We are free to acknowledge free moral agency

 Free Will: What Are the Reasons to Believe in It?

Denyse O'Leary

University of Missouri psychology professor Kennon Sheldon’s message is neatly summed up in an opening statement: “Regardless of whether humans do or don’t have free will, psychological research shows it’s beneficial to act as if you do.”

The author of Freely Determined: What the New Psychology of the Self Teaches Us About How to Live (Basic Books, 2022) responds to philosophers who say that we do not have free will:

All my life, I’ve struggled with the question of whether humans have ‘free will’. It catalysed my decision to become a psychologist and continues to inspire my research to this day, especially as it relates to the kinds of goals people set for themselves, and the effects of goal-striving on people’s happiness and wellbeing.

I’ve come to the conclusion that people really do have free will, at least when it is defined as the ability to make reasoned choices among action possibilities that we ourselves think up…

Regardless of who is correct in this debate, my work has led me to a second conclusion that I consider even more important than whether we have free will or not. It’s that a belief in our own capacity to make choices is critical for our mental health. At the very least, this belief lets us function ‘as if’ we have free will, which greatly benefits us.

KENNON SHELDON, “THE THREE REASONS WHY IT’S GOOD FOR YOU TO BELIEVE IN FREE WILL,” PSYCHE, JUNE 15, 2023 

An Obvious Problem

Now, the obvious problem with his approach is that if we believe in free will simply because that belief is supposed to be good for our mental health, then we really don’t believe in it.

A simple example suffices: We sometimes hear that being optimistic is also better for mental health. In one sense, that’s true. If we focus on the positive things, our lives feel more pleasant and that is bound to be better for mental health. But what if we have no good reason for optimism? What if we live under an active volcano that shows signs of erupting? Optimism (“it probably won’t really happen this year”) could delay evacuation past the point of no return.

So let’s look back at free will in this light: If we believe that we have it — and that belief is true — we are empowered to deal with temptations and addictions, firm in the knowledge that we really can cast the deciding vote for our best possible outcome. But if free will is not true, we are setting ourselves up for delusion if we succeed and needless disappointment and misery if we fail. Not only that but we are participating in an unfair system where people are judged and punished for unwise or bad behavior that they cannot really help. So functioning “as if” we have free will turns out not to be very good at all.

“A Better Person”?

Sheldon goes on to say,

The second reason why I consider belief in free will to be beneficial is that it makes you a better person. Studies in social psychology show clearly that, if people become convinced that they have no free will, there can be negative effects on their ethical behaviour.

SHELDON, PSYCHE, 2023

Perhaps that’s true but it amounts to saying that perhaps we should be deluded for our own good. Even though delusions are said to be bad for us… Is there any light at the end of this tunnel? 

Sheldon offers a reason why some thinkers deny free will:

You might wonder why anyone would choose to believe in determinism, given the clear negative effects of this belief? There are several possible reasons. Some people might think that determinism is the most scientific and intellectually sophisticated position to take, and they like feeling smarter than others.

SHELDON, PSYCHE, 2023

Well, if science matters, the good news is that neuroscience provides sound reasons to believe in free will. As Stony Brook neurosurgeon Michael Egnor has pointed out, the work of neuroscience pioneer Benjamin Libet established that we certainly have “free won’t” — the ability to choose not to do something:

[W]hat he found was, when you made a decision to push the button [in a psychological experiment], you still had the brain wave that preceded the decision by half a second. But when you decided to veto pushing the button, there was no new brain wave at all. It was silent in terms of brain waves. But you did make the decision to veto. So he said that it wasn’t so much that you have free will but you have free won’t. That is, you have the ability to decide whether or not you are going to comply with what your brain is urging you to do. And that compliance is not material. It’s not a brain wave. It’s immaterial.

MICHAEL EGNOR, “HOW A NEUROSCIENTIST IMAGED FREE WILL (AND “FREE WON’T”),” MIND MATTERS NEWS, MARCH 19, 2020 

What Quantum Mechanics Shows

Physicist Marcelo Gleiser also notes that science does not really support the view that free will is an illusion: “[T]he mind is not a solar system with strict deterministic laws. We have no clue what kinds of laws it follows, apart from very simplistic empirical laws about nerve impulses and their propagation, which already reveal complex nonlinear dynamics.” In any event, quantum mechanics shows that nature is indeterminate at the fundamental level and that the observer’s decision of what to measure plays a role in what happens. One outcome is that a number of younger thinkers accept free will as consistent with the evidence.

In other words, we can accept free will based on the evidence. There is no particular need to think that it might be a possibly pleasant delusion.

A theory of devolution?

 Is Adaptation Actually a Fight to Stay the Same?

Andrew McDiarmid

On a new episode of ID the Future, host Casey Luskin talks with Eric Anderson on location at this year’s Conference on Engineering and Living Systems (CELS). The two discuss an intriguing new engineering-based model of bounded adaptation that could dramatically change how we view small-scale evolutionary changes within populations of organisms. In presenting his argument for natural selection, Charles Darwin pointed to small changes like finch beak size and peppered moth color as visible evidence of an unguided evolutionary process at work. Many have adopted this perspective, quick to grant the Darwinian mechanism credit for micro-, if not macro-, evolution. But Anderson and other attendees at the CELS conference are starting to promote a different view. “We need to stop saying organisms are partly designed,” says Anderson. “We need to view them as deeply designed and purposeful, active and engaged in their environments, and capable of adapting within their operating parameters.” To get a fascinating glimpse of this novel approach to biology, download the podcast or listen to it here .

On professor Dave and the bacterial flagellum

 Answering Farina on Behe’s Work: Bacterial Flagella

Jonathan McLatchie

In a previous article, I began a series of four responses to YouTuber Dave Farina (aka “Professor Dave”) about his video reviewing Dr. Michael Behe’s three books. Here I will turn my attention to Mr. Farina’s comments regarding bacterial flagella.

In relation to the flagellum, the video complains about Behe’s “dishonest usage of terminology pertaining to machinery,” including phrases such as “outboard motor,” “drive shaft,” “universal joint,” “bushings,” and “clutch and braking system.” In reality, this terminology is used widely in the scientific literature. It’s not unique to Behe. On the contrary, in reference to flagella, the literature is full of such terms including “motor”,1 “drive shaft,”2 “universal joint,”3“bushing,”4 and “clutch.”5 The word “machine” itself has a wide circulation.6 Is Farina going to charge the entire flagella research community with dishonesty as well?

Co-option Scenarios for the Origins of Bacterial Flagella

According to the video, “A flagellum that merely twitches instead of rotating smoothly would also produce motion and thus could be selected for.” But a type IV pilis, which enables twitching motility (a form of bacterial translocation over moist surfaces), is very different from a flagellum. Twitching motility occurs by extension, tethering, and retraction of the type IV pilus, which functions in a manner akin to a grappling hook. A flagellum, on the other hand, rotates as it is driven by a proton motive force across the cell membrane. The assembly mechanisms of pili and flagella are also quite different.

The video complains that Behe fails to acknowledge the existence of alternative flagellar systems that are simpler than the model system found in Salmonella species and Escherichia coli. However, the fact that an alternative system lacks a specific component that is essential in another system does not mean that the former lacks an alternative mechanism for achieving the same outcome. The most robust concept of irreducible complexity understands it as a property of a system that is contributed to by multiple subfunctions, the removal of one of which causes the overall system to effectively cease performing its job. Note that each individual subfunction could, in principle, be performed by multiple protein components. Likewise, a single protein component could perform more than one of those subfunctions. Furthermore, the identity of the specific components performing each respective subfunction could differ from one organism to the next. It is therefore not the identity of the structural parts that is important in an irreducibly complex system, but rather the essential functions that need to be performed in order for a higher-level objective to be realized.

Moreover, pointing to homologues of flagellar proteins does not undermine the argument from irreducible complexity, since co-opting those proteins to produce a flagellar system requires multiple co-incident changes in order for the new system to be realized. For example, flagellar-specific proteins would not confer a selective advantage until incorporated into the flagellar system. But the necessary proteins that serve roles in other systems will not become incorporated into the flagellar system before these flagellar-specific proteins arise. This is quite aside from the need to have complementary protein-protein binding interfaces, as well as a choreographed assembly system to ensure that the proteins are assembled in the appropriate order.

Resurrecting a Flagellum

In a 2016 article at Evolution News, Behe asks, 

W]hy doesn’t [Kenneth Miller] just take an appropriate bacterial species, knock out the genes for its flagellum, place the bacterium under selective pressure (for mobility, say), and experimentally produce a flagellum — or any equally complex system — in the laboratory? (A flagellum, after all, has only 30-40 genes, not the hundreds Miller claims would be easy for natural selection to rapidly redesign.) If he did that, my claims would be utterly falsified. But he won’t even try it because he is grossly exaggerating the prospects of success.

The video by Farina comments, 

hilariously, [Behe] is oblivious to the fact that this precise experiment was carried out the year before. Here’s the paper. Gene deletion produced two strains of bacteria with no flagellum. They then introduced selective pressure for motility by depleting the nutrients in the colony. Within 96 hours, both strains had regenerated flagellar motility by a pathway involving two successive point mutations in genes that served other purposes.

However, the paper that Farina cites7 does not do this at all. Not for the first time with this video, I wonder if he has in fact read the paper. All that the researchers deleted was the flagellar master switch protein, FleQ, in Pseudomonas fluorescens. After a few days of incubating the bacterial cells on Petri dishes, they reacquired their ability to grow flagella. The genetic basis for this reactivation of the flagella is that another master switch protein, NtrC, that is a structurally similar homolog of FleQ — responsible for turning on genes involved in nitrogen metabolism — already had the ability, to some extent, to cross-bind to the promoter usually bound by FleQ. When produced in excess, as a result of a broken regulator, NtrC was thus able to drive flagellar synthesis. As a consequence of this mutation, the bacterial cell lost its ability to regulate its nitrogen metabolism genes. An article in The Scientist describes this research:

But while the re-evolved flagella enabled the bacteria to access food supplies at the farthest reaches of the Petri dish, the ability came at a price. ‘The bacteria that became much better at swimming were much worse at nitrogen regulation,’ said Johnson. However, she added, ‘sometimes the advantage can be so great that it’s worth paying that cost because otherwise you die.’

Thus, contrary to the Farina video’s claims, this paper does not document the de novo evolutionary origins of a bacterial flagellum at all — far from it. In fact, Behe has already addressed the paper here.

The Waiting Times Problem

In 2004, Michael Behe and David Snoke published a paper in the journal, Protein Science.8 About this paper, Farina has three complaints. The first complaint is that, “Behe and Snoke found that the target sequence did actually evolve, in population sizes and timeframes that are entirely realistic, and if anything, quite small compared to real-world populations. The paper literally proves them wrong and they somehow count it as a win anyway.” Farina mentions Behe’s expert testimony at the 2005 Kitzmiller v. Dover trial:

When questioned about his 2004 paper, Behe tacitly acknowledged that the population size in their model was orders of magnitude smaller than real-world bacterial populations, which had the effect of vastly underestimating the rate at which such “irreducible” traits could evolve… In one striking exchange, Behe acknowledged a paper which indicated that there are more prokaryotes in a single ton of soil than in his model population, and that there is a lot more than one ton of soil on Earth.

However, this objection stems from Farina’s misreading of the paper. As Behe himself explains in the very transcript that Farina cites, “forming a new disulfide bond might require as few as two point mutations. But forming other multi-residue features such as protein-protein binding sites might require more.” The graph below (figure 6 of the paper) shows Behe and Snoke’s estimate of the time to fixation (along the y-axis) versus the number of substitutions needed for a new feature to evolve (along the x-axis). On the top axis, values for the needed population sizes are given. The point is that, as the number of needed co-dependent mutations increases, so too does the needed population size and waiting time to fixation.

As Behe and Snoke explain in the paper, in a scenario where three substitutions are required for a novel feature to arise, a population size of roughly 1011 individuals is necessary for it to become fixed over the course of 108 generations (108 generations is marked as a horizontal bar on the figure). If the complex trait in question requires even more substitutions, it would require considerably more time. If six mutations were needed, the average population size required for it to become fixed in 108 generations would be on the order of 1022 individuals. Given that 1030 is a plausible estimate of the number of microorganisms on the entire planet9, these numbers become prohibitive very quickly.

The second complaint is that, “In their model, Behe and Snoke permitted only single-base mutations and natural selection — no recombination, no duplications beyond the initial presumed one, no other evolutionary changes.” But the authors explicitly say that “Because the model presented here does not include recombination, the results can be considered to be most applicable to a haploid, asexual population.” Nonetheless, they do note in the conclusion to their paper that “the results also impinge on the evolution of diploid sexual organisms,” since large multicellular organisms have much, much smaller population sizes than bacteria. If the evolution of complex features is difficult for microorganisms (with their massive population sizes and short generation turnover times), how much more so for large animals? Though one might counter, in the case of diploid sexual species, that recombination allows for neutral mutations to occur separately in a population and to later combine by sexual recombination, Christiansen et al. have shown, in a paper published in Theoretical Population Biology, that “Recombination lowers the waiting time until a new genotypic combination first appears, but the effect is small compared to that of the mutation rate and population size” (emphasis added).10

Finally, Farina complains that “They also specified a pre-determined target sequence and only considered the simulation to have been ‘successful’ if that specific target evolved.” But this is incorrect. Rather, the paper provides estimates for how many organisms would be required, and over how long a time frame, for multiple co-dependent mutations (none of which by themselves confers an advantage) to become fixed in a population.

Notes

Minamino T, Imada K, Namba K. Molecular motors of the bacterial flagella. Curr Opin Struct Biol. 2008; 18(6):693-701.

Johnson S, Furlong EJ, Deme JC, Nord AL, Caesar JJE, Chevance FFV, Berry RM, Hughes KT, Lea SM. Molecular structure of the intact bacterial flagellar basal body. Nat Microbiol. 2021; 6(6):712-721.

Kitao A, Hata H. Molecular dynamics simulation of bacterial flagella. Biophys Rev. 2018; 10(2):617-629.

Yamaguchi T, Makino F, Miyata T, Minamino T, Kato T, Namba K. Structure of the molecular bushing of the bacterial flagellar motor. Nat Commun. 2021 Jul 22;12(1):4469.

Blair KM, Turner L, Winkelman JT, Berg HC, Kearns DB. A molecular clutch disables flagella in the Bacillus subtilis biofilm. Science. 2008;320(5883):1636-8.

Sowa Y, Berry RM. Bacterial flagellar motor. Q Rev Biophys. 2008 May;41(2):103-32.

Taylor TB, Mulley G, Dills AH, Alsohim AS, McGuffin LJ, Studholme DJ, Silby MW, Brockhurst MA, Johnson LJ, Jackson RW. Evolution. Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system. Science. 2015; 347(6225):1014-7.

Behe MJ, Snoke DW. Simulating evolution by gene duplication of protein features that require multiple amino acid residues. Protein Sci. 2004; 13(10):2651-64.

Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A. 1998; 95(12):6578-83.

Christiansen FB, Otto SP, Bergman A, Feldman MW. Waiting with and without recombination: the time to production of a double mutant. Theor Popul Biol.1998;53(3):199-215.

How hubris sinks the unsinkable.

 Shades of Titanic — Probing the Wreck of the Unsinkable Enlightenment

David Klinghoffer

The week that the submersible Titan was revealed to have been instantaneously flattened on its way down to the wreck of the Titanic, David Berlinski spoke with Jame Lileks and Peter Robinson on Ricochet about the wreck of the Enlightenment. Much like the Titanic, and a bit like the Titan, so much was expected at the glorious launch of the experiment in human reasoning — yet down it went to disaster, not least in the 20th century with its horrors.

Writing yesterday in the Wall Street Journal, Peggy Noonan suggested that the story of the Titanic haunts us in part because its demise came two years before the start of the century’s great catastrophe, World War I: “the reason the Titanic endures is that there was an immediate connection in the public mind with the Great War. The 20th century was to be the century of progress.” Interesting connection. Science and reason were supposed to transform the world for the good instead of soaking it in gore. In his books — Human Nature and his latest, Science After Babel — Berlinski probes the causes behind that failure. “A cold wind is blowing,” the mathematician and philosopher observes, revealing how “fragile” the Enlightenment dream really was. The conversation with Dr. Berlinski begins at 31:45.

Gentleman thief?

Another conspiracy theory become just plain conspiracy?

A wonder of ancient engineering

Speaking of ID...

 How to Discuss Intelligent Design with Friends

Evolution News

On a classic episode of ID the Future, Tom Gilson — author, senior editor with The Stream, and occasional contributor to Evolution News — tackles the question of how best to discuss intelligent design (ID) with friends and associates skeptical of the theory. There is so much misinformation about the theory of ID that many well-intended people reject not the actual theory but a silly caricature, a straw man. They don’t realize that ID is not an argument from ignorance but an inference to the best explanation based on positive evidence for design and negative evidence against competing materialistic explanations. It involves abductive reasoning, a standard mode of reasoning in the historical sciences. When in conversation with someone who understands none of this, Gilson suggests using the Socratic method and, in particular, posing three questions designed to turn down the heat, promote dialogue, and draw the other person into a discovery of the actual theory of intelligent design. Try it with friends, colleagues, and family members! Download the podcast or listen to it here

No Jehovah,no Justice,no Peace here's why.

   The pseudo-religious bureaucracies of this age have given religion/worship a bad name.Likely many would agree with Indian statesman Jawarlal Nehru when he said that the spectacle of organised religion in India and elsewhere filled his mind with horror,and that it seems almost always to stand for superstition,ignorance,bigotry,exploitation,the vested interest of entrenched elites and the like.But long before Nehru now famous religious leader/teacher Jesus Christ had some choice words for the leaders of the dominant religion of his time and place: Matthew23:13KJV "But woe unto you scribes and pharisees,!For ye shut up the kingdom of heaven against men:For ye go in yourselves,neither suffer ye them that are entering to go in.Woe unto you,scribes and pharisees,hypocrites!For ye devour widows houses,and for a pretence make long prayer:Therefore ye shall receive the greater damnation.

   Two things to note in Jesus censure 1)The hypocrisy of these religious leaders separated them from God 2)Their hypocrisy turned others away from the God's truth.How?The bible suggest two ways 1)Matthew23:15ESV "Woe to you, scribes and pharisees,hypocrites!For you travel across sea and land to make a single proselyte,and when he becomes a proselyte,you make him twice as much a child of hell as yourselves."

  2)2Peter2:2 "Many will follow their sensuality,and because of them the way of truth will be blasphemed."

 On account of its bringing his name and kingdom into disrepute pseudo-religion in general and Christendom in particular is in the cross hairs of Jehovah's war machine.The bible tells us that soon pseudo-religion will pay a heavy price for its political meddling, greed and hypocrisy.Revelation19:2"because His judgments are trued and righteous,e

because He has judged the notorious prostitutef

who corrupted the earth with her sexual immorality;

and He has avenged the blood of His •slaves

that was on her hands.g"

There are of course those who urge an abandonment of the quest for the creator God.They claim that accepting a status of cosmic orphanhood and making new gods of chance,necessity,matter and self are the only way to free ourselves from the abuses of the past.To begin with militant atheist have been every bit as unsuccessful on liberating their flock from the racism,nationalism,militarism and greed that have always been the main triggers of conflict as theistic pseudo-religionists have.Additionally there are practical reasons that universal justice and peace are simply not possible apart from Jehovah's assertion of his rightful sovereignty over the globe

 1)Only Jehovah as creator can claim unimpeachable legitimacy as a global governor,there plain and simply is no man or group of men(or angels for that matter)that can be trusted with that kind of authority,apart from the fact that it is a universally accepted legal principle that the creator be recognised as legal owner of what he has produced.Jehovah is totally independent of his creation and is thus morally incorruptible,What could anyone possibly offer him as a bribe?A new luxury car?Tickets to the big game?A case of champagne perhaps?With him in charge mankind will finally have a ruler worthy of utter confidence and loyalty.

2)Jehovah is not learning on the job the very wisest among us human or superhuman is only just beginning to understand how to get the most out of Jehovah's creation Jehovah has been there and done that so to speak.No more guessing games with people's lives,health and prosperity.

3)Only Jehovah has the might/smarts to bring leviathan and his hordes to heal.There is a reason that the criminal and otherwise sociopathic elements of society always seem ahead of the agencies charged with countering them.Why instead they have consistently succeeding in corrupting the wider society.Some might be prepared to acknowledge behind the scenes influences on the human level.They might be less willing to acknowledge the Bible's warning that the corruption of the main institutions of our global civilisation extends to the realm of the superhuman see Ephesians6:12.Until our civilisation is rid of these malignant minds human and superhuman advances in technology will continue to be more of a curse than a blessing.

  4)Only Jehovah can guarantee infallible judgement.Not only is he first hand witness to all wrongdoing and right doing he can read hearts.This means that under his rule not only will we finally have a ruler worthy of our complete trust we will have fellow servants worthy of our complete trust.Picture a society with no need for

police,soldiers,spies,security personnel of any kind,courts,magistrates,judges,jails,locks,keys.Impossible you say?Certainly in the atheistic universe we could entertain no such hope.

 5)Justice delayed is Justice denied the saying goes.What about when justice never arrives?The number of unsolved crimes on the files of this world's law enforcement agencies is in the tens of thousands some of these are horrific indeed heartbreaking murders.What about those who have been erroneously convicted crimes they never committed What about past victims of state sponsored injustice.Jehovah is not only mankind's only hope of a just future he ALONE can counter the injustices of the past.

What is a hominid?

 Fossil Friday: To Be or Not to Be Homo

Gunter Bechly

The fossil hominin Homo habilis was described 1964 by famous paleoanthropologist Louis Leakey and his colleagues from the 1.9 million year old Olduvai Gorge locality in Tanzania (Leakey et al. 1964). Even though this taxon is only known from a small and highly incomplete collection of isolated bone fragments, it has become the crucial hominid species that supposedly bridges the gap between the ape-like australopithecines and our human genus Homo. Because of the association of the bones with stone tools it has been named Homo habilis, which means “handy man.” However, its alleged position as transitional form is quite controversial (also see Gibbons 2011, Luskin 2007, 2015), and even the validity of the species has been questioned because it seems to be “a wastebasket taxon, little more than a convenient recipient for a motley assortment of hominin fossils” (Tattersall 1992). Homo habilis certainly was not the ancestor of later Homo species, because he is too recent and coexisted with early Homo ergaster, thus leaving a distinct gap between australopithecines and the genus Homo (Hawks et al. 2000).

A Dubious Attribution?

Since its small brain volume falls within the range of australopithecines, several scientists very early doubted the attribution of H. habilis to the genus Homo. Also the hand and feet are more ape-like and exhibit clear adaptations for climbing. Walker & Shipman (1996: 132) said that H. habilis is even more ape-like than Lucy, and Spoor et al. (1994) even remarked in their comparative study of hominid labyrinthine morphology that “The specimen Stw 53 provisionally attributed to H. habilis, differs from all other hominids … [and] shows greatest similarities to the pattern observed for large cercopithecoids …[which] suggest that Stw53 relied less on bipedal behaviour than the australopithecines”. Holly Smith (1994) concluded from the comparative study hominid patterns of dental development that gracile australopithecines and H. habilis remain classified with African apes. Wood & Collard (1999a, 1999b, 2001), Collard & Wood (2007, 2015) could show that in none of the crucial character H. habilis is closer to Homo than to Australopithecus.

An Assignment Rejected

Therefore, they suggested that H. habilis should be transferred to the genus Australopithecus, which was also supported by Hartwig-Scherer (1999) and Schwartz & Tattersall (2015). This assignment was rejected by Harcourt-Smith (2007) based on postcranial characters, while Berger et al. (2015) agreed that “postcranial remains of H. habilis appear to reflect an australopith-like body plan”. Spoor et al. (2015) found that the mandible of H. habilis is remarkably primitive and more similar to Australopithecus afarensis. They also reconstructed a slightly larger brain volume for the holotype and clarified the definition of the taxon Homo habilis, but cautioned that the results raise questions about its phylogenetic relationships. It is also very much contradicting Darwinian expectations, that the oldest specimens of Homo habilis, such as the 2.3 million year old specimen no. AL 666-1, possess more advanced characters than the younger holotype specimen OH 7, which lived more than a half million years later. One of the most striking contradictions is the fact that the bones of Homo habilis and many other animals were found in the context of so-called “butchering sites” together with stone tools, and in the neighbourhood of rock circles that very much look like the stone huts still used by modern nomadic tribes of the region (Leakey 1972: 24).

These rock circles and huts demonstrably originated at the same time as Homo habilis, which obviously suggests that this ape-like creature was rather the animal prey of contemporary human hunters than a human ancestor and producer of stone tools. Otherwise, we would have to believe highly implausible hypothesis that an ape-like creature with an ape-sized brain and climbing adaptations built stone huts like modern humans. Anyway, the majority of evolutionists of course ignored all such doubts among the experts and blindly embraced Homo habilis as a cherished “missing link” without asking inconvenient and potentially career-threatening questions.

Reference

Berger LR, Hawks J, de Ruiter DJ et al. 2015. Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa. eLife 4:e09560, 1–35. DOI: https://doi.org/10.7554/eLife.09560

Collard M & Wood B 2007. Defining the Genus Homo. pp. 1575–1610 in: Henke W & Tattersall I (eds). Handbook of Paleoanthropology. 3 vols. Springer, Berlin, 2069 pp.

Collard M & Wood B 2015. Defining the Genus Homo. pp. 2107–2144 in: Henke W & Tattersall I (eds). Handbook of Paleoanthropology. 3 vols. Springer, Berlin, xliii+2624 pp. DOI: https://doi.org/10.1007/978-3-642-39979-4_51

Gibbons A 2011. Who Was Homo habilis—And Was It Really Homo? Science 332(6036), 1370–1371. DOI: https://doi.org/10.1126/science.332.6036.1370

Harcourt-Smith WEH 2007. The Origins of Bipedal Locomotion. pp. 1483–1518 in: Henke W, Tattersall I (eds). Handbook of Paleoanthropology. 3 vols. Springer, Berlin, 2069 pp.

Hartwig-Scherer S 1999. “Homo” habilis ab jetzt kein Mensch mehr. Studium Integrale Journal 6(2), 85–87. http://www.si-journal.de/index2.php?artikel=jg6/heft2/sij62-5.html

Hawks J, Hunley K, Lee S-H & Wolpoff M 2000. Population Bottlenecks and Pleistocene Human Evolution. Molecular Biology and Evolution 17(1), 2–22. DOI: https://doi.org/10.1093/oxfordjournals.molbev.a026233

Holly Smith B 1994. Patterns of Dental Development in Homo, Australopithecus, Pan, and Gorilla. American Journal of Physical Anthropology 94(3), 307–325. DOI: https://doi.org/10.1002/ajpa.1330940303

Leakey MD 1972. Olduvai Gorge: Volume 3, Excavations in Beds I and II, 1960-1963. Cambridge University Press, Cambridge (UK), xix+306 pp.

Leakey LSB, Tobias PV & Napier JR 1964. A new species of the genus Homo from Olduvai Gorge. Nature 202(4927), 7–9. DOI: https://doi.org/10.1038/202007a0

Luskin C 2007. Paleoanthropologists Disown Homo habilis from Our Direct Family Tree. Evolution News August 9, 2007. https://evolutionnews.org/2007/08/paleoanthropologists_disown_ho/

Luskin C 2015. As a Taxonomic Group, “Homo habilis” Is Challenged in the Journal Science. Evolution News September 9, 2015. https://evolutionnews.org/2015/09/as_a_taxonomic_/

Schwartz JH & Tattersall I 2015. Defining the genus Homo. Science 349(6251), 931–932. DOI: https://doi.org/10.1126/science.aac6182

Spoor F, Wood B & Zonneveld F 1994. Implications of early hominid labyrinthine morphology for the evolution of human bipedal locomotion. Nature 369(6482), 645–648. DOI: https://doi.org/10.1038/369645a0

Spoor F, Gunz P, Neubauer S, Stelzer S, Scott N, Kwekason A & Dean MC 2015. Reconstructed Homo habilis type OH 7 suggests deep-rooted species diversity in early Homo. Nature 519(7541), 83–86. DOI: https://doi.org/10.1038/nature14224

Tattersall T 1992. The Many Faces of Homo habilis. Evolutionary Anthropology 1(1), 33–37.

Walker A & Shipman P 1996. The Wisdom of the Bones: In Search of Human Origins. Knopf, New York (NY), 368 pp.

Wood B & Collard M 1999a. The Human Genus. Science 284(5411), 65–71. DOI: https://doi.org/10.1126/science.284.5411.65

Wood B & Collard M 1999b. The changing face of genus Homo. Evolutionary Anthropology 8(6), 195–207. DOI: https://doi.org/10.1002/(SICI)1520-6505(1999)8:6<195::AID-EVAN1>3.0.CO;2-2

Wood B & Collard M 2001. The meaning of Homo. Ludus Vitalis 9(15), 63–74. http://profmarkcollard.com/wp-content/uploads/2014/09/Wood-and-Collard-2001.pdf

Natural antifreeze vs. Darwin.

 Blood Viscosity and Freezing Temperatures — A Titanic Problem

Emily Reeves

Editor’s note: With the RMS Titanic tragically back in the news this week, we thought of this article from last year by biochemist Emily Reeves. She notes a question about the character Jack in the movie Titanic, and addresses a fascinating problem in marine biology.

Dr. Gregory Sloop is a Montana physician who knows a thing or two about the cardiovascular system. He has an article in the journal BIO-Complexity highlighting the sleek design of the Antarctic icefish that allows it to live in super-cold waters without freezing to death.

Icefish, aka the family Channichthydiae, survive at 0oC in the Southern Ocean by maintaining blood viscosity at the set point of 3.27 centipoise — a level nearly identical to human blood. They do this without hemoglobin, which is the primary determinant of human and other red-blooded animals’ blood viscosity.

Since icefish don’t have hemoglobin, how do they maintain blood viscosity? Also, how do they breathe? Turns out they maintain viscosity at freezing temperatures primarily by using a special type of glycoprotein: the antifreeze protein. And because oxygen has a higher solubility at lower temperatures, icefish don’t need an oxygen transport molecule like hemoglobin. 

Why Jack Froze

In case you were wondering, blood viscosity is the technical reason why Jack (Rose’s buddy aboard the Titanic) froze in less than 23 minutes, but icefish can survive for 15 years in water of a freezing temperature. Viscosity increases at lower temperatures, and at 0oC human blood reaches a viscosity that is not compatible with life. This is because hemoglobin as a protein is not able to keep viscosity low enough at freezing temperatures. But the antifreeze protein can (think: custom design).

While a viscosity too high is incompatible with life, a low viscosity is also unsuitable for sustaining life. This is because a properly functioning cardiovascular system must have optimized laminar flow and low vascular resistance, which can be achieved only through coordinated control of blood viscosity and specification of vascular geometry.

Stop Criticizing Icefish

Dr. Sloop says icefish have been criticized for expending nearly 22 percent of their basal metabolic rate pumping their hemoglobinless blood compared to at most 5 percent in temperate fish. But he reminds his readers that’s just the cost of doing business in the chilly — well technically, freezing — waters of the Southern Ocean.

Sloop also emphasizes that everything about the icefish is like a custom-fitted suit — appropriate for niche needs. Features included for dealing with the extreme cold are a high-output, low resistance vasculature where the diameter of muscle capillaries is 2-3 times larger than those of other fish.

These fish also have a heavy heart which delivers a larger stroke and therefore higher volume. Together these features enable a high-output, high-velocity, low-pressure, and low-resistance circulation.

Truly, every part of these incredible creatures is optimized for cold. Could all these custom changes be the result of random mutation? Dr. Sloop thinks that is very unlikely. What do you say?

Continuing to rethink the unthinkable

Yet another shot at explaining black holes

Comb Jelly's have never been a "simple lifeform"

Earliest Comb Jellies Wore Armor — “Remarkable,” Say Researchers

David Coppedge 

What does it take to wear armor? An animal has to be able to make the material and put it where it belongs. To be functional, the armor cannot interfere with the animal’s movement. And the animal cannot simply glue sand particles on its exterior in a haphazard way. The appropriate materials, directed by genetic instructions, must be manufactured and placed holistically so that the finished armor provides a beneficial function. It would be surprising, under an evolutionary view, to find such a complex system in the earliest animal fossils. But that’s what Chinese paleontologists discovered in their country’s early Cambrian rocks.

Phylum Ctenophora (cilia-bearing) has about 150 living representatives. While most of them have tentacles, none have hard parts. Varying in size from a few millimeters to over a meter, they resemble jellyfish (phylum Cnidaria) in being gelatinous and transparent, but are distinct in having eight-fold radial symmetry with comb-like rows of fused cilia that propel them around. Some living comb jellies give stunning light shows as their comb rows reflect light in rainbows of iridescent colors, making them resemble alien spacecraft.

Though not bilaterians, they have complex body plans with a buoyancy organ called a statolith, muscles, a nervous system, an alimentary canal, and the ability to control the direction of their locomotion. The phylum made its appearance in the earliest Cambrian layers, dated 520 million years ago. That takes us to the Chengjiang biota in China, one of the finest exposures of early Cambrian fossils in the world.

A Surprise for Fossil Hunters

Seven Chinese researchers found beautifully preserved comb jellies in lower Cambrian strata — three new species and three reclassified species — all with armor. Their open-access paper in Science Advances, “A vanished history of skeletonization in Cambrian comb jellies,” shows the photographs of the fossils along with diagrams of how they probably looked. Armored struts and plates are arranged in complex shapes along the animals’ exterior, following the eight-fold symmetry and making up complex curves. One of the species has spines along its outer struts. The fossil hunters were quite surprised:

They share a basic body plan characterized by a tentacleless and octaradial body with an oral-aboral axis, eight rigid struts (termed here “spokes”) radiating from the aboral end and arched to converge to the oral end, eight soft-bodied flaps or lobes supported by the spokes, eight pairs of ctene rows, a conspicuous apical (or aboral) organ walled by eight rigid plates and housing a spheroidal or ellipsoidal statolith, and an oral region surrounded by eight apiculate lappets…

The eight arcuate spokes [in one species] bear robust spines (Fig. 2, L to N, and figs. S4 to S6) and retain their structural integrity even when disarticulated, suggesting a remarkable degree of sclerotization.

The plates have “considerable rigidity,” they noticed, retaining their integrity even when separated. Some of the hard parts protrude into different layers of sediments. It’s not clear what the armor is made of, but the authors presume it is chitin, the same protein that makes up the exoskeleton of arthropods. “The spokes and apical plates of scleroctenophores were likely cuticular or chitinous in composition, but the presence of minerals in their skeletons cannot be completely ruled out, given that the epidermis of extant ctenophores can produce Mg-Ca carbonates that partially form the statolith,” they say. The statoliths of some fossil specimens even preserve some organic carbon.

Evolutionary Speculations

The authors are not sure about the function of the armor, but indulge in some evolutionary speculation. The typical evolutionary explanation is to imagine an “arms race” that forced the animals to defend themselves against a new class of predators. It seems obvious, though, that nothing about predation can cause a brainless animal to build a suit of armor. It could more easily just go extinct. 

What’s even more remarkable (a word they use themselves) is that the ctenophores are not alone in being armored compared to living counterparts. They use this observation to support a view from the late Stephen Jay Gould that evolution is highly unpredictable:

The occurrence of sclerotized and armored skeletons in Cambrian representatives of several animal groups — including entoprocts, phoronids, lobopods, scalidophorans, and now ctenophores that are exclusively soft-bodied among modern survivors — is a remarkable phenomenon. The independent skeletonization among these diverse Cambrian animals provides indirect evidence for an intensified level of ecological interactions (for example, arms race) and also highlights the importance of paleontological data in illuminating the evolutionary legacy that would be otherwise inaccessible by studying living animals alone. The widespread occurrence of skeletonization echoes Stephen Jay Gould’s view of the striking morphological disparity of many animal phyla during their Cambrian debut, and the contrasting evolutionary trajectories of skeletonized cnidarians and ctenophores also elucidate the contingent fate of evolutionary innovations such as skeletonization.

Protection from Evidence

This kind of explanation serves only to protect Darwinian evolution from the evidence. If animals are similar, they evolved. If animals are different, they evolved. But the authors noticed that the “morphological disparity” in the Cambrian explosion exists not only between phyla, but between species within phyla. Earlier, they referred to the explosion:

Here, we report several sclerotized and armored ctenophore species, based on new material and reinterpretation of previously published material from the early Cambrian Chengjiang biota (ca. 520 Ma). Along with armored Cambrian entoprocts, phoronids, lobopods, and scalidophorans, the new fossils suggest a vanished Cambrian history of skeletonization in multiple animal groups, imply the ecological importance of skeletonization in the Cambrian explosion, and highlight the remarkable morphological disparity in certain Cambrian animal clades relative to their modern survivors.

A “vanished Cambrian history of skeletonization in multiple animal groups” is inconsistent with Darwinian evolution. “Ecological importance” is incapable of producing genetic programming for an armored skeleton. “Morphological disparity” at the earliest onset of complex animals is the opposite of Darwin’s image of a branching tree gradually separating into more and more complex types.

Designers, by contrast, know how to apply a common solution in different applications. That’s why it’s unsurprising to see complex armor in disparate groups from the beginning. 

Stephen Meyer did not go into detail about ctenophores in Darwin’s Doubt, other than to note they are among the phyla that suddenly appeared in the Cambrian explosion (p. 32). But this revelation that ctenophores are more complex than originally realized, possessing elaborate armor, certainly reinforces his contention that “the best explanation for the explosion of information necessary for the Cambrian animals… remains intelligent design” (see the Epilogue in the paperback edition, p. 448).

Time to end fractional banking?

A case for conditionalism

Rethinking the unrethinkable again

On irreducible complexity

 Answering Farina on Behe’s Work: Irreducible Complexity

Jonathan McLatchie

Editor’s note: We are delighted to welcome Dr. McLatchie as a new colleague. He is Resident Biologist and Fellow at the Center for Science and Culture.

On the Internet, some people are worth responding to and others are not. We have written enough lately in response to YouTuber Dave Farina following his recent debate with Rice University synthetic chemist Dr. James Tour. However, Mr. Farina has also posted a popular video criticizing Dr. Michael Behe’s work, and I will turn to that now.

I am a specialist in molecular and cell biology, and was thus interested in Farina’s video reviewing Michael Behe’s three books — Darwin’s Black Box, The Edge of Evolution, and Darwin Devolves. In this and several subsequent articles, I will offer a rebuttal to Mr. Farina’s analysis of Dr. Behe’s work. Here, I will address Farina’s commentary on Darwin’s Black Box – in particular, his alleged counterexamples of irreducibly complex systems having evolved by natural processes.

Evolution of the Cit+ Mutant

The video contends that Behe’s concept of irreducible complexity is empirically falsified by documented examples of systems that meet Behe’s definition of being “irreducibly complex” yet evolving by unguided mechanisms. The first exhibit is Richard Lenski’s long-term evolution experiment with Escherichia coli, in which it was observed that, after some 33,000 generations (15 years), bacterial cells evolved the ability to grow on citrate under aerobic conditions.1 The genetic basis for this ability was subsequently identified.2 E. coli already possesses the ability to grow on citrate under anaerobic conditions, facilitated by a citrate transporter protein encoded by the gene citT. A 2933 base pair stretch of DNA, containing the citT gene, underwent duplication. The result was that a copy of the hitherto unexpressed citT gene was placed under the control of the promoter of the adjacent gene, rnk, which as a consequence drove expression under aerobic conditions. This is a relatively simple change that does not require multiple co-dependent mutations to bring it about. Indeed, this instance of adaptation does not even require the origin of any novel genes and proteins, or even the modification of existing ones. The citT gene already codes for a citrate transporter which imports citrate into the cell in the absence of oxygen. The duplication event led to a loss of regulation of the citT protein such that it was expressed under both oxygen-rich and oxygen-deficient conditions, rather than in only oxygen-deficient ones.

Furthermore, the ability of the cells to grow on citrate under aerobic conditions was optimized by several other mutations.3 As Behe himself summarizes:

Even before the critical mutation occurred, a different mutation in a gene for a protein that makes citrate in E. coli degraded the protein’s ability to bind another metabolite, abbreviated NADH, which normally helps regulate its activity. Another, later, mutation to the same gene decreased its activity by about 90 percent. Why were those mutations helpful? As the authors write, ‘When citrate is the sole carbon source, [computer analysis] predicts optimal growth when there is no flux through [the enzyme]. In fact, any [of that enzyme] activity is detrimental.’ And if something is detrimental, random mutation will quickly get rid of it. Further computer analysis by the authors suggested that the citrate mutant would be even more efficient if two other metabolic pathways that were normally turned off were both switched on. They searched and discovered that two regulatory proteins that usually suppress those pathways had been degraded by point mutations; the traffic lights were now stuck on green.4

In other words, these mutations that optimized the ability of the cells to grow on citrate were in fact damaging. Since they supported the present needs of the organism, they were preserved by natural selection. As Behe argues at length in Darwin Devolves, the majority of mutations that are subject to positive selection are damaging rather than constructive, since there are far more ways to acquire an advantage by breaking something than there are ways to do so by building something. Readers may find interesting Behe’s response to Richard Lenski’s review of Darwin Devolves, which you can find here.

One researcher who has studied the evolution of citrate metabolism in E. coli is microbiologist Dr. Scott Minnich, a Fellow with Discovery Institute’s Center for Science and Culture. Farina is aware of this fact, and states that “Ironically, one of Behe’s colleagues at Discovery Institute, Dr. Scott Minnich — a professor in the department of agricultural and life sciences at the University of Idaho — co-authored a paper describing this pathway in detail, inadvertently highlighting its irreducible nature. I’m sure he got a slap on the wrist from Meyer and pals for that.” However, the Minnich paper5 in fact supports Behe’s interpretation of these results rather than Lenski’s — that is, that “no new functional coded element was gained or lost, just copied.”6 I am therefore doubtful that Farina has read the paper. Lenski’s original paper had suggested that the adaptation process involved three steps — potentiation (involving initial neutral mutations), actualization (the promoter fusion event described above), and refinement (increasing expression of the dctA gene, encoding a transporter that facilitates recovery of lost succinate during citrate import). In the view of Lenski and his colleagues, the reason the trait took some 15 years to evolve is because of the need for the initial neutral mutations (“historical contingency”) that by themselves do not promote growth but are necessary for the later actualization event. Minnich’s lab demonstrated that the mutants observed by the Lenski lab could be isolated much more rapidly — within 14 days rather than 15 years (and in as few as a hundred generations rather than 33,000) — and that the length of time it took in Lenski’s experiment more probably reflects an artifact of the experimental conditions than a requirement of evolution.

Vpu Protein

The video offers a few other supposed examples of irreducibly complex traits evolving, including the Vpu protein in HIV-1.7 Farina comments, 

This now has a novel function — inactivating a protein of the human immune system called tetherin. Human tetherin is different enough from the same protein in chimpanzees such that simian immunodeficiency virus, from which HIV evolved, can’t counter it. This new trait requires three to seven specific mutations, leading to several completely new protein binding sites. HIV only jumped from chimps into humans around 1930, so this is another recent example of an irreducibly complex trait evolving.

Vigan and Neil (2010) “carried out an extensive mutagenesis of the HIV-1 NL4.3 Vpu TM domain to identify three amino acid positions…that are required for tetherin antagonism.”8 Mutating two of these positions (namely, A14L and W22A) showed a marked defect, whereas the A18L mutant showed only a minor defect. Thus, it is not even the case that all three amino acid positions are crucial for tetherin antagonism. Furthermore, viruses have enormous population sizes and extremely high mutation rates. They are therefore able to evolve complex traits requiring multiple co-dependent mutations far more readily than more complex organisms, including bacteria. Thus, for those two reasons, this is really not a good example to cite in support of Farina’s contention about irreducible complexity arising in more complex organisms.

Horizontal Gene Transfer to the Rescue?

As a further example, the video offers “the many animals that eat photosynthetic algae which appear to be on their way to becoming photosynthetic themselves via endosymbiosis.” Farina cites a paper on “Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica.”9 The paper discusses the acquisition of plastids by the sea slug Elysia chlorotica by ingestion of the photosynthetic algae Vaucheria litorea. Though more than 90 percent of the proteins required for plastid metabolism are encoded in the nuclear genome of the algae, the plastids are nonetheless still able to photosynthesize within the sea slug. The paper determines that the essential plastid proteins are supplied by the sea slug itself, and that the genes which support photosynthesis have been acquired through horizontal gene transfer. But this does not involve the evolution of any new complex traits. The genes and proteins already existed but were simply transferred from one organism to another.

Rapid Lizard Evolution?

Next, the video notes that “There are lizards which are transitioning from laying eggs to live birth, in one case doing both in a single litter,” citing a paper from 2019.10 But it seems more likely that the Saiphos equalis was designed with the capability of switching between laying eggs (“oviparous”) and carrying embryos internally until completely developed (“viviparous”). Indeed, as Farina noted, there was even one case of a female giving birth to a live infant and laying eggs in the same litter. Moreover, it has been shown that very similar genes are expressed between the two modes, suggesting “that reproductive mode is relatively labile in this species,” and that “there may be fewer physiological barriers to transitions between parity modes than previously thought, an assertion that is supported by our gene expression data, in which oviparous and viviparous individuals expressed genes with many of the same functions during the reproductive cycle.”11 Furthermore, it has been previously shown that differences in parity mode between two species of Phrynocephalus are due to differences in gene expression rather than the result of many mutations.12

Multicellular Algae

As a final example, the video argues that “There are the unicellular algae that evolved in the lab to become permanently multicellular,” citing a paper by Herron et al. (2018) — “De novo origins of multicellularity in response to predation.”13 In the study, populations of the unicellular green alga Chlamydomonas reinhardtii were subjected to selective pressure by the introduction of the filter-feeding predator Paramecium tetraurelia. They found that two of the five populations developed multicellular structures. However, the multicellular populations lacked motility and the multicellular structures did not evolve multiple cell types. Moreover, as the authors of the paper note, “The ability of wild-type C. reinhardtii to form palmelloids [i.e. multicellular structures] suggests that the founding population in our experiment already possessed a toolkit for producing multicellular structures.” While the strains that evolved in the experiment are obligately multicellular (meaning that being composed of multiple cells is an essential and permanent part of their life cycle), the authors suggest that the genetic basis of the evolved multicellularity phenotype “involves the co-option of a previously existing plastic response.” If this is the case, the authors note, “the shift from a primarily unicellular (but facultatively multicellular) to an obligately multicellular life cycle may have required only a change from facultative to obligate expression of the genes involved in palmelloid formation.” In other words, the transition from being able to exist as single-celled organisms, while forming multicellular structures under certain conditions, to being permanently multicellular may have involved a shift from being able to turn the relevant genes on or off to the genes being permanently locked on. See also this short article by Michael Behe where he addresses a similar paper.

Straw Man Arguments

A common tactic in debate is setting up and then knocking down a straw man argument — that is, a version of your interlocuter’s argument that has been modified to render it easier to refute. The Farina video complains that ID proponents turn scientific research into a game of whack-a-mole by moving on to some other system and claiming that it is irreducibly complex when prior similar claims have turned out to be false. He comments, “No matter how many times creationists point to a supposedly unevolvable system and then biologists figure out its evolutionary history, there’s always another system creationists will point to and say, ‘But this this one — surely, this one — couldn’t have evolved.” However, I am not persuaded that any of the systems that have been proposed by Behe and other proponents of ID to be irreducibly complex have been shown to be evolvable by naturalistic processes. It would be one thing if there were detailed, plausible evolutionary scenarios that could account for thousands of complex biological systems save for a relative handful. Instead, it is the case that essentially none of the complex systems found in living organisms can be plausibly accounted for in this way.

The video also grossly misrepresents the structure of the inference from irreducible complexity to design. As Farina summarizes, “Humans build things; therefore, everything must have been built.” In fact, the inference is much more nuanced. The argument says that well-matched arrangements of parts that work together to achieve some higher-level objective are the sorts of systems that are habitually associated with conscious agents — since intelligent beings, unlike naturalistic processes, are capable of goal-directedness. Therefore, on the hypothesis that a mind was involved in the creation of biological systems, the existence of irreducibly complex systems is not particularly surprising. However, if the design hypothesis is false, such systems become wildly surprising. Given the top-heaviness of this likelihood ratio (or “Bayes factor”), these systems favor a design hypothesis. Moreover, since each requires a significant appeal to chance, each one is epistemically independent, meaning that the Bayes factors for the many thousands of irreducibly complex systems multiply together, forming a massive cumulative case for design.

Notes

Blount ZD, Borland CZ, Lenski RE. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci U S A. 2008; 105(23):7899-906.

Blount ZD, Barrick JE, Davidson CJ, Lenski RE. Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature. 2012;489(7417):513-8.

Quandt EM, Gollihar J, Blount ZD, Ellington AD, Georgiou G, Barrick JE. Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment. Elife. 2015; 4:e09696.

Behe MJ, Darwin Devolves: The New Science About DNA That Challenges Evolution (HarperOne, 2020), 139.

Van Hofwegen DJ, Hovde CJ, Minnich SA. Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection Requires citT and dctA. J Bacteriol.2016;198(7):1022-34.

Behe MJ, Darwin Devolves: The New Science About DNA That Challenges Evolution (HarperOne, 2020), 188.

Lim ES, Malik HS, Emerman M. Ancient adaptive evolution of tetherin shaped the functions of Vpu and Nef in human immunodeficiency virus and primate lentiviruses. J Virol. 2010; 84(14):7124-34. 

Vigan R, Neil SJ. Determinants of tetherin antagonism in the transmembrane domain of the human immunodeficiency virus type 1 Vpu protein. J Virol. 2010; 84(24):12958-70.

Rumpho ME, Worful JM, Lee J, Kannan K, Tyler MS, Bhattacharya D, Moustafa A, Manhart JR. Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. Proc Natl Acad Sci U S A. 2008; 105(46):17867-71.

Laird MK, Thompson MB, Whittington CM. Facultative oviparity in a viviparous skink ( Saiphos equalis). Biol Lett. 2019; 15(4):20180827.

Griffith OW, Brandley MC, Belov K, Thompson MB. Reptile Pregnancy Is Underpinned by Complex Changes in Uterine Gene Expression: A Comparative Analysis of the Uterine Transcriptome in Viviparous and Oviparous Lizards. Genome Biol Evol. 2016; 8(10):3226-3239.

Gao W, Sun YB, Zhou WW, Xiong ZJ, Chen L, Li H, Fu TT, Xu K, Xu W, Ma L, Chen YJ, Xiang XY, Zhou L, Zeng T, Zhang S, Jin JQ, Chen HM, Zhang G, Hillis DM, Ji X, Zhang YP, Che J. Genomic and transcriptomic investigations of the evolutionary transition from oviparity to viviparity. Proc Natl Acad Sci USA.2019;116(9): 3646-3655.

M.D. Herron et al. (2019), “De novo origins of multicellularity in response to predation,” Scientific Reports 9: 2328.

Primeval nanomachines troll Darwinism again?

Local Fitness Landscape Mapped Out For Green Fluorescent Protein

Cornelius G Hunter  

As we have discussed many times, proteins are a show-stopper for evolution. Proteins consist of dozens, hundreds and even thousands of amino acids and, like most machines, they don’t work very well until most of the parts (amino acids in this case) are in place. Half of the amino acids don’t give you half the function of a protein. Now, a new paper reinforces the problem of protein evolution.

One approach to studying how evolution could create new protein designs is to start with some sort of random sequence of amino acids, see how well it works, and try to evolve it to obtain a protein. This is difficult because the protein design space is astronomically huge and proteins are sparse within that space. Any random sequence of amino acids will merely give you junk. Furthermore, the fitness landscape is flat and doesn’t provide the guidance evolution needs to move toward functional proteins.

Another approach is to start at the end and work backwards. In other words, start with the finished product—a functional protein—and see what the fitness landscape looks like as you swap in different amino acids. This is difficult because, unfortunately for evolution, the fitness landscape drops off precipitously as you move away from the native protein design. Modifying only a few percent of the amino acids leads to a rapid loss of function.

The new paper takes this second approach. It uses a bioluminescent protein known as the green fluorescent protein, taken from the jellyfish, Aequorea victoria. It is a wonderful study that systematically mapped out the protein’s function (as measured by the protein’s fluorescence) for a total of 51,715 different protein sequences that are nearby the native sequence.

The results confirmed what earlier studies had indicated: the protein function drops off dramatically with only a relatively small number of substitutions. But the study also explored the effect of multiple substitutions. It is well known that the effect of two substitutions, for example, are not always simply the sum of their individual effects. They can interact with each other in either positive or negative ways. This is referred to as epistasis.

The new study found that negative epistasis was strong and prevalent. As one of the researchers explained:

We were really surprised when we finally had a chance to look at exactly how the interactions between mutations occur. We also did not expect that almost all the mutations that are only slightly damaging on their own can destroy fluorescence completely when combined together.

It was well understood that evolving a protein is an astronomically unlikely event, and these results indicate it is even more difficult. Those negative results, however, were not reported in the paper. Instead, the paper discussed possible ways that one green fluorescent protein, found in one particular species, may have evolved into other green fluorescent proteins, found in other species. The implications for the initial evolution of a protein were ignored.

The Origin of Life=the origin of information?

 Information and Life’s Origin — A Retrospective View

Eric Hedin

In the late 1980s, I first encountered the science of information theory and its application to theories of the origin of life. My introduction to the subject was a book, Origins and Destiny1, by research scientist Robert Gange. He described the idea of a generalized form of the traditional Second Law of Thermodynamics, based on quantum statistical mechanics. In conjunction with the understanding that the formation of life from non-life constitutes a rise in specified complexity rather than increasing order, this generalized Second Law raised a theoretical barrier against any natural origin of life scenario.

The traditional Second Law of Thermodynamics is viewed as an inviolable arbiter of possible outcomes for all physical processes. In particular, any conceivable proposal for a perpetual motion machine can, without analysis, be rejected based on the Second Law. With regars to the origin and development of life, the generalized Second Law states that any “alleged natural explanation…will be untrue in the same way a patent examiner in Washington, DC, knows an alleged invention for a perpetual motion machine is untrue.”2

A Postdoc Wonders

As a young postdoctoral researcher in physics, I wondered why the quantum statistical version of the Second Law wasn’t more widely recognized as an aspect of physical reality that limited any proposed natural mechanism for the origin of life. However, since the background physics of the generalized Second Law is typically buried in graduate-level texts on quantum statistical mechanics, perhaps its low visibility isn’t surprising.

Since my own physics research trajectory took me from experimental plasma physics to integrated optics to computational nano-electronics, my professional work did not directly intersect with research on the physical aspects of information theory. However, my personal interest in seeing how evidence for intelligent design held up to scientific advances kept my attention focused on relevant developments in cosmology and molecular biology.

In the early 1990s, the graduate library at the University of Washington provided access to research articles by Hubert Yockey on the application of information theory to the origin of life. Noting that “The information content of amino acid sequences cannot increase until a genetic code with an adaptor function has appeared,” Yockey states,

Nothing which even vaguely resembles a code exists in the physico-chemical world. One must conclude that no valid scientific explanation of the origin of life exists at present.3

Unlocking Life’s Enigma

By the mid 1990s, I had read The Mystery of Life’s Origin4, in which the authors distinguish between thermal entropy (related to the distribution of energy in the system), and configurational entropy (related to the distribution of mass — for example, the specific sequence of amino acids comprising a protein). Their analysis of multiple proposals for natural mechanisms to overcome the thermodynamic barrier represented by the high degree of configurational entropy in living systems led them to conclude that all such mechanisms are “clearly inadequate to account for the configurational entropy work of coding.”5

In the documentary video “Unlocking the Mystery of Life,” the premise of intelligent design was cogently defended as an alternative to the shortcomings of naturalism to explain such biochemical enigmas as irreducible complexity and the specific sequences of amino acids comprising functional proteins. The latter example of nature’s inability to increase the information content of a closed system over time led biophysicist Dean Kenyon to disavow his own research, published earlier in his textbook, Biochemical Predestination.

In the late 1990s, my academic schedule allowed me to pursue other source material on the physics of the generalized Second Law, and I obtained copies of two main textbooks on statistical mechanics referenced by Gange. The author of one of these texts gives a fundamental definition of information that emphasizes the relationship between information and the mind:

Information is the entity which makes the difference between knowing and not knowing, between being faced with a number of possibilities and between knowing the one that actually prevails.6

Only in the context of the mind is the difference between knowing and not knowing a meaningful distinction. The author of the other text, Arthur Hobson, affirms that given an initial measurement of a system, predictions of the system at a later time “cannot contain more information (but may contain less information)” than the initial data describing the system.7 This limitation on natural processes, based upon the laws of quantum mechanics, prohibits a system (even the entire universe bounded by the cosmic horizon) from progressing from a state of lower information (pre-life) to a state of higher information (post-life) by any combination of natural forces.

Chance and Necessity

William Dembski affirms the proscriptions of the generalized Second Law by showing that chance and necessity are insufficient to ratchet up the complex specified information (CSI) content of a closed system over time:

What natural causes cannot do, however, is originate CSI. This strong proscriptive claim, that natural causes can only transmit CSI but never originate it, I call the Law of Conservation of Information. It is this law that gives definite scientific content to the claim that CSI is intelligently caused.8

In 2005, while mentoring a senior honors student on a study of the boundaries of science, I read Stephen Meyer’s groundbreaking article outlining intelligent design as a source of biological information.9 Complementing the conclusions of other lines of research, Meyer’s analysis and conclusions added to the scientific literature affirming the validity of the generalized Second Law as a fundamental boundary of nature that disallows an unguided origin of life.

Have the last twenty years produced any experimental research demonstrating how unguided natural processes can successfully produce the complex, specified arrangements of components inherent in functional biomolecules? Any dearth of success in this field is not for lack of trying, nor is it surprising that scientists have not been able to coax even a single biochemically relevant protein into existence from a mix of ingredients likely to be available on the early Earth. 

The Limits of Unguided Processes

A Rice University professor of chemistry, James Tour, who is renowned for his research in synthetic organic chemistry, draws this conclusion regarding any naturalistic origin-of-life scenario:

the requisite molecules (lipids, proteins, nucleic acids, and carbohydrates) are so unlikely to have occurred in the states and quantities needed, that we could never have gotten to the point of figuring out the genesis of the requisite code or information.10

Unguided natural processes, according to the generalized Second Law, cannot systematically increase the information content of a closed system over time. Since the origin of life, represented by the formation of a single-cell organism, constitutes just such an increase in information, natural processes are not expected to be the cause. Intelligence is the only recognized source of information, as inherent in living organisms. What we know of the laws of physics supports this conclusion.

Notes

Robert Gange, Origins and Destiny (Waco, Texas: Word Books, 1986).

Gange, Origins, (1986), 91.

Hubert P. Yockey, “Self Organization Origin of Life Scenarios and Information Theory,” J. Theor. Biol. 91 (1981), 13-31.

Charles B. Thaxton, Walter L. Bradley, and Roger L. Olsen, The Mystery of Life’s Origin: Reassessing Current Theories (New York: Philosophical Library, 1984).

Thaxton, et al, Mystery (1984), ch. 8 (available online: https://www.ldolphin.org/mystery/chapt8.html ).

Amnon Katz, Principles of Statistical Mechanics: The Information Theory Approach (San Francisco: W. H. Freeman & Co., 1967), 14.

Arthur Hobson, Concepts in Statistical Mechanics (New York: Gordon and Breach Science Publishers, 1971), 142-145.

William A. Dembski, “Intelligent Design as a Theory of Information,” (1997); https://www.discovery.org/a/118/ .

Stephen C. Meyer, “The Origin of Biological Information and the Higher Taxonomic Categories,” Proc. of the Biological Society of Washington, 117(2), (2004), 213-239.

https://www.jmtour.com/personal-topics/evolution-creation/.

Before all roads led to Rome.

From the graveyard of empires.

David Berlinski against reductionism

On Reductionism and the meaning of life.

 David Berlinski on the Immaterial, Alan Turing, and the Mystery of Life Itself

Evolution News

The recently published book Science After Babel is again in the spotlight at ID the Future, with its author, philosopher and mathematician David Berlinski, and host Andrew McDiarmid considering various elements of the work. In a new podcast, the pair discuss the puzzling relationship between purely immaterial mathematical concepts (the only kind) and the material world; World War II codebreaker and computing pioneer Alan Turing, depicted in the 2014 film The Imitation Game; and the sense that the field of physics, once seemingly on the cusp of a theory of everything, finds itself at an impasse. Then, too, Berlinski writes, there is the mystery of life itself. If scientists thought that its origin and nature would soon yield to scientific reductionism, they have been disappointed. Life’s “fantastic and controlled complexity, its brilliant inventiveness and diversity, its sheer difference from anything else in this or any other world” remain before us, suggesting, as Berlinski puts it, “a kind of intelligence evident nowhere else.” Download the podcast or listen to it here.

The rise and fall of ancient Egypt.

Sorry design denier that's my line.

 We Can Say It, But You Can’t

Cornelius G Hunter

Highly, Intricately, and Precisely Integrated Networks of Entities and Interactions

As Carl Woese explained in 2004:

The cells we know are not just loosely coupled arrangements of quasi-independent modules. They are highly, intricately, and precisely integrated networks of entities and interactions. … To think that a new cell design can be created more or less haphazardly from chunks of other modern cell designs is just another fallacy born of a mechanistic, reductionist view of the organism.

Mechanistic, reductionist view? It appears Woese put his finger on precisely what he believed in: evolution. Replace “cell” with just about any biological structure and Woese has, in a nutshell, summarized evolutionary theory, what little there is of it. As Richard Dawkins once explained:

The bombardier beetle’s ancestors simply pressed into different service chemicals that already happened to be lying around. That’s often how evolution works.

The future of energy again?