Origins of Life: A Closer Look Part I

Some life scientists believe they can present a truly naturalistic scheme of events for the origin of life from simple chemical substrates, without any appeal to an intelligent agency.

Here is one such scenario, presented by Harvard professor, Jack Szostak.

I invite you to study the video at your leisure.

In this work, I wish to critically appraise each of the steps Dr. Szostak presents in light of the latest research findings that show that any such scheme of events is physio-chemically untenable from a purely naturalistic perspective.

 

Video Clock Time 00.00 -10.00 min

Here Dr. Szostak sets the scene for this thesis, exploring the varied landscapes and environments under which we find life on Earth. Dr. Szostak reasonably suggests that when life first appeared on Earth, it must have done so in an extreme environment with higher temperatures and in aqueous environments with extreme pH values and high salinity. What Dr. Szostak does not acknowledge is that life was already complex when the Hadean environment first cooled enough to permit life to gain a footing. For example, there is solid isotopic evidence that the complex biochemical process of nitrogen fixation was already in place at least 3.2 Gyr ago and possibly earlier still.

References

Eva E. Stüeken et al., “Isotopic Evidence for Biological Nitrogen Fixation by Molybdenum-Nitrogenase from 3.2 Gyr,” Nature, published online February 16, 2015, http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14180.html.
“Ancient Rocks Show Life Could Have Flourished on Earth 3.2 Billion Years Ago,” ScienceDaily, published online February 16, 2015, http://www.sciencedaily.com/releases/2015/02/150216131121.htm.

In a more recent study conducted by a team of scientists headed by Professor Von Karnkendonk, based at the University of South Wales, solid evidence for complex microbial ecosystems in the form of stromatolite colonies were established some 500 million years earlier at 3.7 Gyr ago.

Reference

M..J Van Krankendonk et al, Rapid Emergence of Life shown by the Discovery of 3,700 Million Year Old Microbial Structures, Nature Vol 537, pp 535 to 537, (2016).

Dr. Szostak claims the origin of life must have occurred via a Darwinian evolutionary mechanism, but the self-evident complexity of the first life forms strongly argues against this assertion, as there would not have been enough time to have done so. In other words, the window of time available for the emergence of the first forms of life on Earth is too narrow to entertain any viable Darwinian mechanism.

Dr Szostak continues by considering the vast real estate available for potential extraterrestrial life forms. Szostak presents the emerging picture; the principle of plenitude – that of a Universe teeming with planets. That is undoubtedly the case; there are likely countless trillions of terrestrial planets in the Universe.  However, new research on the frequency of gamma ray bursts (GRB) in galaxies suggests that such violent events would greatly hamper any hypothetical chemical evolutionary scenario. In December 2014, a paper in Physical Review Letters, a group of scientists estimated that only 10 per cent of galaxies could harbour life and that there would be a 95 per cent chance of a lethal GRB occurring within 4 kiloparsecs of the Galactic centre, and the likelihood would only drop below 50 per cent at 10 kiloparsecs from a typical spiral galaxy. What is more, since the frequency of GRBs increases rapidly as we look back into cosmic time, the same team estimated that all galaxies with redshifts >0.5 would very likely be sterilised. These data greatly reduce the probability that a planet could engage in prebiotic chemistry for long enough to produce anything viable.

Reference
http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.113.231102#abstract

In addition to GRB induced sterilization events, Dr Szostak completely ignores the remarkable fine tuning that is required to produce a planetary system that could sustain life for any length of time.

References

http://www.reasons.org/articles/fine-tuning-for-life-on-earth-june-2004

http://www.reasons.org/articles/fine-tuning-the-ratio-of-small-to-large-stars

Dr. Szostak entertains the possibility that lifeforms with fundamentally different chemistry may evolve and that our type of life might be the exception rather than the rule. This reasoning is flawed, as the latest research suggests that carbon-based chemistry in a water-based solvent is overwhelmingly more likely to sustain any biochemical system throughout the Universe. Ammonia has been suggested as an alternative solvent to water but there are some( possibly insurmountable) issues with it.

References
http://www.reasons.org/articles/water-designed-for-life-part-1-of-7

http://www.reasons.org/articles/weird-life-is-ammonia-based-life-possible

Summary: Dr Szostak’s introduction presents a gross oversimplification of the true likelihood of prebiotic chemistry becoming established on Earth and other planets. Szostak does concede that our planet could be unique but is unlikely to be. The emerging scientific data however supports the view that life will be rare or unique to the Earth.

Video Clock Time; 10:00 – 32:00 min
The RNA World
In this section, Dr. Szostak presents the central dogma of molecular biology: DNA begat RNA and RNA begat proteins. Origin of life researchers were completely in the dark about how this scheme of events came into being, but in the mid-1980s, Thomas Cech et al discovered that RNA molecules could act catalytically.
Reference:
Zaug, A. J & Cech, T. The Intervening Sequence of RNA of Tetrahymena is an Enzyme, Science, 231, (1986).

This immediately suggested a way forward; perhaps RNA was the first genetic material and over the aeons, it gradually gave up these activities to its more stable cousin, DNA. Szostak gives some examples of how this ‘fossil RNA’ has been incorporated into structures like ribosomes, the molecular machines that carry out the synthesis of polypeptide chains. His interpretation of these examples as ‘fossils’ is entirely speculative, however.

Szostak then explores hypothetical loci where prebiotic synthesis of biomolecules could have taken place, including the atmosphere, at hydrothermal vents and on mineral surfaces. For the sake of clarity, let’s take a closer look at RNA nucleotides, and in particular, the pentose sugar, ribose. Dr. Szostak mentions the Urey-Miller experiments where supposed prebiotic molecules were produced when an electric discharge was passed through a reducing atmosphere including water vapour. Though widely cited in college textbooks, its validity has in fact, long been discounted by serious researchers in the field. Urey and Miller assumed the atmosphere to be reducing in nature, but it is now known that it was neutral, consisting of nitrogen, carbon dioxide, carbon monoxide and water vapour.

Reference:
The Early Setting of Prebiotic Evolution, Shang,.S
From Early Life on Earth, Nobel Symposium No. 84, Bengtson, S. (ed.), pp 10-23, Columbia University Press (1994).

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Even in the complete absence of molecular oxygen, this atmosphere could not have sustained the production of prebiotic molecules, including ribose. Only in the presence of significant quantities of molecular hydrogen has some synthesis been demonstrated.

Reference:
Schlesinger, G, & Miller, S. Prebiotic synthesis in Atmospheres containing methane, carbon monoxide and carbon dioxide. Journal of Molecular Evolution, 19, 376-82 (1983).

The problem with this scenario though is that molecular hydrogen would rapidly escape from the Earth’s gravitational field and thus is entirely irrelevant to the question of prebiotic synthesis.

An Aside:

Video Clock Time: 20:00 min: The Narrow Time Window:  Reconciling Dr. Szostak’s timeline for prebiotic chemical evolution with impactor bombardment history.

At 20.00min on his slide, Professor Szostak envisages the time during which prebiotic chemical evolution took place on the primitive Earth. He dates it to a period between 4.2 and 3.8Gyr ago (the supposed time of the beginning of the RNA world). Szostak presents a warm, aqueous environment during which all these reactions were taking place. But the planetary scientists modelling the impact history of the inner solar system have revealed a violent early history for the Earth. Extensive isotope analysis of terrestrial and lunar rocks, as well as cratering rate analysis indicate that the inner solar system was subjected to intense bombardment from the debris left over from the formation of the planets, which occurred between 4.5 and 3.9 Gyr ago. The cratering intensity declined exponentially throughout that era, except for a brief episode of increased bombardment between 4.1 and 3.8 Gyr ago. This is known as the Late Heavy Bombardment. One study has estimated that the total accumulation of extraterrestrial material on Earth’s surface during this epoch added a mean mass of 200 tons per square yard over all the surface of the Earth. Thus, Dr. Szostak’s relatively ‘gentle’ scenario is untenable. Realistically, the only oceans to speak of during this epoch are those of magma.

Reference:

Anbar A.D. et al, Extraterrestrial Iridium, Sediment Accumulation and the Habitability of the Earth’s Surface, Journal of Geophysical Research 106 ( 2001) 3219-36.

http://www.reasons.org/articles/no-primordial-soup-for-earths-early-atmosphere

Back to Ribose (a key component of RNA nucleotides discussed by Dr. Szostak). The only plausible mechanism for the synthesis of ribose is the so-called Butlerow reaction (also referred to as the formose reaction) which involves the coupling of the single carbon molecule, formaldehyde (methanal) in spark-ignited reactions forming sugars of varying carbon numbers, including ribose. However, many side reactions dominate formose chemistry, with the result that the atom economy with respect to ribose is very loww; up to 40 other chemical products being typically produced. This is the case in carefully controlled laboratory synthesis (read intelligently designed!), where the reaction is protected from contamination. Experimentally though, the presence of small amounts of ammonia and simple amines (which should be permissible in Szostak’s scheme) react with methanal to bring the formose reaction to a grinding halt.

Reference:
Chyba, C. & Sagan,C., Endogenous Production, Exogenous delivery and Impact Shock Synthesis of Organic Molecules: An Inventory for the Origins of Life, Nature 355(1992): 125-32.

The concentrations of ribose would have been far too low to sanction any RNA world envisaged by Dr. Szostak. Compounding this is the added problem that ribose and other simple sugars are subject to oxidation under alkaline and acidic conditions, and since Szostak presents both hot and cold scenarios on the primitive Earth, it is noteworthy that ribose has a half life of only 73 minutes at 100C (near hydrothermal vents) and just 44 years at 0C.

Reference:

Oro, J., Early Chemical Changes in Origin of Life, from Early Life on Earth, Nobel Symposium No. 84, Bengtson, S. (ed.), pp 49-50, Columbia University Press (1994).

But there are more serious reasons why Szostak’s scheme of events could ever have happened on the primitive Earth. This is encapsulated in the so-called Oxygen-Ultraviolet Paradox.
Szostak envisages prebiotic synthesis in warm aqueous environments, but on the primordial Earth, some 3-4 Gyr ago, the presence of much higher levels of radioactive nuclides such as uranium, thorium and potassium-40 would have presented another proverbial spanner in the works. These would have been more or less evenly distributed over the primitive Earth and when the radiation they produce passes though water, it causes its breakdown into molecular oxygen, hydrogen peroxide and other reactive oxygen species. Oxygen and the associated reactive oxygen species easily and quickly destroy organic molecules; not just ribose and other sugars but the other biomolecules mentioned by Dr. Szostak too, including fatty acids and purine & pyrimidine bases, required for the production of micelles and nucleotides, respectively .

The other part of the paradox pertains to the produce of stratospheric ozone, which requires ultraviolet light. The ozone layer was not present during the epoch in which Szostak’s scheme of events would have occurred. The intense UV irradiance on the primitive Earth would have sundered any exposed prebiotics, further compounding the problem.

References:

Draganic, I.G., Oxygen and Oxidizing Free Radicals in the Hydrosphere of the Earth, Book of Abstracts, ISSOL , 34 (1999) .

Draganic, I, Negron-Mendoza & Vujosevis, S.I, Reduction Chemistry of Water in Chemical Evolution Exploration, Book of Abstracts ISSOL, 139 (2002).

Dr. Szostak appears to be completely unaware of Draganic’s work (though citing Hazen and Deamer’s hydrothermal synthesis work @ 31 minutes) and indeed, in and of itself, would preclude any further discussions of his scheme of events. But we shall nonetheless persevere with this analysis.

 

This work will be continued in a new post (Part II) here.

2 thoughts on “Origins of Life: A Closer Look Part I

  1. I enjoyed reading this essay Neil. I am going to do two things. Keep my mental antenna elevated for further “chatter” on the web, along the lines of the materials you’ve written here. Second, I will pray that, your valid points will be disseminated through the sentient world.

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