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Saturday, August 25, 2012

A Question of Categories

Mount Tahoma: 2.9 million to 840,000 years old
Under the classical definition of life, a mountain is neither alive nor dead, because it is not "organic," by which we actually mean it is not an organism. Organisms are alive while they're alive, and dead when they're not alive.

Yes, that's the sentence I meant to write. Classical biology begins by accepting these definitional tautologies as self-evident. It also begins by drawing a circle around organisms and declaring the contents of this circle to be the subject of biology and everything else not to be. By virtue of that circle, anything outside the circle can be neither alive nor dead, because those are definitions that should only properly be applied within the circle.

Biology's Archaic Foundational Categories
The biggest problem with biology's classical definition of life is that its apparent detail and precision obscure its fundamentally arbitrary and begging-the-question nature. It doesn't actually tell us anything meaningful about its choice of subject matter; it just gives us three categories to sort things into (alive, dead, and not applicable) and rules for doing so, and it utterly depends upon us not questioning any more deeply into the nature of life itself. We can explore details within that threefold frame to our heart's content, but we are not to look at the frame.

The world never agreed with us about how we drew that set of circles, nor have we proved that they were the right circles to draw. We've simply defined ourselves as correct from the outset by deciding that life applies to what we say it applies to.

The entire thrust of this series of posts is to shake up that complacent and stagnant "thinking," not through metaphors but through questioning our unexamined assumption that we have properly categorized the world into organic things that can be described as alive or dead and nonorganic things that can not. What if we are not metaphorically but literally, rigorously, scientifically wrong about how the category of life should be drawn?

Water cycles across our tidy boundaries
As the higher sciences (biology, psychology, systems theory, information science, etc., the sciences whose subjects appear only at higher states of material organization) develop further from their earlier primitive states, we are coming to understand that there are any number of contradictions, paradoxes, and subtler problems that emerge from our insistence that only the organism is alive, that nothing short of the organism is alive. After all, if those categories are by definition, absolutely, categorically separate, then:

1) How did life emerge?

2) Where is the line between life and death?

3) Why does life seem to defy entropy, even temporarily?

4) How can nonorganismic systems have so many living qualities and yet not be alive?

Campion sprouted from 32,000-year-old seed
How are we to respond to these and the many other paradoxes, contradictions, and defects inherent in these unexamined, mutually exclusive categories?

Usually we try to define them away, which may be intellectually satisfying (or not), but still leaves the problems unresolved. Instead of honestly coming to grips with our defective categories, we resort to other sciences and to hand-waving and changing the subject and if that fails to ad hominem attacks to try to dismiss the fundamental flaws in our categories.

When a 32,000 year old seed sprouts, it proves that our categories of alive, dead, and nonorganismic are broken. Hell, even when a brand-new seed sprouts it proves the same thing.

Cowpea Mosaic Virus: alive but not quite an organism
From an overly simplistic but intuitively satisfying take on the laws of entropy, the seed should just rot (and most do), but some of them sprout and grow into trees, defying all our tidy but self-defeating categories. After all, if a seed is nonliving matter, like a machine is, then it should just break down; my toy car doesn't grow into a full-size car, after all. If it's living matter, then what is it about being alive that makes it able to unfold so much order in a way that a realistic carving of a seed made from marble can't do? Somehow, the seed is appropriating non-organismic matter and energy (sunlight, heat, water, air, minerals, etc.) and transporting it across biology's categorical divide to convert it into living matter - and the non-organismic matter and energy does not refuse to participate. That is, non-organismic life - even a simple molecule, such as H2O or O2 - is fully prepared to cross that categorical divide and assemble themselves into living organisms.

DNA: just a molecule
At every organizational level of the cosmos, everything is prepared to participate in life in some fashion, even if we are not prepared to admit it. Beneath the level of complexity of the whole, finished organism, there is a predisposition to life and a varying degree of living structure and systemic relationships that we have no clean, simple way to describe, because we have defined such "anomalies" and "boundary cases" out of existence with our black-and-white definitions. The entire spectrum of cosmic order from vacuum to biosphere is packed with increasing degrees of challenge to our ossified categories, yet still we insist upon them.

We're wrong about our unexamined assumptions about what constitutes life.

No matter how hard we look we will never find a line between living and nonliving.

Life is not best explained with boundaries between discrete categories but with a continuum that spans everything, like mass, or entropy, or temperature do, with a measurable suite of geometric, organizational, and behavioral qualities that we blinded ourselves to long ago with our false categories and definitions but that nevertheless describes both organismic and non-organismic forms of order in a unified theory.

Prions: also just a molecule, yet infectious and reproduce
We do not have to explain how nonliving matter becomes a living organism because there is no nonliving matter, only matter with varying, measurable amounts of life interacting in ways that are more or less alive. Once we begin measuring the amount of life in a system, we can begin to accurately predict how it will combine with other systems, whether the result will be more or less life, based on the nature of their interactions. That is, we can upgrade the foundations of biology from primitive and arbitrary categories suitable only for rough sorting and logical but non-empirical arguments, and replace them with actual science.

Ganges River Delta: measurable, non-organismic life
What Christopher Alexander is doing in his series The Nature of Order is not a categorical mistake, nor is it metaphorical reasoning. He is deliberately spotlighting, criticizing, and replacing our broken categories with something better, something we need, a new framework for conceiving of life and the cosmos. He is leading the way to a better science of biology.

It is an irrational category mistake to assume that only organisms can be alive. These self-contradictory categories themselves are an impediment to science and engineering. We should insist upon new categories of life and death that are drawn up rigorously rather than arbitrarily, that are scrutinized rather than taken for granted and protected from scrutiny.

It's time to let the accumulated evidence of biology and other sciences guide us toward a new definition of life that offers us a more rigorous, coherent, and useful way to understand ourselves and our place in the cosmos.

And a better way to understand complex systems such as the VISTA software.

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PHOTO CREDITS

1) According to the a priori categories of biology, since Mount Tahoma (AKA Rainier) is not an organism it cannot be said to be alive or dead. And yet we name it with a proper noun, and the first peoples of the Northwest say it has a spirit, and we feel something when we look at it or go there that we do not feel when looking at asphalt. According to the new definition of life proposed by Christopher Alexander, it has a powerful form of geometry that is at the heart of what life is, more central to a proper definition of life than merely whether or not something is an organism.

If we shift to the right geometric view of life, we begin to recognize that far from being an inexplicable miracle, the development of organismic life from non-organismic life was inevitable. We are surrounded by things that have the same kind of life that organisms have, just at different scales of complexity that do not reach the threshold needed for an organism to exist. Mount Tahoma is measurably, non-metaphorically, literally alive according to Alexander's new definition.

Photo: Mount Tahoma over the city of Tacoma, Washington, USA. In this view from the northwest (Tacoma), Liberty Cap is the apparent summit with Mowich Face below. Photo taken 10 August 1984 by Lyn Topinka.
Source: USGS, Cascades Colcano Observatory (http://vulcan.wr.usgs.gov/Imgs/Jpg/Rainier/Images/Rainier84_mount_rainier_and_tacoma_08-20-84.jpg)

2) According to biology's foundational categories, because most of the cosmos is composed of non-organismic matter, most of the cosmos cannot be categorized as either alive or dead, and is therefore no fit subject for biology. Hence, only the minority of matter organized into the form of organisms are termed alive or dead. Further, within the domain of organisms, biology prefers to focus on living organisms, since they satisfy its definition of life. Dead organisms, though categorically falling within the domain that is an acceptable topic, nevertheless pose problems since they fail all the definitions of life, so they tend to be the main study of specialists, a minority of biologists. The transitions between these domains are problematic because of their excessively absolute definitions.

The proper study of life must span the full spectrum across these boundaries in order to explain not only how we live, but also how we come into being and how we cease to be. These things remain mysteries to us above all because their investigation is hampered by a priori contradictions in our conception of life.

Image: Venn diagram created using Omni Graffle professional.
Source: Frederick D. S. Marshall, Saturday, 25 August 2012, licensed under Creative Commons Share Alike, Noncommercial, Attribution license.

3) The water inside your body is not an organism, so it is neither alive nor dead under current biological categories, yet you'd be dead in an instant without it. Further, it has to flow from outside you, into you, through you, and back out of you, or you will die. The organism, the proper subject of life, is not actually a separable thing. If we break the flow to prove you are a worthy stand-alone topic, you die, and therefore no longer satisfy the definition of life. You are only alive so long as you are a filter through which massive amounts of non-organismic matter pass, a filter that is created from that flow and continuously replaces itself from it, but somehow under the modern definition of life all of this matter is to be treated merely as nonliving consumables.

According to these categories, every single element of your body is composed of non-organismic matter. If we remove from you everything that is non-organismic, you cease to be an organism. Therefore, there is no life without all of this matter that has been categorized as outside the domain of life.

So what are we left with, after applying these biological categories to you as an organism? Life must be the result of a specialized set of properly energized relationships among and within different kinds of non-organismic matter that results in an organism. A true, rigorous definition of your life, therefore, has to extend outside the boundaries of your skin to include all of the flows of non-organismic matter without which you have no life. Even so, following current categories, the water that flows into you starts out as neither alive nor dead, then becomes organismic as part of you, then becomes neither alive nor dead again afterward.

These categorical boundaries might have been adequate for early cladistics (identifying and categorizing types of living organisms), but now they impede our ability to understand the dynamics of life. The existing definition of life inherently calls itself into question without offering a clear answer about what to replace it with.

Photo: A graphical representation of the global hydrological exchanges. Created 19 October 2012 by Wikipedia user Anishct.
Source: Wikipedia (http://en.wikipedia.org/wiki/File:HydrologicalCycle1.png)

4) Is a seed alive or dead? If the answer is that it is alive if it is viable, that is, if it can produce a plant, then that is no definition at all because it is an indirect tautology. The question is not whether the plant a seed might grow into is alive; the question is whether the seed itself as it is at that moment is alive. The honest answer is that we don't know. Our definitions and categories are a mess in this area.

Let's imagine that the campion the seed grew into has not existed on the Earth for the past 10,000 years. Now it does. Was it extinct during that time? Is it still extinct? Was it ever extinct?

The categorical problem with seeds is related to the problem with organs. Your heart is not an organism, but it also is not non-organismic matter, and it isn't dead, so it falls into none of the categories. We can't say it's alive because it's only a "part." Our categories fail us, not metaphorically but actually. In practice, we just try not to formally categorize hearts, seeds, berries, and other such boundary cases, so we use wishy-washy words such as "viable" that let us call them alive without admitting that's what we're doing.

Photo: From AP/Institute of Biophysics of the Russian Academy of Sciences.
Source: Discover Magazine (http://discovermagazine.com/2012/jul-aug/06-ice-age-flower-blooms-again)

5) Viruses were one of the first non-organismic forms of life to give biologists categorical fits. From Wikipedia:
Opinions differ on whether viruses are a form of life, or organic structures that interact with living organisms. They have been described as "organisms at the edge of life", since they resemble organisms in that they possess genes and evolve by natural selection, and reproduce by creating multiple copies of themselves through self-assembly. Although they have genes, they do not have a cellular structure, which is often seen as the basic unit of life. Viruses do not have their own metabolism, and require a host cell to make new products. They therefore cannot naturally reproduce outside a host cell – although bacterial species such as rickettsia and chlamydia are considered living organisms despite the same limitation. Accepted forms of life use cell division to reproduce, whereas viruses spontaneously assemble within cells. They differ from autonomous growth of crystals as they inherit genetic mutations while being subject to natural selection. Virus self-assembly within host cells has implications for the study of the origin of life, as it lends further credence to the hypothesis that life could have started as self-assembling organic molecules.
In other words, any fool can see that viruses are alive, but likewise we can see they are not organisms, so which is more important to us, that it has the qualities of life, or that it is an organism? If we had a proper definition of life, we would not have to waste a moment on such inane, useless arguments. It is an obvious form of non-organismic life that we have tried to torture to make it fit the Procrustean Bed (http://en.wikipedia.org/wiki/Procrustes) of our biological categories.

In the contest between yourself and the world, back the world. -Franz Kafka

Photo: Structure of the icosahedral Cowpea mosaic virus (CPMV) based on PDB ID 2BFU. Rendered with Cinema 4D on 18 July 2012 by Thomas Splettstoesser.
Source: Wikipedia (http://en.wikipedia.org/wiki/File:CowpeaMosaicVirus3D.png)

6) In the wake of Watson and Crick's discovery of DNA, our understanding of cellular biology has advanced rapidly. The more we study DNA, the more clearly we understand that it behaves like a lifeform, despite being merely a single molecule. Within its proper environment, surrounded by its supporting materials and structures, it satisfies a surprising number of the elements of the classical definition of biology, despite not being made of cells nor being an organism itself.

It is not self-suficient, but then neither are we, as mentioned above. Can a single molecule be alive? If any can, it's DNA. Indeed, the organismic life of a cell is not possible without DNA. Perhaps instead of seeing DNA as merely a part of a living thing, we should see a cell as the unfolded environment of the DNA, as its creation. Where does the life in a cell actually reside?

Classical biology would say it resides in the cell, and in the complete organism made of cells, but that tissues, organs and systems are iffy, and cell components are definitely not alive (even though mitochondria have their own DNA). Christopher Alexander would say they each have their measure of life, as do all the organelles and other centers within the cell, as do the larger colonies, tissues, and so on that are unfolded at larger scales from the cell's own life.

Photo: Static thumb frame of Animation of the structure of a section of DNA. The bases lie horizontally between the two spiraling strands. Derived on 10 March 2009 by Wikipedia user 84user from an original animated file uploaded 4 February 2007 by Richard Wheeler.
Source: Wikipedia (http://en.wikipedia.org/wiki/File:DNA_orbit_animated_static_thumb.png)

7) Prions (http://en.wikipedia.org/wiki/Prion) are "infectious agents" that are not only not organism, nor even almost-organisms such as viruses, but are merely proteins that were folded badly (http://en.wikipedia.org/wiki/Protein_folding).

In brief, a protein is just a long chain of atoms (carbon, hydrogen, oxygen, and nitrogen). Proteins are distinguished not just by which atoms they contain in which order, but also by how they are folded into shapes. It is their distinct shapes that make proteins indispensible to life, since (as with the tools humans make) they can only carry out their biochemical work if they have the right shape for the job at hand. They literally maneuver other molecules mechanically into place, and their shape determines which molecules they manipulate and what they do to them.

Prions are proteins that have been folded into the wrong shape, and not just any wrong shape but an especially bad one. Prions are infectious in a unique way different from viruses, bacteria, amoebae, or multicellular parasites; the work they do is to refold other healthy proteins they encounter into the prion shape. In other words, they reproduce, using your healthy proteins as raw material. Their spread causes diseases such as bovine spongiform encephalopathy (BSE, also known as "mad cow disease") in cattle and Creutzfeldt-Jakob disease (CJD) in humans.

When we were searching for the causes of these diseases, we were not expecting to find a reproducing molecule; we expected to find a pathogenic microorganism. When the prion theory was first suggested, there was a lot of resistance to the idea. After all, dangerous molecules can't infect you; they can only poison you. If I accidentally swallow cyanide, the amount of cyanide in my body does not increase over time, but if I eat mad cow containing prions, the number of prions does multiply, infecting me with the disease.

The idea of a single molecule that reproduces - other than DNA or something close to it (such as RNA) - is just beyond the pale when it comes to categorizing it as life, under the classical categories of biology. It is technically termed an "infectious agent."

Christopher Alexander has not yet applied his definition of life to the molecular level, but a prion would certainly qualify as a simple form of nonorganismic life.

Photo: Illustration of the process of protein folding. Chymotrypsin inhibitor 2 from pdb file 1LW6. Uploaded to Wikipedia on 18 April 2007 by Wikipedia user DrKjaergaard.
Source: Wikipedia (http://en.wikipedia.org/wiki/File:Protein_folding.png)

8) The Ganges River Delta is the largest inter-tidal delta in the world. With its extensive mangrove mud flats, swamp vegetation and sand dunes, it is characteristic of many tropical and subtropical coasts. The vegetation cushions the shoreline from wind and wave action while the mangrove trees provide a habitat and food for aquatic and terrestrial plant and animal life.

By the classical categories of biology, the delta may contain life in the form of living organisms, but the delta itself cannot be alive, except as a metaphor. Any resemblance between its branching patterns and those of blood vessels, lymph vessels, neural pathways, root systems, fungal hyphae, or xylem and phloem is purely coincidence, and biologists recommend you ignore it. Pay no attention to the evidence before your eyes; trust our unexamined, unquestionable categories instead.

By Christopher Alexander's geometric definition of life, the resemblance cannot be a coincidence, because it is the shape itself that contributes to the measure of life in the system. The shape is where the life comes from. All those things have that shape in common because they are all alive in that way, among others. In other words, the evidence before your eyes is evidence of life, life as properly defined. Of course the River Ganges Delta is alive; anyone can see it, if they have not been trained to disregard the evidence.

Photo: Photographed 6 November 1994 as part of the Space Shuttle Mission Report Series: Earth Observations during STS-066 by NASA.
Source: The Earth Observation Gateway at NASA's Johnson Space Center (http://eol.jsc.nasa.gov/debrief/STS066/rep2.htm)

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