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Friday, 14 July 2023

On Origin of Life science's rose colored glasses

 More Scientific Problems with Paul Rimmer’s Views on Origin of Life


In an article here yesterday, I analyzed astrochemist Paul Rimmer’s commentary on the debate between James Tour and Dave Farina. I focused on the specific research Rimmer cited and how his position as an origin of life (OOL) researcher likely shapes his evaluation of its relevance to explaining how a cell could have emerged through natural processes. Here, I will describe additional serious scientific problems with Rimmer’s optimistic assessment of the state of the field.
            
Proposed Path to Life

Rimmer presents the stages toward life’s genesis proposed by leading origins researcher John Sutherland (Figure 1). The postulated path to life entails a continuous series of stable systems gradually increasing in complexity until an autonomous cell emerges capable of Darwinian evolution. Since Sutherland assumes that life must have originated from undirected physical processes, he believes such stable intermediates must have existed. 


Many have attempted to justify this assumption by appealing to such researchers as Jeremy England who have demonstrated that far-from-equilibrium systems can generate self-organizational behavior such as a hurricane’s funnel cloud. Theorists propose that analogous self-organizational processes could have driven a chemical system from one stable state to the next. 

The Underlying Challenge

The problem with such claims is that naturally occurring self-organization is fundamentally different from the order in living systems, and all experiments that demonstrate self-organizational behavior that is even remotely life-like must apply artificial energy sources to systems designed to properly interact with the applied energy. For instance, Bachelard et al. (2017) applied acoustic waves of specific frequencies to meniscus particles in a waveguide to generate desired patterns in the acoustic bandgap (i.e., graph of transmitted frequencies). And Sacanna et al. (2014) applied light within carefully chosen frequency ranges to asymmetric semiconductor spheres in a solution of hydrogen peroxide fuel to generate self-propulsion and crystal formation. I describe other studies in my response to Jeremy England that employed comparable investigator ingenuity. In every example, the self-organizational behavior depends on the expertise of the researchers acting to achieve desired results. 

In contrast, energy sources available on the early Earth properly interact with few, if any, biologically relevant chemical reactions or physical processes. Instead, raw energy tends to break apart complex molecules (e.g., proteins and RNA) and cellular structures. Any interactions that would have allowed a chemical system to move even a tiny step toward life would have been exceedingly rare. 

The same holds true for even the earliest stages of origin scenarios. Tour has detailed how research that purportedly moves a chemical system toward life must start with carefully chosen molecules in concentrations and purities far higher that what could have occurred naturally. They must also employ highly orchestrated experimental procedures (here, here, here, here). Any chain of chemical events on the early Earth that achieved the same results would also have been exceptionally rare. 

Alternative Perspective

These challenges convince scientists who do not assume that life originated through undirected natural processes that the journey toward the first cell should be depicted very differently from that of Sutherland. Consider this figure which realistically presents what is necessary for life to arise: 


Figure 2 depicts four required processes for constructing a minimally complex cell:

The building blocks of life must be synthesized, including proteins, RNA, DNA, and cellular structures. 
The building blocks must be transported to the same location. This step is far more difficult to explain through natural processes than most realize. The origin of the constituent molecules and linking them together require at least eight different environments.
The building blocks must be properly assembled into a functional cell. The number of configurations corresponding to life divided by the number of all possible configurations is an unimaginably small ratio. 

Energy must be harnessed from the environment and converted into biologically useful forms, and that energy must be directed toward constructing a cell and then sustaining it. Continuous and reliable energy conversion and delivery can only be achieved with complex molecular machinery (here, here, here)

Figure 2 also depicts how every step toward life accomplished through a natural process corresponds to very “rare events.” In contrast, the natural processes continuously acting on an emerging protocell would have relentlessly driven it back toward biologically useless complex mixtures. 

Even a 95 percent complete cell would irreversibly decompose into simpler molecules. Every chance step in the local environment toward cellular autonomy (e.g., two amino acids linking) would be matched by physical processes breaking apart the cell membrane, disassembling cellular machinery, and degrading proteins, RNA, and DNA. Every step forward would have been overshadowed by countless steps backward. 

The Chicken or the Egg

Jeremy England elegantly describes the thermodynamic challenge for all life in his book Every Life Is on Fire: How Thermodynamics Explains the Origins of Living Things when he states:

Like all living things, plants are structures that absorb energy from specific sources in ways that lead to internal motions that correct or undo each incremental bit of falling to pieces that happens at every moment. This process goes on not only when a wound heals, but also much more instantaneously every time sunlight is used to regenerate a molecule of chemical fuel that was just burned up, or every time a molecular chaperone burns up some chemical fuel in order to help a protein that has become misfolded to get back into the correct, functional shape. The fuel-consuming, heat-dissipating activities of proofreading, quality control, and self-maintenance lie at the core of what living things are doing all the time to remain alive, and every one of these activities involves some kind of cyclical motion, whereby work absorbed from the environment perpetually drags things back up the mountain as each little downward slip and slide occurs.

The dilemma for life’s origin is that the machineries for “proofreading, quality control, and self-maintenance” are required early along the journey to life, but they can only be built by cells that are already fully autonomous. In other words, life cannot form unless life already exists. 

Final Analysis

As I said in my previous article, I applaud Paul Rimmer’s civility, thoughtfulness, and stature as a committed theist who works in the field of origin of life research. Many might be attracted to his approach, and rightly so. I hope for the opportunity to have a dialogue with him someday. But just as hoping and believing in something doesn’t therefore make it true, being civil and thoughtful does not change the state of the scientific evidence. We must face reality, and when we realistically consider the complexity of biological systems, the quest to explain life’s origin through natural chemical processes shows every sign of being an impossible scientific goal. 

In fact, those not committed to the philosophy of scientific materialism often see attempts to explain life’s origin through natural processes as falling into the same category as alchemy or the quest for a perpetual motion machine. In addition, the minimal requirements for cells, such as information processing, energy production, and error correction, represent indisputable evidence for direct design. The denial of design is not driven by the empirical data or theoretical analyses but by philosophical commitments. 

The fossil record continues to be fuel for doubt re:Darwin.

 Fossil Friday: Cloudina Still Lacks the Guts to Be a Worm


In a previous article series at Evolution News I discussed and debunked various alleged Precambrian animals, including the tube-like cloudinomorphs (Bechly 2020), which had recently been claimed by Schiffbauer et al. (2020) to represent bilaterian worms because of a preserved longitudinal structure that was interpreted by these authors as a digestive tract. This should support the existence of a hypothetical late Ediacaran “worm world.” I criticized this interpretation and the taxonomic attribution and concluded that “cloudinomorphs remain what they were before the recent paper by Schiffbauer et al. (2020): a problematic group of shelly fossils, which were almost certainly not bilaterian worms, but quite possibly related to cnidarians.” My conclusion has since then been strongly corroborated by three new studies.

First Study

Park et al. (2021) identified “derived characters linking some members of an enigmatic animal group, the cloudinids, which first appeared in the Late Ediacaran, to animals with cnidarian affinity from the Cambrian Series 2 and the Miaolingian.” These authors also mentioned that the alleged cloudinomorpha with preserved gut lack the characteristic funnel-in-funnel structure of the tubes and thus may be unrelated to typical cloudinids. This would leave the theoretical possibility that those “cloudinomorphs” (e.g., Saarina and Costatubus) indeed were bilaterian worms with a convergent similarity to cloudinids. However, the authors “propose an alternative hypothesis for the phylogenetic affinity of the cloudinid-like tubular organisms,” because recent cnidarian polyps of coronate scyphozoan affinity produce tubes that are superficially similar and often conflated with polychaete tubes. They also possess a lengthy gastrovascular cavity that could be misinterpreted as an annelid-like gut in the fossils.

Second Study

My hypothesis (Bechly 2022) that all the tube-like Ediacaran fossils with a stacked composition of the sclerotized tubes do represent burrowing cnidarians, has been strongly supported by the discovery that similar phosphatized and annulated tube-like fossils from the Cambrian were not worms but indeed cnidarians (Zhang et al. 2022). The latter authors concluded that “early annulated tubular exoskeletons from the latest Ediacaran and Cambrian are better understood as variations on cnidarian exoskeletons rather than early annelids.”

Third Study

Finally, Dunn et al. (2022) described a supposed crown-group cnidarian from the Ediacaran of Charnwood Forest in the UK. They discussed the affinities of Cloudina and the interpretation of its body structures. Here is what they found:

The affinities of Cloudina and similar taxa are controversial, with some authors arguing for an annelid affinity while others compare them with non-bilaterians, chiefly cnidarians. Proponents of an annelid affinity for Cloudina have argued that the putative presence of direct development excludes a placement in Cnidaria; however, there are several Cambrian, skeletonizing fossil cnidarian taxa known to undergo direct development (see below). Furthermore, the annelids with which Cloudina has been closely compared (Serpulidae and Siboglinidae) both go through indirect development via a trochophore larva, a feature common to many marine annelids and their close relatives. The tube microstructures in Cloudina that are comparable with those of annelids have evolved many times (for example, in Alvinellidae and Siboglinidae), while the granular tube microstructure of Cloudina is found in living cnidarians but is absent in calcareous tube-forming annelids, along with polytomous branching, a lack of attachment structures and a closed tube base (except in individuals that have undergone damage). Further evidence for a total-group bilaterian affinity was provided by the discovery of fossilized soft tissues, interpreted as a through gut. The proposed gut morphology was used as evidence against a cnidarian affinity due to the absence of features characteristic of anthozoans, such as an actinopharynx, and longitudinal septa are also absent from the skeleton. However, these features are not present in medusozoan polyps with many medusozoans having a gut gross morphology that is broadly comparable with that observed in the soft tissues of cloudinomomorphs. Furthermore, there are a variety of annelid-mimicking bilaterian groups known from the Palaeozoic era, although these mostly first appear from the Ordovician period onwards. While recent discoveries have provided critical insights into the tube ultrastructure, growth and soft-tissue structures of cloudiniids, placing Cloudina in the total group of any animal phylum may be premature and we chose not to consider it in our phylogenetic analysis.

In sum: the evidence for an affinity of cloudinids with bilaterian worms does not stand up to scrutiny, while there is stronger new evidence for a cnidarian relationship. This adds to the growing evidence that the Cambrian bilaterian animal phyla were mostly or even totally absent in the Ediacaran and thus highlights the abruptness of the Cambrian Explosion as a discontinuous burst of biological novelty.

It is becoming a striking pattern that we intelligent design proponents make one successful prediction after another, while Darwinism’s track record of failed predictions grows ever longer. This should give our critics some reason to pause and think, but for mainstream science Darwinian evolution must be true by default and intelligent design is a priori ruled out as an acceptable option, irrespective of any conflicting evidence or predictive scores. Unfortunately, not everybody is prepared to follow the evidence wherever it leads.

References

Bechly G 2020. Did Cloudinids Have the Guts to Be Worms? Evolution News January 17, 2020. https://evolutionnews.org/2020/01/did-cloudinids-have-the-guts-to-be-worms/
Bechly G 2022. Let’s Help “Professor Dave” Understand the Precambrian. Evolution News December 2, 2022. https://evolutionnews.org/2022/12/lets-help-professor-dave-understand-the-precambrian/
Dunn FS, Kenchington CG, Parry LA, Clark JW, Kendall RS & Wilby PR 2022. A crown-group cnidarian from the Ediacaran of Charnwood Forest, UK. Nature Ecology & Evolution 6, 1095–1104. DOI: https://doi.org/10.1038/s41559-022-01807-x
Park T-YS, Jung J, Lee M, Zhen YY, hua H, Warren LV & Hughes NC 2021. Enduring evolutionary embellishment of cloudinids in the Cambrian. Royal Society Open Science 8(12):210829, 1–12. DOI: https://doi.org/10.1098/rsos.210829
Schiffbauer JD, Selly T, Jacquet SM, Merz RA, Nelson LL, Strange MA, Cai Y & Smith EF 2009. Discovery of bilaterian-type through-guts in cloudinomorphs from the terminal Ediacaran Period. Nature Communications 11:205, 1–12. DOI: https://doi.org/10.1038/s41467-019-13882-z
Zhang G, Parry LA, Vinther J & Ma X 2022. Exceptional soft tissue preservation reveals a cnidarian affinity for a Cambrian phosphatic tubicolous enigma. Proceedings of the Royal Society B 289(1986): 20221623, 1–9.
   DOI: https://doi.org/10.1098/rspb.

..and one Lord Jesus Christ?

 

The Father is one God his Son is one Lord?

 

For the hyper-titan crushing titans is but a pastime?

 

Continuing to rethink the unrethinkable again.

 

Coming to terms with E.C.T