Later On

A blog written for those whose interests more or less match mine.

Long argument: part 2

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Part 1 is here.

When you look at “reality”—by which I mean the sum total of the universe and everything in it—you quickly encounter emergent phenomena. Emergence is fascinating in itself: the way in which complex systems seem to generate newer, higher-level complexities.

For example, the initial state of the universe/reality was, to our best knowledge, a tiny dot of intensity that immediately started unfolding in time, following rules we later have deduced as “natural laws”, but are really simply descriptions of what stuff (matter/energy, forces, particles) does when interacting with itself through time. And emergence started at the very beginning, creating new things that (so far as I can tell) could not, even in theory, be predicted.

Indeed, Edward Fredkin’s “digital philosophy” posits that the universe/reality is a cellular automaton whose purpose, such as it is, seems to be to work out what happens when the singular event unfolds in space-time. The idea is that some processes are sufficiently complex that by far the fastest way to determine the outcome is simply to let the process run: it’s figuring out the result as fast as theoretically possible.

So what has emerged. First were the forces, which seem to have split, perhaps, from a single force at the beginning. (Gravity is always the outlier—the hypothesis is much stronger for the other forces: electromagnetic, strong, and weak.) Then matter appears—but only hydrogen and helium, no great shakes.

But emergence continues: stars and galaxies form, and from those emerge the other elements and we get chemistry and chemical compounds.

Things roll along like this for quite a while. Every part of the universe seemed to obey one overriding law: follow the path of least effort. This principle seems to hold in all of nature: water flows only downhill, light travels in straight lines and when reflected follows the shortest possible distance. (In quantum electrodynamics, Feynman shows that although many paths exist, they coalesce around the minimal time path. Highly recommended: QED: The Strange Theory of Light and Matter.)

As we later learned, light actually follows the fastest path through space, and if space is curved (by the effects of gravity) light’s path curves as well—but it is still following the overall rule of finding the minimal-effort path.

All of inanimate nature obeys this rule of least effort: physical movement, chemical interactions, and so on.

The next major emergent phenomenon seems to have been life as we know it. So far as we can tell, life originated in deep-sea vents that created tiny chambers for chemical interactions to work through various sequences. As in the case of the pebbles in Part 1 of the argument, everything that was going on affected everything else, so parts of this reaction would mix in with that, and so on—all following the principle of least effort.

New Scientist has an excellent article on how this probably worked, unfortunately locked behind a subscription wall, but fortunately New Scientist is well worth subscribing to. The article contains a link to these 10 steps to the first cells:

We may never be able to prove beyond any doubt how life first evolved. But of the many explanations proposed, one stands out – the idea that life evolved in hydrothermal vents deep under the sea. Not in the superhot black smokers, but more placid affairs known as alkaline hydrothermal vents.

This theory can explain life’s strangest feature, and there is growing evidence to support it.

Earlier this year, for instance, lab experiments confirmed that conditions in some of the numerous pores within the vents can lead to high concentrations of large molecules. This makes the vents an ideal setting for the “RNA world” widely thought to have preceded the first cells.

If life did evolve in alkaline hydrothermal vents, it might have happened something like this:

1. Water percolated down into newly formed rock under the seafloor, where it reacted with minerals such as olivine, producing a warm alkaline fluid rich in hydrogen, sulphides and other chemicals – a process called serpentinisation.

This hot fluid welled up at alkaline hydrothermal vents like those at the Lost City, a vent system discovered near the Mid-Atlantic Ridge in 2000.

2. Unlike today’s seas, the early ocean was acidic and rich in dissolved iron. When upwelling hydrothermal fluids reacted with this primordial seawater, they produced carbonate rocks riddled with tiny pores and a “foam” of iron-sulphur bubbles.

3. Inside the iron-sulphur bubbles, hydrogen reacted with carbon dioxide, forming simple organic molecules such as methane, formate and acetate. Some of these reactions were catalysed by the iron-sulphur minerals. Similar iron-sulphur catalysts are still found at the heart of many proteins today.

4. The electrochemical gradient between the alkaline vent fluid and the acidic seawater leads to the spontaneous formation of acetyl phosphate and pyrophospate, which act just like adenosine triphosphate or ATP, the chemical that powers living cells.

These molecules drove the formation of amino acids – the building blocks of proteins – and nucleotides, the building blocks for RNA and DNA.

5. Thermal currents and diffusion within the vent pores concentrated larger molecules like nucleotides, driving the formation of RNA and DNA – and providing an ideal setting for their evolution into the world of DNA and proteins. Evolution got under way, with sets of molecules capable of producing more of themselves starting to dominate.

6. Fatty molecules coated the iron-sulphur froth and spontaneously formed cell-like bubbles. Some of these bubbles would have enclosed self-replicating sets of molecules – the first organic cells. The earliest protocells may have been elusive entities, though, often dissolving and reforming as they circulated within the vents.

7. The evolution of an enzyme called pyrophosphatase, which catalyses the production of pyrophosphate, allowed the protocells to extract more energy from the gradient between the alkaline vent fluid and the acidic ocean. This ancient enzyme is still found in many bacteria and archaea, the first two branches on the tree of life.

8. Some protocells started using ATP as well as acetyl phosphate and pyrophosphate. The production of ATP using energy from the electrochemical gradient is perfected with the evolution of the enzyme ATP synthase, found within all life today.

9. Protocells further from the main vent axis, where the natural electrochemical gradient is weaker, started to generate their own gradient by pumping protons across their membranes, using the energy released when carbon dioxide reacts with hydrogen.

This reaction yields only a small amount of energy, not enough to make ATP. By repeating the reaction and storing the energy in the form of an electrochemical gradient, however, protocells “saved up” enough energy for ATP production.

10. Once protocells could generate their own electrochemical gradient, they were no longer tied to the vents. Cells left the vents on two separate occasions, with one exodus giving rise to bacteria and the other to archaea.

Notice that all the reactions and developments following the path of least effort: the protons, electrons, and the like in the atoms, the atoms in the elements, the elements in the compounds, and the chemical reactions among them: every single entity, at every level from quark to cell, does what minimizes effort at each step, following the most efficient path.

With this emergence, we get living cells, and as soon as those arise evolution kicks in by logical necessity: resources used by the cells are limited, and cells pass on their characteristics. Cells that make best use of the resources available tend to generate more copies of themselves, and the new process begins: life.

Life at this point is a lot more complex than a rock, but like the rock, life consists of a myriad of particles, each of which simply follows the path of least resistance through space-time, given the context in which it exists.

Things get rather complex. Take a look at this video:

The yellow molecule is messenger RNA (mRNA); it leaves the nucleus; at the ribosome, ribosomal RNA (rRNA) binds to mRNA; transfer RNA or tRNA (in green) can read the three letter code on mRNA or codon; each codon codes for one animo acid (red molecule attached to tRNA); the sequence of codons on the mRNA determines the sequence of amino acids in the protein, which in turn determines the structure and function of the protein.

The video is fascinating: watching the little machine read its instructions and churn out a string of a particular protein. But it’s totally mechanical, in the sense that it is merely matter and forces following the principle of least effort at every level of scale. Of course, what you see in the video is the result of perhaps millions of years of evolution: small simple systems struggling for survival and passing along their characteristics.

Written by Leisureguy

30 August 2010 at 8:52 am

One Response

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  1. The most fascinating video I’ve found is this:

    ATP Synthase, THE most crucial protein, enzyme, or enzyme complex (whichever term you use), isn’t just biochemical, but electrochemical and *mechanical*, using the world’s smallest nanorotor. It’s in the membranes of every free living bacteria and archaea and in the mitochondria descendants of one of those free living bacteria.

    By the way, I think those crucial enzymes of cyanobacteria and their descendant chloroplasts, Photosystem II, which does the water splitting using photons, and Photosystem I that uses the results, would rank second and third.

    Like

    Mark R

    8 January 2011 at 2:36 pm


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