On the cosmogony of the physical and moral universes

 Watch: Brian Keating and Jordan Peterson on All Things Cosmological

Emily Sandico 

Our friend Professor Brian Keating recently joined Jordan Peterson for an intriguing dialogue about all things cosmological and Keating’s book Losing the Nobel Prize: A Story of Cosmology, Ambition, and the Perils of Science’s Highest Honor. Keating is a brilliant astrophysicist, an observant Jew, and a fascinating figure in the dialogue about science and religion. He and Peterson discuss how to fight your personal dragons and find the great adventure of your life, how to distinguish evidence for the multiverse from mere dust, and what we learned in 2015 when scientists found gravitational radiation from the fusion of two massive black holes a billion years ago.  

A couple of years ago on his podcast Into the Impossible, Dr. Keating interviewed our own Dr. Stephen Meyer about his  book Return of the God Hypothesis. Check out both interviews!    

“The Jordan Peterson Podcasts: Black Holes, Time Travel, and the Origin of the Universe with Dr. Brian Keating“

“Into the Impossible with Dr. Brian Keating: Stephen Meyer and the Return of the GOD Hypothesis"

The "hammer of God" saves Christendom.

Darwinism's version of the design inference?

 Meet Intelligent Design’s Naturalistic Cousin: Assembly Theory

Evolution News 

From “A New Idea for How to Assemble Life,” by science writer Philip Ball at Quanta Magazine

Assembly theory started when [Lee] Cronin asked why, given the astronomical number of ways to combine different atoms, nature makes some molecules and not others. It’s one thing to say that an object is possible according to the laws of physics; it’s another to say there’s an actual pathway for making it from its component parts. “Assembly theory was developed to capture my intuition that complex molecules can’t just emerge into existence because the combinatorial space is too vast,” Cronin said.

See if you can spot the notion highly similar to Bill Dembski’s “specification” in this section:

for a complex object to be scientifically interesting, there has to be a lot of it. Very complex things can arise from random assembly processes — for example, you can make protein-like molecules by linking any old amino acids into chains. In general, though, these random molecules won’t do anything of interest, such as behaving like an enzyme. And the chances of getting two identical molecules in this way are vanishingly small. Functional enzymes, however, are made reliably again and again in biology, because they are assembled not at random but from genetic instructions that are inherited across generations. So while finding a single, highly complex molecule doesn’t tell you anything about how it was made, finding many identical complex molecules is improbable unless some orchestrated process — perhaps life — is at work.

We should be crystal clear — calling Assembly Theory the “naturalistic cousin” of ID is OUR take on the work of Cronin’s group. Dr. Cronin himself (pictured above), and his collaborators, would disavow any connection to intelligent design reasoning, and they should not be held responsible for our interpretation. 

But, when one notices conceptual similarities and parallels, it would be remiss for us not to highlight them. Assembly Theory is fascinating and potentially fruitful, and so, we’re over here cheering on the effort. 

The fossil record's uprising against gradualism continues apace.

 Fossil Friday: The Stubborn Mystery of the Tully Monster

Gunter Bechly 

Tullimonstrum gregarium is an enigmatic but abundant fossil organism from the famous locality of Mazon Creek, which is dated to a Carboniferous age of about 307 million years. The Tully monster, named after its discoverer the amateur fossil collector Francis Tully, has been designated as the official state fossil of Illinois, but it has puzzled scientists for more than 50 years since its first description by Richardson (1966). 

Tullimonstrum is a relatively large (about 13 inch), soft-bodied bilaterian animal with an apparently segmented body, unpaired fins, a pair of long stalked eyes, and a long proboscis terminating in a toothed pincer-mouth. Based on the same evidence of thousands of fossils, different scientists have identified Tullimonstrum in dozens of studies either as a relict from the strange Cambrian phyla, anomalocarid-like or rather Opabinia-like arthropod, annelid worm, mollusk, tunicate, or conodont, but until recently never as a vertebrate. A few years ago, two high-profile studies, published in the prestigious journal Nature and involving 22 scientists, surprisingly claimed to finally have solved the mystery. They identified Tullimonstrum not only as a vertebrate (Clements et al. 2016) but more precisely as a relative of modern lampreys (McCoy et al. 2016).

A Very Comprehensive Analysis

These experts based their results on a very comprehensive analysis of more than 1,200 museum specimens. But just a year later a team of seven eminent paleontologists published a new study (Sallan et al. 2017), based on the very same fossil evidence, which strongly disputed this identification as vertebrate and lamprey, as well as the detailed interpretations of the different body structures as trilobed brain, gill pouches, chorda, myomeres, and fin rays. These authors boldly stated that “the ‘Tully Monster’ is not a vertebrate,” and suggested that alternative identifications as mollusk, anomalocarid, or non-vertebrate deuterostome (e.g., tunicate larva) are more congruent with the data. While Clements et al. (2016) found the melanosome structure of the eyes of Tullimonstrum to prove a vertebrate affinity, a synchrotron spectroscopic analysis of the eye pigments by Rogers et al. (2019) found them more similar to those of cephalopod mollusks.

Now, a new paper by a team of five Japanese scientists has published a micro-CT analysis of 153 fossils of the Tully monster (Mikami et al. 2023). These authors also came to the conclusion that it is definitely not related to vertebrates, but represents an invertebrate of unknown affinity.

How Much Confidence?

This is yet another case where groups of renowned scientists, who all look at the very same evidence of numerous well-preserved fossils, can neither agree upon the identification of the preserved body structures nor even the phylum to which the animal should be attributed. How much confidence should we really place in such dubious fossil evidence when it is boldly claimed to prove Darwinian evolution as a fact or to represent long-sought “missing links”?

Notes

Clements T, Dolocan A, Martin P, Purnell MA, Vinther J & Gabbott SE 2016. The eyes of Tullimonstrum reveal a vertebrate affinity. Nature 532(7600), 500–503. DOI: https://doi.org/10.1038/nature17647

McCoy VE, Saupe EE, Lamsdell JC, Tarhan LG, McMahon S, Lidgard S, Mayer P, Whalen CD, Soriano C, Finney L, Vogt S, Clark EG, Anderson RP, Peterman H, Locatelli ER & Briggs DEG 2016. The ‘Tully monster’ is a vertebrate. Nature 532(7600), 496–499. DOI: https://doi.org/10.1038/nature16992

Mikami T, Ikeda T, Muramiya Y, Hirasawa T & Iwasaki W 2023. Three-dimensional anatomy of the Tully monster casts doubt on its presumed vertebrate affinities. Palaeontology 66(2):e12646. DOI: https://doi.org/10.1111/pala.12646

Richardson ES Jr 1966. Wormlike Fossil from the Pennsylvanian of Illinois. Science 151(3706), 75–76. DOI: https://doi.org/10.1126/science.151.3706.75-a

Rogers CS, Astrop TI, Webb SM, Ito S, Wakamatsu K & McNamara ME 2019. Synchrotron X-ray absorption spectroscopy of melanosomes in vertebrates and cephalopods: implications for the affinity of Tullimonstrum. Proceedings of the Royal Society B 286(1913):20191649, 1–8. DOI: https://doi.org/10.1098/rspb.2019.1649

Sallan L, Giles S, Sansom RS, Clarke JT, Johanson Z, Sansom IJ & Janvier P 2017. The ‘Tully Monster’ is not a vertebrate: characters, convergence and taphonomy in Palaeozoic problematic animals. Palaeontology 60(2), 149–157. DOI: https://doi.org/10.1111/pala

OOL Science looks to the heavens for a boost?

 Uracil Discovered on Asteroid Ryugu — What Does It Mean for the Origin of Life?

Carl Linnaeus 

Recently, chemical composition data were obtained from samples retrieved by the Japanese spacecraft Hayabusa2 that was landed in two locations on the asteroid (162173) Ryugu. In December 2020 Hayabusa2 successfully returned to Earth with its precious pristine samples, uncontaminated by residues from Earth (except maybe some metallic material originating from the collection device). Published in Science, early analysis of organic compounds extracted from the collected samples included significantly racemic mixtures of several amino acids, indicating that these samples were relatively free of Earthly contamination from biopolymers.1 (All proteins in life are made of racemically pure L-amino acids.) Prior analysis of meteorites could not boast of such purity uncontaminated by Earth’s biological products. 

Therefore, these Ryugu samples appear to be our first chance to examine which organic compounds may be produced in a prebiotic setting in our solar system. In addition, we don’t have to rely on uncertain estimates of the conditions on Earth when the solar system was forming. Asteroids containing significant amounts of carbon, never visited by extraterrestrials like us, may provide a reasonable idea of what abiotic chemistry can produce.

It Came from Outer Space?

A recent article in Nature Communications reported that uracil, one of the nucleobases found in RNA, was identified in these pristine Ryugu samples.2 For those who place their bets on the RNA world hypothesis, this is a significant finding, at least in their opinion. They finally have evidence that at least one of the nucleobases of RNA has been discovered outside of Earth, thus, they say, upholding the notion that our biochemistry could have been seeded from outer space! As Live Science summarizes, “After becoming trapped on asteroids like Ryugu, these molecules may have eventually hitched a ride to Earth via meteorite impacts, where they sparked the first stirrings of life in primordial oceans.”

This may be our earliest chance to remark on valid data of prebiotic chemicals free of Earthly contamination. So it would be logical to consider first the initial chemical analysis described in Science to broadly classify all organic compounds, identified using two sensitive analytical methods. Concerning the building blocks of life, they found several amino acids, but all in racemic mixtures. This is precisely what chemists predict. It is extremely difficult to produce optically pure compounds from smaller compounds. The chemistry of mirror-imaged compounds is exactly the same, differing only in the spatial orientation of covalently bonded atoms (analogous to your right and left hands being equivalent). Life only uses one of these chemical forms to make proteins, RNA, DNA, complex carbohydrates and many lipids. 

Only the Simplest Amino Acids

On Ryugu just some of the simplest amino acids were detected, including glycine, D/L-alanine, D/L-serine, and D/L-valine, along with other amino acids not used to build proteins (Fig. 1). These results agree well with the earlier experiments by Stanley Miller and others where simple organic structures were readily produced in prebiotic simulations. However, over eight amino acids with more complex critical functional groups have still not resulted among the various permutations of prebiotic reactions tested. It’s not just dealing with racemic mixtures that confounds the supporters of abiogenesis, but how to form those more elaborate amino acids whose side chains play critical roles in the activity and structure of all proteins.

Fig. 1. Chemical structures of the four amino acids identified from Ryugu that match those found in proteins plus examples of three amino acids (among 11) that are not found in proteins.

The chemical analysis also reported thousands of organic compounds, classified in multiple groups, that may or may not be found in the context of living organisms. If a primordial soup were to originate from this mixture, any biomolecules would have to contend with a myriad of possible side reactions with a variety of reactive compounds competing for the rights to produce a biopolymer. Would the situation be different if the asteroid material were to simply seed the Earth with these needed building blocks? The competing contaminants still far outnumber the biologically relevant molecules. 

The RNA Route

Let’s consider whether the prospects are better if we take the RNA route. Uracil was clearly identified from Ryugu. The engineering threshold to form nucleotides, the building blocks for RNA, is much higher than that for proteins. The core unit to which nucleobases and phosphate are bound is the 5-carbon sugar D-ribose. Several mechanisms have been proposed to explain how carbohydrates may have originated in an abiotic environment.3 The challenges to integrate D-ribose into nucleotides abiotically can be summarized as three major chemical barriers. 1) Abiotic production of five-carbon sugars will yield four chemically equivalent stereoisomers in both the D and L forms, thus resulting in eight stereoisomers at approximately equal levels (Fig. 2A). How does D-ribose get selected through random chemistry without even considering that longer chain sugars will also be present? 2) Ribose can interconvert from an open-chain form to a six-membered ring structure (pyranose form) or to a five-membered ring (furanose), both of which present as alpha and beta configurations at carbon 1 (Fig. 2B). At equilibrium the pyranose form comprises 80 percent while the furanose form is 20 percent of the ribose. RNA uses the furanose form, so how does this minor component win out in any abiotic reactions? 3) Nitrogen at position 1 of uracil needs to be bonded with carbon 1 of D-ribose in a beta configuration through a thermodynamically unfavored reaction. How can this reaction occur abiotically?

Fig. 2 Chemistry of 5-carbon sugars. A. Structures of the four D-pentoses are shown with stereochemical projections (bold bars are bonds extending towards the viewer while hatched bars extend away). Note the differences in spatial orientations of all hydroxyl (OH) groups. L-sugars are simply the mirror images of these structures accounting for a total of eight stereoisomers. B. Interconversion of D-ribose between pyranose and furanose ring structures. Arrangements of alpha and beta configurations are indicated by hatched lines at carbon 1. RNA uses only the furanose form with the nucleobase bonded in the beta configuration. C. Enzymatic coupling of uracil to ribose 5-phosphate. The enzyme positions both substrates appropriately to catalyze this stereospecific displacement forming a new chemical linkage.

Ignoring Conundrums

While the first two conundrums are most often sidestepped by those upholding the RNA-world philosophy, the latter reaction is not an impossible task so we will consider how life manages this feat. Most cells can salvage RNA or DNA building blocks normally obtained nutritionally following digestion. The liberated nucleobases can be coupled using D-ribose charged with a pyrophosphate group at carbon 1 in the alpha configuration. Notice the specificity life uses where neither the beta configuration nor the pyranose ring form will work for this reaction. This substrate permits a specifically oriented approach by the appropriate nitrogen of the nucleobase, directed completely by the respective enzyme, to effect displacement of pyrophosphate. This results in the nucleobase bonding to carbon 1 in the beta configuration (Fig. 2C). The release of pyrophosphate fulfills the thermodynamic requirements of this elaborate reaction. 

Attempts have been made to carry out this reaction under purportedly abiotic conditions. These efforts led to some ingenious planning to devise new chemical synthetic schemes involving electrospray of microdroplets containing D-ribose, phosphate, and nucleobases.4 Researchers provide evidence proposing how the microdroplets might make this reaction more thermodynamically favored. It’s feasible for all four nucleotides to be made via this route. 

Other Serious Concerns

But this report did not address the other serious concerns already discussed. They used pure D-ribose, not a mixture of sugars as would be expected prebiotically, and minimally not D/L-ribose. The alpha/beta configuration of the products, or their ring structures, were not indicated (most likely resulting in mixtures of all possible products). It thus becomes difficult to evaluate the relevance of this reaction to producing biologically viable RNA building blocks. Finally, the yields of desired products by this mechanism were low, at 2.5 percent or less. While the attempt to produce RNA building blocks via an abiotic mechanism is to be applauded, this still falls far short of what life needs to get started from the complex mixture of organic compounds present in a prebiotic world. 

Readers are encouraged to investigate further to more fully understand the difficult issues involved in forming life using undirected organic chemistry alone. Chemist Dr. James Tour at Rice University, for one, has addressed abiogenesis including in discussions on his YouTube Channel . See also his chapter in the freely downloadable book Science and Faith in Dialogue.