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Review

DOI: 10.1002/ijch.201500073

Physical Organic Chemistry and the Origin of Life


Problem: A Personal Perspective
Addy Pross*[a, b]

Abstract: The origin of life (OOL) question might be consid- and continues to be, the most relevant one for tackling the
ered physical organic chemistry’s ultimate challenge, yet de- OOL problem. Systems chemistry, a newly emergent branch
spite continuing efforts over close to a century, the problem of physical organic chemistry, which, inter alia, deals with
remains unresolved. In this personal perspective, I discuss replicating chemical systems and the networks they estab-
some aspects of that challenge, and argue that notwith- lish, reveals that physical organic chemistry, though in differ-
standing the general perception that physical organic ent guise, is alive and kicking. The broad direction ahead
chemistry is a research area in decline, the discipline was, seems illuminated.
Keywords: Darwinism · history of science · origin of life · thermodynamics

1 Introduction

Formally, one might think of physical organic chemistry are largely chemical in nature. So what methodology
(POC) as that scientific discipline, which applies physical could be right for considering this vital question – how in-
techniques and principles to problems of organic struc- animate matter self-assembled into the dynamic, far from
ture and reactivity. But that rather dry description belies equilibrium, energy consuming, highly organized, material
a more subtle, more ambitious, less easily defined charac- entity that is a living cell – if not that of physical organic
ter: a methodology for exploring the organic chemistry chemistry? But, strangely, the voice of POC in this ongo-
landscape – seeking broad patterns of behavior with ing debate became increasingly mute. A general percep-
regard to both structure and reactivity characteristics. tion seemed to have set in that the OOL problem was
Though the field was formally established after Louis beyond the reach of physical organic chemistry, that
HammettÏs landmark text of the same title,[1] the POC other more “sophisticated” approaches must be sought.
way of thinking was utilized well before then, strikingly But, as IÏll discuss, to date none of these alternative ap-
by VanÏt Hoff and Le Bel in 1874, when the basic struc- proaches have bagged the Holy Grail, and we continue to
ture of tetravalent carbon was unknown. Was tetravalent await the heralded breakthrough.
carbon planar, or tetrahedral? Without some physical Applying POC thinking to the OOL problem can be
means to “see” the molecule, how was one to know? The traced back to one of the fathers of theoretical biology,
physical organic approach to a solution: count isomers. Alfred Lotka. Almost a century ago, he sought to place
The fact that CH2Cl2 consisted of one isomeric form, not Darwinian theory within a broader physicochemical
two, the fact that carbon bonded to four different groups framework. And, indeed, his early attempt to reformulate
could exist in two distinct isomeric forms, not three, dif- natural selection in physical terms, as articulated in one
fering just in the direction of their optical rotation, solved of his two classic 1922 PNAS papers,[2] was years ahead of
the problem well before physical techniques were avail- its time and appeared to point the way forward. But a cen-
able to confirm that logical deduction. That kind of intel-
lectual versatility has been the mainstay of physical or- [a] A. Pross
ganic chemical thinking ever since, contributing to the es- Department of Chemistry
tablishment of a coherent structural and mechanistic Ben Gurion University of the Negev
framework for the subject. Beer Sheva, 84105 (Israel)
e-mail: pross@bgu.ac.il
Given the scope and range of physical organic chemis-
ap148@nyu.edu
try methodology, it would seem a foregone conclusion
[b] A. Pross
that the origin of life (OOL) problem, one of the most
NYU Shanghai
tantalizing scientific questions ever, and physical organic 1555 Century Avenue
chemistry would make for a happy marriage. After all, Pudong New Area
the building blocks of life are organic, and life processes Shanghai 200122 (China)

Isr. J. Chem. 2016, 56, 83 – 88 Ó 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim 83
Review
tury has passed, and while some progress has been made, from where Lotka took leave, to work towards a physico-
particularly through the development of nonequilibrium chemical framework able to accommodate both chemical
thermodynamics,[3] the OOL question remains unre- and biological systems, one that is hopefully able to inte-
solved. The two grand theories of the 19th century – Dar- grate DarwinÏs biological theory of evolution and the
winian natural selection and the second law of thermody- ubiquitous second law. Happily, a newly emergent area of
namics – remain the odd couple, awkwardly out of step chemistry, termed systems chemistry, established and
with one another. The former unified biology and ex- named less than a decade ago by Gînter von Kiedrowski
plains its irrepressible direction, seemingly towards in- and colleagues, is providing valuable experimental data
creasingly complex, dynamic, energy gathering, far-from- and is now beginning to fill the void.[6,7] In the following
equilibrium systems; the latter downhill, towards equilib- discussion, I outline what I believe to be the central chal-
rium and uniformity – towards what the physicists call lenge, the achievements to date, and the way forward.
heat death. That anomalous situation has troubled biolo- Some of the main ideas summarized here are discussed in
gists and physicists alike. But as Woese and Goldenfeld my recently published book.[8]
recently pointed out, understanding biologyÏs essence en-
tails understanding how the remarkable transformation
from inanimate to animate came about. In their words, 2 Discussion
“biology is a study, not in being, but in becoming”.[4]
2.1 Historic and Ahistoric Facets
Indeed, in an almost messianic cry for redemption, Woese
claimed that biology of the 20th century, with its current In addressing the OOL problem, a necessary starting
focus on the genome and associated molecular mecha- point is the recognition that the problem has two facets –
nisms, had lost its way and needed to be rediscovered, historic and ahistoric.[8,9] The historic facet would seek to
just like physics at the turn of the 20th century.[5] We have reveal the pathway by which life on earth emerged;
here a shrill wake-up call from one of the 20th centuryÏs namely, the central molecular building blocks from which
leading biologists, though one that seems to be studiously the process was initiated, key intermediate forms, and the
ignored. primal energy source that would have enabled the trans-
The POC-OOL story I present is very much a personal formation to simple life to take place. However, this goal
perspective. POC, as applied to traditional organic prob- is not achievable, not even remotely. Simply, the historic
lems, was my scientific field for some three decades record of lifeÏs chemical emergence has long been lost (in
before the siren call of biology jolted me out of my chem- contrast to the historic pathway for biological evolution,
ical tranquility. The realization that initially there was no where paleontological and phylogenetic studies offer sub-
biology, that some 3.5 to 4 billion years ago chemistry stantial historic information). But, of even more concern,
became biology, that evolution must have started with attempts to simulate the historic reaction conditions
a chemical system, and therefore, that biology must ulti- thought to have existed at various sites on the prebiotic
mately be just a very special kind of chemistry, struck me earth, even if feasible, would not prove that life started
like a thunderbolt. To me, a conceptual framework based out that way, as such theories are not falsifiable. So while
on physics and chemistry was the way to proceed, and the chemistry that could be discovered in this way would
that realization has been my focus for the past 15 years. be of interest, experiments of this kind cannot impact di-
My goal: based on years of applying POC methodology rectly on the OOL question. In fact, the plethora of un-
to chemical problems, to attempt to apply that methodol- falsifiable mechanistic speculation surrounding the OOL
ogy to WoeseÏs “becoming” question, to continue on question in the latter part of the last century may well
have contributed to the decline in the status of OOL re-
search as a legitimate scientific pursuit.
Addy Pross received a PhD in organic A momentÏs thought however suggests that the more
chemistry from Sydney University in fundamental OOL question is the ahistoric one, namely,
1970 and took up a lectureship in why would any mixture of chemical materials lead to the
Chemistry at Ben Gurion University of process of material complexification towards life? It is
the Negev in 1973, where he is now
the resolution of the ahistoric question that is the real
Professor Emeritus. He currently holds
a visiting professorship at NYU Shang- challenge. Rather than how did life emerge?, the more
hai, China. His research interests are in pertinent question is why did life emerge?, or for those
theoretical organic chemistry and uncomfortable with “why” questions, how could life have
chemical reactivity with recent empha- emerged? If the ahistoric principles, necessarily independ-
sis on systems chemistry and the ent of time and place, could be identified, then the histor-
origin of life. He has authored two ic path, though still interesting in its own right, would be
books: Theoretical and Physical Princi- of secondary importance – presumably just one of many
ples of Organic Reactivity, Wiley, 1995, and What is Life: How Chemis- feasible pathways. And, indeed, only when that process of
try Becomes Biology, Oxford University Press, 2012.
emergence is finally understood can we seriously hope to

Isr. J. Chem. 2016, 56, 83 – 88 Ó 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim www.ijc.wiley-vch.de 84
Review
duplicate the process – to attempt the synthesis of proto- and do, lead toward thermodynamically more stable
life, that ultimate synthetic challenge. products. For this and other reasons (associated with the
likely availability of lifeÏs essential abiotic building
blocks), the replication-first approach to the OOL prob-
2.2 Darwinian Selection or the Second Law?
lem continues to encounter opposition.
Before the question of process can be addressed, we need The second law, as the primary law governing the OOL
to consider the possibility that lifeÏs emergence occurred process, enjoys widespread support, but also has its diffi-
by chance, that in fact no process was involved at all. But culties. According to this way of thinking, and based on
as Morowitz pointed out some time ago,[10] the likelihood subsequent developments in nonequilibrium thermody-
of a chance sequence of events leading to life can be namics, life is a thermodynamically induced phenomenon,
safely dismissed. The probability of the chance formation a so-called dissipative structure. Thus lifeÏs nonequilibri-
of a bacterial cell from its components was estimated to um character emerged to facilitate natureÏs drive towards
be of the order of 10¢100 000 000 000. That being the case, energy dissipation, an additional means of reaching ther-
there had to be a process, one able to overcome the effec- modynamically stable states.[3] But here also there are
tively zero probability of a chance series of events leading concerns. If living systems are simply nonequilibrium dis-
to life.[11] sipative structures and life is merely one of natureÏs fa-
The two central theories which have been utilized, di- vored ways of dissipating energy, then why did cells
rectly or indirectly, to explain the process underlying evolve to minimize energy dissipation? Why is the pro-
OOL are well known – Darwinian natural selection and cess of cell replication so exquisitely efficient in replica-
the second law. But despite their profoundly important tion, but so miserly in dissipation?[15] Why, for example,
place in scientific thought for over a century, both have donÏt cells dissipate energy deliberately and expeditiously
come up short. Consider first Darwinian selection, which when resources are plentiful? LifeÏs extraordinarily inno-
also forms the basis for the replication-first view of vative and versatile character could easily have come up
OOL.[12] In his classic work on RNA in-vitro replication, with a mechanism for that. But it didnÏt. Examination of
Sol Spiegelman discovered that biologyÏs sine qua non – cell replication makes it evident that the cellÏs “agenda”
the sequence: replication-variation-selection-evolution – is to optimize replication, not energy dissipation. So life
can take place at the molecular level.[13] In other words, processes are consistent with the second law, but not ex-
the chemical equivalent of (biological) natural selection plained by the second law. A strict thermodynamic view
already operates on molecules; natural selection is not re- of evolution appears to have reversed cause and effect:
stricted to living organisms. The implication of that land- replication induces dissipation, not the other way around.
mark experiment conducted almost 50 years ago is pro- Indeed, Lotka, already almost a century ago, recognized
found: the roots of biological evolution lie in chemistry; that thermodynamics is unable to tell us what will
a connection between change in the chemical and biologi- happen, just what cannot happen; thermodynamics is only
cal worlds had been discovered. Since SpiegelmanÏs dis- part of the story.[2]
covery many elegant molecular replication experiments Two additional perspectives on the life phenomenon,
have been carried out, and SpiegelmanÏs early finding much in vogue in recent times, are complexity theory and
that a process akin to Darwinian selection operates at the information theory, and given their fundamental nature,
chemical level has been reaffirmed.[14] Thus according to one might dare hope they could offer insights into OOL.
this Darwinian perspective, once some replicating entity After all, OOL is the process by which biocomplexity and
(or replicating molecular system) emerges, the evolution- bioinformation were created. But despite the considera-
ary process, based on natural selection, begins to operate, ble interest in these approaches, the OOL problem does
leading ultimately to simple life. not appear to have benefited. Even though life could be
Yes, but how? Despite that appealing Darwinian inter- considered as the ultimate emergent complex system, any
pretation, a number of difficulties arise. In the first in- underlying rules of complexity governing the emergence
stance, how were the energy requirements of replication and evolution of living things continue to remain ob-
accommodated? The driving force for all chemical pro- scure.[16] And the claim that biological complexity has
cesses, OOL related or not, is thermodynamic, as ex- more to do with those rules of complexity than with Dar-
pressed by the second law, so it is not clear how natural winian principles[17] remains unproven.[16]
selection was able to transform a relatively simple molec- A similar conclusion is forthcoming regarding informa-
ular system into the staggering complexity of even the tion theory and OOL, as no direct connection between
simplest life form. How would selection at the molecular the two has been proposed to date. In fact, a recently pro-
level lead in a direction seemingly opposed to the ther- posed view that informational imperatives may be able to
modynamic directive – towards complexity and the main- transcend the laws of physics and chemistry[18] remains
tenance of a far-from-equilibrium, metabolic state – unsubstantiated, and in the OOL context, merely serves
rather than downhill towards the “dead” equilibrium to muddy the waters. If life is but an information manage-
state? After all, even kinetically directed processes must, ment and control process, how does that manifest itself in

Isr. J. Chem. 2016, 56, 83 – 88 Ó 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim www.ijc.wiley-vch.de 85
Review
the early (chemical) phase of lifeÏs emergence? In sum- kind is established, it leads directly to a different selection
mary, to the best of my understanding, no practical in- rule to the one that normally operates in chemistry –
sights into OOL have come about through complexity or from DK less stable to DK more stable. The math gov-
informational considerations, as, for example, in being erning the kinetics is explicit – competing exponential
able to suggest possible strategies for synthesizing simple replicators cannot coexist; better replicators drive poorer
protolife. ones into extinction.[22–24] The result – evolution. Howev-
So given the above comments, how are we to proceed? er, based on the existence of two stability kinds, two evo-
In my view, it is time for the OOL problem to return to lutionary processes for governing change in the universe
its natural home – physical organic chemistry. The OOL naturally follow – in the “regular” chemical world,
problem is a physical/chemical problem and its solution change is directed towards greater thermodynamic stabili-
needs to be sought within the established rules of physics ty; in the replicator world (once DK states have been ac-
and chemistry. In fact, this appears to be taking place, as cessed), change is directed towards greater DKS.
the recently emergent area of systems chemistry[6,7] re- Importantly, recognition of the existence of this alter-
flects this way of thinking. Systems chemistry is physical native stability kind enables the two seemingly distinct
organic chemistry par excellence, just focusing more on phases within the replicative world – the emergence of
the relatively unknown chemistry of replicative sys- simple life from abiotic beginnings (abiogenesis), and the
tems.[19] In the classic physical organic chemical perspec- biotic phase, so-called Darwinian evolution, to be unified
tive, chemical process are seen as being governed by and understood as a single continuous physicochemical
a combination of kinetic and thermodynamic factors, and process.[8,11,21d] That process is able to operate within the
there may be no need to forsake that fundamental and entire world of persistent replicating systems, both chemi-
proven approach when dealing with the OOL issue. cal and biological, thereby offering a conceptual basis for
Indeed, it is precisely through a deeper understanding of the replication-first view that rested (somewhat problem-
that kinetic-thermodynamic interplay in the context of atically) on the (biological) idea of natural selection at
replicative systems where we suspect the solution to the the molecular level. Thus the DKS formulation allows the
OOL problem may lie. In recent work, Robert Pascal and conceptual integration of biological evolution within
I have pointed out that there are two mathematical en- a more general physicochemical framework. A more rig-
gines for change in the universe – one based on Boltz- orous physicochemical analysis of that process of emer-
mannÏs probabilistic considerations, the other on Malthu- gence, with particular emphasis on irreversibility and its
sian exponential growth.[20] It is within the chemical world energy requirements, has recently been described by
of Malthusian exponential growth that the relative impor- Robert Pascal.[21e,g,h]
tance of kinetic and thermodynamic factors changes dra-
matically, and in fact, can invert. Thus the kinetic power
2.4 Unifying Darwinian Selection and the Second Law
associated with replicative systems is able, under certain
circumstances, to subsume thermodynamics, leading to While the formulation of another stability kind, DKS, is
the emergence of a qualitatively different kind of chemis- helpful in unifying the OOL process and biological evolu-
try – biology. That kinetic-thermodynamic reversion is tion, the question may be asked: why two stability kinds?
readily understood through an extension of the stability Could there be others? What is actually meant by the
concept; specifically, through the characterization of an “stability” term? I now offer some recent thoughts that
alternative stability kind: dynamic kinetic stability bear on these general questions. Central to those ideas is
(DKS). the proposal of a logical principle of nature, the persis-
tence principle,[20] very much in tune with the physical or-
ganic way of thinking, and which may offer further in-
2.3 A Different Stability Kind: Dynamic Kinetic Stability
sights into the animate-inanimate connection.
Dynamic kinetic stability, a particular kind of kinetic sta- Though we typically think of stability in energy terms,
bility, is distinctly different to the (static) kinetic stability the stability concept has another facet – a time facet, one
that pervades chemical reactivity thinking.[8,11,21] In sim- quite unrelated to energy. A system is considered stable if
plest terms, DKS is the stability kind associated with enti- it is able to persist over time, even if it is thermodynami-
ties able to self-replicate, but able to do so at an exponen- cally unstable, and DKS exemplifies such a stability kind.
tial growth rate, to enable a nonequilibrium steady-state A biological population is stable in that persistence sense
population of replicating entities to be maintained over since it can maintain a continuing presence over millions
time – stability (in the sense of persistence) through self- of years, even though the individuals that comprise that
replication. And being in a nonequilibrium state, DK (dy- population have a limited life span and continually turn
namic kinetic) stable systems are inherently thermody- over. But time stability and energy stability can be relat-
namically unstable, as they depend on a continuing inflow ed, as illustrated in the Venn diagram in Figure 1.
of energy to maintain that replicator steady-state. But to Inspection of the diagram leads to the surprising con-
the central point: once the existence of this other stability clusion that the time facet is more general than the

Isr. J. Chem. 2016, 56, 83 – 88 Ó 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim www.ijc.wiley-vch.de 86
Review
OOL problem: the key to understanding the process is to
understand its driving force, why it got started. Why
would abiotic material of any kind, in any combination,
under any feasible conditions, start out on the long chem-
ical journey towards that highly complex, far from equi-
librium, energy consuming, chemical assembly, that is
life? That question, as posed, is a physical organic
chemistry question, maybe the ultimate one.
While much remains to be discovered, I believe an out-
Figure 1. Diagram illustrating the set of thermodynamically stable
line of a resolution is beginning to materialize. Life is
systems as a subset of the more general set of persistent systems.
a self-sustained, dynamic, nonequilibrium, extended repli-
energy facet. A thermodynamically stable system is nec- cative chemical network, which was initiated by the
essarily persistent, but a persistent system does not have chance emergence of a simple, but persistent, replicative
to be thermodynamically stable, as the DK stability kind chemical system. Replication is not a common chemical
demonstrates. But it is this connection between stability reaction, but it does take place with the right materials
in the replicative world and in the “regular” physico- under the right conditions. Once such an entity was able
chemical world which allows the formulation of a general to emerge and access that nonequilibrium DK state, its
principle governing persistence. Grand recently noted in- road to greater stability – replicative stability – com-
sightfully that “things that persist, persist, things that menced. How? Primarily through a process of complexifi-
donÏt, donÏt”.[25] But that simple truism can be extended cation, that is to say, network formation and its subse-
and reformulated into a principle which describes change quent extension. Greater complexity for greater stability.
in the world: systems will tend from less stable (persistent) Indeed, complexity in the replicative world may be
to more stable (persistent) forms, or, more concisely: thought of as the analog of entropy in the “regular”
nature seeks persistent forms. Note the principle is logical- world. Thus in its broadest sense, life can be understood
ly derived, as the truism can also be expressed as: chang- as a logically dictated process, a direct expression of the
ing things will change, until they change into things that persistence principle – from less persistent to more persis-
donÏt. tent, but within the replicative world. Physicochemical
Importantly, however, the persistence principle, by con- change, whether in the “regular” or the replicative
sidering both thermodynamic stability and DKS in the worlds, reflects the same basic truism: nature seeks persis-
same “persistence” terms, offers a unifying framework for tent forms.[20]
the two stability kinds. Material change towards greater A final point regarding the relative kinetic powers op-
persistence takes place in both worlds – “regular” and erating in the two worlds. Due to the awesome Malthusi-
replicative. It is just the physical/mathematical basis for an power of exponential growth, replicative persistence is
change that differs. Within the physiochemical world, the able to out-compete Boltzmann thermodynamic persis-
driving force is dictated by the second law with its proba- tence, and overwhelmingly so. ThatÏs why life has taken
bilistic directive (towards increasing entropy), while in over our planet, inhabiting almost every conceivable eco-
the replicative world, change is governed by replicative logical niche. The Malthusian power of exponential
variation and the math of exponential growth. But two growth overwhelms the Boltzmann asymptotic slide to-
distinct maths mean two distinct evolutionary processes, wards equilibrium, engulfing all that stands in its way.
each leading to its corresponding material form – living Thus the physics of life is explicit and unambiguous. The
and nonliving – each tending towards increasing persis- uncertainty lies within chemistry, within that new area of
tence. If these ideas prove fruitful, the value of the physi- physical organic chemistry, systems chemistry.
cal organic chemical way of thinking will again have The challenge ahead: to discover which chemical
proven itself. groups are able to facilitate the replication process within
the general framework of nonequilibrium systems, to ex-
plore how energy sources can couple up with and sustain
such systems, and to explore their potential for network
3 Concluding Remarks
formation and possible evolution. Recent work by van
The “what is life?” question continues to torment. Like Esch et al., demonstrating unusual chemically-fueled dy-
the blind men of Hindustan attempting to describe an ele- namic nonequilibrium self-assembly processes akin to cer-
phant, the different sciences “see” different life aspects tain biological ones, is pointing the way forward.[26] For
and reach strikingly different conclusions as to lifeÏs es- those ready to eulogize classical physical organic chemis-
sence. But, as the late and great Carl Woese pointed out, try, the challenge posed by the OOL question is a gentle
life is more a process than a series of things, and there- reminder that, like Mark Twain, rumors of its demise are
fore, to understand those “things”, we need first to under- premature. The ultimate physical organic chemistry ques-
stand the process.[4] And that brings us right back to the tion is very much alive, and beckons.

Isr. J. Chem. 2016, 56, 83 – 88 Ó 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim www.ijc.wiley-vch.de 87
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Acknowledgements [13] D. R. Mills, R. L. Peterson, S. Spiegelman, Proc. Natl. Acad.
Sci. U.S.A. 1967, 58, 217 – 224.
[14] For detailed reviews, see: a) K. Ruiz-Mirazo, C. Briones, A.
I thank Robert Pascal for the productive collaboration de la Escosura, Chem. Rev. 2014, 114, 285 – 366; b) G. F.
which contributed to the ideas expressed here and Leo Joyce, Angew. Chem. Int. Ed. 2007, 46, 6420 – 6436.
Radom for helpful comments on an earlier draft of the [15] J. Monod, Chance and necessity, Vintage, New York, 1972,
manuscript. Thanks are also due to COST Actions pp. 19 – 20.
TD1308 and CM1304 for the exchanges they have facili- [16] S. Weinberg, New York Rev. Books, Oct. 24, 2002.
tated. [17] S. Wolfram, A New Kind of Science, Wolfram Media, Cham-
paign IL, 2002.
[18] S. I. Walker, P. C. W. Davies, J. R. Soc. Interface 2013, 10,
20120869.
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Oxford University Press, Oxford, 2012. versity Press, Cambridge MA, 2003.
[9] M. Eigen, Steps towards Life: A Perspective on Evolution, [26] a) J. Boekhoven, W. E. Hendriksen, G. J. M. Koper, R. Eel-
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Isr. J. Chem. 2016, 56, 83 – 88 Ó 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim www.ijc.wiley-vch.de 88

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