Essay on chemical evolution

Natural drying and re-wetting cycles in a small pool supporting three phases of membranous encapsulation. Hydrated phase top , inset: protocells containing DNA budding out of a dried mixture of DNA and phospholipid, stained with acridine orange. Dehydrated phase bottom , inset: freeze fracture image of anhydrous lipid lamellae of phosphatidylcholine. Micrographs: David Deamer; Image: adapted from Damer, The progenote, a transitional form which occupies the time frame during the origin of life between inanimate matter and living cellular systems, was first defined by Woese and Fox, ; Woese , While the actual form of the progenote is not specified, it is abstractly described as an entity engaged in the collective process of evolving the relationship between phenotype and genotype and is described more specifically by Arnoldt et al.

Progenotes were not well-defined organisms as such, because they had no individuality and no long-term genetic pedigree. Their genes and component parts could come and go, being swapped in or out with other members of the community via horizontal transfer. But because biochemical innovations produced by any member of the community were available to all, evolution at this time was rapid—probably more rapid than at any time since. Selection acted on whole communities, not on individual progenotes.

Those communities that were better at sharing their biochemical breakthroughs flourished. Out of this cauldron of evolutionary innovation, the universal genetic code and its translational machinery co-evolved in response to the selective pressures favoring efficient sharing and interoperability. We hope to show throughout these essays, that as these member protocells are subject to evolution through selection, they can begin to collectively forge and modify their environment, the temporary aggregate we term the progenote. Over time the progenote itself becomes subject to distribution, evolution, growth and adaptation.

In Part 4 we will illustrate that some of this collective evolution will involve the emergence of a regulated network of chemical reactions as the products of metabolic reactions diffuse throughout the protocell aggregate.

Tracing Chemical Evolution of the Human Body Essays

This regulation will also apply to protocell and progenote membranes. This diagram illustrates the entire scenario from the interplanetary synthesis and delivery of meteoritic inputs to a volcanic landscape step 1 , the accumulation and concentration of organic compounds to support the initial chemistry to create membranous vesicles steps 2 and 3 , the influence of a hydrothermally pulsed pool driving the three cycling coupled phases system to generate populations of protocells and form progenotes step 4.

Next come the pathways progenotes must travel, scaling evolutionary gradients to early living microbial populations through distribution and adaptation across a landscape steps Early life then engages in global colonization of both aqueous fresh water settings on the land and the more extreme intertidal and marine shorelines around landmasses step 7. After a great number of additional evolutionary steps, highly robust microbial communities emerge which are advanced enough to leave fossil traces preserved as stromatolites.

Recent stromatolite discoveries provide evidence of life thriving in hot springs in pools on land as far back as 3. Figure 5.


To discover the origin of evolution we have first sought and identified a physical-chemical process, geological setting and unit of selection able to undergo a primitive form evolution, growth, distribution across a landscape, and adaptation through the scaling of selection gradients. The resulting hot spring hypothesis for an origin of life provides an experimentally testable instantiation of this process as well as the unit of selection: a progenote self-assembled from aggregates of protocells.

These protocells are lipid encapsulated systems of interacting polymers cycling through three coupled phases in a periodically filling and drying hot spring pool. The first few steps of this hypothesis have passed empirical testing in the laboratory and in volcanic hydrothermal field analogs of the early Earth Deamer et al. We will next address the proposal that at its origin and throughout its history, life on Earth has been primarily a project of niche construction suffused by a collaborative, networked sharing of resources driven by cycling energy sources.

In Part 1 we took up the question of the origin of evolution , suggesting the underpinnings of the process described so succinctly by Charles Darwin in his book Origins of Species We identified the need for a kinetic trap operating on a self-assembled unit of selection: a population of protocells which undergo three phase changes, one of which temporarily forms a gel aggregate, the progenote. We then introduced a plausible pathway to the arising of the progenote through cycles of selection in hot spring pools on the early Earth.

We put it all together by depicting a journey across a volcanic landscape which large populations of protocells and their progenote collectives might have taken to cross the evolutionary chasm to the first dividing, cellular life. We concluded by suggesting that life on Earth, from its origins and throughout its history, was primarily a process of niche construction paired with emergent collaborative networks. In part 2 we will take up the task of convincing you that it is possible for the processes and structures of biology to arise de novo.

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In other words, that the scenario we are proposing can write the programs of the chemical operating system of life, without a programmer. Figure 6. Charles Darwin and his much-cited letter to J. In Part 1 we described how hot spring pools possess the chemical and thermodynamic properties which support the chemistry that can lead to life. Perhaps this should not surprise us as it was the father of evolutionary biology himself, Charles Darwin, who penned a remarkably similar and prescient vision in a letter to his friend J.

Hooker Darwin, :. If we take his sentence apart with modern understanding, we agree that a little pond would provide molecules the chance to be concentrated enough for reactions to occur and warm enough water provides activation energy for those reactions.

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His light and electricity suggest sources of higher quality energy than simple heat to more precisely drive reactions. His ammonia and phosphoric salts would provide some of the building blocks to link together into a molecule known to Victorian science: proteins. His final statement that a protein compound was chemically formed, ready to undergo still more complex changes is where our part of the story begins.

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These words revealed that Darwin understood that proteins polymer chains composed of monomer building blocks must somehow be synthesized but then re-formed in still more complex configurations. For the past century and a half after Darwin penned this famous phrase, investigators in the origin of life pursued several illuminating but ultimately dead-end chemical scenarios. These scenarios have been situated at many venues including: spark discharge chambers simulating an early Earth atmosphere Miller, , coacervate droplets investigated by Alexander Oparin and Sidney Fox, clay surfaces as an organizing matrix proposed by Cairns-Smith, and the possibility of prebiotically important reactions occurring at energy gradients in deep ocean hydrothermal vents Russell et al.

Until the past decade, a way forward was not visible to most chemists because they are used to working with solutions, that is, wet test tubes of compounds in which reactions occur. The drying down of solutions is anathema to many solution chemists so this was a blind spot for those tackling the problem of the origin of life.

Railway and steamship systems interconnected by telegraph communications networks were only just beginning to inform the future of control theory and automatic computation in the mid-Victorian period.

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Complex chemical networks with their feedback loops would only come to be understood in the 20 th century during the period of the rise of cybernetics, computing and the Internet. As we shall see in a later article in this series, there is a central role such networks can play in the origin of life.

Proteins and other polymers participating in biology such as RNA and DNA all form through condensation reactions in which water must be a leaving group.

Today, enzymes perform the function of removing water to form the ester and peptide bonds of polymers. As described in Part 1, before life there is only one mechanism able to consistently form long enough chains of polymers to express catalytic activity: the removal of water through dehydration. Drying can only occur at the interface between water, mineral surfaces and the atmosphere. On the volcanic land masses of the ancient Earth formed by upwelling magma, distilled fresh water evaporated from the early oceans would have fallen coming into contact with active volcanic systems. Figure 7. Computer graphic of lipid bilayer membranes sandwiching together the building blocks of RNA inset.

If we imagine ourselves bending down to study one of these pools, we will notice that most of the chemical action occurs at its edge where water laps up on mineral surfaces. In ponds, lakes, rivers and the sea shore today, the boundary between water, mineral and air are the richest interfaces for diverse life and this suggests that this boundary may been where life originally began. If you took out a microscope and studied the dried films in that ring, you would see numerous layers sandwiching together smaller molecules from the bathtub, and you may detect some of your own DNA, RNA or proteins!

If the building blocks of these important biopolymers were trapped there, they would be organized and stitched together as water left through the membranous layers figure 7. Our group at UC Santa Cruz and several others have formed these polymers in the laboratory in this way. More recently we have observed the same phenomenon in natural hot spring analogs for the early Earth.

We can produce RNA-like polymers in lengths of hundreds of chain units, long enough to express functions: either folding to create a tool to do a job such as catalyzing a reaction, or to store and express information permitting more polymers to be assembled from a blueprint. The final step in our scenario occurs when the hot little cycling pool refills with water. Contained within some of them will be some of the polymers randomly assembled within the layers. While Darwin was drafting On the Origin of Species , his contemporary Charles Babbage was designing a new breakthrough in Victorian technology: automatic mechanical computation.

The discovery of the structure of DNA suggested parallels to the punched paper tapes and cards of early electronic computers. But how does the formation and combinatorial selection of polymers lead to a system in which life, a sort of program run through chemistry, can write, run, test and rewrite itself all without a programmer?

From the perspective of computer science, a living cell resembles an elaborate chemical computer, but can a chemical computer emerge spontaneously on a sterile yet habitable planet like the early Earth? The answer is obviously yes, because life did begin, but the process by which this occurred remains a fundamental problem in biology. We will argue that by analogy to the development of computers, the hardware of the first, or indeed any form of life, is operated by: organic molecules organized into supramolecular structures capable of capturing free energy available in the environment and using it to drive polymerization and growth.

We propose that the first programs of life spontaneously developed when initially random systems of polymers underwent cycles of selection and amplification to express functions within a system of self-assembling hardware built up from protocells. But you might ask: how it is possible for programs to emerge in the absence of a programmer? Figure 8 illustrates how this can work by referring to early computers that used holes punched in a paper tape as a way to code binary bits. The goal is to generate a program that will turn on a series of light emitting diodes LEDs in a front panel attached to the computer.

At the outset, the tape puncher is linked to a random number generator. The punched tapes are then read one at a time into a simple computer which uses electrical energy to read each tape and then executes the purely random instructions through a primitive processor. This method of programming is inefficient but given enough time it will create a program that switches on all of the LEDs. Figure 8. Metaphor for how a computer program can be developed without a programmer. To apply more chemical terms to the above auto-programming example, 1 a source of energy an electrical current drives a process that punches random holes in a tape.

At some point, one set of holes happens to cause an LED to light up and that set is 2 selected , 3 reproduced and 4 amplified , within a population of continuing random hole punching until another chance sequence of holes causes a second LED to light up, and those sets are ligated together and so on until all of the LEDs are operating.