life

Essay
A Field Trip to the Archaean in Search of Darwin’s
Warm Little Pond
Bruce Damer 1,2
1 Department of Biomolecular Engineering, Baskin School of Engineering, University of California at Santa
Cruz, Santa Cruz, CA 95064, USA; bdamer@ucsc.edu; Tel.: +1-831-459-2158
2 DigitalSpace Research, Boulder Creek, CA 95006, USA

Academic Editor: Niles Lehman

Received: 22 March 2016; Accepted: 20 May 2016; Published: 25 May 2016

Abstract: Charles Darwin’s original intuition that life began in a “warm little pond” has for the last
three decades been eclipsed by a focus on marine hydrothermal vents as a venue for abiogenesis.
However, thermodynamic barriers to polymerization of key molecular building blocks and the
difficulty of forming stable membranous compartments in seawater suggest that Darwin’s original
insight should be reconsidered. I will introduce the terrestrial origin of life hypothesis, which combines
field observations and laboratory results to provide a novel and testable model in which life begins as
protocells assembling in inland fresh water hydrothermal fields. Hydrothermal fields are associated
with volcanic landmasses resembling Hawaii and Iceland today and could plausibly have existed
on similar land masses rising out of Earth’s first oceans. I will report on a field trip to the living and
ancient stromatolite fossil localities of Western Australia, which provided key insights into how life
may have emerged in Archaean, fluctuating fresh water hydrothermal pools, geological evidence
for which has recently been discovered. Laboratory experimentation and fieldwork are providing
mounting evidence that such sites have properties that are conducive to polymerization reactions
and generation of membrane-bounded protocells. I will build on the previously developed coupled
phases scenario, unifying the chemical and geological frameworks and proposing that a hydrogel
of stable, communally supported protocells will emerge as a candidate Woese progenote, the distant
common ancestor of microbial communities so abundant in the earliest fossil record.

Keywords: origin of life; hydrothermal systems; progenote; microbial communities; stromatolites

1. Introduction
Most workers investigating the origin of life confine their horizons to theoretical papers,
computational models or laboratory simulations that use a narrow spectrum of commercial reagents
reacting in buffered aqueous solutions. The results are then related to prebiotic conditions with the
assumption that laboratory or in silico results can plausibly occur in the early Earth environment.
A complementary approach is to visit sites that are analogs to candidate venues for biogenesis. Such
fieldwork broadens our perspective by providing a more realistic assessment of the actual conditions in
which physical and chemical reactions progressed toward life’s beginning approximately four billion
years ago. Furthermore, geologists familiar with the most ancient, Archaean fossil sites can interpret
the rock record and provide knowledgeable advice about geochemical conditions to guide model
building and laboratory experiments.

Life 2016, 6, 21; doi:10.3390/life6020021 www.mdpi.com/journal/life

Life 2016, 6, 21 2 of 14
Life 2016, 6, 21 2 of 14

2. A Field Trip in Deep Time to the Archaean

2. A Field Trip in Deep Time to the Archaean
In July 2015, I joined a unique scientific field trip led by Malcolm Walter and Martin Van
Kranendonk In July
of the2015, I joined
Australian a unique
Centre scientific field
for Astrobiology at thetrip led by of
University Malcolm
New South Walter and This
Wales.
Martin Van Kranendonk of the Australian Centre for Astrobiology at the University of New
3000 km trek (Figure 1) by air, bus, utility vehicle and foot traveled through 3.5 Ga (billion) years of South
Wales. This 3000 km trek (Figure 1) by air, bus, utility vehicle and foot traveled through 3.5 Ga
Earth’s history across Western Australia, from Perth to Hamelin Pool (1) at Shark Bay, northward
(billion) years of Earth’s history across Western Australia, from Perth to Hamelin Pool (1) at Shark Bay,
through the Hamersley Range and Fortescue Group (2–4) to the Marble Bar area (5) and finally to
northward through the Hamersley Range and Fortescue Group (2–4) to the Marble Bar area (5) and
sites (6–8) in the remote North Pole Dome of the Pilbara Craton. During the ten-day tour, new ideas
finally to sites (6–8) in the remote North Pole Dome of the Pilbara Craton. During the ten-day tour,
emerged through
new ideas examination
emerged of evidenceoffrom
through examination the from
evidence earliest known,known,
the earliest Archaean geological
Archaean settings
geological
inhabited
settingsbyinhabited
microbialbylife.
microbial life.

Figure
Figure 1. Routetaken
1. Route taken from
fromPerth, Western
Perth, Australia
Western to Sharkto
Australia BayShark
near Denham,
Bay near north via Paraburdoo
Denham, north via
and Tom Price into the Pilbara region before departure from Port Hedland. Sites visited are
Paraburdoo and Tom Price into the Pilbara region before departure from Port Hedland. Sites visited marked in
red (1–8). in
are marked Source: Government
red (1–8). of Western
Source: Australia
Government of Department of Mines and
Western Australia Petroleum. of Mines and
Department
Petroleum.
3. Living Marine Stromatolites and Inland Microbial Communities
3. LivingThe journey
Marine began with a visit
Stromatolites and to one ofMicrobial
Inland the best examples of living stromatolites, in Hamelin Pool
Communities
at Shark Bay (Figure 2). These shallow water domical and mat-like structures are formed by microbial
The journey began with a visit to one of the best examples of living stromatolites, in Hamelin
communities under conditions of elevated salinity that prevents larger organisms from feeding on
Pool the
at Shark Bay (Figure
communities. 2). Thesethat
The organisms shallow water domical
form stromatolites and
cause mat-like
carbonate structures
minerals are formed
to precipitate in by
microbial communities
distinctive under
layers, forming conditions
structures that of
canelevated salinity
be preserved that prevents
for billions of years inlarger organisms
the fossil record. from
feeding on the communities. The organisms that form stromatolites cause carbonate minerals to
precipitate in distinctive layers, forming structures that can be preserved for billions of years in the
fossil record.
Life 2016, 6, 21 3 of 14
Life 2016, 6, 21 3 of 14
Life 2016, 6, 21 3 of 14

Figure 2. (Left) Underwater view of stromatolites in Hamelin Pool, Shark Bay, Western Australia
Figure 2. (Left) Underwater view of stromatolites in Hamelin Pool, Shark Bay, Western Australia (credit:
(credit:
Figure 2.Marisol Juarez Rivera).
(Left) Underwater view(Center) Eroded section
of stromatolites through
in Hamelin Pool,a Shark
recently
Bay,exposed
WesternShark Bay
Australia
Marisol Juarez Rivera). (Center) Eroded section through a recently exposed Shark Bay stromatolite,
stromatolite, showing
(credit: Marisol Juarezthe domical
Rivera). shape and
(Center) crude
Eroded laminations
section through of athese large,exposed
recently lithified Shark
structures
Bay
showing the domical shape and crude laminations of these large, lithified structures (width of central
(width of central
stromatolite, stromatolites
showing is ~20
the domical cm).and
shape (Right)
crude Oblique view down
laminations onto
of these silt lithified
large, and sand-covered,
structures
stromatolites is ~20 cm). (Right) Oblique view down onto silt and sand-covered, living microbial
living
(widthmicrobial
of centralmat from SharkisBay.
stromatolites ~20 The
cm).ragged
(Right)textured
Obliqueedge
viewindown
the photo
ontoissilt
an and
eroded section cut
sand-covered,
mat from Shark Bay. The ragged textured edge in the photo is an eroded section cut through the
through the microbial
living microbial mat,
mat from which
Shark exhibits
Bay. rubbery
The ragged cohesion
textured edgeasinitthe
is composed
photo is anoferoded
a community of
section cut
microbial mat, which exhibits rubbery cohesion as it is composed of a community of microorganisms.
microorganisms. These mat,
through the microbial contemporary versions
which exhibits of thecohesion
rubbery Earth’s most
as itancient microbial
is composed of aecosystem
community were
of
These contemporary versions of the Earth’s most ancient microbial ecosystem were later compared to
later compared toThese
microorganisms. Archaean stromatolite
contemporary fossils.ofCenter
versions the and right
Earth’s most photos
ancientbymicrobial
author. ecosystem were
Archaean stromatolite fossils. Center and right photos by author.
later compared to Archaean stromatolite fossils. Center and right photos by author.
The stromatolites produced by microbial communities at Shark Bay require near-continuous
The
The stromatolites
immersion stromatolites
in a marine produced
produced by
by microbial
environment. By waycommunities
microbial of contrast, at
communities Shark
Shark Bay
atterrestrialBay require
require near-continuous
microbial near-continuous
mats were also
immersion
observed in a marine
immersiononinthea exposed environment.
marine rockenvironment. By way of
surfaces ofByGallery contrast,
way of terrestrial
contrast,
Hill microbial mats
terrestrial Pilbara
in the semi-desert microbialwere also
mats
region observed
were
near also
Marble
on
Bar the
observed exposed
on3).the
(Figure rock surfaces
exposed arock
Hydrating of Gallery
drysurfaces
mat (by of Hill in the semi-desert
Gallery rainfall)
simulated Hill in the Pilbara
semi-desert
showed that the region
Pilbara near Marble
regionabsorbed
mat quickly Bar
near Marble
the
(Figure
water 3).
Bar (Figure Hydrating
3). Hydrating
and retained a dry mat
it far alonger
dry mat(by
than simulated
(bysurrounding rainfall)
simulated rainfall) showed
mineral showed that
surfacesthat the
the
(as mat quickly absorbed
mat quicklyelsewhere
documented the
absorbed theby
water
water and
and retained
Verrecchia al. [1]). it
retained
et it far
far longer
longer than
Significantly, than surrounding
surrounding
the moistened matmineral
had thesurfaces
mineral surfaces (as
(as documented
same physical consistencyelsewhere
documented elsewhere by
by
as the living
Verrecchia
Verrecchia et
stromatolite et al.
al. [1]). Significantly,
[1]).at
mats Significantly,
Hamelin Pool.the
the moistened
moistened mat
mat had
This microbial the
the same
same physical
hadcommunity physical
inhabitedconsistency
consistency as
as the
a rock-soil living
themargin
living
stromatolite
stromatoliteamats
resembling matsat at
shorelineHamelin
HamelinPool.Pool.
and depended Thisonmicrobial
This community
microbial
infrequent inhabitedinhabited
community
precipitation. a rock-soila margin resembling
rock-soil margin
aresembling
shoreline and depended on infrequent precipitation.
a shoreline and depended on infrequent precipitation.

Figure 3. (Left) Author photos of microbial mats growing on exposed rocks at Gallery Hill; and
(Center)
Figure 3.and (Right)
(Left) hydrating
Author photosaofmat and testing
microbial itsgrowing
mats plasticity.on exposed rocks at Gallery Hill; and
Figure 3. (Left) Author photos of microbial mats growing on exposed rocks at Gallery Hill; and
(Center) and (Right) hydrating a mat and testing its plasticity.
(Center) and (Right) hydrating a mat and testing its plasticity.
Could there have been an evolutionary link between marine stromatolites and these primitive
Couldmats
microbial there have been
pointing backantoevolutionary link between
a common ancestor marine
depending on astromatolites
more reliableand these primitive
fluctuating source
of Could
microbial
fresh there
mats
water? have
If so,been
pointing backanto
how evolutionary
a common
could link between
these ancestor
fresh marine
depending
water mats on stromatolites
have a more toand
reliable
evolved these primitive
fluctuating
survive source
extensive
microbial
dehydrationmats
of fresh water? pointing back
If so, how
and exposure to a
could
to the common
these
much ancestor
fresh
higher depending
water mats
ultraviolet on a more
have evolved
(UV) component reliable fluctuating
to survive
of Archaean source
extensive
sunlight?
of fresh water?
dehydration and
A possible Ifanswer
so, howwas
exposure could these
to suggested
the fresh
much bywater
higher mats have
ultraviolet
examination evolved
(UV)
of to survive
onecomponent
of the many extensive
of Archaean
flat dehydration
rocks sunlight?
littering the
and exposure
surface to answer
A possible
of Gallerythe much
Hill higher
was
(Figure 4). ultraviolet
suggested
The rock (UV)
by lay on component
examination of one
a weathered ofsurface
Archaean sunlight?
of the covered
many flat
by rocks littering
what is knowntheas
surface of
“desert Gallery Hill
varnish”, (Figure canvas
a favorite 4). The rock lay on a weathered
for Aboriginal artists. surface
Beneathcovered
the rockby what
was ais known as
microbial
“desert varnish”, a favorite canvas for Aboriginal artists. Beneath the rock was a microbial
Life 2016, 6, 21 4 of 14

A possible answer was suggested by examination of one of the many flat rocks littering the surface
of Gallery Hill (Figure 4). The rock lay on a weathered surface covered by what is known as “desert
varnish”, a favorite
Life 2016, 6, 21 canvas for Aboriginal artists. Beneath the rock was a microbial community thriving
4 of 14
in moist sediments (center), consisting of cyanobacteria shaded from the ultraviolet component of
Life 2016, 6, 21 4 of 14
sunlight but ablethriving
community to gather enough
in moist diffuse light
sediments for consisting
(center), metabolism of (as noted elsewhere
cyanobacteria shaded in the the
from Pilbara
ultraviolet
by Hoshino component
andthriving
George in of sunlight
[2]). On the but able to gather
early Earth, shade enough diffuse
provided light for metabolism
by rocks and shaded
minerals(as noted
would
community moist sediments (center), consisting of cyanobacteria from the have
elsewhere
protected against in the Pilbara bylight
ultraviolet Hoshino
and and Georgemoisture
retained [2]). On the early Earth,
essential for shadeCracks
life. provided by rocks
within mineral
ultraviolet component of sunlight but able to gather enough diffuse light for metabolism (as noted
and minerals would have protected against ultraviolet light and retained moisture essential for life.
surfaces (right)incan
elsewhere thealso provide
Pilbara such protection
by Hoshino and George for[2]).
cryptoendolithic microorganisms
On the early Earth, thatbythrive
shade provided rocks today
Cracks within mineral surfaces (right) can also provide such protection for cryptoendolithic
in the
andAntarctic
mineralshigh woulddeserts [3].
have protected against ultraviolet light and retained moisture essential for life.
microorganisms that thrive today in the Antarctic high deserts [3].
Cracks within mineral surfaces (right) can also provide such protection for cryptoendolithic
microorganisms that thrive today in the Antarctic high deserts [3].

Figure 4. Author photos of rock next to an impression of its earlier resting place on Gallery Hill
Figure 4. Author photos of rock next to an impression of its earlier resting place on Gallery Hill (Left);
(Left); microbial community in moist sediments beneath it (Center); and view of rock underside
microbial
Figurecommunity
(Right). in moist
4. Author photos sediments
of rock next tobeneath it (Center);
an impression of its and view
earlier of rock
resting underside
place (Right).
on Gallery Hill
(Left); microbial community in moist sediments beneath it (Center); and view of rock underside
(Right).
TheseThese
observations suggested
observations an interesting
suggested comparison
an interesting comparison between
between two
twosites proposed
sites proposedfor
forthe
theorigin
origin
of life: of life: submarine
submarine hydrothermal hydrothermal
vents ventsand
[4–8] and hydrothermalfieldsfields on exposed land surfaces[9,10].
These observations suggested an[4–8]
interestinghydrothermal
comparison between on exposed
two land
sites proposed surfaces
for the
[9,10]. Assuming a source of organic compounds such as amphiphiles, amino acids, and nucleobases
Assuming
origin ofa source of organic
life: submarine compounds
hydrothermal such[4–8]
vents as amphiphiles,
and hydrothermalamino acids,
fields and nucleobases
on exposed supplied
land surfaces
supplied by extraterrestrial infall [11–13] or geochemical synthesis [14,15], these compounds would
by extraterrestrial
[9,10]. Assuminginfall [11–13]
a source or geochemical
of organic compoundssynthesis [14,15], these
such as amphiphiles, aminocompounds would either be
acids, and nucleobases
either be present as a dilute solution in the Archaean ocean [16] or deposited on volcanic land
present as
supplied a dilute solution
by extraterrestrial in the Archaean
infall [11–13] orocean [16]
geochemical or deposited
synthesis on volcanic
[14,15], land
these compounds
masses. Exposed rocky surfaces that support localized pooling from precipitation would provide a
masses.
wouldExposed
rocky venue for early microbial communities, as illustrated by the isolated pools on the ca. 3.4 Ga jasperearly
surfaces
either that
be present support
as a dilutelocalized
solutionpooling from
in the Archaean precipitation
ocean [16] orwould provide
deposited a venue
on volcanic for
land
masses.
microbial Exposed rockyas
communities, surfaces that support
by thelocalized pooling from precipitation
Gawould provide a
formation at Marble Bar illustrated
(Figure 5). Fluctuating isolated poolsby
pools filled on the ca. 3.4 today
precipitation jasper formation
support living at
venue for early microbial communities, as illustrated by the isolated pools on the ca. 3.4 Ga jasper
Marble Bar (Figure
microbial 5). Fluctuating
mat communities (Figurepools filled
5, left) andbyshowprecipitation
evidence of today support
microbial living
chemical microbial
staining when mat
formation at Marble Bar (Figure 5). Fluctuating pools filled by precipitation today support living
communities
dehydrated (Figure
(Figure5,5,left) and
right). showthe
During evidence
Archaean, of organic
microbial chemical
compounds staining
would when dehydrated
accumulate in such
microbial mat communities (Figure 5, left) and show evidence of microbial chemical staining when
(Figure 5, right).
pools and would
dehydrated During
(Figure the Archaean,
During theorganic
be concentrated
5, right).
during cycles ofcompounds
dehydration would accumulate
by evaporation.
Archaean, organic compounds in such
would accumulate in pools
such and
would be concentrated during cycles of dehydration by evaporation.
pools and would be concentrated during cycles of dehydration by evaporation.

Figure 5. Author photos of rock-crevice pool (Left) at Marble Bar concentrating moisture and organic
solutes capable of supporting microbial mats (Inset). (Right) Dried pool illustrating microbial
Figure 5. Author photos of rock-crevice pool (Left) at Marble Bar concentrating moisture and organic
chemical
Figure staining
5. Author on the
photos rock surface. pool (Left) at Marble Bar concentrating moisture and organic
of rock-crevice
solutes capable of supporting microbial mats (Inset). (Right) Dried pool illustrating microbial
solutes capable
chemical of supporting
staining microbial
on the rock surface. mats (Inset). (Right) Dried pool illustrating microbial chemical
staining on the rock surface.
Life 2016, 6, 21 5 of 14
Life 2016, 6, 21 5 of 14

FossilStromatolites
4. Fossil Stromatolites
Well-preserved fossil
Well-preserved fossilstromatolites
stromatolitesare areabundant
abundant inin
thethe 2.72.7
ca.ca. GaGaTumbiana
Tumbiana Formation.
Formation. These are
These
“domical”
are “domical”(dome-shaped) stromatolites
(dome-shaped) (Figure 6),
stromatolites which bear
(Figure a clear resemblance
6), which bear a clearto resemblance
cross-sections to of
the stromatolites at Hamelin Pool (Figure 2, center). The field trip also toured the oldest rocks of
cross-sections of the stromatolites at Hamelin Pool (Figure 2, center). The field trip also toured the
Pilbararocks
oldest region,
of the
the Apex chert,
Pilbara Strelley
region, the Pool
Apexand Dresser
chert, formations.
Strelley Pool andFigure
Dresser6 (right bottom)
formations. shows
Figure 6
a cross-sectional
(right bottom) shows viewathrough ca. 3.4 Ga
cross-sectional stromatolites
view through ca.between beds of blackbetween
3.4 Ga stromatolites chert at beds
the “Trendall
of black
locality”
chert on the
at the Shaw River.
“Trendall Morphological
locality” on the Shaw similarity with modern day
River. Morphological stromatolites
similarity at Shark day
with modern Bay
suggests that at
stromatolites these structures
Shark are indicative
Bay suggests of biogenicity
that these structures [17–19]. Biogenicity
are indicative is also supported
of biogenicity [17–19].
by the fact that
Biogenicity black
is also chert from
supported by these localities
the fact has preserved
that black chert fromrare microfossils
these [20].preserved
localities has Whereasrare the
stromatolites[20].
microfossils of the Strelleythe
Whereas Pool Formation formed
stromatolites in a shallow
of the Strelley Pool marine environment
Formation formed in[21] with at
a shallow
least a local
marine influence [21]
environment of hydrothermal
with at least activity [22], the ca.
a local influence of 3.48 Ga Dresseractivity
hydrothermal Formation,
[22], which
the ca.contains
3.48 Ga
the oldest
Dresser convincing
Formation, evidence
which for life
contains the on Earth
oldest [23,24], was
convincing deposited
evidence within
for life an active
on Earth volcanic
[23,24], was
caldera. The
deposited presence
within of geyserite
an active volcanicprovides
caldera.clear
The evidence
presence of extensive, fresh water
geyserite provides hydrothermal
clear evidence of
systems onfresh
extensive, an exposed land surface, including
water hydrothermal systems on geyser activityland
an exposed [25]. surface,
Furthermore, concentrated
including boron
geyser activity
occurs
[25]. in tourmaline-rich
Furthermore, crusts,boron
concentrated together with
occurs in phosphate in hydrothermal
tourmaline-rich veins,
crusts, together withand clays from
phosphate in
acid-sulfate hydrothermal
hydrothermal veins, and claysalteration. These mineral
from acid-sulfate components
hydrothermal are considered
alteration. to be components
These mineral cofactors of
prebiotic chemical
are considered to bereactions
cofactorsrelated to life’schemical
of prebiotic origin [14].
reactions related to life’s origin [14].

Figure
Figure 6.6.(Left)
(Left)Author’s
Author’s photo
photo of overhead
of overhead viewview
of ca. of
2.7ca.
Ga 2.7 Ga domical
domical stromatolites
stromatolites from the
from the Tumbiana
Formation,Formation,
Tumbiana Fortescue Fortescue
Group. (Right
Group.top) Cross-section
(Right of a Tumbiana
top) Cross-section stromatolite
of a Tumbiana (credit: (credit:
stromatolite Martin
Van Kranendonk).
Martin (Right bottom)
Van Kranendonk). Author’sAuthor’s
(Right bottom) photo ofphoto
cross-sectional view of centimeter-scale,
of cross-sectional domical
view of centimeter-scale,
stromatolites
domical in black chert
stromatolites from chert
in black the “Trendall
from thelocality” outcrop
“Trendall of theoutcrop
locality” ca. 3.4 Ga
of Strelley
the ca. Pool Formation
3.4 Ga Strelley
on the Shaw River.
Pool Formation on the Shaw River.

5.
5. AAnovel
novelModel
Modelfor
foraaTerrestrial
TerrestrialOrigin
Origin of
of Life
Life
“It
“It is
is often
often said
said that
that all
all the
the conditions
conditions for
for the
the first
first production
production of
of aa living
living organism
organism are
are present,
present, which
which could
could
ever
ever have been present. But if (and oh what a big if) we could conceive in some warm little pond with all sorts of
have been present. But if (and oh what a big if) we could conceive in some warm little pond with all sorts of
ammonia
ammonia and and phosphoric
phosphoric salts,
salts, light,
light, heat,
heat, electricity
electricity etcetera
etcetera present,
present, that
that aa protein
protein compound
compound was was chemically
chemically
formed,
formed, ready
ready to
to undergo
undergo still
still more
more complex
complex changes
changes [...]”
[...]” ~Charles
~Charles Darwin,
Darwin, in in an
an 1871
1871 letter
letter to Joseph
to Joseph
Hooker [26].
Hooker [26].
The above speculation by Charles Darwin on where and how life might have begun is prescient
and deeply insightful: a warm little pond in which a useful polymer forms and evolves to ever
Life 2016, 6, 21 6 of 14

The above speculation by Charles Darwin on where and how life might have begun is prescient
and deeply insightful: a warm little pond in which a useful polymer forms and evolves to ever
increasing complexity of structure and function. By expanding Darwin’s insight with today’s
knowledge of chemistry and biochemistry, it is possible to propose a novel scenario for the origin
of cellular life in a small, hot, cycling pool [27]: A source of energy acts on a mixture of simple organic
compounds to produce a large number of random polymers. By chance, a few rare polymers happen to form
protocells defined as functional systems which are encapsulated within membranous compartments that are
subject to combinatorial selection. The encapsulated polymer systems continuously cycle within a kinetic trap in
which the rate of synthesis exceeds the rate of hydrolysis [28,29]. Over a large number of such cycles, populations
of protocells emerge that are capable of growth and replication. Combinatorial selection of protocells that are
better able to survive environmental stresses and more efficient in capturing energy and nutrients, drives the
evolution of populations toward the first primitive forms of life.
It is difficult to imagine how the above scenario could be applied to an origin of life at marine
settings such as hydrothermal vents. First, the continuous presence of water puts thermodynamic
limits on the condensation reactions that are required for polymerization of monomers. Furthermore,
high concentrations of salt and divalent cations at vents or tide pools impose osmotic stresses on
membranous compartments. Life today has evolved complex homeostatic mechanisms to regulate cell
volume by actively pumping osmotically active ions and thereby maintain transmembrane sodium
and potassium gradients as noted by Mulkidjanian et al. [10].
These concerns led to consideration of an alternative scenario that life began in fresh water
hydrothermal fields subject to cycles of dehydration and hydration as outlined by Deamer and
Georgiou [30]. To summarize briefly, given a process that could synthesize functional polymers,
the polymers become enclosed within compartments, referred to as protocells, in order to prevent
dispersion into a bulk aqueous phase. The polymers would resemble RNA and peptides, as well as
possible complexes of RNA and peptides. The boundary membranes of protocellular compartments
must be selectively permeable to permit access to nutrients from the surrounding environment.
A single protocell containing random polymers cannot evolve biologically relevant functions in
isolation. Instead, a combinatorial process is necessary to generate large populations of protocells,
test the functional fitness of encapsulated systems of polymers, and permit these polymers to be
expressed in later cycles of the population. The transition to life is a continuum, along which the
synthesis of functional polymers moves beyond physical self-assembly and comes under the control of
an autonomous set of molecular processes driven by instructions, itself subject to replication, mutation
and propagation through generations of protocells.

6. Linking Chemical Reactions to the Physical Properties of Hydrothermal Pools

Hydrothermal pools may contain mixtures of organic solutes, some of which are potential
monomers, and others capable of forming membranous vesicles. During the evaporation that drives the
dehydration phase of a cycle, layers of lipid membranes form films on mineral surfaces at the pool edge
as the water level fluctuates. Amphiphilic molecules assemble into multilamellar structures in which
monomers are captured between the lipid bilayers [31]. Figure 7, bottom inset shows the multilamellar
character of one such amphiphile, in this case anhydrous phosphatidylcholine. The concentrated
monomers (shown in red) are organized within a two-dimensional reaction space, and reduced water
activity drives condensation reactions in which water becomes a leaving group, resulting in synthesis
of ester bonds and peptide bonds, the primary links of biopolymers today. Assuming that amino
acids and nucleotides are among the potential reactants [32], the synthesis of peptide bonds and
phosphodiesters will occur and this has recently been demonstrated in laboratory simulations [33–37].
By chance, some of the polymers will have functions that are relevant to selection as components
of protocells.
Life 2016, 6, 21 7 of 14
Life 2016, 6, 21 7 of 14

Figure7.7.Protocells
Figure Protocellscycling
cyclingbetween
betweenthree
threecoupled
coupledphases.
phases.Hydrated
Hydratedphase
phase(Top),
(Top),inset:
inset:protocells
protocells
containing DNA growing out of a dried mixture of DNA and phospholipid, hydrated
containing DNA growing out of a dried mixture of DNA and phospholipid, hydrated by by water, stained
water,
with acridine orange. Gel phase (Center), inset: hydrogel of lipid with approximately 50%
stained with acridine orange. Gel phase (Center), inset: hydrogel of lipid with approximately 50% water by
weight showing lipid vesicles fusing into lamellae. Dehydrated phase (Bottom), inset: freeze
water by weight showing lipid vesicles fusing into lamellae. Dehydrated phase (Bottom), inset: fracture
image of anhydrous lipid lamellae of phosphatidylcholine. Micrographs credit: David Deamer.
freeze fracture image of anhydrous lipid lamellae of phosphatidylcholine. Micrographs credit: David
Deamer.
Short term dehydration and rehydration of the pool through periodic fluctuations in hydrothermal
water supply, rainfall
Short term events, and and
dehydration dew from day-nightofcycles
rehydration the orpoolthrough changing
through humidity
periodic cause thein
fluctuations
outer layers of the
hydrothermal driedsupply,
water lamellaerainfall
to disperse large
events, numbers
and dew from of protocells
day-night intocycles
the bulk
or solution. Some of
through changing
these protocells
humidity causewill
thecontain random
outer layers setsdried
of the of polymers
lamellae(Figure 7, top-inset
to disperse shows DNA
large numbers encapsulation).
of protocells into the
The protocells
bulk solution. areSome
then subject
of thesetoprotocells
selective processing
will contain in which
random the sets
aqueous environment
of polymers disrupts
(Figure some
7, top-inset
protocells
shows DNA while encapsulated functional
encapsulation). The protocells polymers
are thenstabilize their
subject to membranous compartments
selective processing in which and the
thereby
aqueous increase their robustness
environment disrupts some[38]. protocells
Stabilizedwhile protocells would persist
encapsulated and return
functional polymers to deposit
stabilize
their
theirsurviving
membranous cargos of polymersand
compartments backthereby
into the lamellae
increase as robustness
their protocells dry [38].down and undergo
Stabilized protocells
fusion.
would In this manner
persist and return the to
polymers
deposit are their“coupled”
survivingbetweencargos ofphasespolymersand back
cycledintowithin a kineticas
the lamellae
trap, permitting
protocells dry generations
down and of polymers
undergo to be re-synthesized,
fusion. In this mannertested and, as Darwin
the polymers intuited, become
are “coupled” between
increasingly
phases andcomplex.
cycled within a kinetic trap, permitting generations of polymers to be re-synthesized,
Theand,
tested kinetic trap provides
as Darwin intuited, scaffolding for the stepwise
become increasingly complex.emergence of encapsulated systems
of functional polymers
The kinetic described
trap provides earlier infor
scaffolding thethecoupled
stepwisephases scenario of
emergence proposed by Damer
encapsulated andof
systems
Deamer [27].polymers
functional Functions emerge earlier
described as selective
in thepressures
coupled phasespresent hurdles
scenario for populations
proposed by Damerofand protocells
Deamer
undergoing chemical
[27]. Functions evolution.
emerge The hurdles
as selective can bepresent
pressures surmountedhurdles by the
for stepwise
populationsaccumulation of
of protocells
functions
undergoingsuchchemical
as membrane stabilization;
evolution. The hurdles osmoticcan be equilibration
surmounted and bytransport
the stepwiseby transmembrane
accumulation of
pores; primitive
functions such as metabolism
membraneutilizing nutrients
stabilization; and equilibration
osmotic energy sources available
and transportin by
thetransmembrane
environment;
feedback controls;metabolism
pores; primitive and catalytic cycles enabling
utilizing nutrientsreplication
and energyofsources polymers. For Darwinian
available selection
in the environment;
tofeedback
begin to controls;
operate, and simple self-assembly
catalytic must bereplication
cycles enabling supplemented and ultimately
of polymers. replacedselection
For Darwinian by activeto
processes
begin to encoded in informational
operate, simple self-assembly polymers.
must beThe RNA-World and
supplemented hypothesis
ultimately[39,40] suggests
replaced that
by active
transfer of proto-genomic
processes sequence information
encoded in informational polymers.could be first expressed
The RNA-World by simple
hypothesis oligonucleotide
[39,40] suggests that
templating
transfer of[41] then later through
proto-genomic sequence theinformation
combinatorial selection
could of expressed
be first a pool of functional
by simpleribozymes [42]
oligonucleotide
some of which
templating arethen
[41] capable
later of RNA-catalyzed
through template-driven
the combinatorial selectionsynthesis
of a poolof ofother RNA ribozymes
functional sequences by [42]
active
someribozymes
of which are [43,44]. These
capable laboratory teststemplate-driven
of RNA-catalyzed of RNA World concepts synthesisrequire
of othercycling, interactionby
RNA sequences
active ribozymes [43,44]. These laboratory tests of RNA World concepts require cycling, interaction
 and combinatorial selection of large numbers of polymers encapsulated in glassware. A natural
kinetic trap of the kind described above may have supported some version of these powerful
laboratory demonstrations of molecular evolution and brought an RNA World, or perhaps more
likely, an RNA-Protein World, into existence.
Life 2016, 6, 21 8 of 14
7. A Gel Phase as Candidate Progenote
It is a common observation that terrestrial microbial life in the form of mats is metabolically
and combinatorial selection of large numbers of polymers encapsulated in glassware. A natural
most active in a moist, gradually dehydrating state following a short term hydration event such as
kinetic trap of the kind described above may have supported some version of these powerful
rain fall [1]. This property suggests a link with an earlier form which can only occur in fluctuating
laboratory demonstrations of molecular evolution and brought an RNA World, or perhaps more
pools: a hydrogel that emerges naturally when sufficiently large populations of stable protocells
likely, an RNA-Protein World, into existence.
crowd together next to mineral surfaces as the pool water level drops. Figure 7, center-inset
7. illustrates
A Gel Phase lipid vesicles (~50%
as Candidate water by weight), which aggregate and form such a “gel phase”
Progenote
during dehydration. In a hydrothermal pool such gel structures would contain concentrated organic
It is a and
solutes common mineralobservation
grains along that terrestrial
with systems microbial life in thesynthesized
of randomly form of mats is metabolically
functional and inert
most active in a moist, gradually dehydrating state following a
polymers. A self-assembled gel aggregate can act as a scaffold for the emergence of short term hydration event
key such as
biological
rain fall [1]. as
functions This propertybysuggests
suggested Tevors anda link with an
Pollack earlier
[45], form which
and possesses can onlysuggesting
properties occur in fluctuating
evolutionary
pools: a hydrogel that emerges naturally when sufficiently large populations
continuity [46] with later microbial communities. A gel aggregate also represents the first example of stable protocells crowd of
together
niche construction described by Odling-Smee [47] in which a micro-environment is modifiedlipid
next to mineral surfaces as the pool water level drops. Figure 7, center-inset illustrates for the
vesicles (~50% water by weight), which aggregate and form
benefit of its members in a primordial example of endosymbiosis [48–50]. such a “gel phase” during dehydration.
In a hydrothermal
A gradient pool such gel
of selective structures
pressures would
would becontain
required concentrated
to give rise organic solutes that
to adaptations and mineral
enable the
grains along with systems of randomly synthesized functional and inert
transition from a non-living gel phase to a primitive microbial population. Examples of such polymers. A self-assembled
gelselective
aggregate can act asare
pressures a scaffold
exposure fortothe emergence of gradients
environmental key biological
suchfunctions as suggestednutrient
as pH, temperature, by Tevorsand
and Pollack [45], and possesses properties suggesting evolutionary
salt concentrations. Stromatolite fossils observed today were presumably produced by continuity [46] with later microbial
complex
communities. A gel aggregate
microbial communities with also represents
a number the first
of finely tunedexample of niche
adaptations construction
(Figure 8, right).described by
These include
Odling-Smee [47] in which a micro-environment is modified for
mat formation using an excreted polymeric substance, specialization of community members the benefit of its members in a
primordial example of endosymbiosis [48–50].
carrying out photosynthesis, chemosynthesis and other metabolic functions, cementation of mineral
A gradient
sediments, andoftolerance
selectivefor pressures
fluctuatingwould be required
hydration to give[51,52].
and salinity rise toItadaptations
follows thatthat enable
the microbial
thepopulations
transition from a non-living gel phase to a primitive microbial population.
forming stromatolites able to tolerate Archaean marine shorelines had advanced Examples of suchfar
selective pressures are exposure
along the evolutionary gradient. to environmental gradients such as pH, temperature, nutrient and
salt concentrations.
A predecessorStromatolite
would therefore fossils possess
observed a today
subset were
of thesepresumably
adaptations. produced by complex
The microbial mats
microbial communities with a number of finely tuned adaptations (Figure
observed at Gallery Hill (Figure 8, center) are suggestive of intermediate form between 8, right). These include mat
an earlier
formation
ancestorusingand an excretedstromatolite.
a marine polymeric substance,
However,specialization
it should beofnoted community memberscommunities
that microbial carrying out as
photosynthesis, chemosynthesis and other metabolic functions, cementation
represented by living examples today as well as in the earliest fossil record arose long after LUCA,of mineral sediments, and
tolerance for fluctuating hydration and salinity [51,52]. It follows that
the last universal common ancestor. The path from an early form of life to autonomous cellular the microbial populations
forming stromatolites
structures defined asable LUCA to is
tolerate Archaean
not expected marine
to be shorelines
tree-like, but will had moreadvanced far along
likely resemble the
the shrub
evolutionary gradient.
metaphor of Doolittle [53].

Figure 8. Desert microbial mats (Center); suggestive of an intermediate form between marine
Figure 8. Desert microbial mats (Center); suggestive of an intermediate form between marine
stromatolites (Right); and an ancestral form of all microbial communities (Left).
stromatolites (Right); and an ancestral form of all microbial communities (Left).

A predecessor would therefore possess a subset of these adaptations. The microbial mats observed
at Gallery Hill (Figure 8, center) are suggestive of intermediate form between an earlier ancestor and a
marine stromatolite. However, it should be noted that microbial communities as represented by living
examples today as well as in the earliest fossil record arose long after LUCA, the last universal common
Life 2016, 6, 21 9 of 14

ancestor. The path from an early form of life to autonomous cellular structures defined as LUCA is not
expected to be tree-like, but will more likely resemble the shrub metaphor of Doolittle [53].
A gel phase (Figure 8, left) can retain moisture and concentrate nutrients, providing for the
emergence, testing and sharing of polymer functions such as membrane stabilization and pores
required for solute transport in and out of protocells. With nutrient solute transport come opportunities
to support primitive metabolic processes within protocells. A gel is also an ideal venue for protocell
competition [54,55]. Furthermore, a gel would tend to retain the components of disrupted protocells,
thereby selecting for surviving protocells that can absorb these in a primitive form of heterotrophy.
A gel would also help to maintain a collective transmembrane solute balance, thereby protecting
all its member protocells against osmotic stress. Lastly, a gel would be subject to group selection in
which a metabolic product or functional innovation from one protocell would diffuse throughout the
gel, benefiting the entire population suggesting an early pattern resembling horizontal gene transfer,
central to microbial evolution today.
I propose that the protocell gel phase is a candidate progenote as described by Woese and Fox [56,57],
in which its member protocells are engaged in the collective process of evolving the relationship between
genotype and phenotype. As individual protocells gradually accumulate and internalize proto-genomic
functions, they will develop more autonomous phenotypic expression. A new evolutionary phase of
the progenote will arise when member protocells can enzymatically replicate encapsulated genomic
and functional polymers and pass them on to daughter cells without depending on dehydration
synthesis. The resulting speciation and specialization of increasingly independent protocells will lead
to communities becoming robust to steeper gradients of environmental pressures. Some individual
protocells will eventually become advanced enough to survive and reproduce independent of their
source community, passing an important milestone on the continuum to life. Wider distribution and
direct competition between free-living cells will drive this early life along the long winding road
to LUCA.

8. The Adaptive Radiation of the Progenote

A protocell gel progenote possesses one more property that supports its central role in the origin
of life: mobility. As soon as the components cycling in a hydrothermal “origin pool” (Figure 9,
upper) reach a steady state incorporating a kinetic trap, they will give rise to a robust, growing
and adaptable progenote. This has the potential to be distributed (Figure 9, center left) as a raft,
transported by gravity downstream in its hydrated phase, or as a film detached by wind from mineral
surfaces and dispersed in the dry phase. Distribution is essential because the initial sustaining
‘Goldilocks’ conditions at the origin pool may not persist. When they arrive at new aqueous venues
dispersed throughout the geological context of an Archaean volcanic island (Figure 9, lower), progenote
aggregates will continue to undergo adaptive radiation by responding to environmental pressures and
accumulating innovations through individual and group selection. Innovations will be continuously
mixed and shared by combining functions from different gel aggregates. The lower figure insets
illustrate some informed guesses as to the effect of various geological venues in the downhill journey
of the progenote as it evolves toward the living microbial communities which ultimately build the
stromatolites so abundant in the earliest fossil record. This unified view of chemical and geological
contexts completes a high level treatment of the terrestrial origin of life hypothesis, offered as a model to
the astrobiology community.
Life 2016, 6, 21 10 of 14
Life 2016, 6, 21 10 of 14

Figure 9. Overview of the unified chemical (Upper) and geological (Lower) contexts and their
Figure 9. Overview of the unified chemical (Upper) and geological (Lower) contexts and their interface
interface through protocell gel progenote distribution (Center) comprises the model of the terrestrial
through protocell gel progenote distribution (Center) comprises the model of the terrestrial origin of
origin of life hypothesis.
life hypothesis.

9. Summary of Novel Features and Testable Predictions of the Model

The novel features of the model are summarized below, each carrying predictions that can be
subject to testing by experimentalists:
Life 2016, 6, 21 11 of 14

9. Summary of Novel Features and Testable Predictions of the Model

The novel features of the model are summarized below, each carrying predictions that can be
subject to testing by experimentalists:

i A kinetic trap cycling polymers through coupled phases of hydration and dehydration will
produce large numbers of random molecular systems synthesized between dehydrated lipid
lamellae (Figure 9, upper left), which become encapsulated within large numbers of lipid
compartments (protocells).
ii Combinatorial selection of encapsulated functional polymers will be observed within this kinetic
trap. The initial selection criterion will be the ability of encapsulated polymers to enhance
the stability of their membranous compartments, which will be tested in the hydrous phase
(Figure 9, upper right).
iii During dehydration, stable protocells will crowd together with concentrated solutes forming
a third, gel phase (Figure 9, center) which provides a protective environment. Interaction of
protocells within the gel will enable early forms of metabolism, competition, and sharing of
functions and products across the gel.
iv These three phases will provide continuous resources and subject molecular systems to a variety
of selective pressures, driving the system to surmount hurdles to achieve stepwise molecular
evolution of new functions.
v Pure self assembly and random synthesis will enable the initial stages of the model, but
eventually, active functions expressed through sets of robust, heritable proto-genomic
instructions will enable Darwinian evolution to take hold.
vi Degradation rates of synthesized polymers will set upper bounds on the permitted dwell
time within each phase suggesting the necessity of reliable, repetitive fluid refilling typical of
hydrothermal fields. Expressing a pattern emerging later as the life cycle, degraded polymers
and other inert byproducts must be periodically reused or expelled and functional systems
continually re-synthesized through proto-genomic blueprints drawing from solute sources
(Figure 9, upper right).
vii A candidate protocell gel progenote capable of growth and evolutionary adaptation will emerge
and become robust to distribution to a variety of watery venues in a plausible Archaean volcanic
landscape. Extensive laboratory growth, testing, and analysis of such progenotes will provide
insight to possible pathways to the first microbial communities and viable free-living cells.

10. Conclusions
A field trip in Western Australia to venues ranging from living marine stromatolites to inland
Archaean stromatolite fossil localities tested the coupled phases scenario for an origin of life. A novel
terrestrial origin of life hypothesis was developed through the unification of chemical and geological
settings. The model is centered upon the insight into a protocell gel progenote, a candidate common
ancestor of microbial communities. It seems inescapable that very soon after the first robust protocells
emerged, they became communal. Primitive protocells floating free in the Archaean environment
would be unlikely to survive, while selection would favor the protective, nutritional and collaborative
advantages of a protocell gel progenote. This progenote is a model for an amphibious, communal
aggregate of protocells that preceded LUCA, a much more highly evolved population of cells able
to independently support their own metabolism and reproduction. The progenote described here
represents a common pool, or roots from which the earliest inhabitants of the tree of life emerged.

Acknowledgments: I would like to acknowledge the assistance of David Deamer, Malcolm Walter,
Martin Van Kranendonk, and Tara Djokic who provided key subject matter expertise in support of this work.
Ryan Norkus is also gratefully acknowledged for his production of graphics for this article.
Resources: A website has been established to support collaboration, testable hypotheses and research results on
the terrestrial origin of life hypothesis at: http://origins.biota.org.
Life 2016, 6, 21 12 of 14

Conflicts of Interest: The author declares no conflict of interest.

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