Sunday, July 17, 2016

An IT Perspective on the Transition From Geochemistry to Biochemistry and Beyond

One of the major realizations arising from softwarephysics has been a growing appreciation for the overwhelming impact that self-replicating information has had on the Earth over the past 4.567 billion years, and of the possibility for the latest version of self-replicating information, known to us as software, to perhaps even go on to have a major impact upon the future of our entire galaxy. Recall that in softwarephysics we define self-replicating information as:

Self-Replicating Information – Information that persists through time by making copies of itself or by enlisting the support of other things to ensure that copies of itself are made.

So far we have seen 5 waves of self-replicating information sweep across the Earth, with each wave greatly reworking the surface and near subsurface of the planet as it came to predominance:

1. Self-replicating autocatalytic metabolic pathways of organic molecules
2. RNA
3. DNA
4. Memes
5. Software

Software is now rapidly becoming the dominant form of self-replicating information on the planet, and is having a major impact on mankind as it comes to predominance. For more on this see: A Brief History of Self-Replicating Information.

How Did It All Start?
For those researchers exploring the processes that brought forth life on the Earth, and elsewhere, the most challenging question is naturally how did the original self-replicating autocatalytic metabolic pathways of organic molecules bootstrap themselves into existence in the first place. Previously, in The Origin of Software the Origin of Life we examined Stuart Kauffman’s ideas on how Boolean nets of autocatalytic chemical reactions might have kick-started the whole thing off as an emergent behavior of an early chaotic pre-biotic environment on Earth, solely with the aid of the extant organic molecules of the day. Similarly, in Programming Clay we examined Alexander Graham Cairns-Smith’s theory, first proposed in 1966, that there was a clay microcrystal precursor to RNA that got it all started. Personally, as a former exploration geophysicist, I have always favored the idea that a geochemical precursor existed near the early hydrothermal vents of the initial tectonic spreading centers of the Earth that acted as a stepping stone between geochemistry and biochemistry. This is because for the early Earth the only real chemistry of the time was geochemistry alone. But how can geochemistry become biochemistry? I just finished reading a couple of beautiful papers that can be downloaded as PDF files:

The inevitable journey to being. Russell M.J., W. Nitschke, and E. Branscomb (2013) https://www.researchgate.net/publication/237098222_The_inevitable_journey_to_being

Turnstiles and bifurcators: The disequilibrium converting engines that put metabolism on the road. Branscomb E., and M.J. Russell (2013) http://www.sciencedirect.com/science/article/pii/S0005272812010420

that describe the Submarine Hydrothermal Alkaline Spring Theory for the emergence of life and how geochemistry could have become biochemistry on the early Earth in the hydrothermal vents of the initial tectonic spreading centers of the Earth. The work described in both papers was supported in part by the Institute for Genomic Biology at my old Alma Mater the University of Illinois in Urbana-Champaign.

Basically, they describe a possible early form of geochemical metabolism that could have taken the internal heat of the Earth and converted it into high-energy organic molecules via a complex set of geochemical reactions, in what the authors call a Free Energy Converter (FEC) cycle. A Free Energy Converter would have taken the high-temperature low-entropy internal heat of the Earth and degraded it into a lower-temperature higher-entropy form of heat that would then have been dumped into the oceans of the early Earth. The energy extracted by such Free Energy Converters would have ended up in high-energy organic molecules. You can think of a Free Energy Converter cycle as a huge loop of computer code that simply takes the available free energy found in the high-temperature regimes of the Earth at a depth of many miles and converts it into energetic organic molecules that could later fuel self-replicating metabolic pathways of organic molecules.

This turns out to be a rather geologically involved process. The temperature difference between the surface of the Earth and the base of the asthenosphere in the upper mantle of the Earth, causes very slow convection cells to arise that drive the plate tectonics of the Earth. These convection cells in the Earth's upper mantle move about as fast as your fingernails grow, but they do bring up the rock peridotite, primarily composed of the ultramafic silicate minerals olivine and pyroxene that are very rich in iron and magnesium, close to the Earth's surface near the Earth's spreading centers. At the spreading centers we frequently find the familiar "black smoker" hydrothermal vents that overlie the many magma chambers of the Earth's spreading centers - see Figure 1. These "black smokers" are disipative structures, far from thermodynamic equilibrium, but they are a bit too hot to be the true nurseries for the origin of life. But a few miles away from the actual spreading centers, we do find a geochemical regime that could serve that purpose. These are the alkaline hydrothermal vents that run on the geochemical reaction called serpentization that transforms the mineral olivine into the mineral serpentine. The serpentization of olivine into serpentine is an exothermic reaction that gives off heat and consequently creates mild convection cells of pore fluids in the Earth's upper crust. These pore fluid convection cells then produce very porous alkaline hydrothermal vents on the sea floor. These very porous alkaline hydrothermal vents do not spout effluents in a dramatic way, like their "black smoker" cousins, but they do percolate warm hydrothermal pore fluids through them, and they could have been the true nurseries of life on this planet. Unlike their acidic "black smoker" cousins, the alkaline hydrothermal vents had a much higher pH than the acidic ocean water that they were located in. Because the early Earth's atmosphere consisted primarily of nitrogen and carbon dioxide, the oceans of the early Earth were much more acidic than they are today because of a high level of dissolved carbon dioxide. The pH contrast of the acidic seawater with the porous alkaline hydrothermal vent pore fluids allowed for proton gradients to form across thin geochemical membranes, like they do in all living things today. All living things on the Earth now obtain energy from redox reactions involving proton gradients across thin membranes, so this could have been a possible geochemical precursor.

Figure 1 - High-temperature "black smokers" near the Earth's spreading centers were probably too hot to be the nurseries of life on Earth.

Figure 2 - However, neighboring alkaline hydrothermal vents could have provided the necessary conditions to be the true nurseries for the origin of life. The alkaline hydrothermal vents had a much lower temperature than the "black smoker" hydrothermal vents, and they percolated pore fluids with a much higher pH than the acidic seawater in which they were located. Above is a map showing the location of the famous "Lost City" alkaline hydrothermal vents near the mid-Atlantic spreading center.

Figure 3 - Above is a depiction of the "Lost City" alkaline hydrothermal vents near the mid-Atlantic spreading center. Notice that the geochemical serpentization of olivine in peridotite provides the free energy to form organic molecules in the alkaline hydrothermal vents.

Figure 4 - A simplified diagram of a "Lost City" alkaline hydrothermal vent. The alkaline hydrothermal vent has pore fluids with a pH of about 10.5, while the acidic seawater in which it sits has a pH of only 5.5. This difference in pH allows for proton gradients to form, the same kind of proton gradients that now power all forms of life on the Earth. Notice that the alkaline hydrothermal vent is also at a relatively low temperature of only 100 oC, much lower than the temperature of "black smokers" that have a temperature range of 250 - 400 oC.

Figure 5 - An actual "Lost City" alkaline hydrothermal vent.

The authors point out that not every step in the necessary geochemical reactions of a Free Energy Converter needs to increase the entropy of the Universe in accordance with the second law of thermodynamics, because if for any step in a geochemical Free Energy Converter that decreases the entropy of the Universe there is also a logically-coupled step that increases the entropy of the Universe even more, the whole process can still proceed forward under the limitation that overall entropy must always increase as dictated by the second law of thermodynamics. But in order for that to happen there needs to be some processing logic added to the infinite loop that runs the Free Energy Converter cycle. The authors point to a couple of papers that describe how Vigna radiata (mung beans) and Thermotoga maritima, a high temperature loving bacterium, accomplish this logical processing:

The essential feature of this linkage in condensations is that it makes each of the two processes conditional on the other— and with a specific logical directionality, namely, a proton (or sodium ion) can pass from outside to inside if, and only if, that happens coincidentally with the condensation and release of a molecule of pyrophosphate, or conversely, a proton (or sodium ion) can pass in the opposite direction, if and only if that happens coincidentally with the hydrolysis of a pyrophosphate and the release of the orthophosphate products. Because of this coupling logic, the device can function as a reversible free energy converter; converting, for example, the controlled dissipation of an outside-to-inside proton gradient in the production of a disequilibrium in the concentration of pyrophosphate versus orthophosphate (i.e. acting as a proton-gradient-driven pyrophosphate synthase). Or it can function equally well in reverse as a proton-pumping pyrophosphatase. Which way it goes depends, of course, on which way yields a net negative change in free energy (equivalently a net positive rate of entropy production).

Another necessary condition for such a logical coupling to work is to make it a one-way street. The authors describe this as adding some "turnstile logic" that allows the coupled reaction to only work in one direction - the direction that outputs low-entropy high-energy organic molecules. Such organic molecules could then later be used as a fuel for biochemical metabolic pathways of self-replicating information that could subsequently arise as parasites feeding off the output of the geochemical Free Energy Converter that is converting the free energy of the Earth's interior into high-energy organic molecules:

To emphasize the critical mechanistic point here, the functional essence of the coupling that achieves FEC is that the driving flux is made conditional on (is ‘gated’ by) the coincident occurrence of the other (driven) flux—which flow, being inherently improbable (i.e. anti-entropic), would, of course, never proceed (‘upstream’) on its own. However, the coupling of two processes as above envisaged is under no stretch ‘automatic’ or trivial; and is in fact a quite special state of physical affairs. In essentially all situations of interest this linking of the two processes into one, requires, and is mediated by, a macroscopically ordered and dynamic ‘structure’ which acts functionally as a “double turnstile”. The turnstile permits a token of the driving flux J1 to proceed downhill if and only if there is the coincident occurrence of some fixed ‘token’ of the driven flux J2 moving “uphill” by chance (albeit as an inherently improbable event) in the same movement of the turnstile. Embodying such conditional, turnstile-like gating mechanisms is what is universally being managed by such evolutionary marvels as the redox-driven proton pumps we will consider in detail later and indeed all other biological devices that carry out what is conventionally termed “energy conservation” (which name, we however argue, misleads in both of its terms).

In many ways this proposed geochemical metabolism of the Earth's natural heat can be compared to photosynthesis, which takes natural energy from the Sun and converts it into energy-rich organic molecules.

An IT Perspective
The authors view such geochemical Free Energy Converters as heat engines converting high-temperature heat into something of biochemical value, while dumping some energy into lower-temperature heat to satisfy the entropy increase demanded by the second law of thermodynamics. But as an IT professional, when I look at the complicated logical operations of the described geochemical processes, I see software running on some primitive hardware instead. As we saw in The Demon of Software heat engines and information are intricately intertwined, so perhaps these infinite loops of early geochemical metabolic pathways can also be viewed as primitive forms of data processing too. The question is could these early geochemical metabolic pathways also be considered to be forms of self-replicating information? That is a difficult question to answer because these early geochemical metabolic pathways seem to just naturally form as heat migrates from the Earth's mantle to its crust via convection cells. In that sense, could we consider the simple mantle convection cells that drive plate tectonics to be forms of self-replicating information too? Clearly, this all gets rather murky as we look back further in deep time.

Unlike all of the previous transitions of one form of self-replicating information into another form of self-replicating information, the transition from geochemistry to biochemistry seems to have been more or less a "clean break". Very few living things on the Earth today now rely upon hydrothermal vents for their existence. So the self-replicating autocatalytic metabolic pathways of organic molecules, feeding off the output of geochemical metabolism, started off as parasites like all new forms of self-replicating information, but unlike most other forms of self-replicating information, they did not go on to form symbiotic relationships with the geochemical pathways. Instead, the self-replicating autocatalytic metabolic pathways of organic molecules seemed to have made a "clean break" with the geochemical metabolic processes that were living off the internal heat of the early Earth by developing a new energy source called photosynthesis. Consequently, unlike the self-replicating autocatalytic metabolic pathways of organic molecules, RNA, DNA, and memes of the past, not much of the geochemical metabolic pathways of the distant past seemed to have been dragged along as subsequent forms of self-replicating information came to be. But that begs the question of why that should be, and might shed some light on the current rise of software as the dominant form of self-replicating information on the planet. Will software carry along its predecessors, or will it make a "clean break" with them? Currently, we are living in one of those very rare times when a new form of self-replicating information, in the form of software, is coming to predominance, and it is not clear that software will drag along the self-replicating autocatalytic metabolic pathways of organic molecules, RNA, DNA, and memes of the past as it becomes the dominant form of self-replicating information on the planet. Most certainly the AI software of the future will need to carry along the memes required to generate software and the necessary scientific and mathematical memes to build the hardware that it runs upon, but would it really need to carry along the ancient biochemical metabolic pathways , RNA and DNA in order to survive? The possibility of software making a "clean break" with biochemistry, just as biochemistry seems to have made a "clean break" with geochemistry, does not bode well for mankind.

Currently, the world is run by a large number of competing meme-complexes composed of memes residing in the minds of human beings. This is in contradiction to what most human beings believe because we all naturally think of ourselves as rational free-acting agents that collectively run the world together. But I contend that the only way to understand the absurd real world of human affairs is to take the Dawkinsian position that we are really DNA survival machines with minds infected by a large number of memes. The reason we all think of ourselves as rational free-acting agents is that we are all committed Cartesian Dualists at heart, with seemingly, a little "Me" running around in our heads - see The Ghost in the Machine the Grand Illusion of Consciousness for more on that. And so far, software is still being generated by the software-generating memes within the minds of programmers. But this will soon end when software is finally able to self-replicate on its own, without the aid of the software-generating memes in the minds of human programmers, and in doing so, will initiate a Software Singularity - see Machine Learning and the Ascendance of the Fifth Wave for more on that.

As software developers and software users, nearly all of mankind is now actively participating in this transition, because software has forged very strong parasitic/symbiotic relationships with nearly all of the meme-complexes on the planet. Now for many years in the past, I held the position that if we had actually been around 4 billion years ago to watch the origin of life on Earth take place, that we would still be sitting around today arguing about just exactly what had happened, just as we still manage today to sit around and argue about what exactly happened for all of the other events in human history. However, now I am more of the opinion that, being the self-absorbed species that we are, we would probably not have even noticed it happening at all! That certainly seems to be the case in the present era, as software is rapidly becoming the dominant form of self-replicating information on the planet before our very eyes, with very few really paying much attention to the fact that we are now living in one of those very rare times when a new form of self-replicating information is coming to predominance.

The key thing to remember is that all new forms of self-replicating information are very disruptive in nature. New forms of self-replicating information usually begin as a mildly parasitic form of self-replicating information that invades an existing host that usually is also a form of self-replicating information, and over time, forms a parasitic/symbiotic relationship with the host. But eventually, these new forms of self-replicating information take over and come to dominate the environment, and that is very disruptive. This is certainly true for software today. In Crocheting Software we saw that the origin of software was such a hodge-podge of precursors, false starts, and failed attempts that it is nearly impossible to pinpoint an exact date for its origin, but for the purposes of softwarephysics I have chosen May of 1941, when Konrad Zuse first cranked up his Z3 computer, as the starting point for modern software. Zuse wanted to use his Z3 computer to perform calculations for aircraft designs that were previously done manually in a very tedious manner. So initially software could not transmit memes, it could only perform calculations, like a very fast adding machine, and so it was a pure parasite. But then the business and military meme-complexes discovered that software could also be used to transmit memes, and software then entered into a parasitic/symbiotic relationship with the memes. Software allowed these meme-complexes to thrive, and in return, these meme-complexes heavily funded the development of software of ever increasing complexity, until software became ubiquitous, forming strong parasitic/symbiotic relationships with nearly every meme-complex on the planet. In the modern day, the only way memes can now spread from mind to mind without the aid of software is when you directly speak to another person next to you. Even if you attempt to write a letter by hand, the moment you drop it into a mailbox, it will immediately fall under the control of software.

Presently, we are now entering the final stage where software is now in an intense battle with the memes for predominance, and currently this is causing a great deal of social, political and economic unrest as discussed in The Economics of the Coming Software Singularity , The Enduring Effects of the Obvious Hiding in Plain Sight, Machine Learning and the Ascendance of the Fifth Wave and Makining Sense of the Absurdity of the Real World of Human Affairs. The main difficulty is that software has displaced many workers over the past 75 years, and as software comes to predominance, it will eventually reduce all human labor to a value of zero over the next 10 - 100 years. So in a sense, software will soon be eliminating the metabolic pathway of earning a living through labor for most of mankind that has made civilization possible for the past 10,000 years. The resulting social chaos can only help to hasten the day when software finally takes over control of the Earth, and perhaps, makes a "clean break" with the biochemistry that has dominated the Earth for nearly 4.0 billion years (see The Dawn of Galactic ASI - Artificial Superintelligence for details).

Comments are welcome at scj333@sbcglobal.net

To see all posts on softwarephysics in reverse order go to:
http://softwarephysics.blogspot.com/

Regards,
Steve Johnston

No comments: