The desperate quest for a purely naturalistic explanation for the origin of life

Imagine you were playing a card game with the aim of getting a set of all 4 queens, but the game manager purposely hid one of them – you would continue playing indefinitely and your efforts would be in vain, as you would never conceivably complete the game. Today we are going to take a trip down the path of how that feels in the context of obtaining an explanation of the origin of life, from purely naturalistic arguments – seeing as this is the constraint that many research institutions impose. Note that the approach we take, from both sides of the argument, is the one described in “Building puzzles with the cosmos”, where we allow the evidence to take us to dead ends; anyone who has done a maze will know that dead ends are actually a good thing as they provide us information on where not to go, and help us, after systematically culling off bad options, to find iteratively more reasonable routes.

We play the devil’s advocate and try, wherever possible, to accept only naturalistic explanations for the origin of life – read to the end.

Our discussion turns to sequence space, referring to all possible amino acid combinations that could conceivably exist, that we think of as an ‘ocean’. Within this space some are not functional while the rest - the functional sequences – form the ‘islands’. While these islands have steep cliffs – proteins are 98% intolerant to changes in amino acid composition since substitutions result in a loss of function, it turns out that the ocean is richly populated, as like a dense meshwork (3), with functional regions. Furthermore, when one amino acid in the protein is successfully changed, it allows invariant positions to change and freely-altered positions to become invariant – thus eventually more than 90% of the amino acids in a protein can be altered.

Furthermore, a team from Georgia Tech investigated the origin of binding interactions between proteins and small molecules, which take place in “pockets” (concave regions) at the protein surface. These pockets are specific about which molecules they may bind with. Remarkably, only 400 different types of binding pockets exist in nature, all of which can be generated randomly from artificial protein-like material. The team argues that each pocket will bind a wide range of small molecules, and that the specificity arises from evolutionary processes as a secondary feature (4,5).

All in all, a purely naturalistic explanation – or pure evolution - for how functional, information-rich molecules are built up looks reasonable… on the surface.

The question evolves into a more crucial form. Why do biochemical systems bear such a close resemblance to man-made systems? And if the analogue is so strong why do we not come to the same conclusion for biochemical systems as we do for man-made systems, i.e. that they were made and not witlessly assembled? Let’s break down what we mean here:

Biochemical information systems – the cell’s biochemical systems are information-based.

Structure of biochemical information – beyond being information-based, which in itself is impressive, biochemical information displays structural attributes like language structure, as well as the organisation and regulation of genes.

Biochemical codes – beyond the above, which is impressive of itself, there is also encoded information – seen in the genetic code, histone code and even parity code of DNA.

Genetic code fine-tuning – beyond the staggering impressiveness of the above, the rules governing the genetic code are better designed than any conceivable alternative for resisting errors when translating stored information into functional information. Researchers have found great difficulty due to the multidimensional optimality and claimed that, “the optimality of the SGC [standard genetic code] is a robust feature and cannot be explained by any simple evolutionary hypothesis proposed so far… the probability of finding the standard genetic code by chance is very low. Selection is not an omnipotent force, so this raises the question of whether a selection process could have found the SGC in the case of extreme code optimalities.”(10)

Considering the incredible parallels between man-made information systems and biochemical information systems, why would one not come to the logical and reasonable explanation that the latter was indeed made by a Creator. And whichever process He used to put it into place simply puts us in greater awe of Him – it certainly doesn’t eliminate Him as the source or the code! A purely naturalistic view of the process appears a little over-enthusiastic.

Furthermore, information we deal with on a daily basis is either analogue (for example records which have become increasingly popular by DJs and the like who appreciate the sound emanating from the continuous grooves) and digital (where information is stored as discrete numbers, e.g. the 0’s and 1s of silicon chip based logic). Researchers Georgi Muskhelishvili and Andrew Travers recently demonstrated, rather remarkably, that information housed in DNA requires both of these types of information to enable effective gene expression. They also found that the coupling between the two represents an “irreducible organizational complexity” (5). 

The nucleotide sequences comprising DNA molecules represent a succession of discrete units – a digital framework. Not all genes in the genome are expressed all the time – they are either on or off, a further logic-type characteristic of digital information. 

Beyond the iconic double helix structure, DNA can adopt various higher order structures; for example super coils where the two ends connect and the resulting loop undergoes a variety of ‘twists’ and ‘writhes’ which too affects gene expression. These distortions are not discrete in nature but continuous – analogue.

The best man-made systems appear, at best, to exhibit mere attributes of natural systems.

Another concept is that of Turing machines. Alan Turing, the father of computer science and critical role-player in cracking the Germans’ enigma code during World War 2 is the inspiration behind Turing machines, which consists of 3 parts: input, output and finite control. Nobel Laureate Sydney Brenner who has made significant contributions to molecular biology, memorable writes, “Biology research is in a crisis and in Alan Turing’s work there is much to guide us. Technology gives us the tools to analyse organisms at all scales, but we are drowning in a sea of data and thirsting for some theoretical framework with which to understand it.”(7) This follows what Leanard Adleman recognised more than 2 decades ago – that the proteins responsible for DNA replication, repair and transcription operate as Turing machines (8). Nucleotide sequences of DNA act as input and output strings, and the operations that can be executed on the DNA “strings” include: modifying, multiplying and reading the DNA nucleotide sequence, cutting and linking together DNA molecules, lengthening and shortening individual DNA strands, and separating and fusing strands of the DNA double helix.

Intriguingly, the biochemical information systems exhibit several advantages over man-made ones. For example, operations take place in parallel (not series like silicone based chips) massively increasing the efficiency. Secondly, in terms of capacity, one gram of DNA stores an incredible 215 petabytes of information, way out-doing man-made (man-created?) counterparts.

Nature has been prolific with examples of unexpected complexity. For example, the single-celled Euplotes which is analogous to a biochemical FSM (finite-state machine – think of the way a vending machine works) in spite of its not possessing even a rudimentary nervous system (9).

This all seems to point towards a revival of the watchmaker analogy (maligned by skeptics over the past century – but nevertheless pertinent) of William Paley (1743 – 1805). A beautifully designed machine points to an intelligent designer, whether the machine is of human or natural origins. And when one thinks of Jesus displaying what the unmerited love of God towards us means and looks like, it seems unthinkable that one would choose not to fully “receive abundance of grace and of the gift of righteousness” [Romans 5:17, NKJV]. Let’s not leave the most important element out of the equation of our lives.

Walter L. Bradley and Charles B. Thaxton, “Information and the Origin of Life” in The Creation Hypothesis: Scientific Evidence for an Intelligent Designer, J. P. Moreland, ed. (Downers Grove, IL: InterVarsity Press, 1994): 190.

Hubert P. Yockey, Information Theory and Molecular Biology (Cambridge, UK: Cambridge University Press, 1992), 246-57

Inna S. Povolotskaya and Fyodor A. Kondrashov, “Sequence Space and the Ongoing Expansion of the Protein Universe.” Nature 465 (2010): 922-26

Jeffrey Solnick and Mu Gao, “Interplay of Physics and Evolution in the Likely Origin of Protein Biochemical Function,” Proceedings of the National Academy of Sciences, USA 110 (June 4, 2013): 9344-49

Sara Imari Walker and Paul C. W. Davies, “The Algorithmic Origins of Life,” Journal of the Royal Society Interface 10 (February 6, 2013): doi:10.1098/4sif.2012.0869

Georgi Muslhelishvili and Andrew Travers, “Integration of Syntactic and Semantic Properties of the DNA Code Reveals Chromosomes as Thermodynamic Machines Converting Energy into Information,” Cellular and Modecular Life Science 70, no. 23 (December 2013): 4555-67, doi: 10.1007/s00018-013-1394-1

Sydney Brenner, “Life’s Code Script,” Nature 482 (2012): 461

Leonard M. Adleman, “Computing with DNA,” Scientific American, August 1998, 54-61.

Ben T. Larson et al., “A Unicellular Walker Controlled by a Microtubule-Based Finite State Machine,” bioRxiv”, preprint (June 17, 2021): doi: 10.1101/2021.02.26.433123.

Stefan Wichmann and Zachary Ardern, “Optimality of the Standard Genetic Code is Robust with Respect to Comparison Code Sets,” Biosystems 185 (November 2019):104023, doi: 10.1016/j.biosystems.2019.104023.

Acknowledgments – Many thanks to Fazale Rana for his insightful knowledge of the field, his passion, his story, for being ready to explain anything unclear and the articles he has posted for more than a decade. This article can be thought of as a taster, and touches on topics which he has researched in his field of expertise; the links to his articles are pasted below.

Intelligent Design: The Right Conclusion but the Wrong Reasons

https://reasons.org/explore/publications/articles/intelligent-design-the-right-conclusion-but-the-wrong-reasons

Too Good to Be True: Evolution and the Origin of Bioinformation

https://reasons.org/explore/publications/articles/too-good-to-be-true-evolution-and-the-origin-of-bioinformation

Digital and Analog Information Housed in DNA

https://reasons.org/explore/publications/articles/digital-and-analog-information-housed-in-dna

Biochemical Turing Machines Reboot the Watchmaker Argument

https://reasons.org/explore/publications/nrtb-e-zine/biochemical-turing-machines-reboot-the-watchmaker-argument

Biochemical Finite State Machines Point to an Infinite Creator

https://reasons.org/explore/blogs/the-cells-design/biochemical-finite-state-machines-point-to-an-infinite-creator

Does New Approach Solve Origin-of-Life Problem?

https://reasons.org/explore/publications/nrtb-e-zine/does-new-approach-solve-origin-of-life-problem

Origin and Design of the Genetic Code: A One-Two Punch for a Creation

https://reasons.org/explore/blogs/the-cells-design/origin-and-design-of-the-genetic-code-a-one-two-punch-for-creation