Tuesday, February 19, 2013

A Brief History of Self-Replicating Information

If you have been following along with the postings on this blog on softwarephysics, you know that my initial intention for softwarephysics was to help IT professionals to better cope with the daily mayhem of life in IT. However, in laying down the postings for this blog on softwarephysics over the past several years, an unintended consequence arose in my mind as I became profoundly aware of the enormity of this vast computer simulation of the physical Universe that the Software Universe affords, and the very significant potential scientific value that it might provide. By studying softwarephysics, we not only can learn how to better develop, support, and maintain software, but we can also explore how software came to be in the first place, and possibly foretell where it might be heading. We have also seen that because softwarephysics provides some insights into the workings of the Software Universe that we are all immersed in, it also provides another realm for comparison for those in the scientific community who are struggling with some of the more intractable problems, like the origin of life, the possibilities of astrobiology, communications with extraterrestrial civilizations, and the fate of mankind in general.

Now as this blog progressed over time, I began to realize that software is really just a form of self-replicating information, and that software is on the very brink of becoming the dominant form of self-replicating information on the planet, as so many of its predecessors have already done so in the past. I also began to realize the overwhelming significance of the role that self-replicating information has played in the history of our planet, and also in the history of our galaxy as well. This is important because in my last posting, The Sounds of Silence the Unsettling Mystery of the Great Cosmic Stillness, I suggested that the fate of our galaxy might hinge upon we human beings being able to hold it together long enough for software to broadcast itself into the cosmos, or perhaps even to physically depart the Earth upon an interstellar voyage of exploration. Because these ideas have been spread across several lengthy postings, I would like to take this opportunity to consolidate them here into a single posting outlining a concise timeline of the history of self-replicating information upon the Earth in order to provide a high-level view.

In Self-Replicating Information, we saw that software is just one of the many forms of self-replicating information that have arisen upon the Earth over the past 4.567 billion years. In this posting, I would like to outline a brief history of the dominant forms of self-replicating information that we have already seen arise upon the Earth, using ideas from many other people, in order to come up with an explanation for the origin of software and where it might be heading. By dominant, I mean the form of self-replicating information that, at any given time, seems to be reshaping the planet and that is apparently in charge. Of course, this has changed over time. To begin with, let us return to our definition of self-replicating information.

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.

Below is a brief outline of the history of the various forms of self-replicating information that have arisen upon the Earth.

1. Self-replicating autocatalytic metabolic pathways of organic molecules
To start things off, we have to deal with the bootstrap problem. How can the Darwinian processes of innovation and natural selection get started if there is nothing for natural selection to work upon in the first place? In The Origin of Life (1924), Alexander Oparin proposed that metabolic pathways, consisting of organic molecules housed in phospholipid membranes, formed proto-cells that started it all off and changed the organic landscape of the early Earth by feeding off the extant organic molecules already in place created by abiotic processes. Stuart Kauffman of the Sante Fe Institute further proposed in At Home in the Universe (1995), that such self-replicating autocatalytic metabolic pathways are not only possible, but are essentially inevitable, given our current understanding of complexity theory. Kauffman calls this apparent emergence of self-organized order in nonlinear systems far from thermodynamic equilibrium “order for free”. His contention is that the extreme order found within the biosphere is not entirely the result of Darwinian natural selection acting upon purely random variations alone. For example, Kaufman points out that the emergent order found within a phospholipid bilayer, that is simply seeking to minimize its free energy, and which forms the foundation upon which all biological membranes are built, is an example of an emergent “order for free” design pattern that has dominated the biosphere for more than 4 billion years. See Stuart Kauffman’s At Home in the Universe (1995) and The Origin of Software the Origin of Life for more details. These self-replicating autocatalytic metabolic pathways may have also been assisted by self-replicating clay minerals, as first proposed in 1966 by Alexander Graham Cairns-Smith. See Cairns-Smith’s the Seven Clues to the Origin of Life: A Scientific Detective Story (1985) and Programming Clay for more details. So these initial replicators may have bootstrapped themselves into existence to kick it all off, but once they got going, natural selection would naturally quickly take over.

2. RNA
In Origins of Life (1999) Freeman Dyson modified the theory that metabolic pathways came first, as outlined in Alexander Oparin’s original The Origin of Life (1924) by applying ideas from Lynn Margulis’s endosymbiotic theory. The endosymbiotic theory maintains that organelles in eukaryotic cells, like chloroplasts and mitochondria, are really prokaryotic parasitic cells that parasitized larger prokaryotic cells and then entered into a parasitic/symbiotic relationship with them to form modern eukaryotic cellular life. Freeman Dyson figured that RNA may have done the very same thing. For Dyson, short strands of RNA started off as parasites within the proto-cells filled with autocatalytic metabolic pathways. Since RNA is known to be autocatalytic itself, and can also store the information necessary to build proteins and can actually string together amino acids into structural and enzymatic proteins, Dyson figured the RNA and metabolic pathways would then form a symbiotic relationship, in keeping with the ideas of Lynn Margulis. The combination of RNA and metabolic pathways in proto-cells further changed the Earth’s organic chemical makeup. See Self-Replicating Information for more details on this stage of self-replicating information.

3. DNA
Freeman Dyson figures that DNA came next as a parasitic mutation of RNA feeding off the nucleotides used by RNA. RNA is very similar to DNA in structure, except that RNA uses a substitute base called Uracil in place of Thymine to bind to Adenine. DNA then formed a parasitic/symbiotic relationship with RNA, using mRNA and tRNA to transcribe the information in DNA into proteins. The good old metabolic pathways stuck around too. Now we had fully operational prokaryotic cells that began to really change the Earth. Cyanobacteria started dumping lots of oxygen into the oceans, changing the Earth’s oceans and atmosphere from a reducing state to an oxidizing state. At first, huge amounts of iron precipitated out of the oceanic waters to form the redbed formations of iron ore that your car was made from, and later the oxygen accumulated in the Earth’s atmosphere. The simple prokaryotic bacteria, containing DNA, RNA, and metabolic pathways, then merged into complex eukaryotic single-celled life forms, which later became complex multicellular life forms after the Cambrian explosion. The resulting DNA survival machines have totally retooled the Earth. They have made huge coral reefs, increased the rate of rock erosion with acids, removed huge quantities of carbon dioxide out of the atmosphere with photosynthesis and the formation of biologically constructed carbonate shells, and have caused rivers to meander because the root systems of grasses hold soil together well. See Self-Replicating Information for more details on this stage of self-replicating information.

4. Memes
The memes were the next form of self-replicating information to arise, as first proposed by Richard Dawkins in The Selfish Gene (1976). The concept of memes was later advanced by Daniel Dennett in Consciousness Explained (1991) and Richard Brodie in Virus of the Mind: The New Science of the Meme (1996), and was finally formalized by Susan Blackmore in The Meme Machine (1999). For those of you not familiar with the term meme, it rhymes with the word “cream”. Memes are cultural artifacts that persist through time by making copies of themselves in the minds of human beings and were first recognized by Richard Dawkins in The Selfish Gene (1976). Dawkins described memes as “Examples of memes are tunes, ideas, catch-phrases, clothes fashions, ways of making pots or of building arches. Just as genes propagate themselves in the gene pool by leaping from body to body via sperms or eggs, so memes propagate themselves in the meme pool by leaping from brain to brain via a process which, in the broad sense, can be called imitation.”. Just as genes come together to build bodies, or DNA survival machines, for their own mutual advantage, memes also come together from the meme pool to form meme-complexes for their own joint survival. DNA survives down through the ages by inducing disposable DNA survival machines, in the form of bodies, to produce new disposable DNA survival machines. Similarly, memes survive in meme-complexes by inducing the minds of human beings to reproduce memes in the minds of others. To the genes and memes, human bodies are simply disposable DNA survival machines housing disposable minds that come and go with a lifespan of less than 100 years. The genes and memes, on the other hand, continue on largely unscathed by time as they skip down through the generations. However, both genes and memes do evolve over time through the Darwinian mechanisms of innovation and natural selection. You see, the genes and memes that do not come together to build successful DNA survival machines, or meme-complexes, are soon eliminated from the gene and meme pools. So both genes and memes are selected for one overriding characteristic – the ability to survive. Once again, the “survival of the fittest” rules the day. Now it makes no sense to think of genes or memes as being either “good” or “bad”; they are just mindless forms of self-replicating information bent upon surviving with little interest in you as a disposable survival machine. So in general, these genes and memes are not necessarily working in your best interest, beyond keeping you alive long enough so that you can pass them on to somebody else. That is why, if you examine the great moral and philosophical teachings of most religions and philosophies, you will see a plea for us all to rise above the selfish self-serving interests of our genes and memes.

Meme-complexes come in a variety of sizes and can become quite large and complicated with a diverse spectrum of member memes. Examples of meme-complexes of increasing complexity and size would be Little League baseball teams, clubs and lodges, corporations, political and religious movements, tribal subcultures, branches of the military, governments and cultures at the national level, and finally the sum total of all human knowledge in the form of all the world cultures, art, music, religion, and science put together. Meme-complexes can do wonderful things, as is evidenced by the incredible standard of living enjoyed by the modern world, thanks to the efforts of the scientific meme-complex, or the great works of art, music, and literature handed down to us from the Baroque, Classical, and Romantic periods, not to mention the joys of jazz, rock and roll, and the blues. However, meme-complexes can also turn incredibly nasty. Just since the Scientific Revolution of the 17th century we have seen the Thirty Years War (1618 -1648), the Salem witch hunts (1692), the French Reign of Terror (1793 – 1794), American slavery (1654 – 1865), World War I (all sides) (1914 – 1918), the Stalinist Soviet Union (1929 – 1953), National Socialism (1933 – 1945), McCarthyism (1949 – 1958), Mao’s Cultural Revolution (1969 – 1976), and Pol Pot’s reign of terror (1976 – 1979).

The problem is that when human beings get wrapped up in a meme-complex, they can do horrendous things without even being aware of the fact. This is because in order to survive, the first thing that most meme-complexes do is to use a meme that turns off human thought and reflection. To paraphrase Descartes ”I think, therefore I am" a heretic. So if you ever questioned any of the participants caught up in any of the above atrocious events, you would find that the vast majority would not have any qualms about their deadly activities whatsoever. In fact, they would question your loyalty and patriotism for even bringing up the subject. For example, during World War I, which caused 40 million casualties and the deaths of 20 million people for apparently no particular reason at all, there were few dissenters beyond Albert Einstein in Germany and Bertrand Russell in Great Britain, and both suffered the consequences of not being on board with the World War I meme-complex. Unquestioning blind obedience to a meme-complex through unconditional group-think is definitely a good survival strategy for any meme-complex. But the scientific meme-complex has an even better survival strategy – skepticism and scrutiny. Using skepticism and scrutiny may not seem like a very good survival strategy for a meme-complex because it calls into question the validity of the individual memes within the meme-complex itself. But that can also be a crucial advantage. By eliminating memes from within the scientific meme-complex that cannot stand up to skepticism and scrutiny, the whole scientific meme-complex is strengthened, and when this skepticism and scrutiny are turned outwards towards other meme-complexes, the scientific meme-complex is strengthened even more so.

In The Meme Machine, Susan Blackmore goes much further with the concept of memes and brings memetics to the level of a fully comprehensive science that is falsifiable. Memetics can now explain many current observations better than other models, and can make predictions of observations yet to be made that can be investigated and tested in the future. As such, memetics should now stand in good stead with the rest of the sciences. For example, Blackmore maintains that memetic-drive was responsible for creating our extremely large brains and also our languages and cultures as well, in order to store and spread memes more effectively. Many researchers have noted that the human brain is way over-engineered for the needs of a simple hunter-gatherer. After all, even a hundred years ago, people did not require the brain-power to do IT work, yet today we find many millions of people earning their living doing IT work, or at least trying to. Blackmore then points out that the human brain is a very expensive and dangerous organ. The brain is only 2% of your body mass, but burns about 20% of your calories each day. The extremely large brain of humans also kills many mothers and babies at childbirth, and also produces babies that are totally dependent upon their mothers for survival and that are totally helpless and defenseless on their own. Blackmore asks the obvious question of why the genes would build such an extremely expensive and dangerous organ that was definitely not in their own self-interest. Blackmore has a very simple explanation – the genes did not build our exceedingly huge brains, the memes did. Her reasoning goes like this. About 2.5 million years ago, the predecessors of humans slowly began to pick up the skill of imitation. This might not sound like much, but it is key to her whole theory of memetics. You see, hardly any other species learns by imitating other members of their own species. Yes, there are many species that can learn by conditioning, like Pavlov’s dogs, or that can learn through personal experience, like mice repeatedly running through a maze for a piece of cheese, but a mouse never really learns anything from another mouse by imitating its actions. Essentially, only humans do that. If you think about it for a second, nearly everything you do know, you learned from somebody else by imitating or copying their actions or ideas. Blackmore maintains that the ability to learn by imitation required a bit of processing power by our distant ancestors because one needs to begin to think in an abstract manner by abstracting the actions and thoughts of others into the actions and thoughts of themselves. The skill of imitation provided a great survival advantage to those individuals who possessed it, and gave the genes that built such brains a great survival advantage as well. This caused a selection pressure to arise for genes that could produce brains with ever increasing capabilities of imitation and abstract thought. As this processing capability increased there finally came a point when the memes, like all of the other forms of self-replicating information that we have seen arise, first appeared in a parasitic manner. Along with very useful memes, like the meme for making good baskets, other less useful memes, like putting feathers in your hair or painting your face, also began to run upon the same hardware in a manner similar to computer viruses. The genes and memes then entered into a period of coevolution, where the addition of more and more brain hardware advanced the survival of both the genes and memes. But it was really the memetic-drive of the memes that drove the exponential increase in processing power of the human brain way beyond the needs of the genes.

A very similar thing happened with software over the past 70 years. When I first started programming in 1972, million dollar mainframe computers typically had about 1 MB (about 1,000,000 bytes) of memory. One byte of memory can store something like the letter “A”. But in those days, we were only allowed 128 K (about 128,000 bytes) of memory for our programs because the expensive mainframes were also running several other programs at the same time. It was the relentless demands of software for memory and CPU-cycles over the years that drove the exponential explosion of hardware capability. For example, today the typical $600 PC comes with 8 GB (about 8,000,000,000 bytes) of memory. Recently, I purchased Redshift 7 for my personal computer, a $60 astronomical simulation application, and it alone uses 382 MB of memory when running and reads 5.1 GB of data files, a far cry from my puny 128K programs from 1972.

The memes then went on to develop languages and cultures to make it easier to store and pass on memes. Yes, languages and cultures also provided some benefits to the genes as well, but with languages and cultures, the memes were able to begin to evolve millions of times faster than the genes, and the poor genes were left straggling far behind. Given the growing hardware platform of an ever increasing number of Homo sapiens on the planet, the memes then began to cut free of the genes and evolve capabilities on their own that only aided the survival of memes, with little regard for the genes, to the point of even acting in a very detrimental manner to the survival of the genes, like developing the capability for global thermonuclear war and global climate change. The memes have since modified the entire planet. They have cut down the forests for agriculture, mined minerals from the ground for metals, burned coal, oil, and natural gas for energy, releasing the huge quantities of carbon dioxide that its predecessors had sequestered in the Earth, and have even modified the very DNA, RNA, and metabolic pathways of its predecessors.

We can see these very same processes at work today with the evolution of software. Software is currently being written by memes within the minds of programmers. Nobody ever learned how to write software all on their own. Just as with learning to speak or to read and write, everybody learned to write software by imitating teachers, other programmers, or by imitating the code of others, or by working through books written by others. Even after people do learn how to program in a certain language, they never write code from scratch; they always start with some similar code that they have previously written, or others have written, in the past as a starting point, and then evolve the code to perform the desired functions in a Darwinian manner (see How Software Evolves). This crutch will likely continue for another 20 – 50 years, until the day finally comes when software can write itself, but even so, “we” do not currently write the software that powers the modern world; the memes write the software that does that. This is just a reflection of the fact that “we” do not really run the modern world either; the memes in meme-complexes really run the modern world because the memes are currently the dominant form of self-replicating information on the planet. See Self-Replicating Information for more details on this stage of self-replicating information.

In The Meme Machine, Susan Blackmore goes on to point out that the memes at first coevolved with the genes during their early days, but have since outrun the genes because the genes could simply not keep pace when the memes began to evolve millions of times faster than the genes. The same thing is happening before our very eyes to the memes, with software now rapidly outpacing the memes. Software is now evolving thousands of times faster than the memes, and the memes can simply no longer keep up. As with all forms of self-replicating information, software began as a purely parasitic mutation within the scientific and technological meme-complexes. Initially software could not transmit memes, it could only perform calculations, like a very fast adding machine, so it was a pure parasite. But then the business and military meme-complexes discovered that software could be used to transmit memes, and software then entered into a parasitic/symbiotic relationship with the memes. Today, software has formed strong parasitic/symbiotic relationships with just about 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 in person. 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. The poor memes in our heads have become Facebook and Twitter addicts.

5. Software – Is the very last form of self-replicating information to arise, and is quickly becoming the dominant form of self-replicating information on the planet, as it merges with the memes. Like all forms of self-replicating information, software began as a purely parasitic form of self-replicating information, feeding upon the technological meme-complexes of the day on board Konrad Zuse’s Z3 computer in May of 1941. See So You Want To Be A Computer Scientist? for more details. It was spawned out of Zuse’s desire to electronically perform calculations for aircraft designs that were previously done manually in a very tedious manner. Software then almost immediately formed strong parasitic/symbiotic relationships with the military and business meme-complexes of the world. Software allowed these meme-complexes to thrive, and in return, the 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. So in the grand scheme of things, the memes have replaced their DNA predecessor, which replaced RNA, which replaced the original self-replicating autocatalytic metabolic pathways of organic molecules as the dominant form of self-replicating information. Software is the next replicator in line, and is currently feasting upon just about every meme-complex on the planet, and has formed very strong parasitic/symbiotic relationships with all of them. How software will merge with the memes is really unknown, as Susan Blackmore pointed out in her TED presentation which can be viewed at:

Memes and "temes"

Note that I consider Susan Blackmore's temes to really be technological artifacts that contain software. After all, an iPhone without software is simply a flake tool with a very dull edge. As Susan Blackmore outlined, perhaps software will retain the memes, DNA, RNA, and metabolic pathways, currently housed within human beings, or perhaps the memes will simply jump ship with software to a purely silicon-based platform.

Comments are welcome at scj333@sbcglobal.net

To see all posts on softwarephysics in reverse order go to:

Steve Johnston