VISTA Enterprise Network - Successful Implementation, World Class Support

Thursday, August 21, 2014

VISTA and the Agile Manifesto

VA's early adoption of the Agile methodology (before the term Agile had been coined) led to remarkable accomplishments and extremely high customer loyalty.

For organizations that contract out much of their software acquisition and development, it can be extraordinarily difficult to stay true to the Agile methodology. Likewise, the more organizations try to get their software acquisition and development under control - as is required to manage contractors - the more they risk letting processes and metrics replace the Agile methodology.

As VA charts its IT course into the future, and as our new Secretary of Veterans Affairs comes to grips with his organization, we can all benefit from a deeper understanding of what Agile is, why it leads to the successes it does, and how contracting and business processes can conflict with or suppress Agile's productive capacity.

VISTA hardhat Sam Habiel introduced me to the best resource I've seen on the subject so far. It is called the Agile Manifesto (http://www.agilemanifesto.org). It is very short, just two pages. The first page is only a few lines long. I quote it here in its entirety:

Manifesto for Agile Software Development
We are uncovering better ways of developing software by doing it and helping others do it. Through this work we have come to value: 
Individuals and interactions over processes and tools
Working software over comprehensive documentation
Customer collaboration over contract negotiation
Responding to change over following a plan 
That is, while there is value in the items on the right, we value the items on the left more.
This short statement encapsulates how VA revolutionized itself with VISTA, by creating Golden Pairs consisting of programmers and medical practitioners who worked together doing medical-software R&D, letting the discoveries, the experimental evidence from trying things out together, shape the organic and extremely rapid evolution of world-class medical software.

The second page draws out some of the important implications of that terse manifesto, in the form of twelve briefly stated principles:

Principles behind the Agile Manifesto
We follow these principles: 
Our highest priority is to satisfy the customer through early and continuous delivery of valuable software. 
Welcome changing requirements, even late in development. Agile processes harness change for the customer's competitive advantage. 
Deliver working software frequently, from a couple of weeks to a couple of months, with a preference to the shorter timescale. 
Business people and developers must work together daily throughout the project. 
Build projects around motivated individuals. Give them the environment and support they need, and trust them to get the job done. 
The most efficient and effective method of conveying information to and within a development team is face-to-face conversation. 
Working software is the primary measure of progress. 
Agile processes promote sustainable development. The sponsors, developers, and users should be able to maintain a constant pace indefinitely. 
Continuous attention to technical excellence and good design enhances agility. 
Simplicity--the art of maximizing the amount of work not done--is essential. 
The best architectures, requirements, and designs emerge from self-organizing teams. 
At regular intervals, the team reflects on how to become more effective, then tunes and adjusts its behavior accordingly.
I encourage everyone interested in helping VA achieve the most from its healthcare software to learn about and spread the Agile Manifesto. This brilliant and concise frame of reference could help VA shape its next generation of IT policies in the most productive directions, to increase our ability to improve healthcare for humanity.

Friday, April 19, 2013

VEN Webinar 1 - Introduction to VISTA Architecture

The new VISTA Onion Diagram, grandchild of Tom Munnecke and George Timson's original diagram.
VISTA is modular, but not in the naive sense of the word.

VISTA is not modular in the sense of being a structure built by snapping together packages like Legos, which is why projects designed around updating or replacing those Legos invariably fail. A VISTA package is not a Lego.

Instead, VISTA is modular in the sense of being a complex architecture of extensible frameworks, each of which has different kinds of Legos that can be plugged into it. A VISTA package is a collection of different kinds of Legos, each of which is plugged into its appropriate framework to activate it.

The core architecture of VISTA, then, can only be understood by understanding what these extensible frameworks are and how they work together to accomplish the system's functions. The components of all of VISTA's user-oriented packages (like Lab, Pharmacy, Scheduling, and so on) are extensions of those frameworks rather than separable "pieces" of the system.

For example, the Lab package doesn't automate a hospital's Lab department. Instead, it adds numerous plug-in components to VISTA's extensible frameworks until *they* can automate a hospital's Lab department. In other words, VISTA Lab is not a separable program like a word processor that does Lab things. It is in a sense data that the core VISTA architecture uses to know how to do Lab things.

So long as people plan VISTA projects assuming the widespread but naive model of packages as Legos, their projects will fail, often at great expense. Understanding VISTA's unusual form of modularity and how its architecture is built from it is the first step toward being able to carry out successful VISTA projects.

This first webinar in our series on VISTA fundamentals introduces these ideas. You can watch it at the vxJourney VISTA Webinars site here: https://www.vxvista.org/display/vx4Learn/Introduction+to+VISTA+Architecture

My thanks to Fabian Lopez for creating the vxJourney VISTA Webinars series and encouraging me to create and deliver this presentation.

Sunday, January 20, 2013

FLAP Presentation at 26th VISTA Community Meeting


Our Director of Technology, Sam Habiel, recently gave a presentation on the Fileman/Lab Agile Project (FLAP) at the 26th VISTA Community Meeting. You can have a look at his slides at the following link.

http://www.vistaexpertise.net/docs/flap_slides.pdf

Friday, October 19, 2012

Another installment of Expo synopses


  • "Moving Beyond Scrum Into Organization-wide Agile Practices" by John Stenbeck
  • "Nothing is Missing from the EHR" by Tom Munnecke
  • "How to Ask for What You Want: Including Open Source in the RFI/RFP Process" by Carol Monahan and Sam Williams
  • "VISTA Hardhats: Training the Next Generation" by Luis Ibañez
Check them out on the VISTA Expo website!

Monday, October 15, 2012

More Expo synopses


We have posted more synopses of the presentations from the 2012 VISTA Expo & Symposium, such as:

  • "Patching: How it Works For VA, IHS, and the Rest of the World" by Rick Marshall
  • "Data-Centric VISTA" by Conor Dowling
  • "National Drug File and VA Pharmacy: Current Problems and Future Solutions" by Don Lees
  • "A New Drug-File Lifecycle" panel with Don Lees, Rick Marshall, and Dr. Luis Ibañez
Check them out on the VISTA Expo website!

Friday, October 5, 2012

VISTA Expo presentation synopses


Our 2012 VISTA Expo was a great success! We've begun to post synopses of some of the presentations from the event, such as the keynote address:

  •  "Why the VISTA Open Source Community Should Care About RPMS (and why IHS cares about you . . .)" by Dr. Howard Hays
Have a closer look on the VISTA Expo website!

Saturday, September 1, 2012

The Geometry of Life

Phospholipids: their shape makes organismic life possible.
We are looking for a new definition of life that encompasses the organism but also includes other things that are not organisms but are clearly alive, like an organ, an organelle, an ecosystem, and other forms of living structure. Where the classic definition uses factors that represent fully formed living processes, we're looking for a definition whose factors are much simpler, rudimentary, preconditions for organisms and living processes that are not themselves those organisms or processes.

Our goals in doing this are:

a) to replace the self-contradictory and rigid categories underlying the foundations of biology with measurable qualities, that is, to shift from a rational but arbitrary understanding of the world to an empirical one;

Micelles: Phospholipids in water form spheres.
b) to make our science describe the cosmos rather than merely try to define it, to create a new concept of life as a continuum that permeates all things to greater or lesser degrees as do other physical qualities of the cosmos, so we can learn to directly perceive the amount of life in a thing or system; and

c) to give us a context for discussing complex, adaptive systems like VISTA, which until now have had to hobble along without a coherent vocabulary or conceptual framework.

In The Nature of Order, Volume 1: The Phenomenon of Life, Christopher Alexander posits a new definition of life based on his decades-long search for an unambiguous way to distinguish living architecture from nonliving. Because a work of architecture is so different from an organism, so much less complex (at least, until you add in its relationships with people, that is), the natural factors of such an architecturally oriented definition will drive us far away from our organismic prejudices, which is exactly what we want in a more fundamental definition of life.

Vesicles: micelles with water inside and outside.
That is, it's not an accident that a discipline like architecture that is so seemingly far from biology is where we must look for a more fundamental definition of life. We have to be shocked out of our prejudices to see the subject with fresh eyes.

Instead of defining life in terms of organismic living processes, Alexander defines it in terms of geometry. This would seem natural for an architecturally based definition of life, given the importance of geometry to architecture, but it also turns out to be a natural foundation for a complete definition of biological life.

Cell membranes: complex vesicles with proteins.
Any full study of biological organisms will include more elementary forms of organisms, such as worms, jellyfish, sponges, kelp, protozoa, amoebae. The more elementary the lifeform, the greater a role geometry can be seen to obviously have. Spacial geometry is also vital to the living qualities of complex organisms; the role of geometry may be obscured in complex lifeforms, but it remains fundamental. The plant orients itself toward the sun, and toward many other things besides. The animal orients itself to food, water, warmth, safety, gravity, light, mates, and so on. The circulatory system is above all a geometrically precise system of connecting every cell in the body to the outside, to air and nutrients and water and waste disposal. The list is seemingly endless.

From every perspective, at every scale, proper geometry turns out to be a prerequisite for life. Life depends upon its geometry. Disrupt a lifeform's geometry and you damage or kill it. Assemble the geometry of life, and life self-organizes in seeming defiance of the laws of entropy.

Cells: the geometry of inside & outside creates organisms.
It turns out the classic definition of life takes us only about one sixth of the way toward understanding the basic nature of life, discussing the "finished product" of the organism and leaving incomprehensible to us the layers of living geometry, living structure, and living processes necessary for the organism to unfold into life as classically defined.

In his definition of living geometry, Christopher Alexander cites fifteen interrelated geometric properties:

1) levels of scale,
2) strong centers,
3) boundaries,
4) alternating repetition,
5) positive space,
6) good shape,
7) local symmetries,
8) deep interlock and ambiguity,
9) contrast,
10) gradients,
11) roughness,
12) echoes,
13) the void,
14) simplicity and inner calm, and
15) not-separateness

In the posts ahead, we will define and explore these fifteen properties and show how they are as essential to living organisms and other living systems as they are to living architecture.

PHOTO CREDITS

1) A phospholipid (http://en.wikipedia.org/wiki/Phospholipid), like the nutrient lecithin (aka phosphatidylcholine), is an organic molecule with the shape of a tuning fork, in which its tails are repelled by water, but its head is attracted to it. Just like a magnet's geometry is aligned by its magnetic properties toward magnetic north and south (or toward other magnets), a phospholipid's geometry is aligned by its chemistry toward and away from water. Although much less complex and exciting than DNA, phospholipids are every bit as essential to the creation of cells, since their chemical orientation toward and away from water create the geometry of cells - the inside and outside.

Photo: Space-filling models of sphingomyelin (a) and cholesterol (b). This figure shows the inverted cone-like shape of a common sphingolipid (sphingomyelin) and the cone-like shape of cholesterol based on the area of space occupied by the hydrophobic and hydrophilic regions. Diagram created on 26 April 2009 by Wikipedia user Wlstutts.

Source: Wikipedia (http://commons.wikimedia.org/wiki/File:Space-Filling_Model_Sphingomyelin_and_Cholesterol.jpg)

2) Micelles (http://en.wikipedia.org/wiki/Micelle) are the geometric solution to a geometric/chemical problem: dump a bunch of phospholipids in water, and the molecules will have to find a way to hide their water-hating tails. The solution is to form balls of phospholipids in which the water-loving heads face out toward the water and the water-hating tails face inward together away from the water. That is, the phospholipids align themselves into balls to mutually protect their tails. The tails are repelled by water because are made of fatty acid chains, so like oil they won't mix with water. As a result, a micelle can't store water, since that would repel all the tails inside the micelle; they can only keep water out.

Photo: Scheme of a micelle formed by phospholipids in an aqueous solution. Diagram created using Inkscape on 12 October 2007 by Wikipedia user SuperManu.

Source: Wikipedia (http://en.wikipedia.org/wiki/File:Micelle_scheme-en.svg)

3) Vesicles (http://en.wikipedia.org/wiki/Vesicle_(biology_and_chemistry)) are how phospholipids solve the problem of storing water as well as keeping water out. In addition to forming into solid balls (micelles), phospholipids can also form into hollow balls that can contain water. They do this by creating a second layer of phospholipds; the water-hating tails of each layer of phospholipids point toward each other to keep away from the water inside and outside. This clever geometric structure creates the next level of biological structure, in which we not only have water outside, we also have water inside - and most importantly, the two liquids can be different, since they are insulated from each other. This is the geometric precondition for all cellular life, which must be able to carry its necessary fluid conditions for life around inside itself. It can only do that by building upon the vesicle shape that phospholipids automatically generate in the presence of water because of their own geometry.

Photo: Scheme of a liposome formed by phospholipids in an aqueous solution. Diagram created using Inkscape on 15 October 2007 by Wikipedia user Supermanu.

Source: Wikipedia (http://en.wikipedia.org/wiki/File:Liposome_scheme-en.svg)

4) Cell Membranes (http://en.wikipedia.org/wiki/Cell_membrane) are vesicles with additional structure. The double-phospholipid layer of the vesicle is augmented with proteins, whose different shapes allow them to carry out different biochemical work, such as opening and closing holes in the membrane to allow selected molecules (like sugar or oxygen) to pass through the membrane, or providing anchor points for a cell's internal skeletons to attach to, or detecting specific substances outside the cell so the cell can react to them. But when we ignore all the added complexity, the underlying structure of all cell membranes is still the vesicle's structure, so much so that when the cell wants to bring in materials from outside, the membrane folds around it and pinches off to create a new vesicle that contains the substance, a process called pinocytosis (http://en.wikipedia.org/wiki/Pinocytosis). Cells are full of vesicles that store materials for the cell's use, and these vesicles are continually budding off the membrane or reuniting with it. Cell membranes are what happen when phospholipids and proteins join forces to protect their geometry.

Photo: The cell membrane, also called the plasma membrane or plasmalemma, is a semipermeable lipid bilayer common to all living cells. It contains a variety of biological molecules, primarily proteins and lipids, which are involved in a vast array of cellular processes. It also serves as the attachment point for both the intracellular cytoskeleton and, if present, the cell wall. This diagram was derived from 13 to 16 June 2008 by Wikipedia user Dhatfield from originals created from 31 January to 24 August 2007 by Wikipedia user LadyofHats.

Source: Wikipedia (http://en.wikipedia.org/wiki/File:Cell_membrane_detailed_diagram_4.svg)

5) Cells (http://en.wikipedia.org/wiki/Cell_(biology)) may be controlled by the way their DNA defines their proteins and RNA, and in turn by the way those molecules manage the cell's life processes, but cells are structured by their many membranes. Vesicles, plastids, the endoplasmic reticulum, the Golgi apparatus, mitochondria, vacuoles, the nucleus, lysosomes, and many, many other kinds of organelles within cells are made up of these kinds of phospholipid membranes. The geometry of the phospholipid is thus the basic building block of the geometry of the cell, making it possible to separate the organism from its environment, and to separate all its internal resources and functions. Without that ability to control the separation and recombination of resources and functions, they would mix chaotically according to the laws of entropy, and the cell would be impossible.

In our era we focus on DNA as the building block of life, but DNA is so complex that it is fragile and easily damaged; unless it can be very well insulated from the surrounding environment and from most of the cell's own operations, DNA too quickly breaks down. Phospholipids and the layers, balls, spheres, and membranes they naturally self-organize into create the geometry that makes stable DNA possible, along with all the other preconditions for cellular life.

Photo: The cells of eukaryotes (left) and prokaryotes (right). This image is from the Science Primer (http://www.ncbi.nlm.nih.gov/About/primer) a work of the National Center for Biotechnology Information (http://en.wikipedia.org/wiki/National_Center_for_Biotechnology_Information), part of the National Institutes of Health (http://en.wikipedia.org/wiki/National_Institutes_of_Health). This version of the Science Primer was revised 30 March 2004. The image itself was vectorized using Inkscape on 23 May 2007 by Wikipedia user Mortadelo2005.

Source: Wikipedia (http://en.wikipedia.org/wiki/File:Celltypes.svg)

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.

=====

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)

Wednesday, July 18, 2012

Problems Equating Life and Organism


1) Earth: alive but not an organism
In mathematics and logic, a paradox is a sign that we have screwed up. Something we assume to be true must not be so, or we would not have run into the contradictions in our equations or assertions.

In real life, paradoxes have a more interesting meaning, but here too they are a sign that something's wrong with our perspective. They mean we're onto something important, that something profound is trying to reveal itself through the flaws in our understanding that have obscured it until now.

Equating "life" with "organism" has created a raft of problems for biologists. Critics of biology are unerringly drawn to these problems, but biologists have defensively dug in their heels and tried to rationalize each one rather than deal with the the underlying common problem. Here are just a few:

1) If only the organism is alive, then that must mean that every living system is an organism. Thus we end up with James Lovelock's conclusion that since the biosphere is obviously a living system, it must therefore be an organism, which he calls Gaia. And yet, Gaia does not actually satisfy the classical definition of life; it fails the reproduction test, and many of the others it satisfies only vaguely or metaphorically. So, by the classical definition, the biosphere must be dead, even though it's obviously a living system.

2) Organs: not organisms; are they then dead?
2) The boundaries of this definition are filled with small things that seem to hover between being classically alive or dead. Is a virus alive or dead? How about a prion? What about a cell's organelles, like the mitochondria? Is it dead? As with division by zero, the only clear answer adherents of the classical definition can give is "Don't ask that question."

3) If it takes all these characteristics to count as alive, and anything less is dead, then how did life emerge? It is extraordinarily unlikely that they could all happen at once - we have been unable to make them all happen at once in an experimental setting, despite decades of trying. This is why critics of biology point to God - with the classical definition of life, nothing short of a natural-laws-defying divine miracle could create life. Since the proper realm of science is rational empiricism, it is ironic that biological scientists have settled on a definition of life that forces us to introduce unnatural interventions to explain the origins of one of the most everyday features of the natural world.

3) Waterfall, river, ecosystem: dead or alive?
4) In The Timeless Way of Building, architect Christopher Alexander set out to explore why some architectural spaces make us feel oppressed and dead while others fill us with wonder and vitality. This objectively observable effect architecture has upon our subjective life inhabits a gray zone where we lose our ability to describe what's happening, yet with photographs and language Mr. Alexander wrestles the problem into clarity for us. He tries to name this quality that good architecture has and even considers calling it "life," but in the end he accepts that according to the classical definition of life he cannot do it. By process of elimination, he is left having to call it "the quality without a name."

4) Staircase: dead?
In 1979, that classical definition paints him into a corner in which he has no name to describe a nonorganismic living system. The very same problem plagues those of us trying to describe organically organized complex software systems - the classical definition of life bans us from naming what can only be described as a form of life, unless we submit and agree not to name it at all.

By 2001, Mr. Alexander has rightly concluded the problem lies not with architecture (nor with software engineering) but with the classical biologist's false equation of life with the organism. If we break this arbitrary equation, all of these paradoxes disappear.

But without the classic definition, how should we define life?

===

PHOTO CREDITS

1) Earth's biosphere as a whole contains all life and consists of complex living systems, but since it is not an organism according to the classic definition it must therefore be dead.

Photo: NASA/GSFC composite photograph from 20 June 2012. Synthesized view of Earth's Northern Hemisphere showing the Arctic, Europe, and Asia. Taken from the low-orbiting satellite Suomi NPP.
Source: Wikipedia (http://commons.wikimedia.org/wiki/File:Arctic_from_low_orbiting_satellite_Suomi_NPP.jpg)

2) Organs cannot survive on their own as independent organisms, and despite being made of cells they fail many of the other components of the classic definition of life. Therefore, they are dead. Therefore, human beings (who are alive) are made up of dead things, so we are - what? Zombies? Frankenstein's monsters? Paradoxes abound when the organism is the standard of life. Doctors and nurses intuitively understand that the classic definition of life is an obstacle to medicine, so they refuse to abide by it and insist on referring to hearts and lungs as being alive or not when doing transplants.

Image: Gray's Anatomy of the Human Body (20th U.S. edition), 1918. Etching of human heart and lungs.

3) A waterfall cannot be alive according to the classic definition of life. It is not an organism, no matter how many living characteristics it contains, no matter that it inspires so much awe in human beings that our natural response is to assume it has been touched by the divine, no matter how much life depends upon it. Dead dead dead. Likewise, an ecosystem cannot be alive, because only the individual organism is alive, so the combination of living things creates something supposedly dead: the ecosystem. It takes significant training to learn not to see any of this as alive, since its life is so obvious to anyone else.

Photo: The Fulmer Falls, a waterfall located in the Childs Recreation Area in the Pocono Mountains, Pennsylvania, USA. Photo by and ©2006 Derek Ramsey (see Wikipedia page for license and technical details).

4) According to the classic definition of life, nothing Christopher Alexander has written makes any sense. Architecture cannot be more or less alive. Space cannot be more or less alive. It does not matter whether every single human being who ever lived or will live can immediately feel the difference between the oppression of a prison staircase and the joyful vitality of this outdoor one - these are subjective feelings and therefore imaginary. The classic definition of life is itself a conceptual prison that teaches us to ignore the obvious reality before us, that there is more to life than the organism. The organism is a special case. Life is something more fundamental, something that boundary cases like organs and viruses can have, something that water can have, something that space can have, something a staircase can have. When we break out of this trap, we realize that the emergence of the organism stops being a baffling miracle and becomes a universal miracle, an inevitable miracle, because life is all around us to varying degrees. An organism is merely a more concentrated expression of life. Living things are drawn to life wherever we find it, whether in a loved one, in a flower, in a waterfall, or in a staircase. That "subjective" feeling is no more subjective than vision or sound. As Christopher Alexander has shown us it can be quantified and measured even more readily than the supposedly superior classic definition of life. A newly expanded and more mathematically rigorous science of biology awaits us if we recognize that the organism is an example of life, not the definition of it.

Photo: Outdoor stairs, photographer unknown.

Saturday, June 23, 2012

Classical Definition = Life, or Something Else?


A nudibranch and a sea squirt, both classically alive
More precisely, does the classical definition define all forms of life?

"The unexamined life is not worth living for a human being" (ho de anexetastos bios ou biôtos anthrôpôi — ὁ δὲ ἀνεξέταστος βίος οὐ βιωτὸς ἀνθρώπῳ), said Socrates, according to Plato in The Apology. Among the many reasons to live an examined life is that the greatest revelations usually await us in the things we take for granted, the things we do not examine.

Chief among those overconfident blind spots is our habit of framing the bounds of discussion and then letting that frame go unquestioned. This discussion of whether VISTA is a living system hinges on our definition of life, so let's put the spotlight on that.

Sure, VISTA may not fully fit the classical definition of life, but does that definition actually define life? Most biologists agree it does, more or less, but what does that really mean? It means it defines something they equate with life, but that's not the same as saying it actually defines life.

Could this definition be defining something else, something other than life per se? If so, what is it? What is so close to life that biologists would nearly universally confuse it with life?

The wording of the definition - especially certain clauses - gives it away. What is made of cells, metabolizes food into energy, and reproduces? The definition even answers the question for us by using the answer as a synonym for life: an organism. This definition equates life with an organism. It cannnot conceive of non-organismic life, because it has bundled together multiple characteristics - some of which are different in kind from one another - into a single definition and then made an implicit assertion about the subject of the definition.

This definition has begged the question of what is life by offering a definition that only claims to define life. We can all see it defines an organism, and we assume a priori that an organism is the only form life can take.

Is it?

About the Photo

A nudibranch (Nembrotha lineolata, right) lays eggs in a spiral pattern on a sea squirt (Polycarpa aurata).

Nudibranchs are a kind of sea slug, marine gastropod mollusks in the family Polyceridae and class Gastropoda (which includes sea slugs, slugs, and snails). They are often spectacularly colorful, and their external gills rise from their backs like floral plumes.

Sea squirts are a kind of tunicate, immobile filter-feeding marine animals found in shallow waters throughout the world’s oceans. Tunicates preserve the original form and life-patterns of the earliest chordates; all vertebrates—including Homo sapiens—are descended from creatures much like tunicates. In their larval form, tunicates have a notochord, a stiff, spine-like rod that is the ancient predecessor of the spine. Tunicates lose their notochord by the time they reach adulthood, so we evolved from animals like them via neoteny—the retention of juvenile characteristics into adulthood.

Photo: Nick Hobgood
Source: Wikipedia

Monday, June 18, 2012

VISTA and the Classic Definition of Life


A buff-tailed bumblebee (Bombus terrestris)
[A symbiotic relationship between two living systems, each of which unambiguously satisfies the classic definition of life. Photo credit: Joaquim Alves Gaspar Source: Wikipedia]

Does VISTA satisfy the classic definition of life? Let's answer this point by point.

1. Some VISTA software exhibits homeostasis (Task Manager for example), but a lot of VISTA software does not - or, at least in isolation it does not. Once you add users and programmers into the equation, VISTA's software lifecycle exhibits strong homeostasis; but as plenty of organizations have proved, it is possible to impose alternative software lifecycles on VISTA that destroy this higher-level homeostasis. Also, some systems within VISTA that started out without homeostatic mechanisms had them added later, and many more can still be added. So the answer is yes, some of it does, sometimes, under some conditions, but the answer is also no, not all of it, not even most of it, and not always. Yes and no seem entirely inadequate for this point.

2. Ah, organization! VISTA has lots of it, lots of structure built up from basic units to create many higher layers of order. To those of us who understand VISTA's architecture, its overall organization is elegant and often beautiful (though plenty of it is ugly and in need of refactoring). Unfortunately, the classic definition of life pretty much demands cells as the basic unit, and this is not true of VISTA (metaphorical cells don't count).

3. No, VISTA definitely does not have a metabolism (metaphorical metabolism does not count, either). VISTA is completely dependent on an electrical supply, which is the mechanical equivalent of an animal that is only "alive" as long as it is plugged in - we call that a machine. That's pretty much the opposite of a metabolism, so a big no on this point.

4. Yes, VISTA has growth. Oodles of it. Its data multiplies, its software extensions increase, its routines and globals, its files and options, even its extensible frameworks and documentation grow in number over time. At all its layers it grows. Some of this growth requires interaction with other living things (like people); some happens even when VISTA is left to itself. Controlling VISTA's growth is often the real challenge in managing a VISTA system.

5. In isolation, most of VISTA does not adapt, though some of it does, but with programmers and users involved much of it adapts very well indeed, both in the short term and the long. VISTA's adaptabillity is one of its core strengths. Adding heredity to the question, as this definition does, only muddies the picture. VISTA has nothing really like DNA or heredity, but neither is it limited to mechanical copying for its reproduction, as we'll discuss below. What it has instead makes it in some ways amazingly more adaptable than most biological organisms. As with homeostasis, the answer here is mixed and can improve over time, leaving us with more ambivalence.

6. Yes, VISTA is extremely responsive to stimuli, just not the kinds of stimuli or responses biological organisms are tuned to (not motion, for example). In terms of both quantity and variety of information it responds to, VISTA has all biological organisms beat many, many times over. In terms of survival-positive responses to the kinds of stimuli that might threaten its survival, VISTA flunks out with a big fat zero. It has no survival common sense at all, leaving it utterly dependent on its caretakers for its survival. Of course, it does have a strong symbiotic relationship with biological organisms that leads them to fill in this defect completely; most VISTA systems are better protected than most people.

7. Freud said it's all about the sex, so how fitting that we end with this characteristic. We've put it off long enough. Now it's time to answer the question we've all been waiting for (unless we haven't): does VISTA reproduce? The answer is: not like any biological species does. First, like many overbred domestic species, it cannot reproduce without human help - a lot of help. Second, new VISTA systems are derived from existing ones, yet are not clones; each VISTA system is unique. Third, VISTA systems do develop and adapt mainly by exchanging new features with one another to create new combinations of features; dozens of VISTA systems supply new features to each other and all other VISTA systems. It is as though animals were continuously mutating and then sharing their mutations with all the other animals, advancing their DNA while still alive - and not just a little bit, but dramatically over time. So, VISTA systems are overbred, domestic, polygamous, repeat-offender mutants that reproduce asexually from a single parent organism. VISTA has completely separated the twin goals of reproduction: increase in number of entities and genetic change. In other words, weird reproduction and weird sex, requiring the dedicated help of its biological symbionts.

So, no VISTA cannot be called alive under the classic definition of life. There were too many noes on the list above, and too many yeses are partial.

But that being said, there are also too many yeses to simply dismiss them. VISTA may not be a living organism, but it has more than a few of the characteristics of one.

And more importantly, before resting our case we need to explore these questions: Does something have to satisfy the classic definition of life for it to actually be alive? Is this definition complete? Does it actually define life?

Saturday, June 16, 2012

The Classic Definition of Life


The coconut octopus (Amphioctopus marginatus)
[The coconut octopus (Amphioctopus marginatus) satisfies the classic definition of life. Photo: Nick Hobgood. Source: Wikipedia.]

My friend, student, and coworker David Wicksell has pointed out that in my writing I use terms like "alive" and "living system" without specifying what I mean. Am I using these terms metaphorically, or do I somehow mean that VISTA is actually alive?

He raised this question because in Tuesday's webinar, An Introduction to VISTA Architecture, I said it's not a metaphor, that VISTA's literally alive - but how can that be true? Software is part of a machine, so how can it be alive? I agreed with him that I'm long overdue to spend some time laying out what I mean by these loaded terms.

The problem with calling VISTA alive is that it does not appear to satisfy the classic definition of life. I quote at length here from Wikipedia, whose article Definition of Life contains pretty much the definition I was first exposed to back in high school, and that most biology textbooks use:

Since there is no unequivocal definition of life, the current understanding is descriptive, where life is a characteristic of organisms that exhibit all or most of the following phenomena:


1. Homeostasis: Regulation of the internal environment to maintain a constant state; for example, electrolyte concentration or sweating to reduce temperature.


2. Organization: Being structurally composed of one or more cells, which are the basic units of life.


3. Metabolism: Transformation of energy by converting chemicals and energy into cellular components (anabolism) and decomposing organic matter (catabolism). Living things require energy to maintain internal organization (homeostasis) and to produce the other phenomena associated with life.


4. Growth: Maintenance of a higher rate of anabolism than catabolism. A growing organism increases in size in all of its parts, rather than simply accumulating matter.


5. Adaptation: The ability to change over a period of time in response to the environment. This ability is fundamental to the process of evolution and is determined by the organism's heredity as well as the composition of metabolized substances, and external factors present.


6. Response to stimuli: A response can take many forms, from the contraction of a unicellular organism to external chemicals, to complex reactions involving all the senses of multicellular organisms. A response is often expressed by motion, for example, the leaves of a plant turning toward the sun (phototropism) and by chemotaxis.


7. Reproduction: The ability to produce new individual organisms, either asexually from a single parent organism, or sexually from two parent organisms.

One may quibble about terms or ideas here or there, but overall most biologists would agree that this is the current working definition of a living organism, more or less.

Does VISTA satisfy this definition?

Friday, June 15, 2012

Webinar: An Introduction to VISTA Architecture

(See the version of the diagram at the webinar for a larger image.)
On Tuesday at 1:00 p.m. PDT I gave my first webinar, An Introduction to VISTA Architecture. It was in support of Fabián Lopez's webinar series for his VISTA Extensions Hub website, www.vxvista.org. It's the first in a series of webinars we'll be doing together, most of which will be about VISTA architecture, software lifecycle, and policy and planning.

This first webinar focused on a new diagram depicting the layers of VISTA's architecture. This is a great grand-child of Tom Munnecke and George Timson's original Onion Diagram, which they drew on a napkin back in 1978 when they were first planning VISTA's architecture.

Where later onion diagrams developed by VA have increasingly emphasized VISTA's architecture as being constructed of plug-in packages, Tom and George's original diagram was trying to capture the idea of a health-information space, in which a small set of carefully thought out initial conditions would provide all the organization necessary for large numbers of autonomous developers working on their own could nevertheless create a coherent organic architecture. This is the same model used to build the Internet, and it is just about the opposite of the command-and-control model VA had been using up until then to try to do software development.

As VA later slipped increasingly back into the centralized authority model, then lost sight of the organic-growth model of design and reverted to trying to pre-specify the content of the system. This specification-driven model is what VA has been trying and fail to do for the last fifteen years without notable success, and it's what they're still trying to do in the new round of VISTA replacement projects (which try to part out the development of replacement VISTA packages (for their new iEHR initiative). This model cannot work because it is incapable of organizing such a complex system full of so many unknowns. It's what all this discussion of organic growth on this blog is about, that you cannot constrain reality at these scales without overreaching. Instead, you have to forward-bind your system, to leave room for future innovation and growth that you cannot presently foresee - in fact that most of your future development is going to be things you cannot foresee organized in ways you cannot foresee. Trying to plan all this out at the beginning - when we know as little as possible about how it eventually needs to look for it all to work - is building failure into the process from the outset.

The later generations of the Onion Diagram reflect this misunderstanding of Tom and George's original ideas, paying scant heed if any to the idea of an organically evolving health-information space in favor of a Legos approach to snapping together packages.

This webinar with its new Onion Diagram tries to remedy that situation by at least presenting the alternative viewpoint that the true architecture of VISTA is not package-based, that packages are just an organizational trick we use to divide up the work, that the true architecture of VISTA arises from plug-ins into dozens of extensible frameworks and the engines that run them, all of which is built upon a Von Neumann database-management system that allows the creation of an arbitrarily growing, arbitrarily interconnected network of integrated files and routines, which in turn is built upon a simple portability and integration layer.

I welcome your feedback about this new (or perhaps I should say return to the old) Onion Diagram. I'm hoping that in the comments section below the webinar, we can explore these ideas together.

The webinar is here: https://www.vxvista.org/display/vx4Learn/Introduction+to+VISTA+Architecture

Wednesday, May 30, 2012

. . . Part three: Begriff

Verstand's illusion about life: make wholes from parts.
Begriff thinking is not synthesis to Verstand's analysis. Both forms of thinking are capable of analysis and synthesis, but they do it in different ways that result in different products. Here is where the nature of the two forms of thought becomes clearest.

Verstand thinking is mechanistic, abstracting, and rules-based, so it performs analysis by breaking things into parts and rules, and it performs synthesis by following the rules for assembling the parts into "wholes" that are mechanisms. Verstand thinking is motivated by the profound belief that the truth is found in the building blocks of things - that all things are built out of building blocks - and that he who can identify these blocks and the rules for putting them together acquires God-like control over the realm of things those blocks are used to build. At its core, Verstand is a form of reductionism - the belief that truth and power are found by reducing things to irreducible components. Verstand is thus a form of atomism, a kind of logic, a kind of mathematical thinking, a mindset of scalpels and puzzles.

Monsters, not people, are made of parts.
There are many things Verstand thinking is good for; it works well with things that are made of parts, like cars, molecules, equations, and logical arguments. Unfortunately, it works poorly with living systems, as Victor Frankenstein discovered to everyone's horror. Sewing together the best available parts does not result in the best person - any more than interfacing together the best individual medical software packages results in the best medical system.

Living systems are not made of parts. A living organism is not made of parts. Although our language and thinking are so deeply contaminated that we think of our arm as a part that is connected to the rest of the body, that is thoroughly, profoundly false. Our arm did not begin separate for us - we were not assembled by adding arms to an armless torso - and it would do terrible violence to us to remove it. It is not a part. Nor is it connected to us - one connects parts to create a mechanical whole. Its relationship to us cannot be explained in terms of parts and connections - yet that is how we talk and think about even our own body.

Life's true structure: integrated centers.
If we can come to grips with how terrible a job Verstand thinking does of understanding even something as familiar to us as our own body, if we can escape that mode of thought long enough to consider what really is the relationship of our arm to the rest of us, then we can begin to comprehend what it is about living systems that Verstand is so blind to. Thinking effectively, successfully, pragmatically, powerfully about that nameless quality is what Begriff does so very well.

As Christopher Alexander writes in The Nature of Order, Volume One: The Phenomenon of Life, rather than being made up of parts, living systems are made up of centers. In a living system, although these centers are distinguishable and therefore nameable, they are not truly separable from each other. They cannot be separated because they are integrated into a whole - not in the way Verstand thinking would have it, in which they would begin as separate parts and then be snapped or woven together, but rather in a way that only living systems are capable of.

Life unfolds new centers, one after another.
The process of creating life is fundamentally different from the process of creating a mechanism. As Dr. Alexander writes in The Nature of Order, Volume Two: The Process of Creating Life, instead of being constructed from parts, living systems unfold new centers from existing centers. In mechanical construction, parts are visibly present before being attached together. In living construction, centers that are not visible or present develop, grow, and unfold as new levels of order from the order that was already present.

The clearest example of this is the way an acorn grows into an oak tree. The acorn does not contain a miniature oak that merely increases in size, nor does it contain the parts of an adult oak waiting to be assembled. It contains three things instead: (1) it is itself a center, (2) it contains rules for how new centers can be unfolded around the existing center to expand the strength of this initial center, and (3) it is alive, so that it interacts with the other centers around it in ways that permit both them and itself to thrive, so it can gain strength from the presence of the other centers it needs to live. The seed weaves itself into the ecosystem around it, draws upon its resources, and uses them to develop itself into a new center within the larger center. As it increases its own strength, so at the same time it contributes to the larger center around it.

Our arms and legs form as buds, new centers unfolding.
In the same way, your arms were neither present in miniature form in your initial fertilized egg, nor did the egg contain full-sized arms waiting to be bolted onto you. The arm is a center that unfolded from earlier centers that ultimately unfolded from the egg, all following the egg's rules for developing itself through the unfolding of new centers. Each of the centers of your body - your head, your arms, your legs, your fingers, your heart, and all the rest - is both a center in its own right and also a participant in the larger center that is all of you, and most of them are participants in other centers, too (your heart contributes to your circulatory system, but also to your torso, and also to your endoderm, and so on). This quality of being both a "part" and a "whole" at the same time is something the many cascades of centers in living systems all embody naturally, effortlessly, and essentially.

Not a machine, but an ecosystem.
Yet for all its ubiquity this is a quality that Verstand thinking cannot comprehend. This is not a mechanical, zero-sum game directly answerable to Newton's Third Law of Thermodynamics; through the subtle and sophisticated process of life, when one living thing increases its own life it also increases the life around itself. To paraphrase Gary Larson, all Verstand thinking can make of a sentence like this is "blah blah blah part blah blah blah," because the concept of wholes without parts, wholes that cannot be reduced to irreducible components - wholes that are not things - is inconceivable.

So, in truth, your arm is not a part connected to the rest of you. It is a living center integrated with the whole of you. Verstand cannot comprehend this, but Begriff can. Here's why.

Where Verstand trusts in parts and the rules for manipulating them, Begriff deals in wholes, in complete living systems and their behavior. This is why Begriff only accumulates around topics we have immersed ourselves in for long periods of time, to give the subjects time to re-form our minds to fit the complex truths about them. When you have a Begriff understanding of a subject, you don't need rules or parts most of the time to figure out what the subject will do; you just know, because you have experienced it in all its details for so long. How does this work?

All the world's a stage - to us. Mimesis powers Begriff.
The name of our species, Homo sapiens, is fundamentally false. We should be called Homo mimesis, because our true gift is mimicry. We are the world's greatest mimics. We evolved to be capable of so fully immersing ourselves in the behavior of our prey that we could become the prey, could anticipate its actions, its migrations, its needs, its feelings. Art, acting, music, singing, and so many other capabilities of our species owe their existence to the power to imitate, the drive to imitate. Memes and turns of phrase spread through our culture like wildfire until they get old and worn out because we can't stop ourselves from imitating what we see and hear. Earworms get stuck in our heads, playing over and over endlessly until we are driven to distraction because our mind naturally remembers and imitates anything that captures its interest.

In his mind, Einstein role-played light.
When one of us (Homo mimesis) immerses ourself in something - anything - for years and decades at a time, we come to know that subject intimately because our brain is recording and remembering everything about it, anticipating it, lavishing our memory on the details and behavior of it, until in our minds we have grown our subject as a living, holographic representation of it. That actors' capacity, that need, that reflex, is in each of us. The longer we spend with a subject, the more we become the subject.

I'm one of the three experts in the world (along with Wally Fort and Dr. Dave Wilson) on VISTA's Task Manager module. Part of what makes me great at troubleshooting Taskman is that I anthropomorphize him. I know what he will do, how he acts, what he wants, so equally strongly I know - in my gut - when his behavior is off-kilter, because that's not what he would do. But of course, I'm not really anthropomorphizing him - I've become him. In my mind, when I'm troubleshooting Taskman, I am Taskman. I know what I would do in his shoes, which is why my intuitive response is so visceral when he's misbehaving. So it is with most great masters of any subject. Whether they're consciously aware of it or not, in their mind (both thoughts and feelings) they have memorized the role of their subject and can role-play it through all its lines and permutations. They know the role so well, they not only know what would be in character for their subject, they also know what would be out of character.

Learning through mimesis (age 2).
This Begriff thinking, this experience-driven comprehension, can easily achieve precise modeling of the behavior of highly complex, sophisticated systems - can almost trivially do what Verstand cannot - because we are hard-wired to empathize with and mimic things. It's free, built-in processing for human beings. Unlike Verstand, which must be learned, we are born with powerful Begriff capabilities.

Begriff is the basis for much of the rapid learning and maturation by which the infant mind becomes the adult mind, physiological transformations aside. As we learn through education to shift from Begriff thinking to Verstand thinking, we lose our ability to learn rapidly and become increasingly rigid and brittle in our thinking. It is because of this abstractivizing mindset that we lose the ability to see past our own prejudices, because Verstand prefers abstract theories about things over the actual, concrete experience of them. This is why a generation of scientists had to die off before the theory of continental drift - which is so obvious that any child with a globe could see it in the shapes of the continents - could overcome the abstract prejudices against it. Rationalism - an overreliance on the power of reason alone, too independent of concrete, empirical evidence - is a dangerous faculty equally at home leading us away from the truth as toward it; Verstand is the thought process most involved in the pure exercise of reason unrestrained by concrete evidence.

Verstand sees parts. Begriff sees life.
When Begriff is informed by Verstand, we can learn to decompose a living whole into the living subsystems that make it up, rather than just its hypothetical parts or role-playing behaviors. Hardly anyone is competent to do this, to combine both forms of thinking to produce accurate results. Almost no one is born knowing how to do Verstand, and the process of education teaches us to suppress our naive Begriff in favor of Verstand rather than to inform our Begriff with Verstand. Educated or not, we end up being one form or the other of half-wit rather than integrating the two forms of thought to unleash their full potential.

Complex living systems of the kind Dr. Alexander writes about can only be created through living processes. Planning for such development processes cannot be done in the mechanistic ways that dominate modern architecture and project-management theory. And the organic planning methods needed will only ever be conceived and executed by those capable of informed Begriff thinking, by those capable of seeing the world in terms of complex organic systems rather than reductionist tinkertoy machines.