Fall Semester 2022 Archean Fossils & Life's Origins
Banded iron formation
Key Points:
•Whatever definition you use, life requires homeostasis, metabolism, and reproduction.
•LUCA, the last universal common ancestor, was a chemosynthetic autotroph that lived in a hot anoxic environment.
•Life seems to have arisen immediately after end of the Late Heavy Bombardment ~ 3.8 Ga.
•Photosynthesis fundamentally changed Earth environments.
•the earliest microfossils are ~3.77 Ga tubular microfossils from a hydrothermal environment.
•Complex eukaryotic cells seem to have emerged between 2.7 and 2.2 Ga.
"By firm immutable immortal laws Impress'd on Nature by the GREAT FIRST CAUSE,
Say, MUSE! how rose from elemental strife
Organic forms, and kindled into life;
How Love and Sympathy with potent charm
Warm the cold heart, the lifted hand disarm;
Allure with pleasures, and alarm with pains,
And bind Society in golden chains.
(Erasmus Darwin, 1803. 'Production of Life', The Temple of Nature; or, The Origin of Society: A Poem, with Philosophical Notes)
Definitions of Life
There is no single standard definition of life. Different definitions tend to reflect the priorities of their authors. One that Merck is fond of:
"Living things are systems that tend to respond to changes in their environment, and inside themselves, in such a way as to promote their own continuation."
Metabolism: Chemical systems for converting external chemicals and the energy of their bonds into life-system components and energy.
Reproduction: The ability to produce new living units.
Isua metaconglomerates
Environmental conditions at time of life origins.
Life is thought to have arisen (for the last time?) shortly after the end of the Late Heavy Bombardment, between 3.9 and 3.8 Ga. The environment in which this happened differed markedly from what we know today.
Atmospheric composition.
Early atmosphere was result of volcanic outgassing of volatiles.
Highly reducing atmosphere. Rich in CO2.
Some free oxygen derived from photochemical dissociation by UV in upper atmosphere.
2 H2O + uv --> 2 H2 +O2
This would have generated enough oxygen quickly to oxidize chemical building blocks of life near ocean surface.
Oceanic conditions. Initially strongly acidic, precluding precipitation of carbonate rocks. This was because atmospheric CO2, dissolved in sea water, forming carbonic acid.
Land conditions: Here is one spot of optimism. By 3.8 Ga, we have continental conglomerates in Isua, Greenland (right), showing that streams of water were flowing on surface.
Requirements for life:
Energy source: For most that's the Sun, but some deep-sea ecosystems depend on chemical energy from hydrothermal vents.
Proteins: Polymers of amino acids. Structural elements and catalysts.
Nucleic acids: Regulate synthesis of proteins in proper cells, acting both as information templates and enzymes.
Semipermeable membranes: In which to package and isolate the components of life.
Proteins: These end up being surprisingly easy to form under natural circumstances.
The simple experiment of Miller and Urey, 1959, in a classic experiment, showed that amino acids are readily synthesized from presumed primordial components of Earth atmosphere. Indeed, the Murcheson meteorite (a CM carbonaceous chondrite) has been shown to contain numerous amino acids (some of types employed in protein synthesis and others not.) (Matson, 2010)
Fox et al., 1959 saw that concentrated solutions of amino acids form proteinoids (short polymers of 18 common amino acids) if heated to 140 deg. C. When cooled, proteinoids form suspiciously cell-like spheres. Fox ultimate found "wild" proteinoids in pools associated with Hawaiian volcanoes. It's not a huge stretch to speculate on a similar origin of proper proteins.
Nucleic acids: Here we have a more complex problem, as the nucleotides of which they are composed are more complex than amino acids, and coaxing them to polymerize is more difficult. Research has focused on the identification of non-living substrates that could serve as a polymerization template:
A. G. Cairns-Smith observed that RNA nucleotides can bind to the edges of clay minerals like smectite to form RNA-like polymers. (For an overview, see Genetic Takeover: And the Mineral Origins of Life).
RNA World? - Altman et al., 1986 demonstrated that RNA is capable of acting not only as a template for protein synthesis, but, in limited ways, as a biochemical catalyst. (Particularly interacting with phospholipids like those occurring in cell membranes). Sidney Altman went on to propose an early stage in the origin of life, called RNA World. in which simple "biochemical" processes were carried out entirely by RNA. In this scenario, double-strand DNA is derived from RNA at a later time. Recently, however, Gavette et al., 2016 observed that intermediate forms of nucleic acid that would have figured in this transition are unstable, making the RNA -> DNA transition problematic.
Only later did nucleic acids and proteins join forces.
PNAs: Because ribose, the sugar component of the RNA polymer is difficult to synthesize from a Miller and Urey-style primordial soup, but amino acids are easy, some researchers have proposed that the first gene-bearing molecules were "peptide-nucleic acids" that used amino acids instead of ribose as the polymerizing "backbone" of nucleic acids. Not crazy: PNAs have been synthesized, and recently identified in cyanobacteria by Banack et al., 2012. And yet, the substitution to RNA seems to have happened very early.
Membranes:
In living cells, these are made of highly impermeable phospholipid bilayers. (Indeed, protein channels regulate transport across the membrane.) The lab of Jack Szostak of Harvard has shown that fatty acids that would have been common in the Archean oceans can form vesicles that are permeable to nucleotide monomers and amino acids, but not to polymers of these. (See Szostak, 2012.)
Osmotic pressure from nucleic acid polymers causes larger vesicles to "steal" fatty acids from smaller ones that they encounter. Mechanical forces cause larger vesicles to fission.
The result, the beginning of natural selection, in which fatty acid vesicles that grow faster dominate.
For a clever review of Jack Szostak's ideas, link to this video.
Energy source: The crucial fact in the foregoing is that the both cell membranes and proteins seem to have originated in environments that are at least intermittently hot.
Synergies: The foregoing research suggests that the major components of life were able to self-assemble independently of one another in the primordial soup, Don't assume from this that the components of life necessarily evolved independently. Black et al., 2013 show that the simple fatty acid decanoic acid binds preferentially to the four RNA nucleotides found in RNA (adenine, guanine, cytosine, and uracil). Moreover, in their bound state, the nucleotides buffer decanoic acid against the disruptive effects of salt water. The result is a natural affinity between fatty acids and RNA nucleotides.
The Ultimate result: Cells in which information encoded in DNA is the template for the synthesis of proteins. The structure of DNA was discovered in 1953, and its role as the physical repository of genes illuminated in the following decades. A brief review of how information encoded as nucleic acid is expressed as proteins goes like this:
DNA at rest in the nucleus is a double helix (spiral staircase) whose corresponding base pairs are connected through weak bonds.
RNA polymerase separates the DNA helices and uses one of them as a template for assembling a single-strand messenger RNA molecule (mRNA).
mRNA passes from the nucleus into the cytoplasm, where it encounters the two components of the ribosome.
The ribosome grabs passing transfer RNA (tRNA) molecules. tRNA have nucleotide triplets (codons) exposed at one end. Each nucleotide triplet combination is associated with a specific amino acid, that is bound to the opposite end of the tRNA.
The ribosome matches nucleotide triples on the mRNA to corresponding tRNAs, moving down the mRNA strand. Amino acids connected to adjacent tRNAs bind to form a protein, an amino acid polymer, that forms part of the cell's structure or does work in it.
Current thinking maintains that life probably originated in hydrothermal vents (right). These environments were:
Sheltered from free oxygen, which is toxic
Rich in thermal energy
Interestingly, phylogenetic analyses suggest that among the most primitive organisms are thermophylic prokaryotes known as Archaea. Their special features:
Live only at near-boiling temperatures
Obtain energy from exotic reactions involving materials readily available in minerals, esp sulfur.
Find oxygen to be toxic.
The environment in which these conditions are routinely found is near deep sea hydrothermal vents. For some time the most likely locations for the origin of life. Weiss et al., 2016 have attempted to identify genes conserved across all major domains of life (Archaea and Prokaryota) in order to characterize LUCA's environment and ecology. Their conclusions:
LUCA has genes for energy metabolism through the combination of H2 and CO2 to form methane (CH4). It must have lived in an anoxic environment where hydrogen and carbon dioxide were common.
It was a chemosynthetic autotroph, employing sulfur compounds as an energy source but was unable to feed heterotrophically
It's environment was hot
It possessed the biochemical machinery for the translation of DNA to proteins (thus significantly advanced over hypothetical RNA-world organisms.)
It relied heavily on molecules in its external environment for many metabolic functions that are handled internally by living cells today.
Mojzsis et al., 1996 reported a 3.85 Ga banded-iron formation with biogenically fractionated carbon from Akila island, Greenland. The rocks are considered by Fredo and Whitehouse, 2002 to be a
metavolcanic with its carbon being an abiotic metasomatic product.
Rosing, 1999 reporting 3.7 Ga fractionated carbon in deep sea sediments from Isua, Greenland. This is a mere 100 my after the planet-sterilizing Late Heavy Bombardment. Largely unchallenged.
Brocks et al., 1999 report hopanes in 2.7 Ga rock from West Australia that seemed to clinch the presence of cyanobacteria at that time. More recent work by Rasmussen et al., 2008 has called this into question. They maintain that the oldest unambiguous cyanobacterial body fossils are roughly 2.15 ga.
Body fossils:
Schopf and Barghoorn, 1967 reported the oldest body fossils in the ~ 3.4 Ga Fig Tree Cherts of South Africa.
Schopf, 1993 suggests the Apex Chert (Australia 3.485 Ga) contains "microfossils." Probably bits of organic matter in a hot-springs solution deposit. Brasier et al., 2002 skeptically note that shapes grade from reasonable bacterial shapes to wholly inorganic, suggesting supposed biological forms are just part of shape spectrum.
More recently Wacey et al., 2011 note sulfur-metabolizing microfossils from the 3.4 Ga Strelley Pool Formation of Australia, on morphological and geochemical evidence.
Nutman et al., 2016 have reported on 3.7 Ga stromatolitic bacterial mats, also from Isua, Greenland.
Dodd et al., 2017 reported on microscopic tubularstructures in a marine hydrothermal environment preserved in the 3.77 Ga Nuvvuagittuq belt in Quebec.
Baumgartner et al., 2019 report pyritized stromatolites in the 3.5 Ga Dresser Formation of West Australia. These demonstrably contain organic matter.
For a while, organisms got away with chemosynthesis in vent environments (E.G. LUCA), and heterotrophically absorbing the organic materials that were floating around in the ocean. As these started to get scarce, one group, the cyanobacteria, came up with a new method of autotrophically capturing energy from the environment - Photosynthesis,
6 CO2 + 6 H2O + energy (sunlight)---> C6H12O6+ 6 O2
Note that oxygen is a product.
We can't tell from looking at microscopic fossils which were photosynthesizers, but photosynthesis had momentous consequences for life and Earth environments.
Living cyanobacteria probably provide a good picture of ancient photosynthesizers. Indeed, all other photosynthesizing organisms ultimately rely (directly or indirectly) on cyanobacterial symbionts. Phylogenetic studies of living cyanobacteria suggest a minimum divergence age of roughly 2.8 Ga.
The Gunflint Chert (1.88 Ga - Michigan) represents a well preserved Paleoproterozoic cyanobacterial flora containing forms that can be directly compared with living ecomorphs.
Banded iron formation
Great Oxidation Event: ~ 2.4 Ga oceanic oxygen concentrations begin to rise, indicating that cyanobacteria had become widespread by this point. This accords well with the minimum divergence age of 2.8 Ga.
This oxygen didn't initially escape the oceans. Rather it reacted with soluble ferrous iron (Fe2+), oxidizing it to less soluble ferric iron (Fe3+). This precipitated out, staining ocean sediments that are preserved as
Banded Iron formations (BIFs): Late Archean - Early Proterozoic (~3.0 - 1.8 Ga) Cherts with alternation of gray and rust red bands of hematite (Fe2O3).
The earliest BIFs were limited in extent, forming in localized deep marine environments, but spreading to encompass a wider environmental range.
The disappearance of BIFs around 1.8 ga indicates the saturation of oxygen sinks and signals the beginning of accumulation of high concentrations of oxygen in atmosphere.
Bar River formation - the first red bed
Terrestrial red bed deposits begin to appear at around 2.2 ga. and start to become common around 1.8 ga. This tells us that the oceanic oxygen-sinks had become saturated and free oxygen was now building up in the atmosphere. This stabilized at ~1% at 1.85 Ga and didn't change significantly for a billion years, the "boring billion" of geochemistry. During this time, oxygen sinks on land were gradually filled.
Atmospheric effects: were significant:
Methane: CH4 was originally common in Earth's atmosphere, acting as a powerful greenhouse gas. (It's presence is a partial solution to the "young weak Sun" paradox of Earth environmental history.) Oxygen quickly oxidizes it to CO2 and H2O, weaker greenhouse gasses. As oxygen began to enter Earth systems ~2.4 Ga, global climates cooled, resulting in the Huronian glaciation (2.4 - 2.1 Ga).
Ozone: As it accumulated, free oxygen in upper atmosphere recombined to form ozone layer (O3). Ozone is opaque to ultraviolet light. The appearance of the ozone layer thus allowed life to colonize surface waters and, eventually, land.
Oceanic acidity: Of course, by eating up atmospheric CO2, photosynthesizers caused the acidity of the oceans to diminish, allowing the direct precipitation of carbonate rocks for the first time. Once that was possible, CO2 concentrations fell very rapidly. as carbon became locked up in rock.
Respiration: The earliest organisms used nitrate or sulfur as electron receptors in the synthesis of ATP. As oxygen began to appear in the environment, some organisms evolved the ability to use it instead. To such aerobic critters, oxygen became a necessity rather than a poison. Today anaerobic organisms are restricted to marginal environments.
C6H12O6+ 6 O2 ---> 6 CO2 + 6 H2O + energy
Look familiar? It's just photosynthesis run backwards. In this case, the energy powers cell activities.
Stromatolite in cross-section
The Age of Slime
Stromatolites: Beginning about 3.0 Ga, we begin to see abundant fossil stromatolites - the body fossils of laminated bacterial mats. (Not necessarily photosynthesizing.) The earliest are from the 3.5 Ga Dresser Formation of Australia (Baumgartner et al., 2019) and possibly the 3.7 Ga Isua metasediments (Nutman et al., 2016). These were very common for most of the Proterozoic, but declined during the Neoproterozoic, when, presumably, critters appeared that could eat them.
Stromatolites form when sediment falls onto a thin film of bacteria. The bacteria bind the sediment, and grow up through it. At any moment, only the top layer is alive.
When there was nothing around to eat them, stromatolites were very common. Today, they only live in hypersaline environments that exclude other critters, like Shark Bay, Australia
Cladogram of the domains of life showing Eubacteria (blue), Archaea (green), Eukaryota (red)
Eukaryota and the two domains of life:
Traditionally we distinguish between basic cell types:
Prokaryotic: Small simple cells lacking nuclei and organelles. E.G.: bacteria.
Eukaryotic: Large complex cells with nuclei and organelles, capable of forming multicellular bodies.
Woese and Fox, 1977, recognized that some prokaryotic organisms were distinct from bacteria based on their DNA transcription biochemistry and on molecular systematics. These have come to be known as Archaea. It would be simple to say that Eubacteria, Archaea, and Eukaryota are the three domains of life, but no.
Typically much larger than prokaryotic cells. > 60 microns as opposed to < 20.
DNA contained in nucleus (phylogenetically related to the archaean genome)
Specialized organelles bound by double-layer cell membranes, possessing their own genome. Especially
Chloroplasts: photosynthesizers (derived form cyanobacteria)
Mitochondria: (sing. "Mitochondrion") aerobic respirers (related to Rickettsia, an obligate endocellular parasite that causes typhus.)
Nuclear genome organized into distinct, pairedchromosomes. Capable of reproducing by:
Mitosis: Simple cell division where daughter cells are diploid (Have both chromosomes of each pair.)
Meiosis: Cell divisions resulting in four haploid daughter cells, each with only one of each chromosome set.
Fusion of haploid cells into diploid composite. Sexual reproduction!
Endosymbiosis
Why:
Archaean nuclear genome?
Double membranes on organelles?
Organelles with distinct genomes?
Eukaryotic cells are presumed the result of endosymbiosis, the "colonization" of one type of prokaryotic-grade cell by others. Note that two prokaryotic groups that have been mentioned in passing are taxonomically distinct:
Archaea
Eubacteria (proper bacteria)
Eukaryota is, in a sense, a composite of these, being the result of the "colonization" of an archaean by photosynthesizing cyanobacteria (-> chloroplasts) and/or aerobically respiring eubacteria (-> mitochondria). (Williams et al.)
Eukaryote complexity seems to be largely a response to the challenges of the Great Oxidation Event.
Mitochondrial symbionts enable the cell actually to use the poisonous oxygen metabolically.
The complex genome structure and sophisticated reproductive strategies enable the possessor to to get rid of DNA damaged by oxygen through the reshuffling of genes.
In the rock record:
Oldest biochemical markers characteristic of eukaryotes are steranes ~2.7 Ga. (Brocks et al., 1999) Could possibly have belonged to archaean precursors.
Oldest eukaryotic body fossils: 2.2 Ga of South Africa, reported from a terrestrial paleosol (!) by Retallack et al., 2013.
Oldest definite fungi at 1.0 - 0.9 Ga from Grassy Bay Formation of Canada (Loron et al. 2019.)
