Audio recording of this lecture

Previous lecture

Reading for this lecture:

• Rasmussen, B. 2000 Filamentous microfossils in a 3,235-million-year-old volcanogenic massive sulphide deposit. Nature 405:676-679

REQUIRED READING FOR THIS LECTURE:

• Woese CR 2000 Interpreting the universal phylogenetic tree. PNAS 97:8392

Early evolution

The 'last common ancestor'

Woese CR 2000 Interpreting the universal phylogenetic tree. PNAS 97:8392

Features common to all three 'Domains' were inhereted from the last common ancestor, including:

• DNA, the Universal code, and most genes
• transcription and RNA polymerase
• RNAs of all types (rRNA, tRNAs, etc)
• translation and the translational apparatus
• most proteins, and the metabolic pathways they generate
• membrane and cellular structure

In other words - pretty much everything! Most biochemical evolution must have predated the last common ancestor. The phenotype of the last common ancestor was probably thermophilic and autotrophic (sulfur &/or H2 metabolism), because all deep/primative branches are thermophilic and at least facultatively autotrophic. The last common ancestor, if it existed as a single organism, was probably alot like Thermococcus celer is today. Most of evolution since has been peripheral.

However, the last common ancestor may not really have been a single organism, but rather a population of organisms (like 'mitochondrial Eve') or a 'communal' organism. There is theoretical reason to believe that lateral gene transfer may have been pervasive prior to the last common ancestry, and the 3-way split between Bacteria, Archaea, and Eukarya may have been lifes first real experiment in geneological diversification.

Before the Last Common Ancestor

Most of evolution (at least biochemical evolution) predates the last common ancestor.

The "progenotes" in the figure above refer to organisms in which genotype & phenotype had yet to be tightly linked, i.e. in which translation was inaccurate or not well-developed. The last common ancestor, and even the last common ancestors of each of the 3 Domains, may have been progenotes.

The Earth's formative meteor/comet bombardment ended ca. 3.8Bya. Prokaryotic fossils from 3.6 Bya and cyanobacterial-like fossils 3.2Bya have been found, so life originated & most of evolution occurred in a fraction of the Earth's history. Some people interpret this as evidence that life originated elsewhere in the solar system (or beyond) and came to Earth on meteorites. I'll let you judge the idea of "Panspermia" for yourself. Regardless, there is probably no need for life to have originated elsewhere. As organisms became increasingly complex, the rate of evolution would be expected to slow, and so there was probably plenty of time for life to emerge and develop into complex organisms.

The RNA World

Because:

1. DNA functions only through RNA intermediates, and
2. the protein synthesis machinery is entirely RNA-based,

RNA must (perhaps) predate both DNA and protein, and therefore there must(also perhaps) have been some form of an "RNA world" before the evolutionary invention of either DNA or protein. (An alternative is that the three macromolecules co-evolved - somehow)

The RNA world hypothesis is plausable because:

1. RNA can serve as genomes (information storage) - e.g. RNA viruses
2. RNA can serve as biocatalyst - i.e. catalytic RNAs

Known catalytic RNAs:

• group I and II introns - self-splicing
• nuclear splicing snRNAs - splice pre-mRNAs
• hammerhead & hairpins of plant viroids - self-cleaving/ligating
• hepatitus delta virus + & - strand RNA - self-cleaving/ligating
• RNase P - pre-tRNA 5' endonuclease
• Varkud mitochondrial RNA in Neurospora - self cleaving
• the ribosome - the lsu-rRNA is the peptidyl transferase

What could the RNA world have been like?

Two extreme scenarios are the "simple RNA world" and the "complex RNA world" scenarios.

Simple RNA world view

Single self-replicating RNA - a 'one molecule' RNA world, coding & function in same molecule, or perhaps an RNA genome encoding an RNA replicase (separation of coding & function)

or

In this scenario, proteins took over right away, so that only the genome, replicase, & translational apparatus were ever RNA:

The replacement of the RNA genome with more chemically stable DNA yeilds the modern system:

Complex RNA World view

In this scenario, an entire RNA-based metabolism, with all of the current metabolic pathways & functions catalyzed by RNAs rather than proteins. These RNAs were then replaced one-at-a-time by more efficient protein enzymes.

Proponents of this view consider nucleotide cofactors (e.g. ATP, GTP, NAD, FMN, etc) to be the remnants of the original RNA enzymes. In this view, the RNA organisms would be cellular organisms (unlike the previous hypothesis).

Problems with the RNA World hypothesis

1. Where do the activated nucelotides come from for RNA polymerization?
2. RNA is far too complex isomerically - each nonfunctional isomer is an inhibitor!
3. RNA is very unstable, especially sensitive to metal ions, high temp & pH

The avoid these problems, some have suggested that early precursors of RNA may have contained only purines, & a non-ribose backbone (e.g. glycerol).

The emergence of life

The Oparin Ocean hypothesis : 'Primordial Soup'

The RNA World hypothesis deals only with the 'information' of life - the software. Metabolisn, the hardware of life, is an entirely separate issue. The first realistic suggestion about how metabolism could have originated was the Oparin Ocean hypothesis. The idea was that chemical reactions & meteoric influx concentrated organics in the ocean, creating an ocean (or at least tidals pools) of nutrient-rich organic 'soup'. Spontaneous and random polymerizations created self-replicating molecules that eventually evolved into metabolism and life.

There were two sources of organic material in the early Earth: in situ synthesis and meteoric influx.

In situ chemical synthesis from primal atmospheric components

Irradiation of methane/ammonia/water/hydrogen/cyanide/ and other possible atmospheric mixtures yields lots of organic compounds, including adenine, amino acids, etc. This is the classic Miller experiment:

Meteoric influx

Many comets, asteroids, etc are rich in carbon & organics. In fact, comets are similar in composition to life!

Metabolism was thought to be the result of sequential exhaustion of substrates & utilization of precursors instead, i.e. when X is exhausted from the primordial soup, Y was used by converting it to X

Y --> X

then when Y was exhausted, Z was used by converting it to Y, then to X:

Z --> Y -->X

over-&-over, generating the metabolic pathways we know today.

Problems with the Primordial soup:

1. An entire ocean of primordial soup?
2. Activated precursors are unstable, especially at high temperatures, & so wouldn't likely have accumulated.
3. Too many isomers of everything. The useful compounds end up at trivial concentrations, and overwhelmed by inhibitory isomers.
4. Polymerization is strongly disfavored in aqueous solution (55M H2O), and so accumulation of polymers is unlikely.

Not a great theory, but it was the best available until ....

Wäctershäuser's hypothesis of surface metabolism

The basis behind this hypothesis is that life originated in the organic scum on mineral surfaces, not in solution! The hypothesis comes with a very elaborate set of chemical features that solve most of the problems with the Oparin Ocean hypothesis:

1. Surfaces can concentrate trivial concentrations of solution organics to very high local concebntrations by absorbtion
2. polymerization is favored on surfaces (little available water)
3. surface chemistry is stereospecific
4. activated precursors aren't required to drive reactions

Pyrite and similar minerals binds anions, e.g. organophosphates, but let them diffuse around in 2-D. This explains the observation that the most fundamental metabolic pathways use phospho-intermediates - the other pathways were probably invented later.

These surface metabolic reactions may have been catalyzed only by cofactors before the invention of enzymes (protein or RNA); i.e. metabolism predates both genomes & biocatalysts!

Cellularization, in this scenario, is thought to have occurred when lipid by-products of metabolism later enclosed the surface reaction centers, creating a kind of simple 'cytoplasm', followed by the escape of these surface organisms from their mineral substrate.

The RNA World, then may have originated within this proto-biotic metabolism.

Microbial fossils from long ago

"Fossils" are the traces of previous life. Fossils can range from the actual remains of an organism (e.g. an amberized insect) to scant traces of unusual isotope ratios (e.g. the Greenland banded iron formations). The further back in time you wish to examine, the harder it gets to obtain and interpret these fossils. Samples are harder to get because of plate tectonics - really old rocks are actually quite rare, since most have been heavily or completely transformed by passage into the mantle. Before about the Cambrian explosion, when all or nearly all of the animal phyla appeared a short 540 Mya, only microbial fossils exist. In later formations, these are common, but very old fossils are few and far between. Most of these have been found in Australia and Greenland, where the oldest untransformed deposits reside. Here we'll talk about evidence for microbial life early in Earth's history.

In attempt to try to bring these time scales into focus, here is a time scale of life (very approximate) compared to the length of this classroom (~45ft):

Notice that life seems to have originated and evolved into recognizable forms very quickly, within about 200 million years. After this, for the next 3 billion years, 80% of Earths history, life was entirely microbial. During this time the concentration of oxygen in the atmosphere was not high enough to be breathable. Remember this when people dismiss other planets for being "uninhabitable", or say that even if there could be life there, it would "only" be microscopic. This was so for this planet over most of its history. And, of course, microbes still rule the ecosystems; in the words of Stephen J Gould, a very famous animal evolutionary biologist, "This is the Age of Bacteria - as it ever has been and always will be."

It is clear is that life on Earth has existed for at least 3.5 Bya, and probably more, although not before about 3.8 Bya because the large impacts that took place before then that would have vaporized the oceans and, in some cases, a fair amount of the crust of the planet. Before 3.8 Bya, the planet may have gone through alternating cycles of sterilizing heat from impacts, and crushing cold with completely frozen oceans.

In the last 3.8 billion years, life has survived many trials in the history of the planet, some of it's own making. Large impacts are now rare, and not of 'sterilizing' intensity, but do occur. The most famous is the K-T impact that probably played a role in the extinction of dinosaurs about 0.65 Bya, but previous impacts were much larger, such as the Permian impact 240 MYA that extinguished 95% of all macroscopic species.

The temperature of the planet has also changed, and seems to be less stable than previously thought. It seems likely that Earth has looked a lot like Europa, with completely frozen-over oceans, perhaps several times over the last 4 billion years, the last time about 0.6 Bya, just before the Cambrian explosion. The planet is in a delicate balance between the energy provided by the sun and how much of this is retained via greenhouse gases. Today, the major greenhouse gas is carbon dioxide, produced by photosynthesis, without which the Earth would freeze. Prior to about 2 Bya, however, methane was probably the major greenhouse gas, and this methane was apparently also the product of life (methanogenesis).

Another issue is atmospheric oxygen. Although we think of oxygen as an essential for life, high concentrations of oxygen are a recent feature of Earth's atmosphere. Oxygen concentrations before about 2.8 Bya are immeasurably small, less than 0.01% of the current level. Oxygen produced by photosynthesis was absorbed by the planet before 2 Bya, when the 'buffering' capacity was exhausted and the oxygen concentration in the air increased dramatically to as much as 2% - 10% of the current level. This has been described as the greatest climactic change ever to have occurred on Earth. Although animals need oxygen, it is not an innocuous compound - imagine if the Earth's atmosphere suddenly rose to 2% chlorine or ammonia! Over most of the last 1 billion years, the oxygen concentration has risen about 10-fold to it's current level, most of this change occurring at about the time of the Cambrian explosion.

Rasmussen, B. 2000 Filamentous microfossils in a 3,235-million-year-old volcanogenic massive sulphide deposit. Nature 405:676-679

This paper describes fossil filamentous microbes from the geological remains of a hydrothermal vent that existed over 3.2 Bya and about 1 kilometeer below the surface of the Archaean ocean. These are not the oldest microbial fosssils known - there are a few from between 3.5 and 3.6 Bya - but these are of more typical rods and cocci from shallow sediment deposits, and are much less visually striking and with less of their 'environmental context' clear. There is some reason to doubt the origin of these earlier fossils.

This paper contains a great deal of geological and geophysical description that is difficult to decipher - in other words, I don't understand it. Suffice it to say that this site has been described in great detail by previous geologosts and there is a clear picture of the environment that the organisms that became these fossils lived in. This was a deep-sea hydrothermal vent system, much like those that exist today, with hot (ca. 300C) mineral-laden hydrothermal fluid rising through the fractured rock to the floor of the ocean. As this water neared the surface, it mixed with cold ocean water in the upper levels of rock and the minerals (mostly silicates and sulfides) precipitated to form the 'massive sulfide deposit'. There were probably parts of this deposit that reached the surface of the ocean floor, to emerge as chimneys and black smokers. (Of course, there were no vent worms, etc, as there are in modern deep-sea vents - animals of any complexity being more than 2.5 billion years in the future.) This vent, like many modern vents, contains bitumen deposits, tar, and oil. Although the authors don't point this out, these are all signs of life, since they are produced from the transformation of organic remains. The fossils are found on the surface of what aappear to have been cracks, fissures, and open spaces is the vocanic rock. Probably the water flowing through these open spaces was hydrothermal fluid mixed with the surrounding ocean water at less than 100C, providing a rich supply of geothermal energy and even organic material (oil).

Fig 3. Photomicrographs of filaments from the Sulfur Springs VMS deposit. Scale bar, 10um. A-F, striaght, sinuous and curved morphologies, some densely intertwined. g, Filaments parallel to the concentric layering. h, Filaments oriented sub-perpendicular to banding.

The filaments are clearly the remains of microbial life. They are nearly, but not quite, uniform in diameter and length, and are oriented preferentially rather than randomly. The filaments cross crystal boundries in the rock, and, perhaps most convincingly, they are not branched. The organisms seem to have first nucleated the precipitation of silica around themselves, become 'petrified', and then later the silica was replaced by pyrite, and so the fossils are threads of pyrite in the original shape of the organisms. The morphology and habitat of the organisms is strikingly similar to the filamentous sulfur-oxidizing Bacteria that currently inhabit hydrothermal vents, although because there was no oxygen they would most likely have had some other metabolism.

Questions for thought

• What do you think of the RNA World hypothesis? What are the alternatives? How could you go about testing this?
  
  
• Presuming the RNA World hypothesis to be correct, what do you think about the simple vs complex RNA World scenarios? How would you go about testing your hypothesis?
  
  
• Make a list of all of the RNA-encoding genes you know about in Bacteria (say, E. coli). Of course you'd start with rRNAs and tRNA, but hat other non-protein-encoding RNA genes are there? For any of these, how would you determine whether it is an ancient RNA and so perhaps a relic of the RNA world, or a recently invented RNA?
  
  
• The last "sterilizing" impacts on Earth occurred about 3.8 Bya, and there is good evidence for the presence of microbial life (fossils) at about 3.6 Bya. Do you see this is evidence that life may have originated elsewhere? Why or why not?
  
  
• Space aliens visit the planet Earth in search of intelligent life. What are the chances for them finding it? What are the chances of them finding macroscopic life? What are the chances of them finding a 'breathable' atmosphere?
  
  
• As a microbiologist, you are willing to accept the geologists description of the history of a rock sample from the isotope data. However, microbial fossils are usually identified on the basis of morphology - what they look like, despite the fact that morphology can be severely distorted during fossilization and in the geological transformations of the rock. What, then, would you look for in a potential microbial fossil to convince yourself that it really represents the remains of living things? What kinds of things would convince you that it might not be a real fossil? What kind of rocks would you examine in your search for microbial fossils?