By JAMES KNAUER
This is the second of a three-part series dealing with life, its constituency, and some prophesy regarding its future here on Earth. You can read part one here.
I am related to a plant pathologist, Dr. Skinner, a geneticist who specializes in grasses. As he precedes me by ten years, my role has ever been his student, and when he began his career, our discussions were of Mendel’s Laws, regressive traits, and these new devices that were handy for analysis and had come down in price so that many more of them could be employed: mass spectrometers. These were used to identify base pairs for later genetic sequencing. We postulated that computers would do more of the heavy lifting, and wondered aloud if something as complex as a single cell could even be represented digitally.
Then came the Human Genome Project. Our language then was of genes and RNA and enzymes. And though much work had been done sequencing the genomes of creatures less complex than mammals, it remained a mystery how such splendid coordination among life’s various traits of movement, balance, shape and hue could possibly arise. There were predictions that as many as 100,000 genes could be involved, with most of that under the general heading of regulation. When the Human Genome Project concluded, and the tape read out, only 21,000 protein-encoding genes were found, barely one thousand more than the humble roundworm. Worse – and you knew trouble was coming from the phraseology – most of what was found was labeled junk.
It was a most untidy result.
But it did usher in an intense review of all aspects of cellular biology, providing pathways for experimentation that would eventually overturn our understanding of what, precisely, life does during the process of all that living. One key discovery was that cells were not about to wait around for random mutations to add or remove traits. Dr. Skinner himself confirmed this routinely by planting fields of otherwise genetically identical specimens, and watching their mutation rates over time, now that computing power had arrived to do the analysis. His results confirmed that local environment played a much larger role; that cells would adapt their genetic programming much faster to local conditions; and that this was all done by processes identical to that of software. It can all be represented with boolean logic.
In the present, all my classes with Dr. Skinner are on the subject of software, either he is describing software he has written to process genetic data, or he’s telling me about the results he’s found. I am especially glad to hear of his breakthroughs in disease prevention. But we’re always talking software. The processes of the cell have been mapped to those of what are called virtual machines, independent computing environments where hardware and software merge, and form becomes function.
A compute space is essentially the hall we’ve rented in which to carry out all this software business. It exists wherever computation occurs, at every scale of the universe. A single living cell is composed of a large number of overlapping compute spaces, some fixed, many more transitory, coming and going as messages are processed. There are two things which guide every aspect of a compute space:
- The list of things we care about;
- The list of things we intend to do those items in list 1.
Nothing else exists. Nothing else can exist. Therefore, nothing unreal exists within a compute space.
When we apply this model to the results from the Human Genome Project, and end up 80,000 genes short in one hand, and junk in the other, it’s clear we did not have our arms around our compute space, and that the list of things we cared about was woefully incomplete, to say nothing of the interactions between them. Something was missing, and it turned out to be huge.
In the present, the focus has shifted to include the whole microbial world. None of us travels alone. We are host to untold trillions of microscopic organisms, mostly bacteria, that have evolved with us. They are absolutely fundamental to the continuation of the processes of life. And microbes are just the beginning. We are also home to creatures slightly more complex than bacteria all the way up to skin mites. We are far outnumbered by these passengers, most of whom we cannot even see. Of their interdependencies, next to nothing is known.
So, what, exactly, are we?
Software written by humans shares a fundamental trait with both writing and music: the conversion of symbolic instructions into a form that can be understood, heard, or clicked. Each has a design period, where time has essentially stopped, and the author/composer/developer putters around mountains of words, notes, and end ifs. Then comes the performance. The lights dim. The book is cracked, the maestro gives the downbeat, and the icon is clicked. The show must go on.
Like writing and music, the execution of software creates a narrative. Each narrative in a piece of running software is known as a thread, and compute spaces generally have many threads running through them simultaneously. They communicate with one another through well-established protocols, executing their instructions in precise order. A modern factory floor is the visualization of software executing within a compute space. It’s not the robots that are taking over; it’s their programming.
Where microorganisms come into play is in their messaging systems, the chemicals they emit and absorb, which are in turn processed by the host’s cells. They form vast communication networks that we are just beginning to understand. Microbes signal on two general pathways, much like a home network. There is the local part, shared by microbes of the same species. And there is also a shared part, messages able to be read by all microbes. They have many crisscrossing internets on which they communicate. Because we all came up together, we’re all singing from the same genetic hymnal, an eternal, richly layered symbiosis.
Mapping these networks is theorized to reveal the shared portions of our genome with those organisms we carry with us, a larger scale picture that accounts for some of the “missing” genes. The junk has since been revealed to have many functions not related to the creation of proteins, including copy protections, wear redundancy, and local compute spaces. Further, these messaging systems span great distances, as the entire planet is connected by these networks through the top ten miles of earth’s crust, which is where the vast majority of the planet’s bacteria live. What we do not know is how much of that mass of networks is required for any one population of larger-scale organisms – including humans – to exist for any length of time.
This presents challenges for humans on earth as they confront climate change brought on by pollution. How much degradation can the human-dependent biome endure? If humans intend to leave the planet, how much of this biome is required for long-term sustainability? When we say, “beam me up, Scotty,” what are we beaming, exactly? Only a tiny handful humans has yet been outside the Van Allen Belts protecting this planet from deadly radiation blowing out from the sun, and all of them later developed cataracts after only a week of exposure. How much life will we need to take to live?
The software of today – particularly that on which we depend – has been through multiple generations of testing and analysis under live conditions, and the best traits have been preserved. The rest has been discarded, and that accounts for the vast majority of all the software ever written. Going back to the previous version only makes things worse.
Organic software, that which arises from abiogenesis, has no such software publishing house. It has no design teams, no testers, and certainly no help desk. The most intricate constructions of evolution take millions of years to perfect, and the environment of the moment is the only real feedback. There is no central planning, no thought given to the future. Organic software meets the definition of first fit, that programming which worked long enough for the host to pass on its genetic material. The vast majority of organic software has gone extinct. Since organic software merges form and function, there is no need of source code, those instructions which must first be written and compiled in a human-designed compute space. Computation obeys the shape and electric charge of the molecules upon which organic life depends.
About two and a half million years ago, the organic software we would recognize as our ancestors experienced a mutation in the genes governing the shape of a jaw muscle, causing it to shrink dramatically. This opened up space in the skull for more brain tissue, setting in motion a cascade of events that would lead to us. Larger brains led to more survival. There was no guarantee of that, nor is there one for tomorrow. Life abides today.
At some point, some subset of our ancestors decided it would be a good idea to tend the sick. There are fossils indicating broken bones that had mended dating back well over a million years. A broken leg requires setting, and someone to see to your needs for at least two weeks, longer without access to a pharmacy. There came a realization that these lives we have are precious, something which extended beyond the having of children, though the seeds of it were sown there. We recognized value in others, and tending the sick practiced compassion. It was and remains a free choice to continue to do so.
What business would function with first-fit software? Would we trust an air traffic control system to the first piece of software that didn’t crash the first plane trying to take off? I supported Windows 1.0 and that was after thousands of internal builds at Microsoft. Not ready for prime time. It would take until version 3.5 for any kind of trust to build. About ten years of real time elapsed in between. The rational reaction to this was simple: lower the expectations of what the system can accomplish.
If we are willing to forgive the behavior of tested software, what expectations ought we have for first-fit organic systems about which we know so little, and cannot (as yet) be rewritten? Does the presence of a large brain magically undo all the implications of going with whatever worked first? What unreasonable demands are we making of each other in the present simply because we cannot recognize, by ourselves, reason? Human to human, armed with this awareness, the slack seems to cut itself. A big brain is merely another trait as far as evolution is concerned. What we need most seems to be help from one another.
And lest we forget, even the most excellent software ever written was created by first-fit beings made of energy and light, based on a kind of everlasting life, and floating in space. I’ve often wondered if we were already in heaven, and are just disappointed it doesn’t seem, you know, more classy.
Genetic engineering has been with us for some time. The debate around genetically modified organisms (GMOs) touches an intrinsic awareness that it represents first-fit systems tinkering with other first-fit systems in order to get a “better” result, while having to necessarily ignore the expanse of the underlying microbial networks needed to pull it off. While well-intended, we all know mutations will occur. We feel it in our bones. And we cannot know all the myriad possible outcomes in advance. But we press on because for now, disease is down, and yields are up. And many patients would suffer without it.
There will come a point where a critical mass of the biome is mapped, and genetic engineers will be able to craft organic solutions from scratch. Not just improvements or transplants, but wholesale new genomes. No bionic half-machine, but grown structures which build on successful bioengineering principles. Your grandchildren will likely argue with their children over the age-appropriateness of extra limbs, fur, and gills. Family planning will require a genetic engineering consultant. And all the while pressing deeper into the simulated multiverse through ever-expanding online adventures.
And when these modified people roll off the line, what will they think of us?
In part one of this series, we determined that the ancient processes of life cannot be taken, nor given away, meeting the basic definition of inalienable. Will Homo Sapiens 1.0 be so forgiving? Will HS 2.0 want to throw out all versions before that? Once we can eliminate those traits found to be undesirable, what happens to the current holder of the inalienable rights? The coming longevity assures many versions of humans will exist together for scores of decades, if not centuries. How will they live?
There are many questions coming soon that extend well beyond the notion of increased lifespan. Would you take a modification, say, for a handy touch on/off bioluminescent tattoo in your fingertip you can use as a flashlight? Would you grow another finger? Wings? Eyes in the back of your head? More brains? A clone? To what extent is all this regulated by the state? Will it be legal to add or remove memories, with or without consent? Add them without the underlying experience? Add or remove personalities? A second head, perhaps?
Science will not be stopped, and creative minds are already at work. Is there time left, much less the will, or even the awareness, to have the debates we clearly need to have?
In the third and final part of this series, we’ll explore life as a simulation, the fundamental patterns this reveals, and a quantum case for preserving our inalienable rights. You can also read part one here.
Resources Not Linked Above
How Stuff Works, DNA Computing
Discovery, New Plant Language Discovered
Popular Science, Dandruff Fungus Found In Deep Sea Vents
Popular Science, Microbes Thrive In Asphalt Lake And Sunless Glacial Water