Saturday, July 15, 2017

The Bootstrapping Algorithm of Carbon-Based Life

The August 2017 issue of Scientific American features a cover story entitled Life Springs that outlines a new explanation for the origin of carbon-based life on this planet that Dave Deamer and Bruce Damer out of the University of California at Santa Cruz have developed in recent years. A few years back, I had some very interesting email exchanges with Bruce Damer regarding using the origin and evolution of software on this planet as a useful analogy for the origin and early evolution of carbon-based life. Now Bruce Damer is one of those fascinating computer geniuses and pioneers that you just never get a chance to meet during the normal course of business during the typical workday in a large corporate IT department, so that was a very exciting change of pace for me. Bruce Damer has a very long and colorful history of working with computers, and he even has his own museum, the DigiBarn Computer Museum, of ancient computers and computer artifacts. For more about Bruce Damer, take a look at his very interesting personal webpage at:

http://www.damer.com/

Bruce Damer received his Ph.D. for his work on the EvoGrid, an attempted computer simulation of the origin of carbon-based life on the Earth. But Bruce Damer's work on the EvoGrid led him to realize that our current computers are just not up to the task, and will probably not have enough computing power to simulate the origin of carbon-based life for the foreseeable future. Since then he has teamed up with the renowned biochemist Dave Deamer who has been working on the origin of carbon-based life since the early 1980s. The basic idea arising from their collaboration is to simply let the untold number of organic molecules to be found in a single thimbleful of solution do the huge number of chemical computations needed to bring forth carbon-based life for us, by setting up a primitive Earth-like chemical environment, and automating the necessary laboratory processes to run a large number of small samples of organic molecules through the simulated primitive-Earth conditions that they think brought forth carbon-based life on this planet. But in order to do that you need an algorithm. A quick check with the Wikipedia tells us:

Algorithm
In mathematics and computer science, an algorithm is a self-contained sequence of actions to be performed. Algorithms can perform calculation, data processing and automated reasoning tasks.

An algorithm is an effective method that can be expressed within a finite amount of space and time and in a well-defined formal language for calculating a function. Starting from an initial state and initial input (perhaps empty), the instructions describe a computation that, when executed, proceeds through a finite number of well-defined successive states, eventually producing "output" and terminating at a final ending state. The transition from one state to the next is not necessarily deterministic; some algorithms, known as randomized algorithms, incorporate random input.


Figure 1 – The Quicksort algorithm was developed by Tony Hoare in 1959 and applies a prescribed sequence of actions to an input list of unsorted numbers. It very efficiently outputs a sorted list of numbers, no matter what unsorted input it operates upon.

Based upon the above, it seems that in order to form a bootstrapping algorithm for the origin of carbon-based life you need to know what organic molecules to start with as input, and what actions to put them through, in order to successfully simulate the origin of carbon-based life on the early Earth as output, and that is the rub. Now figuring out the organic molecules to use is pretty easy because you can easily pick them up at any grocery store. Unfortunately, the ones you find in grocery stores have all been pre-packaged and shrink-wrapped by living things into larger molecules, so you do have to do a little work to bust them up into smaller molecules called monomers - like lipids, amino acids, nucleotides and simple sugars. But the real challenge is trying to figure out the correct processing steps in the bootstrapping algorithm, and that is where some softwarephysics might be of help. Recall that one of the fundamental findings of softwarephysics is that living things and software are both forms of self-replicating information, and that both have converged upon similar solutions to combat the second law of thermodynamics in a highly nonlinear Universe. For those working on the origin of carbon-based life, the value of softwarephysics is that software has been evolving about 100 million times faster than living things over the past 76 years, or 2.4 billion seconds, ever since Konrad Zuse first cranked up his Z3 computer in May of 1941, and the evolution of software over that period of time is the only history of a form of self-replicating information that has actually been recorded by human history. In fact, the evolutionary history of software has all occurred within a single human lifetime, and many of those humans are still alive today to testify as to what actually had happened, something that those working on the origin of life on the Earth and its early evolution can only try to imagine. Again, 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.

The Characteristics of Self-Replicating Information
All forms of self-replicating information have some common characteristics:

1. All self-replicating information evolves over time through the Darwinian processes of innovation and natural selection, which endows self-replicating information with one telling characteristic – the ability to survive in a Universe dominated by the second law of thermodynamics and nonlinearity.

2. All self-replicating information begins spontaneously as a parasitic mutation that obtains energy, information and sometimes matter from a host.

3. With time, the parasitic self-replicating information takes on a symbiotic relationship with its host.

4. Eventually, the self-replicating information becomes one with its host through the symbiotic integration of the host and the self-replicating information.

5. Ultimately, the self-replicating information replaces its host as the dominant form of self-replicating information.

6. Most hosts are also forms of self-replicating information.

7. All self-replicating information has to be a little bit nasty in order to survive.

8. The defining characteristic of self-replicating information is the ability of self-replicating information to change the boundary conditions of its utility phase space in new and unpredictable ways by means of exapting current functions into new uses that change the size and shape of its particular utility phase space. See Enablement - the Definitive Characteristic of Living Things for more on this last characteristic.

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 that see: A Brief History of Self-Replicating Information.

Getting Started
Above all else, the one thing that any new form of self-replicating information necessarily needs is some kind of copying algorithm, otherwise it will not be able to self-replicate. For example, we call the copying algorithm that memes use to spread from mind to mind "learning", and we are all familiar with the copy/paste algorithm that is used to copy chunks of software from one file to another, and we have all downloaded software from the Internet and installed it on our computers, sometimes in an unwitting manner that downloads some parasitic malware. Finding a copying algorithm for a new form of self-replicating information might not be so difficult for most new forms of self-replicating information because most new forms of self-replicating information start as a parasitic invader of a host that is also a form of self-replicating information, and most forms of self-replicating information are algorithms. For example, many memes are algorithms, like the meme for properly weaving a basket, or the meme to make a flint flake tool, or the meme to solve a first-order linear differential equation. Similarly, most software also consists mainly of algorithms, and carbon-based life itself can also be viewed as a large collection of biochemical algorithms in play. That means that there must already be some kind of infrastructure in place to support the existence of algorithms for most new forms of self-replicating information trying to get a start. What happens is that the eighth characteristic of self-replicating information comes into play, as a new parasitic form of self-replicating information comes into existence. In order to self-replicate, the new parasitic form of self-replicating information simply exapts an already existing natural algorithm into the new purpose of replicating the new form of self-replicating information. For example, software originally exapted 2400 electomechanical relays, originally meant for switching telephone calls, on board Konrad Zuse's Z3 computer in May of 1941, and it also exapted countless mathematical algorithm memes as well, in order to come into existence. Given the above, it is easy to see how a new form of parasitic self-replicating information can come to be, as it exapts a copying algorithm from an already existing host, but what about the original self-replicating autocatalytic organic molecules? They did not have a self-replicating host to exploit. How did they obtain a copying algorithm?

The Initial Bootstrapping Algorithm
The answer must be that the original self-replicating autocatalytic organic molecules obtained a copying algorithm from a naturally occurring geochemical cycle of some sort. In An IT Perspective on the Transition From Geochemistry to Biochemistry and Beyond we discussed Mike Russell's alkaline hydrothermal vent model which proposes that a naturally occurring pH gradient in alkaline hydrothermal vents arose as alkaline pore fluids containing dissolved hydrogen H2 gas came into contact with acidic seawater that was laden with dissolved carbon dioxide CO2. The alkaline pore fluids were generated by a natural geochemical cycle that was driven by the early convection currents in the Earth's asthenosphere that brought forth plate tectonics. These initial convection currents brought up fresh silicate peridotite rock that was rich in iron and magnesium bearing minerals, like olivine, to the Earth's initial spreading centers. The serpentinization of the mineral olivine into the mineral serpentinite created alkaline pore fluids and dissolved hydrogen H2 gas, which later created alkaline hydrothermal vents when the alkaline pore fluids came into contact with the acidic seawater containing a great deal of dissolved carbon dioxide CO2. The model proposes that the energy of the resulting pH gradients turned the hydrogen H2 and carbon dioxide CO2 molecules into organic molecules, and it is proposed that they also fueled the origin of life in the pores of the porous hydrothermal vents. Researchers have been trying to replicate this process in the lab for a number of years, but so far they have only been able to produce very dilute solutions of organic molecules, and some contend that what has been produced so far is only what one would expect to find at equilibrium. For example, at equilibrium we have hydrogen H2 and carbon dioxide CO2 at equilibrium with the organic molecule formate HCOOH as:

H2  +  CO2  ↔  HCOOH

But at equilibrium most of the atoms are on the left side of the equation, with only a very few on the right side as formate HCOOH. Since so far we have only seen very dilute amounts of formate being created by the lab simulations of alkaline hydrothermal vents, it seems likely that pH gradients are not forming them. They probably are just arising from a natural equilibrium reaction. So more work needs to be done in this area to definitively demonstrate that alkaline hydrothermal vents can indeed generate organic molecules and could have been the environment that brought forth carbon-based life.

Now Dave Deamer and Bruce Damer have come up with a different bootstrapping algorithm that also uses a naturally occurring geochemical cycle. For a condensed presentation of Dave Deamer's and Bruce Damer's model see:

In the Beginning: The Origin & Purpose of Life | Dr. Bruce Damer | TEDxSantaCruz
https://www.youtube.com/watch?v=6qiW4aUqtvA

For a more rigorous presentation see their talk at the SETI Institute:

A new model for the origin of life - Bruce Damer and Dave Deamer (SETITalks)
https://www.youtube.com/watch?v=nk_R55O24t4

Below you can download their original paper on the subject. This is a very accessible paper that anyone can easily comprehend, much like Darwin's Origin of Species:

Coupled Phases and Combinatorial Selection in Fluctuating Hydrothermal Pools: A Scenario to Guide Experimental Approaches to the Origin of Cellular Life
http://www.biota.org/origins/docs/2015/Damer-Deamer-Coupled-Phases-Life2015.pdf

The paper below by Bruce Damer features the full Terrestrial Origins Hypothesis for the bootstrapping algorithm for the origin of carbon-based life on this planet:

A Field Trip to the Archaean in Search of Darwin’s Warm Little Pond
http://www.mdpi.com/2075-1729/6/2/21/pdf

Below are the slides from a presentation they made to the Australasian Astrobiology meeting in Perth, Australia in July of 2016 that you should be able to easily follow once you have reviewed the above material:

An Origin of Life in Salt Water or Fresh Water?
http://www.slideshare.net/bdamer/an-origin-of-life-in-salt-water-or-fresh-water

Figure 2 below is a pictorial depiction of their new bootstrapping algorithm. Basically, their new bootstrapping algorithm calls for organic monomers and polymers that are encased in lipid protocells in hot and very wet fresh water puddles to dry out before becoming wet again. The organic monomers that are the feedstock for this algorithm are to be found in the molecular clouds from which stars are formed, and they end up in the leftovers of forming a solar system. So we now find many organic monomers in the comets of the Oort cloud and the asteroids of the asteroid belt and the Kuiper belt too. The water that is found in carbon-rich chondritic meteorites, that resulted from collisions between asteroids, has a similar Deuterium/Hydrogen ratio as the Earth's seawater. So many now believe that a good portion of the Earth's water supply came from collisions with asteroids early in the Earth's history, and those asteroid collisions would have also brought large amounts organic monomers along with them. This accumulation of water and organic molecules was enhanced by the Late Heavy Bombardment 3.8 - 4.1 billion years ago. It is thought that the Late Heavy Bombardment was caused by Jupiter and Saturn entering into a 2:1 orbital resonance, with Jupiter making two orbits for every single orbit of Saturn. This meant that the combined gravitational attraction of both Jupiter and Saturn would add up at the same location in the Solar System with each orbit of Saturn. That combined tug perturbed the orbits of Uranus and Neptune, and also the asteroids of the asteroid belt and the Kuiper belt, causing many asteroids to fall into close orbits around the Sun, and eventually to collide with the Earth and the Moon.

Because this bootstrapping algorithm requires that the monomers and polymers of life in protocells be dried out each cycle of the algorithm, this bootstrapping algorithm can only take place above sea level. Consequently, they envision that this bootstrapping algorithm operated on the initial volcanic islands of the early earth about 4 billion years ago. These early volcanic islands would have hydrothermal fields of geysers and pools similar to the ones we find today at Bumpass Hell on Mount Lassen in California and on Mount Mutnovski in Kamchatka, Russia. As the water level in a hydrothermal pool rose and fell, it would form a bathtub ring around the hydrothermal pool, and this bathtub ring would run through the bootstrapping algorithm each time the water level fell and rose again. When the bathtub ring was fully submerged in water, the organic molecules of life would find themselves enclosed in cell-like lipid bilayer vesicles. But as the water in a hydrothermal pool evaporated, it would concentrate the protocells into a gelatinous protocell mat, much like the stromatalitic structures of today and of the distant past. In the gel phase, the protocells would be put under a great deal of stress as they tried to survive in a new and rapidly changing environment. Finally, when the protocell mat totally dried out in the last step of the bootstrapping algorithm, it formed layers of lipids that preserved the surviving organic molecules from the latest iteration of the bootstrapping algorithm. This final drying out step of the bootstrapping algorithm is crucial in building new polymers, as water molecules are chemically removed from between monomer molecules in the lipid laminae to form polymers. When the dried out protocells in the lipid laminae are wetted again in the bootstrapping algorithm, they then bud out into vesicles containing a new mix of polymers to be tested by natural selection once again.

Figure 2 – Dave Deamer's and Bruce Damer's new bootstrapping algorithm requires that a bathtub ring around a hydrothermal pool periodically dry out. The resulting desiccation chemically squeezes out water molecules between monomers, causing them to be glued together into polymers.

You can easily replicate their bootstrapping algorithm while making breakfast. First make some toast. After you butter the toast, you will find a greasy layer of butter all over your knife that will not wash off when you run the knife under the kitchen faucet. Now run some water over your fingers and then rub them on the bar of soap at your kitchen sink. Next take your wet soapy fingers and rub them all over the greasy layer of butter on your knife. Now run the knife and your fingers under the kitchen faucet, and make sure you catch everything in a small mixing bowl. Amazingly, your knife will now be totally clean with no residual grease at all when you dry it off! This is because the lipids in the bar of soap have surrounded a huge number of little drops of greasy butter molecules with a lipid membrane called a micelle that has its water-loving heads on the outside. This creates a huge number of little lipid vesicles enclosing greasy butter molecules. That is how soap works. The lipids break the high water surface tension of the polar water molecules, and they create grease cutting micelle vesicles too. Now break a couple of eggs and beat them with a wisk in a small metal mixing bowl for your scrambled eggs. After you finish cooking your scrambled eggs, pour the reserved water, butter and soap mixture into the metal mixing bowl that was used for beating your eggs, which contains a small amount of leftover beaten egg mixture too. Then wisk the contents of the metal mixing bowl and place it on the stove over a very low heat. Now to be fair, we do need to remove the oxygen from the atmosphere of our little breakfast-style simulation of the origin of carbon-based life because the early Earth had an atmosphere composed primarily of nitrogen and carbon dioxide gas, with no oxygen at all. Oxygen is a powerful oxidizing agent that is pretty tough on organic molecules, so it is important for us to remove it, and the modern atmosphere of the Earth is about 21% oxygen, which is a considerable amount. The modern Earth atmosphere is also about 78% nitrogen, so there is plenty of nitrogen around for our breakfast-style simulation, but getting the proper mix of nitrogen and carbon dioxide gas would be a bit of a kitchen laboratory challenge. So let's go with a pure carbon dioxide atmosphere. Take a shot glass and fill it 1/3 of the way with baking soda, and place it in the bottom of the metal mixing bowl. Then slowly dribble in some vinegar, but don't let it bubble over into the mixing bowl. That will create lots of heavy carbon dioxide gas that will totally displace all of the current Earth's atmosphere and its nasty oxygen gas.

You have now completed step one of the bootstrapping algorithm, as displayed in the top portion of Figure 2, because you now have a water mixture of lipid vesicles called liposomes that contain various organic molecules. As the water in your mixture evaporates, it will begin to form the gooey gel of the second step in the bootstrapping algorithm. Finally, when all of the water has evaporated you will have completed the third step of the bootstrapping algorithm, yielding a laminated structure of dried out lipids preserving polymers that have survived. Now you probably have already performed this experiment hundreds of times in your lifetime, and have also come upon the joy of trying to clean a mixing bowl with a bunch of dried out gunk in its bottom. And somebody probably even taught you how to complete the final step of the bootstrapping algorithm by letting the messy mixing bowl soak in warm water before trying to wash it out. Letting the dried out mess soak in warm water allows for lipid vesicles to form, and to bud out, and that brings you back to step one of the bootstrapping algorithm. Now all you have to do is to repeat the steps in this bootstrapping algorithm for about 100 billion trillion times, and after that, there will be a good chance of you finding living cells forming! Now that would not be such a big deal if you were not planning on do much else for the next 100 million years, and you could also run the bootstrapping algorithm in every kitchen in the United States simultaneously. Similarly, Dave Deamer and Bruce Damer propose that if you had run this same bootstrapping algorithm for about 100 million years in a huge number of hydrothermal pools on a very large number of volcanic islands four billion years ago, you would indeed see living cells appear too. Or maybe it could happen much faster. Right now, we just don't know how much time it would take, and that is why Dave Deamer and Bruce Damer are currently researching this in their lab with a little machine that automates their bootstrapping algorithm.

Figure 3 – The lipids in a bar of soap have water-loving polar heads and water-hating nonpolar tails. The soap lipids can form a spherical micelle with all of the water-hating nonpolar tails facing inwards. A spherical micelle can surround the greasy nonpolar molecules of butter and allow them to be flushed away by a stream of polar water molecules. The lipids in a bar of soap can also form a cell-like liposome with a bilayer of lipid molecules that can surround the monomers and polymers of life.

The Very First Parasite
Now if we take the view that carbon-based life, like all new forms of self-replicating information, began as a parasite feeding off the extant organic molecules to be found on the early Earth, and was using the existing geological environments and geochemical processes of the time, then we can see that this new bootstrapping algorithm runs the incipient protocells through a variety of forms and host environments, like all parasites with complex life cycles love to do, in order to complete one protocell life cycle. In SETS - The Search For Extraterrestrial Software we saw that throughout historical time, parasites have usually been undeservedly disparaged by the biological community as degenerate forms of life, when in reality, parasites usually have much more complicated life cycles than most of the "higher" forms of life, and have had to learn to adapt to a multitude of environments and to a multitude of hosts in order to complete a single life cycle. I would suggest that Dave Deamer's and Bruce Damer's new bootstrapping algorithm mimics the rigors of a complex parasitic life cycle, and would therefore favor the development of the parasitic form of self-replicating information known to us as carbon-based life.

The Present is the Key to the Past
One of the founding principles of geology has been the Uniformitarianism of James Hutton presented in his Theory of the Earth (1785) and Charles Lyell's Principles of Geology (1830), and is best summed up by the phrase "the present is the key to the past", meaning that the geological processes that operate in the present also probably operated in the past and in exactly the same manner. So if you want to figure out how the rocks in the deep past came to be, just go out on a field trip to where similar rocks are being formed today and observe how it is done today.

Figure 4 – The cross bedding found when digging into a modern sand dune explains how the cross bedding in ancient sandstones came to be.

Figure 5 – Cross bedding in sandstones arises when sand is pushed by a fluid, such as wind or water. The cross bedding tells you which way was "up" when the sandstone was deposited and which way the fluid was flowing too.

And that is what Dave Deamer and Bruce Damer have done in their quest for a bootstrapping algorithm for the origin of carbon-based life by making field trips to hydrothermal fields like the Bumpass Hell on Mount Lassen in California and Mount Mutnovski in Kamchatka, Russia. They are now trying to replicate what they observed in the field with experiments in the lab.

Figure 6 – Above is Bumpass Hell, a hydrothermal field on the volcanic Mount Lassen in California that Dave Deamer and Bruce Damer cite as a present day example of the type of environment that could have brought forth carbon-based life about four billion years ago, using their new bootstrapping algorithm.

Conclusion
I have long suggested that the researchers working on the origin of carbon-based life on this planet are now working just one level too low. Since carbon-based life is just one form of self-replicating information that we currently have at our disposal, it would make sense to first explore the characteristics of all the forms of self-replicating information that we currently have at hand, and the interactions amongst them all, before focusing on the origin of carbon-based life. For example, we are now living in one of those very rare times when a new form of self-replicating information, known to us as software, is coming to predominance. The parasitic/symbiotic relationships between the memes residing in the minds of human DNA survival machines, and the software on their computers is truly fascinating. In today's world most software is now created and spread by memes, and most memes are now spread by software. Understanding the complex interacting behaviors of all the forms of self-replicating information is critical because not only do they explain where we came from, they might also explain where we all are headed. After all, no one can now deny that civilization might come to a screeching halt because of a single poorly worded Tweet.

Addendum
Bruce Damer was kind enough to send me a PDF of their poster from the last ISSOL - The International Society for the Study of the Origin of Life - meeting. I have encoded it down below in HTML. Please note that the color coded text corresponds to the color coded sections on the poster image. They have also renamed their Terrestrial Origins Hypothesis as the more descriptive Hot Spring Origins Hypothesis.

A Hot Spring Origin of Life and Early Adaption Pathway in seven steps:

1. Synthesis of organics (a), key primordial building blocks for life, occurs in space prior and during the formation of the Solar System;
2. Accumulation of in-falling organics and other compounds generated within hot springs on an active volcanic landscape combine and undergo self-assembly of structures such as lipid membranes;
3. Concentration of compounds in small pools utilizes sunlight, heat and chemical energy to drive key prebiotic polymerization reactions and self assembly of membranous structures;
4. Cycling of the products of these reactions in a wet-dry fluctuating hot spring ‘origin pool’ drives them through three phases: organic membranes in the pool i) Dry down to form layered Films between which organic building blocks bond together to form polymers; on refilling the films ii) Wet and bud off trillions of lipid Protocells some encapsulating random polymers. Each protocell undergoes a iii) Test, the first form of natural selection, and stable survivors accumulate into a moist Gel as the pool level drops. Through many iterations polymers iv) Interact, within the Gel and the Films evolving ever more complex functions until a form of pre-life (b) called a Progenote emerges that is able to grow and adapt;
5. Distribution of robust progenotes occurs by water or wind to other pools, rivers, and lakes, where they acquire and share evolutionary innovations including an early form of photosynthesis. Eventually protocells develop the complicated innovation of cell division and initiate the transition into early life (c);
6. Adaptation of early microbial communities to stressful salt water estuaries prepares them for access to the more extreme marine environment;
7. Large tides at the ancient sea coast select for microbial communities able to cement sand grains together forming the layers that build the stromatolites so abundant in the fossil record. Global life (d) enables Colonization of many niches on the land and in the sea, setting the stage for free-living cells and, after billions of years, complex multi-cellular organisms.

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