other wilderness areas. In these natural environments, the Earth provides the grandeur and beauty, while human involvement seems to serve best with the motto, “Less is more.”
Hiking a mountain trail to a remote lake in the North Cascades would have been overwhelmingly difficult, however, without the efforts of those who made and maintained the trails that penetrated into some extremely rugged terrain. Many people each year find needed refreshment from the stress of everyday life by visits to scenic recreation areas. Again, we can discern design by seeing the complementary aspects of human need and the beneficial meeting of those needs through appropriate stewardship of Earth’s resources.
Shifting our focus now to the “need” expressed by humans for the products of our technologically sophisticated society, design is evident in both the availability of the many essential raw materials and in our intelligence and ingenuity to be able to create from these materials the astounding array of products that most of us have come to regard as essential.
Did civilization need readily available fuel to power a developing technology? Fossil fuels, produced over hundreds of millions of years on Earth, have provided the majority of our energy needs for generations. Forests have provided structural materials for houses, furniture, and more. Limestone quarries have yielded building material for cathedrals and courthouses. The surface crust of our Earth has been enriched to provide metallic ores and almost every other element in the periodic table. A wide variety of these minerals are critical for civilization to continue to develop, including the transition to more “Earth-friendly” Technologies:
The types of mineral resources used vary by technology. Lithium, nickel, cobalt, manganese and graphite are crucial to battery performance, longevity and energy density. Rare earth elements are essential for permanent magnets that are vital for wind turbines and EV [electric vehicle] motors.
Foresight and Design
In almost every conceivable aspect of our lives, what we perceive as a need can be met by resources made available to us by events in Earths history that long pre-date our existence. Foresight and design certainly come to mind as suitable descriptions of this beneficial arrangement.
Although this subject lends itself to avenues of discussion leading in many directions, I would like to return to the traditional sphere of garden as a park-like enhancement to nature’s palette. When visiting a beautiful park, one is struck by the cultivated beauty resulting from the complementary effects of the gardener’s efforts and nature’s resources.
When I lived in Washington State, my family visited the beautiful Butchart Gardens in British Columbia. This transformed limestone quarry is a stunning example of human design and stewardship, healing, as it were, a scar on Earth’s surface left from extraction of material to meet our needs.
With a former quarry as a canvas, Jennie Butchart envisioned transforming this space into a beautiful garden haven, overflowing with lush greens and colourful blooms. The result of her vision is The Gardens…
Complementary design is seen (and enjoyed) through humans imagining and creating beauty beyond the possible outcomes of natural forces or non-human life.
Nurturing Life and Beauty
In Tolkien’s Return of the King, Gandalf expresses his understanding of the service of stewardship, nurturing life and its beauty:
…the rule of no realm is mine… But all worthy things that are in peril as the world now stands, those are my care. And for my part, I shall not wholly fail of my task…if anything passes through this night that can still grow fair or bear fruit and flower again in days to come. For I also am a steward.
J. R. R. TOLKIEN, THE RETURN OF THE KING (NEW YORK: HOUGHTON MIFFLIN COMPANY, 1994), 741-2.
Our stewardship of nature involves a choice. Choosing to put forth our effort and creativity to enhance and beautify the natural realm available to us implies that we are not merely physically complex objects governed by the laws of physics. We participate as sub-creators in a designed system — a physical realm in which our own freedom allows us to complement the outcomes of nature to our mutual benefit.
Tuesday, 11 July 2023
The empire of the gene restored?
Genes Rule? The Evidence of Identical Twins
For some decades, we heard claims from studies of identical twins (formed when one fertilized egg splits) that everything from exam results to homosexuality might hinge on genetics. Therefore, any similarity in later choices or behavior might be due to genetic factors (read “predetermined” or “inevitable” here). How has that assumption held up, especially in the age of genome mapping?
Identical twins comprise roughly 1 in every 250 births. Studies of twins who were separated at birth have been especially prized because the twins were assumed to grow up in different environments. Thus any significant similarities pointed to genetic influences.
Several problems emerged, though. For one thing, what about the assumption that separation at birth means that twins experience different environments? Children may be born into practically any environment but they are generally adopted into middle-of-the-road ones. Twins separated at birth may also be aware of each other’s existence; they may even know each other. Plus, the psychological tendency we have when encountering twins is to notice similarities more readily than differences so similarities, rather than differences, tend to be socially reinforced. But the critics who raised these issues were typically ignored in the rush to see genetics behind every similarity.
Meanwhile, there were two bigger problems.
Identical Twins Diverge Genetically as They Age
Genome mapping has changed the picture a good deal. The fact that twins diverge as they age was reported in Nature back in 2005. A 2021 study found that about 15 percent of identical twins vary from each other significantly in genetics. In any event, a 2022 UC Berkeley open-access Study found that “age plays a more important role than genetics in determining which genes in our bodies are turned on or off, influencing our susceptibility to disease”:
In other words, while our individual genetic makeup can help predict gene expression when we are younger, it is less useful in predicting which genes are ramped up or down when we’re older — in this study, older than 55 years. Identical twins, for example, have the same set of genes, but as they age, their gene expression profiles diverge, meaning that twins can age much differently from each other.
YAMAMOTO, R., CHUNG, R., VAZQUEZ, J. M. ET AL. TISSUE-SPECIFIC IMPACTS OF AGING AND GENETICS ON GENE EXPRESSION PATTERNS IN HUMANS. NAT COMMUN 13, 5803 (2022)
So, it turns out, even if we didn’t start out that way, we all end up being unique.
The Effort to Prove that Genes Rule! Involved Some Avoidable Lapses
In an article published at Aeon last month, science writer Gavin Evans, author of Skin Deep: Journeys in the Divisive Science of Race (OneWorld 2019), who follows twin studies, looks back on an era when the haste to establish genetic explanations for human behavior involved throwing ethics aside.
In the mid 20th century, Sir Cyril Burt (1883–1971), a British psychologist and eugenics enthusiast, claimed to have participated with colleagues in studies on separated identical twins that established the importance of heredity. But then, as Britannica decorously puts the matter:
After Burt’s death, striking anomalies in some of his test data led some scientists to reexamine his statistical methods. They concluded that Burt manipulated and probably falsified those IQ test results that most convincingly supported his theories on transmitted intelligence and social class. The debate over his conduct continued, but all sides agreed that his later research was at least highly flawed, and many accepted that he fabricated some data. However, the soundness of his earlier work justified his reputation as the foremost pioneer of educational psychology in Britain.
BRITANNICA, THE EDITORS OF ENCYCLOPAEDIA. “SIR CYRIL BURT”. ENCYCLOPEDIA BRITANNICA, 27 FEB. 2023. ACCESSED 8 JULY 2023
Evans tells the same story a bit more colorfully:
Shortly after he died in 1971, Burt’s records and notes were all burnt, after which his reputation imploded. Two of his researchers, whose names appeared as co-authors on his papers, could not be traced (when asked about them, Burt had said they’d both ‘emigrated’ — but he didn’t know where) and a third he clearly invented. In The Science and Politics of IQ (1974), the American psychologist Leon Kamin noted that in 1955, when Burt claimed to have tested 21 separated identical twins, he put the correlation between their IQs at 0.771, yet in the 1960s, when his twins cohort numbered 53, he gave the identical three-decimal figure, which Kamin said had a statistically minuscule chance of occurring. Some circumstantial details that Burt claimed to have found among his twins also raised eyebrows: of a pair born to a wealthy mother and then adopted, he claimed one was raised in splendour on a Scottish country estate, and the other was left to a shepherd (like Perdita in The Winter’s Tale). The killer blow was delivered by his approved biographer, Leslie Hearnshaw, a one-time Burt enthusiast who in 1979 concluded that all of Burt’s twin studies were invented.
GAVIN EVANS, “THE MYTH OF MIRRORED TWINS,” AEON, JUNE 27, 2023
Evans found similar, though less dramatic, problems with Thomas J. Bouchard ’s research at the Minnesota Center for Twin and Family Research:
his methods and conclusions did not impress other researchers. One problem was self-selection. His identical twins had known each other for an average of nearly two years before contacting him; some had known each other as young children; and it seems likely that those who were most alike were most likely to contact him. Kamin, the professor who rumbled Burt’s fraudulent studies, and his colleague said there was pressure on the twins to come up with cute stories, and that Bouchard’s studies had ‘a number of serious problems in the design, reporting, and analyses’.
“THE Myth OF MIRRORED TWINS,” AEON, JUNE 27, 2023
What Is It About Twins?
Is there something existential about twins that draws (and maybe, skews) research? Evans thinks so:
Much of the magic evaporates when we lift the lid on the sensational tales of parallel lives. What emerges in place of this seductive mirror myth of the hidden double are more mundane tales of everyday difference, revealing the unique selfhood that is part of the inheritance of all people — including those with genetic doppelgängers.
“THE MYTH OF MIRRORED TWINS,”. AEON, JUNE 27, 2023
Yes, it seems we are all condemned to just be ourselves, even if we are one of a set of twins.
Merodach: the Watchtower society's Commentary
MERODACH
The Hebrew form for Marduk, the most important Babylonian god, whose downfall was foretold to coincide with Babylon’s overthrow.—Jer 50:2.
The Babylonian Kings Merodach-baladan (Isa 39:1) and Evil-merodach (2Ki 25:27) were undoubtedly named after this god. With the rise of Babylon to prominence, because of King Hammurabi’s making it the capital of Babylonia, Merodach likewise increased in importance. The attributes of earlier gods came to be assigned to him, and it is thought that the Babylonian priests altered the mythological accounts to make Merodach the slayer of Tiamat and the creator of the world and of man. Babylonian texts identify Marduk (Merodach) as the son of Ea (the god presiding over the watery element), the consort of Sarpanitu, and the father of Nebo.
The kingship over Babylon was closely associated with the image of Merodach at his temple, Esagila, for the rulers of Babylon were not installed by coronation but became kings by taking hold of the hand of Merodach. The ceremony was repeated each year at the New Year’s festival. Even during the time that Assyria controlled Babylonia, the kings of Assyria were required to come to the city of Babylon each year for the New Year’s festival and legalize their claim to the throne by taking hold of Merodach’s hand.
Jeremiah the prophet, with respect to Babylon’s fall, foretold that Merodach would “become terrified.” This came true in the sense that Merodach proved to be unable to preserve the dignity of the Babylonian World Power, and since the conquerors of Babylon were worshipers of other deities, his future became very uncertain, filled with foreboding.—Jer 50:2;
Ancient humans and the case for devolution/revolution.
Our Ancestors Are Evolving, Just to Keep Up!
Recently, archeologists came up with an interesting find from 30,000 years ago in what is now Moravia, part of the Czech Republic: Ravens lived among humans.
over 30,000 years ago, during the Pavlovian culture, ravens helped themselves to people’s scraps and picked over mammoth carcasses left behind by human hunters.
Ravens live in human settlements today, of course, with one notable difference:
The archeologists from the University of Tübingen and the Senckenberg Centre for Human Evolution noted that “The large number of raven bones found at the sites suggests that the birds, in turn, were a supplementary source of food, and may have become important in the culture and worldview of these people.”
UNIVERSITY OF TÜBINGEN, “RAVENS IN PREHISTORY: SCIENTISTS UNEARTH A 30,000-YEAR-OLD RELATIONSHIP WITH HUMANS,” SCITECHDAILY, JUNE 29, 2023. ONE OF THE PAPERS IS OPEN ACCESS.
Today we barbecue chickens instead of ravens…
Famed for Their Smarts
We are also told, “Ravens have a very wide food spectrum, and are curious and flexible in their behavior.” They are also famous for their intelligence. One consequence is that they likely figured in the culture of that day, as the researchers suggest, just as they do in many modern cultures. But this is a much more complex picture of an early society than we are accustomed to hearing about.
Another recent find has been Neanderthal cave engravings from 57,000 years ago:
Research in recent decades has revealed a great deal about the cultural complexity of Neanderthals. However, relatively little is known about their symbolic or artistic expression. Only a short list of symbolic productions are attributed to Neanderthals, and the interpretation of these is often the subject of debate. In this study, Marquet and colleagues identified markings on a cave wall in France as the oldest known Neanderthal engravings… Based on the shape, spacing, and arrangement of these engravings, the team concluded that they are deliberate, organized and intentional shapes created by human hands.
PUBLIC LIBRARY OF SCIENCE, “NEANDERTHAL CAVE ENGRAVINGS IDENTIFIED AS OLDEST KNOWN, MORE THAN 57,000 YEARS OLD,” PHYS.ORG, JUNE 21, 2023. THE PAPER IS OPEN ACCESS.
Some of us can remember when Neanderthal artwork was an “academic Bombshell.”
Why a Bombshell?
Because materialists need to maintain the idea that the human mind arises purely from animal instincts. That’s hard to establish unless researchers can find human forms with less-than-human minds. Therefore some group must be co-opted into the role. And, while many of us have Neanderthal genes, Neanderthals no longer exist as a separate group. So they can’t lobby against such treatment.
Nonetheless, the weight of evidence will eventually force a confrontation with a stark fact: The human mind has no evolutionary history. It appears suddenly and invents technologies with increasing speed over time. More than that we don’t really know and maybe can’t know. The history was made up, not dug up.
For some, it’s a hard swallow. As paleobiologist Rui Diogo, associate professor at Howard University, notes, negative biases of all kinds about our forebears have long been part of science, education, and popular culture.
One example of how biased narratives are still present in science today is the numerous depictions of human evolution as a linear trend from darker and more “primitive” human beings to more “evolved” ones with a lighter skin tone. Natural history museums, websites, and UNESCO heritage sites have all shown this trend.
RUI DIOGO, “HOW POWER PERVADES PORTRAYALS OF HUMAN EVOLUTION,” SAPIENS, 20 JUN 2023.
David Coppedge made the same Observation — about evolution as a “path to whiteness” — at Evolution News back in 2021.
Professor Diogo quite properly singles out racist and sexist portrayals. But an overarching theme has been the need to promote the idea of a gradual development of human-like intelligence. As it happens, ancestors way stupider than their descendants are just not what paleontologists have been digging up. And histories that are made up rather than dug up tend to collapse.
Even yet more primeval tech vs. Darwinism.
How the “Other” ATP Synthase Saves the Planet
ATP synthase has been featured here many times because of its exquisite rotary mechanism and efficient operation. Viewers of animations like ours on YouTube usually need little convincing that it looks designed. And when they learn more details, like its 6,000-rpm speed, its crankshaft, and three-part ATP manufacturing center, the intuition becomes difficult to dislodge, even when evolutionists insist it emerged by chance. It’s a well-deserved icon of intelligent design.
The one most often referred to is the F-type of ATP synthase shown in the video. But there’s another one — the V-type ATPase — that is no less wondrous. It looks similar to the F-type, but V-type ATPases (let’s call them VHA) work in reverse: instead of using the proton motive force generated by the electron transport chain to manufacture ATP, they spend the ATP “energy currency” molecules to pump protons into organelles, thereby increasing the acidity. They are often found on the membranes of vacuoles that need H+ ions to lower the pH for phagocytosis or other types of digestive or recycling functions. Scientists have now shown they are more widely distributed in the cell than thought.
Our body cells contain both types of ATPase. But why do I say that these VHA rotary engines save the planet? A report by Daniel P. Yee in Current Biology tells the story.
It Begins in the Ocean
Diatoms, dinoflagellates, and coccolithophores are dominant groups of marine eukaryotic phytoplankton that are collectively responsible for the majority of primary production in the ocean.
Primary production represents the bottom of the food chain, on which higher organisms depend. Photosynthetic microbes in the ocean are the major players. For present purposes, we can ignore the authors’ evolutionary story about how these marine microbes obtained their VHAs by some “selective advantage.” It suffices to focus on what the molecular machines do:
Since intracellular digestive vacuoles are ubiquitously acidified by V-type H+-ATPase (VHA), proton pumps were proposed to acidify the microenvironment around secondary chloroplasts to promote the dehydration of dissolved inorganic carbon (DIC) into CO2, thus enhancing photosynthesis.
We report that VHA is localized around the chloroplasts of centric diatoms and that VHA significantly contributes to their photosynthesis across a wide range of oceanic irradiances.
More photosynthesis means more primary production, and more support for a diverse biosphere.
Based on the contribution of diatoms to ocean biogeochemical cycles, VHA-mediated enhancement of photosynthesis contributes at least 3.5 Gtons of fixed carbon per year (or 7% of primary production in the ocean), providing an example of a symbiosis-derived evolutionary innovation with global environmental implications.
Once again, the evolutionary tale is non-essential for the surprising implication: all life benefits from the enhancement of photosynthesis provided by VHA molecular motors in diatoms. The 7 percent number is undoubtedly much higher if the other dominant groups of marine phytoplankton are factored in. Additional tests showed the research team that similar VHA-mediated enhancement of photosynthesis occurs in coccolithophores, dinoflagellates, and probably in all photosynthetic organisms.
The paper’s diagram of VHA in Figure 2 looks almost identical to the F-type ATP synthase except for the direction of proton (H+ ion) flow. Both types could be described by ID proponents as irreducibly complex molecular engines based on the parts list alone:
The VHA is a holoenzyme protein complex that is composed of 16 subunits, with a membrane spanning V0-domain and cytosolic facing catalytic V1-domain (Figure 2A). Transcriptomic analysis of synchronized cultures of T. pseudonana [a centric diatom] demonstrated constitutive mRNA expression of all VHA subunits, suggesting that VHA is important throughout the cell cycle (Figure 2B). However, the VHA holoenzyme can have multiple subcellular localizations and functions.
While the familiar F-type ATP synthase is localized to the mitochondria (in animals) or chloroplasts (in photosynthetic microbes and plants), V-types are found in other subcellular locations. They perform more functions due to their proton-pumping action that can adjust pH of their surroundings. This has made them difficult to study. A few functions are known.
But How Many Others Are There?
In diatoms, VHA has been reported in the membranes of vacuoles, chloroplast endoplasmic reticulum (cER), and silica deposition vesicles (SDVs), where it is strictly required for biomineralization of the silica cell wall and cell division. The complexity and functional versatility of VHA are challenges for genetic manipulation approaches that would constitutively destabilize multiple physiological functions and confound phenotypic interpretation. They also rule out the use of transcriptomics to infer the physiological role(s) of VHA, as these analyses cannot not provide information about the subcellular localization of the VHA holoenzyme.
The authors were excited about another implication of their discovery: carbon sequestration. Because VHA machines substantially enhance photosynthesis, it means more carbon is converted into CO2 which the chloroplast needs for sugar synthesis. The slight pH decrease provided by the VHA proton pumps changes the chemistry to favor CO2 production, which would be bad; but simultaneously, it creates a gradient that favors moving the CO2 into the chloroplast instead of into the cytoplasm where it would escape into the atmosphere. As a result, more oxygen is released by photosynthesis, less CO2 is released into the atmosphere during photosynthesis, and when the diatoms die and fall to the ocean floor, they take the solid carbon with them. V-type ATPases thus perform another global function for the biosphere: a carbon-concentrating mechanism (CCM).
VHA is a universal feature of eukaryotic cells and is present in a number of organelles, including endosomes, phagosomes, macropinosomes, lysosomes, Golgi, and melanosomes. Since VHA invariably acidifies the lumen of each of these organelles to pH ≤ 6, we deduce that VHA in the cER/PP membranes of T. pseudonana must accomplish a similar effect. This is significant, because at pH ≤ 6.3, the majority of DIC [dissolved inorganic carbon] equilibrates to CO2. Hence, we propose that VHA promotes CO2 accumulation in the microenvironment external to the chloroplast. Consistent with model simulations of DIC fluxes in the diatom CCM, some of the CO2 would diffuse back into the cytoplasm (pH ∼ 7.2). However, the higher pH in the chloroplast stroma (pH ∼ 8.15) establishes a more favorable partial pressure gradient for CO2 diffusion into this compartment (Figure S3B). The next steps follow the established CCM of microalgae. In the stroma, CO2is immediately hydrated into HCO3− under catalysis by carbonic anhydrase, which is shuttled into the thylakoid lumen where pH is ≤ 6 due to H+ pumping associated with photosynthetic electron transport chain. At the acidic pH, HCO3− dehydrates into CO2 and diffuses into the pyrenoid matrix, saturating RuBisCo to maximize carbon fixation rates.
A Remarkable Synergy
This shows a remarkable synergy of molecular machines and chemistry in a highly localized microenvironment. VHAs acidify the chloroplast exterior, helping carbonic anhydrase use the excess CO2 to produce more bicarbonate ions. The pH gradient favors these negative ions to flow toward the proton motive force being generated by the electron transport chain (Complexes I-IV) that are powering the F-type ATP synthase motors (Complex V). As the bicarbonate ions dehydrate back to CO2 where the pH drops inside the chloroplast, they saturate Rubisco enzymes that convert the CO2 into nutrients for life.
Notice this careful pH-mediated series of delicate chemical reactions. Within this microenvironment, CO2 gets utilized where needed, but is not released into the atmosphere. The products of Rubisco favor carbon compounds that will get buried in the ocean floor. The result? A carbon-concentrating mechanism that helps the atmosphere gain more oxygen but less carbon dioxide, while enriching the biosphere with nutrients. VHA, the “other” ATP synthase, saves the planet! VHA should be seen as a key player in the carbon cycle, the oxygen cycle, the food chain, and the climate.
Nearly Unrestrained Wonder
The authors can hardly restrain their wonder at all this:
In summary, O2 production, 13C-NanoSIMS, and 14C-P-E measurements demonstrated that VHA significantly contributes to photosynthetic carbon fixation that is retained as biomass. Given that diatoms contribute nearly 50% of carbon fixation in the ocean, the component of photosynthesis that depends on VHA represents between ∼7% and 25% of oceanic primary production, or between 3.5 and 13.5 Gtons of fixed carbon per year (Table S3). These numbers can only increase after accounting for VHA-mediated photosynthesis in other secondary endosymbiotic phytoplankton (Figure 1) and photosymbiotic invertebrates. In addition, diatoms constitute about half of the biomass that sinks into the ocean’s interior. Based on our measurements of the contribution of VHA on both gross and net productivity in diatoms, VHA-mediated carbon fixation is poised to significantly contribute to the biological pump that shuttles organic carbon to the ocean’s interiorand, on a geologic time scale, to the biomass buried in the continental margin that formed fossil fuel deposits. Even by the most conservative estimate, the cooption of VHA for the enhancement of photosynthesis is a symbiosis-derived evolutionary innovation with global environmental implications.
Some future day, when biologists finally admit that evolution is incapable of innovation of complex finely tuned cooperative systems, all scientists will marvel at the intelligent design that gives us air to breathe and edible carbon to ingest under a moderate climate. Some of us are ahead of that time.
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