VISTA Enterprise Network - Successful Implementation, World Class Support

Thursday, March 30, 2017

Vista and Mumps: What's in a Name

During the Underground Railroad, Vista had no name
The name Vista dates back to the mid 1990s, when the U.S. Department of Veterans Affairs held a contest to rename their medical software. Here's how that came about.

During the Second Underground Railroad of 1977 through 1981, when VA staff secretly developed the original versions of what would later become Vista, they had no name for it. Ted O'Neill and Marty Johnson, two of the fathers of Vista, called it the "field-based systems" to distinguish it from the systems being developed (slowly, expensively, and ultimately futilely) in VA Central Office (VACO). Sometimes they called it the "MUMPS systems" in reference to the programming language it was written in. The "Hardhats" (software engineers) who worked with them often referred to the endeavor as "committing portability," as though it were a crime, which is how VACO treated the doctors, nurses, other medical professionals, and programmers who "dared" to disobey orders from DC by writing their own medical software to solve their problems and improve care for their patients. People were fired, equipment was confiscated and sometimes destroyed, Ted O'Neill was hauled before Congress on fabricated charges, and agents of VACO committed arson at the Washington DC VA Hospital before, in the end, the corrupt Office of Data Management & Technology collapsed in well deserved failure, and the upstart "VA systems" became officially recognized as VA's medical software going forward.

DHCP name but no logo, 1989-06
In 1981, as VACO was finally embracing the VA's homegrown software, someone there (I still do not know who) figured out the software needed a name. They coined the awkward but accurate initialism DHCP for Decentralized Hospital Computer Program, reflecting some of the most important qualities that had led to its success. It had no logo, but at least it had a name. Other agencies that adopted the software followed suit with their own four-letter acronyms (Indian Health Service's RPMS, the Department of Defense's CHCS). Many of the software applications we wrote were given long names and referred to just by their initials (OE/RR, ADT, IFCAP, and so on). From 1981 to the mid 1990s, VA software development was awash in initials.

But the computer industry was innovating rapidly, and the limitations of 80 x 24 character terminals was holding back development of our physician-oriented software, so VA's DHCP developers began working intently on developing graphical user interfaces (GUIs) designed to run on graphical workstations that supported windowing interfaces, like MS Windows, Apple Macintosh, and Unix.

At the same time the DHCP developers were delivering the new windows-based user interfaces (named CPRS for Computerized Patient Record System, a new name for new software in the old DHCP style of initialism), VACO was under intense pressure from Congress, who in turn since 1981 had continued doing their best to represent the interests of commercial EHR vendors by struggling to find some justification for replacing the efficient, effective, homegrown DHCP with more lucrative DOD-style contracts like ODMT&T used to do.

Roy Baker and new grandson, 2012-07-28
VA upper management decided in time honored tradition to rename the existing software at the same time the new windows-based clients were rolled out, and to sweep all of Congress's complaints under the rug of DHCP. The name DHCP, standing now for the "old" VA software, would take the blame for everything the congressional lobbyists had figured out they could get to stick. Meanwhile, the same software - which VA staff liked just fine, lobbyists be damned - with a new, shiny interface that everyone liked, would get rolled out with a new name.

So VA held a contest with a $500 reward to name the "new" VA software. the goal was to get some honest-to-goodness branding that carried more emotional appeal than the cryptic DHCP.

Roy Baker, the director of the Dallas Information Systems Center (Dallas ISC, one of the seven VA regional offices [ISCs] responsible for developing DHCP), was at the Washington Vista Hotel (15th and M Streets NW, Washington, DC 20005) attending an ISC directors' meeting, where they were discussing the evolution of DHCP, with special focus on new interfaces, technology, and architecture, so he had those ideas on his mind. During one of the breaks, he played around with making the name of the hotel into an acronym that captured the core ideas of what we were all working to accomplish for veterans, and came up with Veterans Health Information Systems and Technology Architecture. He showed it to Cameron Schlehuber, VA's Database Administrator (DBA), amused by how it came together. Unbeknownst to Roy, Cameron later decided to submit it to the competition, and it won, surprising them both. Roy got his $500 reward, though as he says "I probably still owe Cameron half."

Cameron Schlehuber in a classic mood, 2015-08-27
Cameron told me this story maybe fifteen years ago, and Roy just confirmed it today, so that's where the name comes from.

VACO's strategy worked for a while. The new, much prettier DHCP, named VISTA, got all the credit for DHCP's good qualities, and the older, terminal-interface DHCP took the blame for its shortcomings, real or perceived. The name change plus the new GUIs bought VISTA more life in VA, allowed users and developers for a while to continue improving the software, before politicization, commercialization, and corruption bogged down VISTA development in a quagmire - a subject for another day.

As for the new name, as a new acronym, VISTA would be spelled in allcaps, by the general rules of English capitalization, and for a while it was.

But then some documenters (and I don't know who came up with this innovation) had the idea of trying to create a logo for VISTA, which is not a bad idea. They went with a typographic treatment, to convert the "ist" in the middle to spindly pseudo-smallcaps and italicize them, thus overemphasizing the V and the A (VA? Get it?). Instead of just using it as a logo, though, they then started inserting this special type treatment into the documentation in every place where the name VISTA should have appeared, creating what master typographer disparagingly calls a logogram, a logo masquerading as a word. Since we were all technical people, not editors or typographers, we did not understand how this violated the rules of capitalization in text matter, so we went with it. I confused things further by inventing the "VistA" logogram in a misguided attempt to create a version of the documenters' logogram that could be used in in emails and other contexts that lacked italics or smallcaps. Since I was teaching national classes frequently back in those days, I spread my misinformation far and wide, and VistA eventually replaced the documenters' logogram as the "right" way to capitalize VISTA.

But it wasn't right.

Roy and Cameron had it right to begin with: VISTA.

In text settings with proper typographic tools, smallcaps could be brought to bear to tame the SHOUTING of using allcaps, to help the name blend in better with the surrounding text. Ten years ago, I wrote a set of three blog posts proposing this, and that's how the Vista Expertise Network spelled Vista for the next decade.

But there was always another option, a better option.

If the name VISTA caught on widely enough, then by the same rules that replaced RADAR with radar and LASER with laser, we could replace most of the capitals with lowercase letters, but as a proper noun describing a specific body of medical software, it would always need to retain the capital V. Twenty years later, it's clear Vista has played a decisive historic role in protecting the health and lives of millions of people, as well as being a powerful influence on the development of medical software.

Ken McGlothlen is pleased with his Choffee, 2013-10-29
I did not notice that the time for the name to be capitalized "Vista" had come until typographer, programmer, and all around renaissance man Ken McGlothlen pointed it out to me. Although smallcaps are better than allcaps, lowercase letters are far superior. Those Byzantine and Carolingian monks who spent centuries working to improve the readability of the Latin alphabet knew what they were doing. The greater variety of shapes, the ascenders and descenders, dots and crossings, all help to break up the wall of capital letters, to help the brain distinguish the characters, so we can read and write far more swiftly in lowercase than we can in upper or smallcaps. As the Vista Expertise Network began its next set of publishing initiatives and new employee Ken got a look at all those smallcaps, he shook his head and reminded me of the rules by which acronyms eventually become words.

Since then, we've begun replacing VISTA and VistA and Vista-with-smallcaps with just Vista. In the near future, we're even getting our name officially changed from VISTA Expertise Network to Vista Expertise Network. We're doing the same thing with the name of the programming language Mumps, which was always MUMPS (or M), for the same reasons.

Aside from following the rules of decent capitalization, improving readability and writability, making it easier to typeset, being less precious, standing against the pernicious spread of logograms, deflating the aggressive pompousness of the COLD WAR, and all the other reasons, there is one more interesting reason to spell VISTA as Vista and MUMPS as Mumps: to honor the historical jokes that led to their creation.

You can't thrive in life without a sense of humor. Only the dull or dull-witted think it's more adult to avoid humor. As countless medical dramas - and real-life medical experience - teach us, the seriousness of medical situations can too easily become oppressive over time, so that professionals either begin to break down into addiction and other forms of escape or begin to shut down emotionally and become disengaged from caring about their patients. Successful medical practitioners often address this by honing their sense of humor. Some of the funniest people I know work in lab departments, pharmacies, cancer wards, and other places where the seriousness of their endeavor must be balanced by the cultivation of their own humanity. The same is true of medical software developers, whose every software bug is a potential hazard to some patient, and yet who work at levels of complexity at which mistakes are inevitable. You have to be able to keep laughing to stay sane and to stay focused.

Octo Barnett, whose pun changed the world
It is therefore not a coincidence that Octo Barnett coined the name Mumps the same way Roy Baker coined the name Vista - as a type of pun called a backronym (a term that is itself a neologist pun).

As the founder and former Senior Scientific Director of the Laboratory of Computer Science at Massachusetts General Hospital, Octo oversaw and guided the work of the three men who more directly created Mumps originally (Bob Greenes, Kurt Marbles, and Neil Papallardo). When it came time to name this new medical programming language he and his team had invented, like many medical and medical-software professionals, he began with humor.

In 1966/67, how can you name a medical computer language and get its point across? You could name it after a disease, but that would be gross. For example, you could name it Mumps. Let's see: Massachusetts General Hospital Utility Multi-Programming Systems.

Years later, ruefully, Octo said if he'd had any idea that damn pun would take on such a life of its own, he never would have suggested it, but the humor is not a flaw. Fifty years later, it preserves the spirit in which it was created - humane, at once going about something serious while remembering to laugh at ourselves along the way.

It's the same mood Roy was in thirty years later, during a short break from the serious business of guiding DHCP's evolution, when he started with the name of the hotel they were meeting at and tried to work backwards, for fun, to fit the ideas behind our serious work into an attractive name for absurd reasons.

Since then, VACO has tried numerous times to pull the same DHCP-to-Vista renaming and scapegoating trick that worked in the mid-1990s, but we won't let them, because Vista is the name we needed. We don't need any more. Multiple renaming just causes confusion, making it hard to talk about the continuity and development of this great work over the decades. We are not interested in bureaucratic obfuscation but in clarity. It's time to talk clearly about what we did and how it has changed the world, to help educate a new generation of caregivers, developers, managers, policymakers, and lawmakers. Vista needs some Sonny Montgomery of the new generation to learn what this is all about, to stand against the endless wasteful replacement efforts, to support VA staff in returning to the business they know so well and have proven themselves so capable of - meeting their own medical-software needs themselves, to improve their ability to care for their patients.

So, seriously, the names are Vista and Mumps. No need for trickery in the capitalization or spelling. There's enough healthy playfulness in the origins of the names to balance out the serious business we are engaged in - improving health and saving lives.

Related Posts:

2007-04-28: VISTA, discusses why we use the name Vista when there are so many competing alternatives out there. (https://vistaexpertise.blogspot.com/2007/04/vista.html)

2007-05-07: Capital Confusion, discusses how the capitalization VistA came about and how we preferred to solve the problem (https://vistaexpertise.blogspot.com/2007/05/capital-confusion.html)

2009-06-03: Small-capital Confusion, discusses the history of small caps and its implications

Friday, October 24, 2014

Database Elements Problem 2: Version Control of Init Routines

For VISTA hardhats, here's the latest post in my series introducing and explaining the OSEHRA Forum project.
"If the answer so far to the question "What is VISTA made of?" is only the tip of the iceberg when it comes to the complexities introduced by non-routine software elements, what else makes up this iceberg?
"Flattening data and definitions into Init routines might result in convenient, flat structures (routines) that lend themselves to version control, but the purpose of these routines is to regenerate these data and definitions at the destination VISTA systems, not to support version control. An Init routine is not a snapshot of a file; it is software that regenerates that file in another VISTA system.
"If our goal is to keep track of the Init routines for their own sake - and that is one of our goals - then loading them into Git or other version-control repositories makes good sense. If, however, our goal in so doing is to successfully version-control the data and definitions they transport, we're in for numerous disappointments. . . ."

Wednesday, September 24, 2014

Future VISTA: A Technical Townhall

VISTA Expertise Network executive director Rick Marshall gave a presentation at the 2014 OSEHRA Open Source Summit called Future VISTA: A Technical Townhall. This session, intended for experienced VISTA developers, addressed priorities for technical development within the VISTA EHR. Topics included the code convergence challenge and a new proposal for broker consolidation. The presentation can be viewed here:
Part I
Part II

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.

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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)

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?

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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?