Molecular Magic or Deus Ex Machina?

Senior researcher Ramanarayanan Krishnamurthy at The Scripps Research Institute (TSRI) has recently made a captivating, if not fanciful, statement regarding the remarkable capabilities of a little molecule bearing a quite mundane moniker: diamidophosphate, or DAP:

“It [DAP] reminds me of the fairy godmother in Cinderella, who waves a wand and poof, poof, poof, everything simple is transformed into something more complex and interesting.”1

Krishnamurthy is referencing DAP’s newfound, transformative qualities as described in an article published in Nature Chemistry: “Phosphorylation, oligomerization and self-assembly in water under potential prebiotic conditions.”2 The title is a bit more detached but sure to invoke at least a bit of giddy excitement among those who follow the origin-of-life (OOL) question. Has a new incarnation of spontaneous generation, a DAP phoenix, risen from the ashes? Has the secret recipe for “life in a jiffy” been revealed? Is prebiotic soup back on the table? In the researcher’s own whimsical words, “Poof, poof, poof!”

Remarkably, DAP can phosphorylate three distinct types of biologically significant molecules: nucleosides/tides, amino acids, and lipid precursors. Adding phosphoryl groups to these molecules allows a progression of chemical reactions necessary to advance bottom-up OOL scenarios. DAP reacts with these diverse prebiotic molecules so that they may further assemble into larger biologically significant molecules: oligonucleotides, peptides and liposomes, respectively. Furthermore, DAP’s phosphorylating reactions occur readily, not requiring condensation reactions to drive particular chemical processes to completion.

To their credit, the research team carefully crafted their experimentation using as many plausible prebiotic reagents and primordial conditions as possible. Even so, the initial DAP reagent was synthesized from the “prebiotically available trimetaphosphate by reaction with ammonia, at relatively high pH.” This synthesis is problematic since ammonia levels were very low on the early Earth3 and because the subsequent experimentation was carried out in neutral conditions. The scientists acknowledge that alternative DAP production pathways should be sought out. Intelligent agency, courtesy of the research team, may still a de facto catalyst in these reactions.

It is also important to note that although the experimental conditions were similar for each synthesis, the various molecular assemblages were all acquired separately. The researchers later hypothesized that “the commonality of conditions for the oligomerization [assembly] of different building blocks suggests that productive and mixed chemistries might be possible.” On the other hand, mixed chemistries might compete or otherwise prove to be detrimental, yielding undesirable products that interfere with the production of the targeted compounds as well as with the original experimental conditions that have been so carefully standardized. Robust reactivity can both work for you and against you in a chemical milieu.

Although this work strives to create uniform prebiotic conditions for the emergence of first-life, one must note that life would immediately alter its own habitat upon arrival. Waste products and metabolites change the environment in short order, so adaptability (which presupposes genetic information) would seem to be necessary from the start. Although conflicting environments cannot be plausibly posited for bottom-up OOL scenarios, the inevitability of changing environments must be considered. Hence the importance of a bilayer phospholipid cell membrane that can both provide both a protective barrier and homeostatic intermediary. In The Cell’s Design: How Chemistry Reveals the Creator’s Artistry, Fazale Rana concurs that “[t]he origin of cell membranes has to be one of the first steps in the origin of life.”4

In Krishnamurthy’s research, the lipid-building DAP experiments formed “micelles and vesicle-like bilayer and multilamellar structures in the range of 30–110 nm…[as well as] liposome-like structures with diameters around 280 nm.” In addition, transmission electron microscopy images “impl[ied] the formation of giant bilayer vesicle-like structures with diameters of 9.2 µm on average, with some structures nearing 20 µm.” Impressive as these structures might sound, the unilamellar, phospholipid bilayer required for critical cellular function is notoriously difficult to produce and sustain.5 Micelles and multilamellar structures are much easier to generate, but they are not likely to have formed the first cell membranes. On the other hand, more promising lipid bilayer compositions are “generally impermeable to the types of molecules needed to maintain the activity of encapsulated self-replicators.”6

As previously noted, genetic information is required to invoke and sustain adaptation. The OOL-linchpin molecule, RNA, is quite fragile and relatively short-lived as a “naked replicator,”7 but intact RNA seems to operate quite well within its wide variety of living hosts. As clearly demonstrated in extremophiles, the hardiness of a whole organism is greater than that of its constituent parts. In this way, homeostatic mechanisms appear to be irreducibly complex and are only afforded the fully viable entity.

Just as the DAP-induced liposomes do not necessarily become biologically responsive phospholipid bilayer membranes, DAP-induced assemblies of sugars8 and nucleotide strands do not necessarily form self-replicating molecules, much less bio-relevant information. Likewise, the selective phosphorylation of certain amino acids may not necessarily lead to the production of bio-functional proteins. In naturalistic terms, there is absolutely no reason for chemicals to preferentially tend towards increased complexity in an ongoing fashion, and there can be no meaningful form of natural selection until a reliable replication system is in place to reproduce favorable selections. In the end, the phosphorylation and subsequent oligomerization reactions made possible by DAP might lead to the rapid, concurrent assembly of some potentially useful cell components. Top-down OOL researchers, who already possess all the fully developed components, know that the complete assembly and arrangement of the parts is another very real OOL challenge.

Although ardently opposed to intelligent design arguments, OOL researcher Iris Frye makes the following statement (which strangely sounds like an acknowledgement of irreducible complexity):

“Every living system, as revealed particularly at the molecular level, is organized in a much more complex way than any ordered physical system known to us. The unique character of this complexity lies in the ability of an organism to maintain and reproduce its organization according to specific internal instructions, or information, manifested in specific macromolecules. This character is connected with the purposeful, functional nature of biological organization, in which each part serves the survival of the whole.”9

Frye actually attributes this “informed organized complexity” to evolutionary processes with “natural selection,” “physiochemical constraints,” and “alleged principles of self-organization” making potentially significant contributions towards this end.10 The researcher’s quote above is in sharp contrast to her own description of Steven J. Gould’s initial response when meteor-bound evidence of past Martian life was discovered (and mischaracterized) in 1996:

“Pointing out that life arose on Earth almost as soon as environmental conditions permitted,’ Gould went on to state ‘the standard expectation of paleontologists’: We can only infer from this rapidity, he said, “that it is not ‘difficult’ for life of bacterial grade to evolve on planets with appropriate conditions. The origin of life may be a virtually automatic consequence of carbon chemistry and the physics of self-organizing systems, given favorable conditions and the requisite inorganic constituents.”11

Regarding “the requisite inorganic constituents” as they relate to the DAP research, we should not overlook the obvious: phosphorous is clearly a life-essential element. It is critical to both structural and metabolic chemistries (e.g., adensosine triphosphate). Although the Earth’s crust is “the most phosphorous-rich source known,” it yields a concentration of only about a thousand parts per million.12 Phosphorous is a limited resource, irregularly distributed across the Earth and rarely found in concentrated forms.13 Minerals containing phosphorus are almost always in the maximally oxidized state,14 and it is well-known that oxidative conditions are destructive to prebiotics. So, inorganic phosphorous would be necessary, yet not conducive, to naturalistic OOL scenarios.15 Ross and Rana note that “[w]ithout life molecules (already assembled and operating), no known natural processes can harvest the amounts of phosphorus necessary for life from the environment. All the phosphate-rich deposits on Earth are produced by life.”16

At the most basic level, there is no naturalistic reason for any chemistry-enabling atoms (phosphorous or otherwise) to exist at all. Why should the Big Bang have yielded anything more than widely distributed, discrete subatomic particles or, alternatively, nothing more than all-consuming black holes?17 If mainstream physicists can accept the existence of additional dimensions beyond our experience18 or multiverses beyond our detection,19 why then is it unscientific to consider that life’s source of information and irreducibly complex design features might lie beyond our full apprehension? At an intuitive level, we sense that materialism’s mechanisms are more reductionist than rational, and a DAP fairytale featuring molecular characters does not suffice. There is no reason to expect a purposeless naturalistic process to ultimately produce an organism that seeks to understand its origin, but we humans insatiably seek our story — our grand meta-narrative in which both mystery and meaning ring true.

The Fellowship of Performing Arts (FPA) founder and artistic director Max McLean recently recounted a common criticism of their group’s theater performances:

“One of the critiques of FPA’s productions is that we rely on supernatural or improbable events to solve a play’s main problem…God comes in and changes the outcome. This device is known as “deus ex machina.” I didn’t realize this has become a literary taboo…To guardians of contemporary theater, this literary device generates an eye roll. It might be okay for children, but educated people know that ‘real’ life doesn’t work that way. The world is naturalistic. There is no divine intervention.”20

Although the artistic elites now echo the theme so familiar to scientists, McLean goes on to defend the much-maligned “deus ex machina” plot solution:

“It doesn’t cheapen or weaken the story. Rather, it reintroduces a reality that many have forgotten: that ‘God is there, and He is not silent.’ We believe it makes for a far greater story.”21

The fact of life’s origin is incontrovertibly grounded in realism, yet its veiled narrative is as mystical a fairytale. Only the concurrent immanence and transcendence of Christ the Creator can reconcile these seemingly divergent storylines into a unified plot that accounts for the harshest of realities while eagerly awaiting the happiest of endings. He is the only satisfying denouement in a drama truly Divine.

“Have you not known? Have you not heard? The LORD is the everlasting God,
the Creator of the ends of the earth. He does not faint or grow weary;
his understanding is unsearchable.” Isaiah 40:28

1 Scripps Research Institute. “Potential ‘missing link’ in chemistry that led to life on Earth discovered.” ScienceDaily. www.sciencedaily.com/releases/2017/11/171106112301.htm (accessed December 7, 2017).
2 Clémentine Gibard, Subhendu Bhowmik, Megha Karki, Eun-Kyong Kim, Ramanarayanan Krishnamurthy. Phosphorylation, oligomerization and self-assembly in water under potential prebiotic conditions. Nature Chemistry, 2017; DOI: 10.1038/nchem.2878.
3 Fazale Rana and Hugh Ross, Origins of Life: Biblical and Evolutionary Models Face Off (Covina, CA: Reasons to Believe, 2014), 105.
4 Fazale Rana, The Cell’s Design: How Chemistry Reveals the Creator’s Artistry (Grand Rapids: Baker Books, 2008), 273.
5 Ibid, 229-32.
6 Ibid, 240.
7 Fazale Rana and Hugh Ross, Origins of Life: Biblical and Evolutionary Models Face Off (Covina, CA: Reasons to Believe, 2014), 90-1.
8 Krishnamurthy, R., Guntha, S. & Eschenmoser, A. Regioselective αphosphorylation of aldoses in aqueous solution. Angew. Chem. Int. Ed. 39, 2281–5 (2000).
9 Iris Fry, The Emergence of Life on Earth: A Historical and Scientific Overview (New Brunswick, NJ: Rutgers University Press, 2000), Chapter 14.*
10 Ibid.*
11 Ibid.*
12 Fazale Rana and Hugh Ross, Origins of Life: Biblical and Evolutionary Models Face Off (Covina, CA: Reasons to Believe, 2014), 96.
13 Wikipedia contributors, “Peak phosphorus,” Wikipedia, The Free Encyclopedia, https://en.wikipedia.org/w/index.php?title=Peak_phosphorus&oldid=805719116 (accessed December 8, 2017).
14 Wikipedia contributors, “Phosphorus,” Wikipedia, The Free Encyclopedia, https://en.wikipedia.org/w/index.php?title=Phosphorus&oldid=814149017 (accessed December 8, 2017).
15 Fazale Rana and Hugh Ross, Origins of Life: Biblical and Evolutionary Models Face Off (Covina, CA: Reasons to Believe, 2014), 203-5.
16 Ibid, 96.
17 See Why the Universe Is the Way It Is by Hugh Ross.
18 See Beyond the Cosmos: The Transdimensionality of God by Hugh Ross.
19 See Who’s Afraid of the Multiverse by Jeffrey Zweerink.
20 McLean, Max. 2017. “Deus Ex Machina.” Fellowship Circle, Fall 2017.
21 Ibid.

*Page numbers not available in Kindle version.

Extreme Origin or Extreme Originality?

Enceladus, icy moon of Saturn

Icy water plumes spray forth from the frozen surface of Enceladus and provoke speculation that life resembling Earth’s psychrophiles may be lurking in a liquid ocean beneath. Credit: NASA/JPL-Caltech (Artist’s concept)

As soon the Earth’s molten mass cooled following the Hadean Era, moon-forming event, and late heavy bombardment, life was present and proliferating in all of its diverse and mysterious glory.1 The oldest rocks are 3.9 billion years old (bya) and radiometric bio-signatures date to earlier than 3.8 bya.2,3 Because life appeared so rapidly and under such hostile conditions, some origin-of-life (OOL) researchers believe that Earth-life may have originated elsewhere and then arrived via meteorite during the fray.4 Perhaps life even initiated independently both on Earth and on other planets or moons. Alternatively, the planet’s earliest life-forms may have lurked in deep places, easily riding out catastrophic conditions raging above on the surface. In order to posit novel naturalistic OOL scenarios, scientists look to some exotic little microbes harbored within some of the world’s most extreme environments.

Extremophiles demonstrate that life can exist in a wide variety of conditions: high temperatures, low temperatures, high pH, low pH, high salinity, or high pressure.5 Life can be found nearly everywhere, so first-life must have been fast and easy, even simple – so it would seem. Because they exhibit some of the smallest genomes of independently living, non-symbiont, non-parasitic organisms, various extremophilic organisms appear to be rooted at the base of the of the evolutionary tree.6,7 Maybe OOL researchers have simply not been looking in the right places. Even so, finding life in any locale is not the same as finding its origin.

Thermophiles and hyperthermophiles are early-life candidates that presumably developed as the mostly molten Earth started to cool. They can withstand temperatures up to 70°C and 113°C, respectively, and may also occur in the high-pressure environments near hydrothermal vents. Research has shown that deep ocean chemistry can produce peptides, amino acids, and other bio-precursor molecules.8 In general, however, most prebiotic molecules are unstable in extreme conditions. OOL-critical RNA has been found to be particularly delicate.9  In addition, the cycling of the ocean through these superheated, underwater vents is physically destructive.10 Though some OOL chemistry might be favored at these sites, it is unlikely that all the necessary reagents would remain viable throughout the necessary sequence of OOL reactions. Even though life is still inadequately characterized and ill-defined, it still seems to be an “all or nothing” proposition for the most part.

It is also important to note that thermophilic biochemistry is not “simple.” Rather, “heat-loving” proteins are customized for the stability in hot environments, and they do not adapt well to mesophilic environments. Special interactions between the proteins’ amino acids stabilize their three-dimensional structure, but these same interactions result in a maladaptive rigidity in mesophilic conditions.11 Furthermore, experimentation seems to indicate that the rRNA of the presumed LUCA would have possessed insufficient guanine and cytosine content to have been a thermophile.12 Stanford University and NASA Ames Research Center have determined that as early Earth cooled, “temperature[s] would have persisted within a thermophilic window for at least 100,000 years but for no more than 10 million years – a time window far shorter for life than that on which natural process life-origin models depend.”13 Just as a gradual formation of thermophilic life-form is difficult to imagine, its transformation into a mesophile seems equally unlikely. It appears that they were created in-place, fully customized from the start, with a low likelihood of relocation to mesophilic conditions.

As thermophiles potentially expand the OOL timeline, psychrophiles theoretically expand the OOL habitable zones out to the icy moons of Saturn and Jupiter.14 Such microbes have been found living comfortably in the Antarctic Ocean at around 4°C.15 Bada and Lazcano have noted that low temperatures stabilize some biomolecules, and that some putatively necessary prebiotic reactions only occur in the laboratory at temperatures near 0°C.16 Since the bio-necessity of liquid water remains, psychophiles find ways to lower the freezing point of water. They utilize concentrations of certain molecules17 or antifreeze proteins to this end. This means that these special accommodations would need to be present during the naturalistic construction of the first psychophile in addition to all the “standard” OOL reactants and chemistry. Otherwise, as water began to freeze, cold denaturation would have arrested the hydrophobic effect that allows membrane aggregation, protein folding, and formation of RNA and DNA replicator molecules.18 We find that the whole organism is more robust that its constituent parts, which makes a purposeless and gradual, step-by-step construction process seem implausible.

Sub-surface life is found as far as 3.7 miles deep in the Earth’s crust and has prompted even more OOL speculation. Scientists believe that a deep-biosphere may offer realistic early-Earth conditions for first-life or alternatively provide insight into how OOL scenarios transpired beneath the surfaces of other planets and moons.19 Underground or underwater ecosystems in regions devoid of sunlight are often found to depend on organics trickling down from photosynthetically derived products closer to the surface.20 A few microbial populations are truly isolated from surface organics, however, and can live off of crustal carbon dioxide and hydrogen gas generated as water interfaces with rock at tectonic plate boundaries. This, however, is a rare and finely tuned phenomenon that could not occur where tectonic activity is not present (e.g., Mars). In addition, the deeply localized organics have been biogenically produced by these organisms, leaving the origin of their initial organic precursors a mystery.21 Paul Davies asserts that LUCA likely “lived deep beneath the Earth’s surface, at a temperature well above a hundred degrees Celsius, and probably ate sulfur,” but he also concedes that “it is clear that this little creature was already a sophisticated life form with complex features like coded protein synthesis.”22 Furthermore, deep-Earth organisms typically possess extremely low metabolic rates,23 rendering them incapable of sufficiently rapid replication rates required to promote the fast-paced evolutionary advances required by naturalistic models.

Although the search for a mechanistically initiated origin of life continues, extremophiles seem to have originated in-place, optimized and operational from the start.

Then the LORD answered Job out of the whirlwind and said: “Who is this that darkens counsel by words without knowledge? Dress yourself for action like a man; I will question you and you will answer me. “Where were you when I laid the foundation of the earth? Tell me, if you have understanding…Have you entered into the sea, or walked in the recesses of the deep?…Have you comprehended the expanse of the earth? Declare, if you know all this.” Job 38:1-4,16,18

1 Fazale Rana and Hugh Ross, Origins of Life: Biblical and Evolutionary Models Face Off (Covina, CA: Reasons to Believe, 2014), 175-6.
2 Ibid, 176.
3 Takayuki Tashiro et al., “Early trace of life from 3.95 Ga sedimentary rocks in Labrador, Canada,” Nature 549 (2017): 516-8, http://www.nature.com/nature/journal/v549/n7673/full/nature24019.html.
4 Paul Davies, The Fifth Miracle: The Search of the Origin and Meaning of Life (New York: Simon & Schuster Paperbacks, 2000), 186.
5 Fazale Rana and Hugh Ross, Origins of Life: Biblical and Evolutionary Models Face Off (Covina, CA: Reasons to Believe, 2014), 177.
6 Ibid, 178.
7 Rana, Fazale. “Lesson 9: Assembly Of Life, Part 2.” Lecture Notes, Advanced Origin of Life Seminar, Reasons Institute, 2006 (revised 2017).
8 Fazale Rana and Hugh Ross, Origins of Life: Biblical and Evolutionary Models Face Off (Covina, CA: Reasons to Believe, 2014), 178.
9 Ibid, 182.
10 Ibid, 104-6.
11 Ibid, 181.
12 Ibid, 181-2.
13 Ibid, 181.
14 Ibid, 182.
15Ibid, 177.
16 Ibid, 182.
17 Ibid, 182-3.
18 Ibid, 183.
19 Ibid, 184.
20 Ibid.
21 Ibid, 184-5.
22 Paul Davies, The Fifth Miracle: The Search of the Origin and Meaning of Life (New York: Simon & Schuster Paperbacks, 2000), 186.
23 Fazale Rana and Hugh Ross, Origins of Life: Biblical and Evolutionary Models Face Off (Covina, CA: Reasons to Believe, 2014), 184.

Directionally Challenged

Origin of life research is generally conducted in two different, but related, ways: “bottom-up” and “top-down.” “Bottom-up” researchers seek a combination of chemical reactions that could have yielded a simple, first life-form on the early Earth. “Top-down” researchers seek to understand the simplest of contemporary life-forms, primarily by ascertaining their minimum genome requirements.1 Pathways forged by “bottom-up” and “top-down” camps theoretically meet somewhere in the middle to catch a glimpse of the first-life’s mysterious appearance as well as its transition into the no-less-elusive last universal common ancestor (LUCA).

Both routes must reckon with the empirically determined essentials of life: energy production and metabolism (including catalysts and/or enzymes), information-bearing replicating molecules (including translation mechanisms), and a cell barrier to partition off life from non-life (yet allow interaction with the external environment). Befuddled by simplest life’s innate complexity, both camps would desire to simplify their labors by jettisoning any nice-but-unnecessary, auxiliary cellular functions in order to find a “basic” unit of life that is relatively simple.

Bottom-up researchers are continually plagued with the finding the appropriate prebiotics in realistic concentrations and determining the mechanisms by which they could all come together to successfully produce living cells given the conditions of the early Earth. First, they possess an inadequate knowledge of such conditions, and what they do know seems to mitigate against life. To make matters worse, each hypothetical (and often convoluted) chemical pathway thought to produce a single nascent necessity seems to work against other pathways that lead to products no less important. Yet, all the parts seem to have arrived simultaneously to work in concert rather quickly – a little too quickly. Finally, there is the perpetual problem of the experimenters themselves, who continuously inject their own intelligent influence to purportedly produce a naturalistic outcome. Bottom-up researchers are therefore caught in a maddening loop that still yet lacks life.

Whereas the bottom-up approach seeks a feasibly authentic origin of Earth-life starting from simple chemical compounds, the top-down approach starts with existing organics and bioinformation and seeks to gain mastery over it. A comprehensive knowledge of the life’s minimum genome requirements not only allows an enhanced characterization of LUCA, but it also affords the opportunity to refashion life into new, synthetic forms. These scientists seek not only enlightenment but empowerment. Life can be stripped down and refurbished for specific purposes such as the production of tailored biomedical compounds or renewable energy resources.”2 Like those pursuing a bottom-up approach, these top-down researchers also search out the mechanisms required to build biomolecules, but they are less concerned about the chemical history of “life as we know it.” All available ingenuity, materials, and technologies are fair play when constructing “life as it could be.”3

If top-downers could successfully synthesize a living cell “from scratch” (simple, inorganic compounds) as they are instructed in the lessons of life by today’s simplest organisms, this would provide a much-desired proof-of-principle for the bottom-up researchers; it would show that life can be constructed from chemicals. For now, however, these researchers can fundamentally change the characteristics of existing cells, but they must rely heavily on existing organics and bioinformation.  Quite remarkably, Craig Venter’s team at Synthetic Genomics, Inc., have apparently transformed Mycoplasma capricolum into Mycoplasma mycoides by implanting a synthetic genome of the former into the latter. 4 They cannot yet initiate life, though they soon might.  Even so, though the nature of the physical world may be further elucidated, the necessity of intelligent agency will be simultaneously affirmed. Scientists may manipulate existing matter and information systems in ways that produce physical life demanding at least hundreds of genes,5 but this is a minimum complexity that is still uncomfortably complex from a naturalistic, bottom-up perspective. Yet according to Scripture, various forms of life are more than merely physical and may also manifest that which is soulish and spiritual.6 When scientists look beyond where empiricism can probe, they may find more meaning in the mysteries than the mechanisms.

“Let no one deceive himself. If anyone among you thinks that he is wise in this age, let him become a fool that he may become wise. The wisdom of this world is folly with God. For it is written, ‘He catches the wise in their craftiness,’ and again, ‘The Lord knows the thoughts of the wise, that they are futile.’ So let no one boast in men.” 1 Corinthians 3:18-20

1 Fazale Rana, Creating Life in the Lab (Grand Rapids: Baker, 2011), Chapter 3.*
2 Ibid, Chapters 3-4.*
3 Ibid, Chapter 4.*
4 Ibid, Chapter 3.*
5 Ibid.
6 Fazale Rana and Hugh Ross, Origins of Life: Biblical and Evolutionary Models Face Off (Covina, CA: Reasons to Believe, 2014), 79.
*Page numbers not available in Kindle edition.

Commentary on Reasons to Believe’s Interview with an OOL Insider

By Holger.Ellgaard (Own work) [CC BY-SA 3.0 (https://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons

Photo by Holger.Ellgaard (Creative Commons)

This commentary is based on an interview conducted by Reasons to Believe (RTB) with origin-of-life researcher Robert Shapiro. It was recorded on an unknown date prior to his Dr. Shapiro’s death in 2011.

One cannot listen to Dr. Robert Shapiro without being struck by this synthetic chemist’s brilliant mind and impressive credentials. He is well-studied in the multi-disciplinary field of origin-of-life (OOL) research, and the elegant simplicity of his illustrations belies his depth of understanding. As an independent thinker, he sustains an unrelenting critique of the OOL community from a position of agnostism. From this detached perspective, he evaluates experimental details without philosophical duress or (apparent) financial reprisal. He asserts that unfounded assumptions hinder the advance of the OOL discipline and that the research community needs to start over from scratch with a more open-minded intellectual agility. His self-described exile by the scientific community seems to expose the establishment’s pre-commitments that are grounded in something that is less constructive than the scientific objectivity that Shapiro seems to demonstrate more authentically. The fact that life’s definition is elusive and ill-defined seems to justify his position: “When I get to something [where] I do not know the complete answer (which covers, I think, even the mystery of our existence), I’m not ashamed to say I don’t know and to go on from that. So, [agnosticism is] the best label to apply to me.”

Shapiro is able to step back from the detailed chemistry that confounds most and view the big OOL picture. He then authoritatively states what the layperson had hoped was obvious: organic molecules are not alive, irrespective of their abundance and diversity. Moreover, more time does not solve the problem. Life requires more than just chemical reactions; it requires complex organization. We simply do not comprehend its origin.

Shapiro dislikes the use of the term “prebiotics” when applied to meteor composition due to the unfounded assumption that such chemicals would become “biotic” under some yet-to-be-determined circumstances. Rather, he believes that the “massive molecules” that characterize biological systems on the contemporary Earth run counter to what chemists currently know and can explain. He points out that the very scientists who claim to recreate the first unguided steps toward life on early Earth are actually conducting carefully controlled experiments, magnificent in terms of their design by intelligent agency. After all, organizing complexity is not what we typically find in chemical milieus governed by second law of thermodynamics. Is it reasonable to believe that, once upon a time, some highly significant, albeit unguided, reactions somehow capitalized on localized releases of energy to self-organize and advance in their complexity when no experiments have been conducted to support this notion?

It is beneficial, as well as somewhat refreshing, that all critiques are not being made by creationists. Internal disagreements between replicator-first and metabolism-first OOL camps provide insight into the shortcomings of each. Few secular researchers are willing to openly acknowledge the flaws of both positions and suggest taking an entirely different approach. Shapiro is critical of bottom-up research of chemical mechanisms carried out in pristine laboratory settings as guided by ingenious investigators. He is also critical of top-down paradigms. Whereas biologists see the uniformity of materials that compose living organisms as our greatest clue towards a viable OOL solution, Shapiro considers the continuity of life’s structure as something that may be misleading scientists, diverting their attention from the exotic reactions that might be found to spawn life.

Shapiro seems to think that life should occur fairly readily under the right conditions, so that’s what researchers should be looking for — but we don’t seem to be finding it here on Earth. He seeks a self-sustaining set of reactions that might occur under a set of circumstances and conditions of which we are not yet aware. This is why he believes that the exploration of other celestial bodies within our solar system (and experimental reach) is important. He is excited by the prospect of finding novel, independently developed life-forms on the icy moons of Saturn, but he likewise acknowledges that such life might not relate to the origin of contemporary life on Earth. He makes a subtle but important distinction between finding life and finding the origin of life. Furthermore, recognizing that directed panspermia only re-locates the OOL question, he views this position as a last resort when all other feasible exploration and research endeavors provide no answer. He espouses “science of the gaps,” then perhaps “aliens of the gaps,” but never “god of the gaps.”

Though Shapiro rightly points out the proactive role of the investigator in OOL research, he by no means accepts intelligent design as a tenable explanation for the origin of the universe or life. He politely, but rigidly, insists upon both philosophical and methodological naturalism, and he fully anticipates that naturalistic answers will be found through ongoing research. This provides the opportunity for Hugh Ross, PhD, to explain the importance of the RTB creation model that offers testable, scientific predictions based on various worldviews in order to see which one yields the best empirical results as more and more scientific data becomes available.

Referencing the RTB model, Fazale Rana, PhD, remarked that the extremely unlikely appearance of life during the hostile conditions of early Earth might be in accord with Earth’s description in Genesis 1:2. (Interestingly, Shapiro basically equates the term “miracle” with highly improbable natural occurrences.) After all, there appears to be both fossil and isotopic evidence supporting the presence of fairly complex life right after the inhospitable conditions of the late heavy bombardment around 3.3 to 3.8+ billion years ago. The ensuing divide between Rana and Shapiro shows the RTB creation model at work. Rana has no problem with data supporting life soon after the late heavy bombardment or even before. In contrast, Shapiro doubts the data on naturalistic grounds, moving first-life to a more comfortable data point — 2.8 billion years ago, “when life was probably very peaceful.” Accumulating evidence will increasingly support either Rana or Shapiro on this matter, yet even Shapiro’s accepted date for first-life doesn’t elucidate the mechanism of its arrival. Shapiro admits that “only time will tell, and time is not amicable to us.”

Shapiro finds his time and place in the universe to be limiting but, in reality, they are most favorable:

“From one man he made all the nations, that they should inhabit the whole earth; and he marked out their appointed times in history and the boundaries of their lands. God did this so that they would seek him and perhaps reach out for him and find him, though he is not far from any one of us.” Acts 17:26-27

When confronted with the possibility of the supernatural, Shapiro respectfully relegates anything beyond human senses and empirical proof as being something other than the science and the subject at hand. He stalwartly insists upon keeping the domains of science and philosophy separated into non-overlapping magisteria (NOMA), yet he is not immune to a desire for something more. It is with some vulnerability that he states, “Well, to me, our very existence is a wonder…a wonder, a surprise, something that’s awesome.” Perhaps his affection for “a [fictitious] place called Xanth where every human being had some magical property” is a trace of the unrealized capacity for eternity burning within.

“[God] has made everything beautiful in its time. Also, he has put eternity into man’s heart, yet so that he cannot find out what God has done from the beginning to the end.” Ecclesiastes 3:11

Why would materialism lead to the conclusion that anything (much less everything) can be known? That which is bound by time and space cannot reach up to transcendence but rather transcendence must reach down to bestow not only knowledge but the very capacity for it. In a way, NOMA assumes that the philosophical realm does not align with the natural world – a dichotomy which is consistent with the naturalistic worldview, as alluded to by philosopher Kenneth Samples. Even so, the naturalist uses the same human brain to carry out the philosophical reasoning and logic as he does to conduct and accept science.

During the interview, Shapiro acknowledges that no one knows why there is something rather than nothing but then stops short. Perhaps the mystery of life is meant to lead us beyond the boundaries of empirical investigation – not to life’s origin but rather to its Source.

It is the glory of God to conceal things, but the glory of kings is to search things out.” Proverb 25:2

Make your own tracks…Another synthetic chemist, James Tour, PhD, addresses his colleagues regarding the search for life’s origin: http://inference-review.com/article/an-open-letter-to-my-colleagues.

Frustrating Extraterrestrials, Part 2

Extraterrestrial impactors of the late heavy bombardment are thought to have made Earth’s surface inhospitable to the prebiotic chemistry and biomolecules, frustrating origin-of-life scenarios. Image Credit: NASA’s Goddard Space Flight Center Conceptual Image Lab

The advent of Big Bang cosmology narrowed the history of universe to 13.8 billion years. From a naturalistic perspective, both chemical evolution and biological evolution must fit within this timeframe. (The production of extraterrestrial prebiotic and organic molecules would not be constrained to Earth’s formation 4.5 billion years ago [bya].) As plausible dates for the last universal common ancestor (LUCA) recede further and further into the past, less time is available for complex chemistry to birth first-life.

Fossil and geochemical data indicate that earliest life dates back to 3.7 bya, perhaps to 3.8+ bya.1  For example, rocks in Australia and South Africa dated at 3.3 and 3.5 bya bear the signs of fossilized prokaryotes. The carbon-12 enrichment of the samples implies past photosynthetic activity.2 Researchers do not question the early appearance of life but rather “the rapid emergence of cyanobacteria and complex photosynthetic processes.”3 pushing dates for a more chemically simplistic LUCA back even further. Chemical evolution and biological evolution therefore must vie against one another for the available cosmic time.

But as potential dates for first-life work their way further into the past, chemical evolution is pushed back into less-than-hospitable time in Earth’s history.  During the late heavy bombardment (LHB), impact collisions produced a hot, molten surface that would deter the formation of a permanent land and ocean features until about 3.85 bya.4,5 A very recently published paper asserts that ancient rocks in western Greenland and Eastern Canada show signs of life from as early as 3.95 bya.6 These new dates begin to overlap with this turbulent time period when warm, little, life-friendly ponds were not likely. Appeals to the Hadean Era (prior to the LHB) appear no more accommodating and require not just one, but “multiple, independent origin-of-life scenarios.”7 Neither do hydrothermal vents scenarios provide safe haven. Scientists estimate that the entire ocean cycles through such vents every 10 million years. This destructive process once again severely limits the timeframe for origin of life (OOL) and, once again, thwarts attempts to provide a naturalistic mechanism to produce life.8

“Traditionally, origin-of-life researchers have posited that chemical evolution took place over hundreds of millions, if not billions, of years. More recent assessments allow only about ten million years for life’s origin to take place.”9 Given the available timeframe, scientists like Antonio Lazcano and Stanley Miller must simply retrofit their time estimates for the evolution of cyanobacteria to suit.10 Furthermore, all OOL scenarios require the development of delicate RNA molecules that must be soon incorporated into living systems or degrade quickly11 – an independent indicator that life must develop rapidly. Meanwhile, no viable mechanisms have been determined to potentially produce life on early Earth – slowly or rapidly.

1 Fazale Rana and Hugh Ross, Origins of Life: Biblical and Evolutionary Models Face Off (Covina, CA: Reasons to Believe, 2014), 75.
2 Ibid, 70-4.
3 Ibid, 69.
4 Ibid, 63.
5 Ibid, 88.
6 Takayuki Tashiro et al., “Early trace of life from 3.95 Ga sedimentary rocks in Labrador, Canada,” Nature 549 (2017): 516-8, http://www.nature.com/nature/journal/v549/n7673/full/nature24019.html.
7 Fazale Rana and Hugh Ross, Origins of Life: Biblical and Evolutionary Models Face Off (Covina, CA: Reasons to Believe, 2014), 91.
8 Fazale Rana, Lecture #10: “Early Earth’s Environment,” Reasons Institute “Origin of Life” online course, 2017.
9 Fazale Rana, Creating Life in the Lab (Grand Rapids: Baker, 2011), Chapter 8.*
10 Fazale Rana and Hugh Ross, Origins of Life: Biblical and Evolutionary Models Face Off (Covina, CA: Reasons to Believe, 2014), 87, 90.
11 Ibid, 90.
*Page numbers not available in Kindle version.

Frustrating Extraterrestrials, Part 1

Artist’s depiction of extraterrestrial impactors of the late heavy bombardment striking Earth, perhaps the most significant origin-of-life frustration event. Image Credit: NASA’s Goddard Space Flight Center Conceptual Image Lab

In order to understand how the requirements for life might have first been met, origin-of-life (OOL) scientists must determine the chemicals, conditions, and time(s) available to meet first-life’s requirements. Nucleosynthesis of hydrogen and helium began minutes after the Big Bang, then elements of increasing mass developed over time in burning stars and through supernova events. The formation of hydrogen, carbon, nitrogen, oxygen, sulfur, and phosphorous are of particular interest since they are the elemental constituents of peptides, nucleotides, and phospholipids;1 these polymers are the organic precursors to proteins, nucleic acids, and cell membranes.2 “Chemical evolution and planetary evolution are [therefore] inextricably intertwined,” according to Alan Schwartz and Sherwood Chang.,3

Life-essential elements, prebiotic compounds, and even organic molecules, occur in interstellar space,4,5 comets,6  meteorites,7 asteroids, planets, and moons.8 Schwartz and Chang thereby assert that “organic matter occurs throughout the Universe as an integral component of cosmic evolution…[T]he prospect of identifying other life-harboring solar systems seems inevitable.”9 OOL researchers must yet determine how closely the prevalence of life directly corresponds to the proper abundances of necessary reagents, catalysts, and energies.

More specifically, Earth’s history and formation as part of the larger solar system must be considered in order to assess the plausibility of proposed OOL scenarios. The presence of interstellar organics might be thought to seed and speed Earth’s chemical evolution process; however, a steady pummeling of high-energy impactors during the Hadean Era, Moon-forming event, and late heavy bombardment (LBH) would have likely destroyed complex molecules, vaporized surface water, and significantly altered atmospheric conditions.

At this point, it should be noted that an inadequately founded assumption regarding the composition of the early atmosphere reduced (pun intended) the Miller-Urey proof-of-principle experiment from a milestone to a mile marker on the road to first-life. But during the OOL’s “greatest frustration event,” the LBH, impact collisions produced a hot, molten surface that would deter the formation of a permanent land and ocean features until about 3.85 billion years ago.10,11 Fossil and geochemical data indicate that earliest life dates back to 3.7 billion years ago (bya), perhaps to 3.8+ bya.12 The plausible window of opportunity for elaborate chemical pathways to produce Earth’s first life closes, nearly shut. “Origin-of-life researchers [now] recognize that life had no more than tens of millions of years to emerge”13 – a far different scenario that what could have ever been imagined by earlier scientists who accepted a steady-state model of the universe. A rapidly increasing understanding of how cosmological events impacted (pun intended) the early Earth is reshaping OOL models. Those seeking purely naturalistic scenarios find that life is hard and its origin frustrated.

1 William J. Schopf, ed., Life’s Origin: The Beginnings of Biological Evolution (Berkeley, CA: University of California Press, 2002), 33.
2 Ibid, 46.
3 Ibid.
4 Ibid, 51.
5 Ibid, 52.
6 Ibid, 59.
7 Ibid, 62.
8 Ibid, 47.
9 Ibid.
10 Fazale Rana and Hugh Ross, Origins of Life: Biblical and Evolutionary Models Face Off (Covina, CA: Reasons to Believe, 2014), 63.
11 Ibid, 88.
12 Ibid, 75.
13 Ibid, 27.

Welcome to RNA World! Carefully watch your steps…

The proposed RNA World is a linchpin concept in origin-of-life (OOL) research. RNA seems to conveniently solve the chicken-or-egg dilemma faced by scientists who observe double-stranded DNA coding for the very same protein-based enzymes responsible for its own replication, transcription, and translation processes. In contrast, single-stranded RNA seems to multi-task well, both replicating and providing enzymatic functions. Furthermore, different RNAs mediate critical steps in the process of protein synthesis from DNA; their pivotal intermediary roles assumed to be embedded traces of a past RNA World. Yet the RNA World does not fare well in bottom-up chemical evolution models, especially when carefully managed proof-of-principle experiments in pristine laboratory conditions are compared to the environmental conditions likely present on the early Earth.

The RNA World is a necessary destination on the broader naturalistic pathway called chemical evolution. Upon entry to this phenomenological place of great OOL promise, some assembly will be required. Herein lies many problems. First, water breaks down nuclide polymers, “casting doubt on any soupy version of the RNA world – [e]ven the synthesis of the four bases required as building blocks is not without serious problems.”1 The two known synthetic pathways to produce cytosine are unlikely to have existed in sufficient quantities on the early Earth. Competing chemical interactions would be problematic and the half-life of the desired product insufficiently brief.2 Spark-discharge experiments and meteorites (assumed analogues of the primordial landscape) have even failed to produce any cytosine.3

Next, consider production of the five-carbon sugar ribose required for the RNA molecule’s backbone. The only known mechanism to assemble long-chain sugars is the formose reaction, which produces over forty different sugars along with many more unintended products when contaminants are present. Ribose yield is low and its instability high. Rapid breakdown is inevitable as evidenced by the striking lack of sugars in meteorite samples.4

Finally, phosphates play a crucial role in RNA (and DNA) backbone structure as well as for adenosine tri-phosphate molecules that can generously liberate energy for necessary chemical reactions to take place. Proposed chemical routes to produce polyphosphates encounter typical OOL problems when taking the primordial environmental conditions into consideration: inadequate concentrations of reactants, low product yields, chemical interference, and/or rapid degradation. In addition, although is Earth’s crust in the most phosphorus-rich material in the universe, it bears an elemental abundance of only 1,000 parts per million. Ross and Rana note that “[w]ithout life molecules (already assembled and operating), no known natural process can harvest the amounts of phosphorus necessary for life from the environment.”5

Synthesis of RNA’s homopolymer backbone is contingent on precisely controlled laboratory conditions and a high level of researcher involvement,6 and the characteristic right-handed chirality of RNA sugars only occurs in living systems. Outside a cell, enantiomers almost always tend towards racemic mixtures in relatively short order.7 The purported evolutionary capabilities of RNA also depend on a high level of intervention,8 which better supports intelligent design than chemical evolution by naturalistic processes. Despite their many successes in the laboratory, even the researchers have yet to make truly, self-replicating RNA molecule.9

Given the seemingly intractable problems of the RNA World, as well as dissatisfaction with metabolism-first OOL scenarios, researchers now look back further to a Pre-RNA World to set the stage. Achiral peptide nucleic acid (PNA)10 or threose nucleic acid (TNA) alternatives appear to solve some problems but concurrently add layers of complexity to an already daunting challenge.

“It may be claimed, without too much exaggeration, that the problem of the origin of life is the problem of the origin of the RNA World.” — Leslie E. Orgel11

1 Paul Davies, The Fifth Miracle: The Search of the Origin and Meaning of Life (New York: Simon & Schuster Paperbacks, 2000), 134.
2 Fazale Rana and Hugh Ross, Origins of Life: Biblical and Evolutionary Models Face Off (Covina, CA: Reasons to Believe, 2014), 114.
3 Ibid.
4 Ibid, 115-6.
5 Ibid, 96.
6 Ibid, 119-120.
7 Ibid.
8 Fazale Rana and Hugh Ross, Origins of Life: Biblical and Evolutionary Models Face Off (Covina, CA: Reasons to Believe, 2014), 121.
9 Ibid, 121.
10 Ibid, 135.
11 Leslie E. Orgel, “Prebiotic Chemistry and the Origin of the RNA World,” Critical Reviews in Biochemistry and Molecular Biology 39 (March-April 2004): 99-123.
*Page numbers not available in Kindle version.