Digital Biology

Peter Wayner writes: "Metaphors drawn from biology have always fascinated computer scientists. No one speaks of subroutines that cp themselves through undocumented remote procedure calls because talk of 'computer viruses' carries all of the portent and weight of polio, anthrax, German Measles and tuberculosis. Invoking these mysterious and deadly images is more colorful than tech speak, even if most of the so-called viruses are closer to the common cold than the black plague. Why use a three-letter acronym when a biological metaphor is available?" Wayner wrote the following review of Peter J. Bentley's book Digital Biology, which may just answer that question. Digital Biology author Peter J. Bentley pages 272 publisher Simon and Shuster rating 7.5 reviewer Peter Wayner ISBN 0-7432-0447-6 summary Does a good job of bridging the analogical gap between the worlds of computers and biology; may not be deep but will probably enlighten readers with an interest in either or both of these fields.

It should come as no surprise that the infatuation is requited because some biologists are just as fascinated with the bits that live in computers. They love to wonder whether the software crosses the line and become a sentient being, whatever that may be. They want to know whether a programmer can play Dr. Frankenstein and create life or at least an indistinguishable imitation. They are entranced with the computer's ability to boil vast amounts of data into a coherent answer and they want to harness this power to solve problems about truly organic creatures.

Peter J. Bentley's new book, Digital Biology is a lively tour through some of the research that joins both of these worlds. It's a quickly paced, colorful examination of how computer scientists and biologists can share metaphors like "the immune system" or "growth." If both groups sit down and compare metaphors, computer scientists may learn something about building robust, self-healing, self-reproducing software from looking at carbon- based creatures while biologists will learn something about creatures by studying them with silicon-based software software.

The book is aimed at the same market that embraced the meme of "Chaos" through reading James Gleick's book. The book is light on equations and heavy on showmanship. In many cases, this is more than satisfying. One description of digital flocks of birds describes how three simple rules can keep the birds floating and swarming with all of the coordinated rolling and swooping. There's no need to invoke numbers or distance measurements to convey what's happening.

At other times, the examples can be so tantalizing that the lack of depth can be a bit frustrating. Bentley promises "The number of different applications that we have successfully used evolution for is immense." To explain this, he offers an example of a coffee table designed by a computer program mixing, matching and cross-breeding varieties. After each generation, the computer cuts some desks apart, creates new combinations and then uses an equation to find the most fit and desirable desks. Eventually, a reasonable candidate emerges. After explaining that genetic algorithms may find patterns of credit card fraud and help us find better jet turbine blades, there's no space to tell us the finer details. We do learn that stunning results can emerge when computer programmers mix the three principles of inheritance, variation and selection. But no book can include everything.

While the book is aimed at a broad market, it does not come with many of the traditional flourishes of journalism. Bentley is research fellow at University College in London, not a newspaper hack who churns out stories for a living. So when he introduces other researchers and colleagues, he doesn't bother with dressing them up with details about their homes, their wives, or the usual chestnuts journalists offer in the hope of humanizing the subjects. The book focuses on the ideas and metaphors themselves and doesn't bother with the window dressing. The names are just incidental markers to give credit and a pointer for further research. Scientists will love the lack of distraction, but casual readers looking for colorful anecdotes about the wacky geniuses in labcoats will need to look elsewhere.

The book, as expected, is generally enthusiastic and heavily invested in the field. Software modeled on biological systems, we are told, will, "detect crime for us, identify faults, ... design new products for us, create art, and compose music."

Despite this partisan flavor, the book shines in the few paragraphs where Bentley pauses to discuss some of the limitations of the systems. "We cannot prove that evolution will find us a good solution-- but it almost invariably does. And we certainly cannot predict that solutions that evolution generates," he notes as a caveat to everyone planning to use genetic programming to solve world peace.

At one point, he discusses one of the principle criticisms of the entire area. After describing flourishing digital forests filled with fractal ferns, problem solving viruses, and swooping swarms of evolving birds and insects, he pauses and offers this quote from another biologist: "Where's the experiment?" He notes that most of these creatures are flights of our imagination untested in the lab against real ferns, viruses or birds. Nor is there any real way to test a fern hypothesis. The digital versions look real, but there's little gritty lab work to establish them as true metaphors for sussing out the secret laws of nature. Is looking real enough? Can you measure verisimilitude? Do any traditional experiments measure anything better than the quality of a simulacrum? Is appearance enough or is it only skin deep? After a pause, though, the book is on to more talk of big payoff and grand promises.

In its heart, the book is more a document that shows evolution of problem solving techniques. If you want to get the sales pitch from the computational biology world, you can turn to this book. When there were no machines, scientists used symbols, algebra, calculus and other mathematics to describe the world. Biologists have long employed differential equations to describe the booms and bust in ecologies of predators and prey. Now that we have computers capable of billions of operations in a second, we don't need the old school of mathematics to provide a closed-form solution. The computers can just simulate the world itself. There's no need to struggle for a set of equations that is both easy-to-solve and appropriate. We can just use little worlds of sims creatures, sim fronds, sim viruses, and sim antibodies.

Bentley's book is an ideal way to learn just how and why some biologists are absolute enraptured with the new powers discovered by these computer simulations of genetics, growth, flocking and other natural phenomenon. These models don't offer the kind of concrete certainty of mathematical models, but there's no denying that something is somehow there. Is it as much a breakthrough as Bentley believes? Well, maybe you the reader can create a genetic experiment to cross fertilize the ideas from the book with the ideas in your experience. After a few generations of thought, perhaps a few generations of beer, an answer might evolve.

Peter Wayner is the author of Free for All, a book on the open source software movement and Disappearing Cryptography , the second edition of a book on steganography expected to appear later this spring. He is also the author of several articles on simulation including studies of studies of the relationship between sex and AIDS , segregation , and the length of baseball games. (Each of these links includes a Java applet so you can run the simulator from your browser.) You can purchase Digital Biology from Fatbrain. Want to see your own review here? Just read the book review guidelines, then use Slashdot's handy submission form.

Comments

Stop READING SLASHDOT!

[LunchLady]

The Twelve Steps, originated by Alcoholics Anonymous, now applied to Slashdot. This is the spritual foundation for personal recovery from the effects of Slashaholism, not only for the slashaholic, but also for their friends and family.

Many members of 12-step recovery programs have found that these steps were not merely a way to stop commenting, reading, and retardedly clicking on every link (including all those Goatse links you fags like), but they became a guide toward a new way of life.

Step 1: Honesty
After many years of denial, recovery can begin when with one simple admission of being powerless over CmdrTaco -- for Slashaholics and their friends and family. The Goatse man also owns you, so you should admit that too.

Step 2: Faith
Have faith in the fact that if you stop now - you will be saved. Not only saved but you will never ever have to read or hear about Jon Katz again. Well, I take that back - you will hear about him again, on a legitimate news site where you read that he was finally caught and convicted to the Goatse Man chamber for raping kids.

Step 3: Surrender
A lifetime of slashdot will destroy your soul. Keep in mind that Slashdot is worthless. It does you no good and it is hurting your family. Surrender to the temptation of posting a useful article to slashdot. Surrender to the temptation of even visiting this disease.

Step 4: Soul Searching
Search your soul - why did you first come to Slashdot? WHY? What is here for you? These people are not your friends. They are disgusting dirties that give a general smell to themselves and everyone around you. You all probably notice it when you go places at people look at you funny. It's because you smell like shit.

Step 5: Integrity
Integrity. Not much more needs to be said here. Of course to have integrity one must not smell, and one must have a positive self image. This is also to say - you cannot be the dirty hippie you want to be. So, stop praying to your sun crystals and take a shower.

Step 6: Acceptance
Accept that you will never visit the Slashdot site again. Katz wants you around because you are most likely 14 and he digs little kids.

Step 7: Humility
Practice some humility in your life. Know your place - it is not being a bottom rung goatse link follower at slashdot. The sooner you break the chains of slashdot the sooner you can raise yourself out of the gutter.

Step 8: Willingness
Making a list of those harmed before coming into recovery may sound simple. Becoming willing to actually make those amends is the difficult part. Think of what your parents think about you...are they proud of their dirty anti-shower homosexual hippie child? What about your friends - and not your imaginary friends you fuck hippies. The trees are not alive.

Step 9: Forgiveness
Making amends may seem like a bitter pill to swallow, but for those serious about recovery it can be great medicine for the spirit and soul. Once you have stopped visiting Slashdot - you should take the steps to appologize to your friends (not your imaginary friends, fags) and your family about what an ass you have been over the past X months/years at slashdot. Tell them you are sorry and you didn't know. Tell them you were sucked in my the Goatse Man's ass chamber.

Step 10: Maintenance
Nobody likes to admit to being wrong. But it is absolutely necessary to maintain spiritual progress in recovery. You've visited slashdot and actively engaged in the slashdot moderation system. While this makes you a complete flaming homosexual - there is still hope. You've done wrong in the past - let's make the future a brighter and better place, for everyone.

Step 11: Making Contact
Break the bonds of slashdot that hold you prisoner. You can simply GO OUTSIDE! You fuck hippies could probably use the fresh air - at least it would give your parents a chance to clear out the old smelly air within your room.

Step 12: Service
As a community service. Stop using the internet for at least 1 year. Why you ask? You do this because you have committed sins against the internet community by actively being a part of slashdot. This year off will give you time to reflect about what you have done and about who you have hurt. Also, keep in mind - by the time your year is up - there is no way in hell Slashdot will be online. For one, Jon Katz will surely have been found raping children in the slashdot offices which will destroy the company. If not Katz then the website will fail with it's to be introduced subscription services. Not only will the temptation of slashdot be gone - but the year off of the internet will give you a chance to meet real people - and actually make friends.

Follow these steps are your life will be rich and full.

Digital?

[tenman]

Does anybody remember when analog biology was good enough?

yeah right

[oever]

I know what they mean:

1-0-1

Re:yeah right

[bigjames]

Is that something to do with dalmations ?

Warning

[Anonymous Coward]

This book, like so many other supposedly balanced books on biology, assumes that evolution is true and pushes it at every possible opportunity. People with open minds may want to avoid this book, and members of the moral community will definitely not want to read this. "Analog" biology is a controversial enough subject, there is no need to read about digital biology.

Re:Warning

[PD]

It's easy to see why evolution is a hard concept for you to grasp. Trust me, after you go through it once, things will be much easier for you.

Re:Warning

[supernova87a]

Although the message above this has been marked as flamebait, I'd like to comment briefly.

For those who (inexplicably, through brainwashing or other) don't believe that evolution happens, computers (and their software) provide an unequaled example of evolution in progress.

The speed of computers is the main reason we can actually witness technological evolution happening. Here we have the essense of evolution -- a multitude of different technologies that compete in a marketplace, people writing software and bringing "mutations" into the system to improve it. Look even only at the past 20 years of computer history -- can you simply ignore the evolution going on from Commodore 64 to Apple IIe to Mac to Windows box (to linux box, he he)?

I think this is a very apt idea -- that the forces of biology (call it something else if you want, silicon dynamics)can be seen in our own creations -- with all the implications that that brings. It makes no sense to put your fingers in your ears, evolution is happening.

Well, maybe not in Kansas, or Texas...

Re:Warning

[Anonymous Coward]

What a wonderful generalization about why Evolution MUST be true! Idiot.

Re:Warning

[Gannoc]

can you simply ignore the evolution going on from Commodore 64 to Apple IIe to Mac to Windows box

Unless, say, an Apple IIe in the wild mated and birthed a mutant Apple IIgs, which due to advantages in the environment lived to mate more and more with other machines, then thats not evolution. Just because something is advancing doesn't mean its "evolution".

Re:Warning

[PD]

Oh oh, your compelling argument has convinced me!

Re:Warning

[boaworm]

For those who (inexplicably, through brainwashing or other) don't believe that evolution happens, computers (and their software) provide an unequaled example of evolution in progress

Indeed. For those familiar with Artificial Intelligence, Genetic Algorithms and Genetic Programming, this should already be familiar.. but to enlighten the rest :-)

When talking about AI you have to make a differentiation between the "body" and the "brain". In a computer simlulation you can say that the simulation environment is the body and the "genome" (phenotype) is the brain. Intelligence does not lie in either, but in the cooperation between them. Rather simple.. how much is your brain worth without eyes, arms, legs, nerves etc ? And the other way around.. what to do with your body if you cannot process the data.

So, back to the reflection on the comment above, most people tend to say that humans evolve through the brain, while it is more true to say that the brain and the body coevolve. The same goes for computers, both software and hardware coevolves, keeps getting better and matching each other.

The interesting part here is that if we can understand the body (not that hard, just molecular biology and stuff), then we have one of two keys to human intelligence. That is why biology and computer interaction is so interesting, if we can simulate biology (body) on a computer (body), then we have an increased ability to learn about the brain. A few months ago, an Israeli company successfully performed calculations on human cells. This is the reversed way, using biology as the "body" and computer algorithms as the "brain". Very interesting results, and very promising. This generation or the next should have a fairly good chance of screwing up this planet totally :-)

Re:Warning

[Brian Boitano]

uhh... but computers (etc) have a significant amount of design built into them ;)

Re:Warning

[hoggoth]

> ... evolution bad ... moral = stupid ... etc...

You must be a beginner. Flame bait has to be a little more subtle than that.

... blah blah blah ... abortion ... blah blah blah ... racism ... blah blah blah ... religion ... blah blah blah ... nazi ... blah blah blah ...

Re:Warning

[lohen]

In saying that this work believes in the reality of evolution, you are saying that it works on the assumption that the current scientific orthodoxy is accurate. And believe me that, as a biologist, we are just as certain about evolution as rocket engineers are that their designs are propelled by fuel etc rather than the will of God.

Of course, 'believing' in the current scientific orthodoxy would be wrong too, in terms of having faith in it being 100% correct. Almost everybody who can call themselves a scientist would feel quite certain that they cannot be certain of its accuracy, and shouldn't try to be. Science works on scepticism and guesswork based on the data available, not faith.

Re:Warning

[Seehund]

Just because something is advancing doesn't mean its "evolution".

But that is exactly what it means. Not necessarily evolution due to natural selection, but still evolution.

Re:Warning

[WotanKhan]

Actually, evolution, in its most general sense, is simply change in a certain direction. This comes up often when I am unfortunate enough to discuss evolution with a creationist. They are rarely well-informed enough to understand that what they disagree with is biological macroevolution and end up trying to debate whether things change at all, in order not to appear to be giving ground. *sigh*.

Re:Warning

[Alexis Morissette]

The "moral community"? Gee, there's no unwarranted elitism in that, is there? From my life experiences, people who accept evolution as true are generally of a higher moral calibre than those who believe in the "theory" of creationism. Funny how that works...

Re:Warning

[esper]

That one cuts both ways. 10 years ago, when I was furiously debating both sides of evolution vs. creation at any opportunity, the standard textbook example to prove evolution was that a mostly-white species of moths turned mostly-black when industrialization hit the area. That's nice and all, but very few people seemed able to grasp that changing the statistical distribution of existing phenotypes has little-to-no bearing on the development of new genotypes, much less new species. There are underinformed people on all sides of every issue.

Re:Warning

[Anonymous Coward]

This comes up often when I am unfortunate enough to discuss evolution with a creationist. They are rarely well-informed enough to understand that what they disagree with is biological macroevolution

Funny. I find the same problem exists among evolutionists...

Re:Warning

[Chiasmus_]

Unless, say, an Apple IIe in the wild mated and birthed a mutant Apple IIgs, which due to advantages in the environment lived to mate more and more with other machines, then thats not evolution.

It's not biological evolution. Then again, that ought to be pretty obvious, since it's not biology.

I think it is safe to say that the Apple IIg had advantages in the business, economic, and academic environments, which enabled it to survive (for a time) - while the Apple IIe went extinct (at least, extinct in the sense that no more are being made).

Sure, you can be a purist and say this has nothing to do with evolution, but this discussion is *all about* drawing analogies between biology and computing.

Re:Warning

[Yet Another Smith]

Actually, it does mean that its evolution, however, its not natural evolution, and its not natural selection. Its human selection and intelligent design. And don't go there, 'cause thats a whole can of worms :P

The opinions expressed above do not represent the opinions of the author.

Re:Warning

[zoydoid]

I can't believe the numbers that bit on this. Very funny.

Re:Warning

[Anonymous Coward]

It doesn't have to happen in the physical world, it could happen in people's heads. The designs could merge and produce offspring, which then compete in the marketplace or something.

Of course that's not what happenned either...

Wait...

[joshjs]

the review will answer the question... ? =D

The Solution to all

[xSterbenx]

Software modeled on biological systems, we are told, will, "detect crime for us, identify faults, ... design new products for us, create art, and compose music."

It will also take out the trash, make your bed, screen calls from your annoying ex-girlfriend, make sure your milk is still good, tell you you're looking skinnier, and reprogram your TV to get all the good channels.

Re:The Solution to all

[Anonymous Coward]

...but it still won't open the pod bay doors.

Re:The Solution to all

[damien_kane]

With a little bit of ingenuity and good old-fashioned coding you can already make a box screen calls from your ex (caller id), monitor expiry dates (simple database, possibly + barcode reader), and 'reprogram' your TV (TiVO?) Add to that a complicated mess of actuators and hydraulics (robotic arms) and it can easily make your bed and take out the trash. With a soundcard you can make the computer say anything you ask it to, and leaps and bounds have been made in the field of simulated AI chat programs.

Re:The Solution to all

[Anonymous Coward]

I want an omelet!

Truly an American icon

[Anonymous Coward]

Peter J. Bentley is a great author. I think that his most well-known book is Jaws, which was later made into a widely successful movie by Stephen Spielberg. I have to wonder, though .. this seems like a different career turn for him. Has he done any non-fiction before, or is this his first foray into that genre?

Software IS a living thing

[qurob]

At least to some programmers....

Writing a living, breathing program would be the goal of many of us, not just AI programmers

Amazon's Review

[LunchLady]

Here is Amazon's Review. Not bad, and much better than the slashdot review above.

Re:Amazon's Review

[L0rdkariya]

I don't know, that Amazon review had some gaping holes in it. Not as big as the ones on Slashdot, though.

COMMON SLASHDOT MYTHS

[returnofthe_spork]

Myth: Linux is ready for the desktop.
Fact: Linux is not, and never will be, ready for the desktop. If you use Linux as your desktop choice, you are an anti-social nerd who will never get laid.

Myth: Open-source is a viable business strategy.
Fact: No it isn't.

Myth: Slashdot is a nice place to go for intelligent conversation about technology and political issues.
Fact: Slashdot is full of 14 year-old fanboys who toe the party line for the "approval" of people they will never meet and fascist Janitors who resort to low minded trickery and censorship to further their narrow world-view and agenda. If you want to read posts that are Insightful and Funny, read at -1.

Myth: Information wants to be free.
Fact: Musicians want to be paid.

Myth: Constantly putting down popular music and culture shows your uber-intelligence and good taste.
Fact: Constantly putting down popular music and culture shows you are a stuck-up fuckwit with no friends.

Myth: The government is taking away our rights. WAAAAH!!
Fact: While you're busy complaining and stuffing your fat face with pork rinds and cheese puffs, the government is busy keeping you, and the American way of life, safe from harm.

Myth: Libertarianism is a good solution to our problems.
Fact: Libertarianism would result in a worse country than the USSR, with political and economic instability, horrific human rights violations, and exploitation of workers of a scale not seen since slavery was outlawed.

Myth: Microsoft is an evil monopoly bent on world domination.
Fact: Microsoft is a software company based in Redmond, WA, that produces fine software and believes that programmers should get paid for their work.

Have I missed any?

Re:COMMON SLASHDOT MYTHS

[Anonymous Coward]

MYTH: CowboyNeal will lose weight by sitting on his fat ass all day reading Slashdot and playing with Linux.
FACT: CowboyNeal is having a heart attack, even as we speak.

-WireTap

Re:COMMON SLASHDOT MYTHS

[LunchLady]

Myth: Being a dirty faggot slashdot reader is a healthy enterprise to be in. Thus, having no friends is good.
Fact: Being a friendless dirty hippie will get you know where - you are on a crash course. See here for instructions on how to quit.

Self Organizing Systems

[Sarin]

This is one of the courses I followed at the university, during my artificial intelligence study.
Lots of examples of this book, came back in our practicums, there are nice links to sites about this subject on the page and also the complete course is online for you to download (not sure if my professor is going to be happy about this, but who cares, I passed the grade:)

another gay review

[neal n bob]

while they did not mention the day-to-day buggery that is slashdot, the homosexual undertones of this book are clear.

Biologists and Psychologists Abuse this...

[Ieshan]

To the worst extent possible.

My psych professor explained our language lecture using layman's computer terminology, instead of psychology. I wanted to strangle him the entire time. "So... you've got this memory stuff... and it get accessed - that is - processed, by this other bit over here, right, this area of the brain... let's just call that the "software"."

It was enough to make any techie of any note sick. He actually used Microsoft as a language. Talk about wanting to shoot someone.

But what can we do? Everyone thinks they're a programmer or a techie these days, and everyone thinks that because kids use IM they must have some other association with the grey box.

Sorry fellers, that's wrong. Most kids today don't know jack about computing, much less are able to relate better when you babble incessantly about things in your half-tech, half-psychologist manner. Stick to the psychology or the biology, instead of using computer terms to explain simple concepts. It's just more confusing and more hellish. :(

Re:Biologists and Psychologists Abuse this...

[Anonymous Coward]

Just what do you call a computer virus then? It sure can't be called a virus because thats mixing biology and computers.

Re:Biologists and Psychologists Abuse this...

[DeadVulcan]

My psych professor explained our language lecture using layman's computer terminology, instead of psychology.

My understanding is that psychology has always chased the latest technology in its efforts to explain the mechanics of the brain. The brain has been compared to steam engines and grain mills, in their time (so I hear).

The biggest irony is when psychologists describe the brain as a neural network (the kind that's been modeled in computers), because the origin of idea for the neural network was the workings of neurons in the brain!

For this reason, many people insist that computer neural networks should be called artificial neural networks. Indeed, the artificial neural network is an interesting mathematical algorithm that takes its inspiration from "real" neural networks. It was never meant to be a model of the human brain by any stretch of the imagination.

You have to admit, though, the analogies are getting better. The brain is definitely more like a computer than a steam engine.

Re:Biologists and Psychologists Abuse this...

[Anonymous Coward]

As a neuroscientist and former CS major in college (and long time Slashdot reader) I can also assert that programmers abuse biology metaphors just as badly!

I'm tired of the comprarison of viruses to computer viruses, as well as DNA to computer code. Everytime an article on neural/silicon interactions comes on - here come the stupid Neuromancer "jacking-in" references! Every time a genetic engineering article comes here, people whip out "Jurassic Park" and "Chaos theory" to explain why they don't consider GM a good idea!
Mixing some computer and biological metaphors on a very BASE level has its uses, but people on both sides all too often become overly enamoured with these simple comparisons and forget the very REAL and often subtle differences that invalidate the metaphors.

A lot of coders I've met need to learn as much REAL (not popular) biology as the biologists you are complaining about need to learn about computers! Basically - I thought your comment was more than a bit one-sided and somewhat condescending - knowing alot about bits, pointers and registers doesn't make you any more qualified to mix metaphors than knowing alot about neurons, genes, and molecules does!

Sincerely,
Kevin Christie
Neuroscience Program
University of Illinois at Urbana-Champaign
crispiewm@hotmail.com

Re:Biologists and Psychologists Abuse this...

[ramb]

Even worse the metaphor begins to fall apart fairly rapidly the moment you poke deeper than the metaphor's skin.

Metaphor is a difficult thing, because you are attempting to illustrate an independant reality using something that is familiar to the listener. The danger is that the listener may mistake the analogy for formal equivalency. I tend to open my lectures with bold metaphor (the brain is a swiss army knife...)to try to grab students attention and give them a conceptual framework, and then often spend the rest of the lecture (term?) fighting this phantom notion of formal equivalency (no a ligand is not a key, and a receptor is not a lock). Formal concepts are difficult to absorb, just think of metaphor as the vehicle that carries ideas (whoops there I go again). Of course if your professor does not pick apart his/her own metaphor by the end of the term, then perhaps he/she is doing a disservice to the less engaged students.

What I find really fascinating is how teaching and general discussion is limited by metaphor. When discussing things among collegues there is little elaboration of many things because they grok the independant reality of a phenomena as well as I do (probably better). The metaphors come out when you need to discuss/explain something to the less-expert. I don't think that anyone ever believed that working memory was a "scratch-pad" or that long-term memory was a "tape-recorder". While many of my collegues might argue for the brain as universal-Turing-machine in the formal conception, I don't think any of us believe that the brain is a computer like the one on your desk (we are analog). All of us in our technical capacities just lack the language to express our ideas to the less technically adept.

Re:Biologists and Psychologists Abuse this...

[Yet Another Smith]

Welcome to the hell that we physicists have been dealing with when philosophers start talking about the Heisenberg Uncertainty Principle. Trying to explain that it doesn't mean "nothing is true" is a bit like explaining the entire history of the East India company to a tea leaf.

Re:Biologists and Psychologists Abuse this...

[Pentagram]

I'm tired of the comprarison of viruses to computer viruses, as well as DNA to computer code.

Excuse me? Surely both examples you give are excellent analogies of each other. Viruses parasitically use the machinery of their hosts to spread themselves... and so do computer viruses (well, worms at least.)

And DNA is a digital series of instructions that are interpreted to express something... and so is computer code. Has anyone proved you can build a Turing machine in DNA yet? Admittedly, DNA is processed in a rather more analogue fashion than most computer code, but as an an analogy, it's better than most; (for example) the old one about breaking computer systems/ breaking into a house.

Re:Biologists and Psychologists Abuse this...

[Anonymous Coward]

You took the words right out of my mouth! MOD PARENT WAY UP and keep non-computer related science off Slashdot. I cringe everytime I see Einstein's ugly mug because I know it's some misunderstood hodge-podge which ended up as a story because it contained "k00l" words like "gene", "DNA", "virus" or "mutant".
For crying out loud, the reviewer didn't even bother to introduce the author with more than that he's a "research fellow".

AC, physician (f*ck those disgusting patients - doing a study on angioneogenesis instead) ;)

Re:Biologists and Psychologists Abuse this...

[lukesl]

On some superficial level computer virus and DNA code analogies are good, but the problem is when people take them too far. What makes these analogies bad is that you don't have to take them very far to go too far. The computer virus analogy, to have any value, would require that programs are like cells, for example. They're not, at least in the important ways. The DNA code analogy is a very, very dangerous one that is emerging. Perhaps the best comparison I can make is to the brain-computer analogy. There are very few things more damaging to understanding of the brain than this intuitively appealing piece of idiocy. The DNA code analogy is already starting to lead people astray--I've seen papers from CS people making evolutionary arguments about coding in base 2 vs base 4 (ACTG = 4 bases) and that kind of thing, but the arguments are completely irrelevant because they take one detail and ignore everything else of what's known about the biochemistry of nucleic acids and the molecular biology of cells. Bad analogies are dangerous because they poison the way people think. Unfortunately, since biological systems are invariably orders of magnitude more complex than the systems they're being compared to, it's usually the conceptual understanding of the biological issues that suffers and not the other way around.

Re:Biologists and Psychologists Abuse this...

[Anonymous Coward]

Computer viruses and real viruses (besidse the fact that one is a reah physical entity composed of proteins, polysaccharides, and nucleic acids, while the other is a string of 1's and 0's and must be interpreted by a man-made machine language) don't fit together on a phemonenological level.

The current hypothesis regarding virus evolution is that they arose from the host genome themselves - they are not an externally-evolved entity that merely exploits another organisms replication machinery - they are themselves modified PART of that machinery! Computer viruses, on the other hand, are created by external forces (people) to exploit a man-made translational mechanism (memory systems and program execution systems) of UNRELATED programs. The metaphor jives on a BASIC level, but when you go any deeper, it falls apart, and I just don't see what purpose it sevrves other than to confuse the biology and the computer science.

With regards to DNA - the fact is, is that DNA->RNA->protein expression is an INFINATELY more complex and less understood system than high-levelcode->lower-level code / assembly->machine language instructions. The former has an insanely complex web of interactions with promoters, enhancer regions, transposons, developmental effects, odd things like RNAs which can code for proteins as well as act as the catalytic subunits of enzyme systems themselves!

DNA instructions are much less precise and much more distributed and generalized than computer code. Computer code says "Do this, this, and this, put THIS value in THAT register, etc.". DNA creates merely a VERY basic and generalized "scaffolding" for cellular development, structure, and metabolic function. After that - complex intacting systems take over. DNA simply codes for protiens - which inteact with each other, metals in cells, DNA, RNA, etc. The system has so many loops, twists and systems affecting systems that affect themselves! Again, I must say that the analogy works - but only on a very basic level, but many computer people, especially people here, try to take that further -and think themselves deep and insightful for it. The result is inane comments of "When will I be able to 'hack' my own DNA???", and the general understanding of biology suffers for that.

I'm not saying we shouldn't use metaphor and analogy to facilitate discussion and understanding, but people have to know how far a metaphor will go before it breaks - to the detriment of those attempting to use it for learning and understanding.

Sincerely,
Kevin Christie
Neuroscience Program
University of Illinois at Urbana-Champaign
crispiewm@hotmail.com

Re:Biologists and Psychologists Abuse this...

[Pentagram]

With regards to DNA - the fact is, is that DNA->RNA->protein expression is an INFIN[i]TELY more complex and less understood system

It's not infinitely more complex. Ignoring computational power, I see nothing there that can't be reproduced in code. Just because the code we usually write is quite straightforward doesn't mean it has to be. Self-modifying code, code based on chaotic equations, etc. are all possible. In fact I'm working on a research project at the moment looking at how programs can be evolved in similar representations to biological genomes.

Incidentally, if it was infinitely less understood, or infinitely complex then we wouldn't be able to understand any of it. Perhaps the mathematicians should take you to task for mangling their terminology?

The former has an insanely complex web of interactions with promoters, enhancer regions, transposons, developmental effects, odd things like RNAs which can code for proteins as well as act as the catalytic subunits of enzyme systems themselves!

So? Just because the systems are complex doesn't make your argument better. It certainly didn't warrant an exclamation mark. Try interpreting Windows XP in binary sometime. Besides, I think most (or all) of the things you mentioned have been used in GAs/GP.

Interestingly, I have heard more than one geneticist call the genome 'essentially a computer program'.

Re:Biologists and Psychologists Abuse this...

[Anonymous Coward]

With regards to DNA - the fact is, is that DNA->RNA->protein expression is an INFINATELY more complex and less understood system than high-levelcode->lower-level code / assembly->machine language instructions.

Maybe, but the top level there, DNA high-level-code is quite good analogy. Large computer programs are often far more complex than even the most complex genomes. The complexity comes from how they are intepreted - computer programs in a fairly predictable manner, genomes in a much mmore ujnpredictable chaotic way.

At higher levels, the analogy holds!!

Re:Biologists and Psychologists Abuse this...

[koekepeer]

[quote]
As a neuroscientist and former CS major in college (and long time Slashdot reader) I can also assert that programmers abuse biology metaphors just as badly!
[/quote]

amen!

i was very amused for example by the incorrect parrallel drawn by linus & friends on the LKML lately, regarding linux development as an evolutionary process. linux development is directed by a (group of) person(s), which can hardly be compared to the way nature randomly applies selective pressure onto a living organism.

i could take this argument further, but i don't want to be filtered out as a page-lengthening post ;-)

nevertheless, the parallel was instrumental in the sense that it got the discussion going. and let's face it, this particular discussion even made it to slashdot, so it must have been important... ;p

Re:Biologists and Psychologists Abuse this...

[cookie_cutter]

I don't think the poster was saying that biological systems cannot be modelled computationally. Sure, one can design code which evolves much like genomes do. The point is that most code does not behave in this manner, so that comparing most computer algorithms to biological algorithms is weak at best.

Re:Biologists and Psychologists Abuse this...

[lukesl]

I agree with most of what you're saying, but I think there's a fundamental hole in your logic. If one is to believe that the genome is a computer program, then the cell must be the computer. Or, more precisely, the transcriptional machinery the previous poster mentioned, in addition to signal transduction networks in the cytoplasm, epigenetic influences, and a few other things are part of the computer that runs the program of the genome. But where are these things in the digital computer implementation you speak of? They're in SOFTWARE. In your example, a closer analogy is that of the computer to the laws of physics which regulate interactions among proteins and nucleic acids. The computer program is therefore analogous to the regulatory machinery of the cell, and the genome is analogous to data in an array (although the program can use the information in the array to modify its own code). In your example, the genome is NOT analogous to a computer program, but to data ACCESSED BY a program. This might seem like a subtle distinction, but it's really not. With a few exceptions, programs don't dramatically alter the setup or basic functions of the chip they're run on, but the genome does. In some sense, that's most of what the genome does. Neurons and muscle cells have the same "program," but the "computer" is different. That is one reason why the genome:program analogy is stupid. The geneticists you've been talking to almost certainly know better and should be more careful what they say.

Re:Biologists and Psychologists Abuse this...

[Thurn und Taxis]

DNA and computer code have one very important thing in common -- 90% of the code is junk!

Re:Biologists and Psychologists Abuse this...

[westfirst]

You have to admit, though, the analogies are getting better. The brain is definitely more like a computer than a steam engine.

Okay, I'll bite. I don't think that's the case at all. Steam engines take in stored energy, release it , and move down a track. So do humans. The cells taken in ATP, release it, and move down some track. We don't know much about how these turn into decisions about whom to marry, which beer to drink, or how to mix the two together, but we know that energy is going in, and decisions are coming out.
A computer, on the other hand, is filled with logical gates that make straight-forward, well-defined decisions like AND, OR, or NOR. I hate to remind you, but there are many people that don't seem to have any connection with logic. They're really out to lunch. But they do take in energy and move down some track.
So just for the sake of argument, I think that the computer metaphor is moving in the wrong direction. Your track isn't pointed in the right way. You took in that energy, but it's not helping us at all.

Re:Biologists and Psychologists Abuse this...

[Rogue_Sage]

A single cell is vastly more complex than any computer in existance today. Each cell is essentially a massively parallel system. The great limitation of the analogy is that computers can only execute one instruction at any given time. Whereas within a cell each protein (and in some cases other molecules) might be compared to a program or function, millions and billions of them running all at once interacting with each other by chance in the absence of any type of clock but that which their concentrations and interactions may provide. Sure the overall way that genes have mutations and 'matings' introduced can be easily replicated in strings or whatever you may prefer. But computer programs and systems, because we design them from scratch and come up with every specification are vastly more understood than cellular biology currently is.

Re:Biologists and Psychologists Abuse this...

[DeadVulcan]

Far be it for me not to bite back. :-)

Steam engines take in stored energy, release it , and move down a track. [...] The cells taken in ATP, release it, and move down some track.

Well, I think that's a rather superficial similarity, and it's not quite comparing apples to apples. If the brain converted sugars into mechanical energy and chugged its way along the spine, I would be more inclined to agree with you.

A computer, on the other hand, is filled with logical gates that make straight-forward, well-defined decisions like AND, OR, or NOR. I hate to remind you, but there are many people that don't seem to have any connection with logic.

Just because the base components are logic gates doesn't mean that the final output of the whole system needs to be logical. Why, there are probably huge numbers of people who would already describe computers as being unpredictable, irrational, and self-destructive... and this is when they weren't even programmed to be that way! (Okay, that's a half-joke.) (But only half.)

So just for the sake of argument, I think that the computer metaphor is moving in the wrong direction. Your track isn't pointed in the right way. You took in that energy, but it's not helping us at all.

I'll have to agree that the computer analogy doesn't help that much, and it's a point of argument whether it gives us any more insight into human psychology than a steam engine metaphor.

However, I didn't say the analogy was good; I just said it's better. And I would maintain that the computer, which, after all, helps us to make decisions (with varying degrees of perceived and real effectiveness), is closer to the brain than a steam engine, whose purpose is not related to decision making.

Re:Biologists and Psychologists Abuse this...

[crush]

Surely both examples you give are excellent analogies of each other.Viruses parasitically use the machinery of their hosts to spread themselves... and so do computer viruses (well, worms at least.)

Computer viruses do not physically dis-assemble the host computer (or its OS), chopping it up into pieces that are re-assembled to from new infections computer viruses. A big difference.

And DNA is a digital series of instructions that are interpreted to express something... and so is computer code.

Digital series indeed!! DNA is more like a recipe as S.J.Gould and others never tire of pointing out (evidently for a good reason). If it were a program it would be the buggiest, crappiest program that had been maintained for years with different compatability layers added to it. If it were a program it would be as though COBOL had been kept and had new libraries added to it, some of which worked sort-of, and others were completely b0rken.

The point of this is that the analogies/metaphors/comparisons are not really useful beyond a simple level. Interesting analogies or metaphors are ones that reveal _unexpected_ details about the analogised subject. The code/DNA one does not. It is just two cool things lumped together with superficial similarity.

Re:Biologists and Psychologists Abuse this...

[texchanchan]

Yes. DV is right. For instance, naturall Philosophers compared thought to a system of air pumps when air-pumps were new (can't find a reference). You can also see the constellation "Air-Pump" in the southern hemisphere as a result of the awe generated by this new technology.

Later, about the time of Ben Franklin and Mary Shelley, they began to talk about thought as electricity. This really was a lot closer.

After another few decades, your brain became an internal telegraph-and-railroad system, and then a telephone exchange; and that brings us up to the era of the Giant Computing Machines that have afflicted the analogies of non-techies for the last 50 years.

Re:Biologists and Psychologists Abuse this...

[SparafucileMan]

Actually, computer viruses are programs that were written by someone with intent. Real viruses and their ancestors evolved from nothing (read: non-organic matter) and are an instrinsic feature of life on this planet...unless a computer viruses spontaneously organizes itself out of nowhere and spreads throughout the networks, the anaology really isn't that tight. My linux box at least isn't running around, writing its own code yet.

Re:Biologists and Psychologists Abuse this...

[Lictor]

>Has anyone proved you can build a Turing machine in DNA yet?

Depends on what you mean by 'building a Turing Machine in DNA'. Your question is rather analogous to saying 'has anyone proved you can build a Turing machine with SDRAM yet?'. DNA is a storage medium and requires external mechanisms to operate on it for computation.

If you take DNA and the DNA-processing mechanisms from stichotrichous ciliates, then yes, you *can* build a Turing Machine. See:

Reversable Molecular Computation in Ciliates. Kari, L., Kari, J., Landweber, L.F., _Jewels are Forever_ (Karhumaki, J. et. al eds.), Springer-Verlag, 1999, pp 353--363

Thats particularly interesting because its _in vivo_ computing, but there are also tens (probably hundreds) of proposals for _in vitro_ DNA computing. Do a google search on 'DNA Computing' and look for the proceedings of the International conferences on DNA-based Computers (I believe the one this summer in Japan is number 8)... IIRC they're published under a DIMACS series. If you want a 'canonical' paper for _in vitro_ methods, I guess starting at the beginning would be the best:

Adleman, L., "Molecular Computation of Solutions to Combinatorial Problems," Science, Vol. 266, 11 November 1994, pp. 1021-1023.

Re:Biologists and Psychologists Abuse this...

[rabidcow]

Digital series indeed!! DNA is more like a recipe as S.J.Gould and others never tire of pointing out (evidently for a good reason).

I'm sorry, DNA can obviously be percieved as a digital sequence. There are four distinct states encoding the information. ("recipe", whatever) I hope it's clear that it's not analog at least.

And as for recipe vs. program, they're the same thing! A sequence of instructions describing how to perform some action. Computer code is usually laid out in a more deliberate and structured form because the "operator" is so much simpler and more precise, but that doesn't really change the core nature of the thing. In the case of DNA, things are different yet again.

Of course if you don't understand anything about a recipe, comparing recipies and computer code is useless as well. The analogy to computer code is valid, but not perfect. You can't really use it unless you know where it doesn't work. Just because you can over-extend it doesn't mean it's complete trash.

Re:Biologists and Psychologists Abuse this...

[Pentagram]

In your example, the genome is NOT analogous to a computer program, but to data ACCESSED BY a program. This might seem like a subtle distinction, but it's really not.

No, I have to disagree. There is no difference philosophically between a computer program and the data accessed by a computer program. Any interpreted code, for example, (Perl scripts etc.) are data that are processed by a program. A Turing machine doesn't make the distinction on its infinite roll of tape.

Neurons and muscle cells have the same "program," but the "computer" is different.

The computer is exactly the same in both cases. The genome is interpreted differently in muscle cells and neurons because the genome itself turns on or off parts of itself in different places in the body.

Or, more precisely, the transcriptional machinery the previous poster mentioned, in addition to signal transduction networks in the cytoplasm, epigenetic influences, and a few other things are part of the computer that runs the program of the genome. But where are these things in the digital computer implementation you speak of? They're in SOFTWARE.

All that transcriptional machinery is built up from instructions in the genome: ie in SOFTWARE.

The geneticists you've been talking to almost certainly know better and should be more careful what they say.

I haven't got time to try and find a quote from someone authoritative on it, but Matt Ridley in Genome which seems to be looked upon favourably by most geneticists calls the program/genome comparison something like a perfect analogy.

Obviously the structure of a program and a biological genome are typically very different, but I think from an abstract sense a program is very similar to a genome.

Re:Biologists and Psychologists Abuse this...

[Anonymous Coward]

Might happen soon though... a little mistake through line noise in copying a binary, and you've got yourself a virus.

Re:Biologists and Psychologists Abuse this...

[Anonymous Coward]

Each cell is essentially a massively parallel system. The great limitation of the analogy is that computers can only execute one instruction at any given time

Duh. Any parallel computations you can do can be done serially as well, so this doesn't mean much. Besides, you can have multiple processors or clusters.

Re:Biologists and Psychologists Abuse this...

[Anonymous Coward]

>Your question is rather analogous to saying 'has
>anyone proved you can build a Turing machine with
>SDRAM yet?'. DNA is a storage medium and requires
>external mechanisms to operate on it for
>computation.

As he writes somwehre else, the external mechanisms are made up from DNA instructions.

Re:Biologists and Psychologists Abuse this...

[lukesl]

The computer is exactly the same in both cases. The genome is interpreted differently in muscle cells and neurons because the genome itself turns on or off parts of itself in different places in the body.

I think I agree with everything except one point, and some lack of clarity in my previous post is getting in the way. The only thing (besides the genome itself) that has not changed between neurons and myocytes is the underlying laws of physics. Whether or not it is your intention, I think this is the computer you're referring to, which is what I ultimately agree with. When I said the computer has changed, I was referring to the idea that the things that actually act directly on the genome were the computer, i.e. the transcription factors and RNA polymerase. Since both of us think that's incorrect, we can stick to the idea that the computer is analogous to underlying physical laws. What you're saying is that the different transcription factors and so forth that mediate differentiation are also in software, which I agree with too. I think we actually agree on all of that. The one difference is that you're arguing that there's no difference between a program and data accessed by a program, so the genome is like a program written in an interpreted language. Actually, I can agree with that too, in a formal sense. The problem is that this argument can be extrapolated all the way out to any deterministic system, and almost anything can be analogous to a computer program. So what's the point of the analogy?

I think the issue is less whether the analogy is formally correct at some arbitrarily abstract level and more whether it's a "good" analogy or not. A human being and a donut are topologically equivalent (donut hole:mouth->anus), but I'm not aware of any analogy based on that fact that most people would call "good." If you say that the genome is analogous to a program written in a very high-level interpreted language that partially codes for its own interpreter (e.g. photoshop macro language with extensions), then I would agree that this could be formally valid. Nevertheless, it's a bad analogy. First, it's not specific to the genome--almost anything can be said to be analogous to a computer program if you apply that level of abstraction. More importantly, it's misleading. Unless you already understand a significant amount about molecular biology and computer science, the analogy is going to mislead you. The genome:computer program analogy is bad, and no number of pop science books is going to change that. Of course, it may be much better than the genome:immortal soul or genome:collective unconscious analogies...

Re:Biologists and Psychologists Abuse this...

[lukesl]

I'm sorry, DNA can obviously be percieved as a digital sequence. There are four distinct states encoding the information. ("recipe", whatever) I hope it's clear that it's not analog at least.

This statement is formally correct, but highly misleading. The whole digital vs. analog paradigm implies that DNA simply contains a signal as a function of position, but this is not the case. It's an actual molecule in the real world; the conformation of the molecule matters for important things like transcriptional regulation. This is more easily illustrated with protein sequences. They are also "digital," with twenty states instead of four. However, the behavior of protein molecules of known sequence is not ab initio predictable in practice for sequences of any useful length.

Re:Biologists and Psychologists Abuse this...

[Winged Cat]

However, the behavior of protein molecules of known sequence is not ab initio predictable in practice for sequences of any useful length.

Take a ~1 MB (source code) computer program, written in a language you don't understand. Try predicting what it will do without actually compiling and running it. Same problem...so I'm not surprised this is the case. OTOH, very small sequences can be predicted, it's just that the sizes which we can predict don't happen to be usably long.

Re:Biologists and Psychologists Abuse this...

[Lictor]

Its called the 'bootstrapping' problem. Look it up.

Re:Biologists and Psychologists Abuse this...

[Pentagram]

Taking your points in reverse order...

The genome:computer program analogy is bad, and no number of pop science books is going to change that

A cheap shot :) I only quoted Ridley because I wanted to demonstrate that a geneticist agreed with me. I expect that finding a paper comparing genomes with computer programs from the mountain of non-online biology literature would be a bit of a task.

A human being and a donut are topologically equivalent (donut hole:mouth->anus), but I'm not aware of any analogy based on that fact that most people would call "good."

Oddly enough I remember a biology lesson in school where a teacher used exactly that analogy. I found it useful as a way of understanding that the alimentary canal was a tube through the body and not actually "inside" the body.

The problem is that this argument can be extrapolated all the way out to any deterministic system, and almost anything can be analogous to a computer program.

To counter that statement properly would probably require moving into the realms of information theory and lots of statements about entropy. I don't think I'm up to that, but IMHO there are plenty of similarities between the two that few other systems would share; a finite alphabet, a modular structure, variables, mechanisms to alter their interpretation. Both are linear, abstract lists of instructions that can repeatably influence the macroscopic world when encapsulated in the right medium.

So what is the point of the analogy?

An analogy doesn't have to have a point. It can just be a similarity between two things. (Look up the definition.) But if you mean what use is it, then I can think of two:

• Generating ideas in computer science; creating programs as new structures in ways inspired by genomic ones, looking at programming in different ways, improving evolutionary computing etc. It works for me.
  
• Helping to understand biological genomes; directly through comparing their action to a computer program, attempting to replicate them bottom-up through computer code etc.
  

Going back to the original thread, I was listening to a speaker today about how he was developing artificial immune systems to counter (computer) viruses. Another example where a biological analogy helps.

Re:Biologists and Psychologists Abuse this...

[crush]

the behavior of protein molecules of known sequence is not ab initio predictable in practice for sequences of any useful length.

Exactly. Even if one is able to use a method like threading, or multiple-alignment to find similarities or shared motifs the behaviour of the protein depends upon the complement of other molecules in its vicinity. If anything the whole deal is much closer to an analog system than a digital one.

Re:Biologists and Psychologists Abuse this...

[paulsnx2]

Tired of the comparisons? You should be, for the very reasons you sight. There *are* comparisons, but they have been missed by almost everyone, biologists and programmers alike.

DNA isn't code, because DNA doesn't *do* anything. DNA defines the total set of processes that can be expressed in a cell for an organism. This can be seen by the fact that the roughly 200 cell types in a human only express 10 percent or less of the available DNA.

Thus DNA is the definitions avaiable for a system. Just like that pile of installation disks that an MIS department holds for configuring a computer system.

When DNA is expressed, it results in RNA (to really simplify the transcription process). RNA is the "program store" for a cell. RNA defines the processes that are active in a cell. This isn't at all unlike the programs you have installed on your computer system. What processes a cell will perform and its configuration is driven by the particular genes that have been expressed (copied into RNA) for that cell. These are selected in such a way that the cell can effectively perform its role.

Yet actually carrying out these processes requires yet another step, the translation of RNA into the proteins that drive biological processes. Just like loading a program into memory and executing it is required to have something happen in a computer, building proteins is required to make a process occur in a cell.

A program store serves a very useful purpose. Both in computer systems and biological cells, it allows a cell to be instantly ready to perform the tasks required of it. If another protein is needed, the RNA is ready and able to translate another copy. Or on a computer system, if you need to run that spreadsheet, that program is ready to be load another copy in to memory for your use.

The Central Dogma of Molecular Biology states:

DNA -> RNA -> Proteins

More generally, this can be understood as:

definition -> expression -> function

What we need to learn to do in computer systems is understand how the architecture in biological systems results in self configuring distributed processes. We can do it the hard way (where we fight the mechanical metaphors such that every positive step to more configurable computer systems requires a non-intutive step against the mechanical metaphor), or we can do it the easy way (where we recognize that biological systems have already *solved* the configuration and distribution problems).

The really amazing thing to me about biological systems and computer systems is how long this simple observation has escaped everyone. The mixed-up metaphors (like Microsoft's DNA) are simply painful.

--Paul
http://groups.yahoo.com/group/SoftwareGe netics

Wacky scientists

[SirSlud]

> Scientists will love the lack of distraction, but casual readers looking for colorful anecdotes about the wacky geniuses in labcoats will need to look elsewhere.

If you want that kind of thing, this book is amazing for presenting both sides (ie, the science & the people) of the stories:

http://www.amazon.com/exec/obidos/ASIN/067187234 6/ qid=1015865367/sr=8-1/ref=sr_8_67_1/103-9949968-63 91849

It's called Complexity. It is a kind of answer to 'Chaos', and it has much info on the kind of biological software that the Santa Fe Institute crowd was working on a few years ago. A very highly recommended read.

The Digital Divide

[Klerck]

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.narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you .don't .have .enough .charaters .per .line .that .really .sucks .when .that .happens .and .you .have .to .put .some .lame .lameness .filter .defeater .text .in .there .i .wonder .how .many .people .will .read .this .whole .comment .I .certainly .hope .it .doesnt .annoy .too .many .people .This .is .just .the .beginning .because .PAGE .WIDENING .IS .BACK .I .like .wide .pages .I .wish .all .pages .could .be .as .wide .as .this .dont .you .wide .pages .are .much .cooler .than .those .narrow .pages .you .are .used .to .reading .because .you .dont .have .to .worry .about .the .lameness .filter .telling .you .that .you

Information wants to be Anthropomorphized...

[Bonker]

Humans have a tendancy to cast biological, and even human, behaviors on anything that is outside their ken.

Case in point. When I was helping my mother restore her computer after she was infected with Code Red, she was infuriated at the worm. While she is a computer professional, she is not a coder and has no understanding of... say... how machine code executes a loop or a goto. She talked about Code Red as if it really was a living thing despite the fact that she knew better. One of the things she said that stuck in my head was 'Why would it do that to me?'

Re:Information wants to be Anthropomorphized...

[Anonymous Coward]

We do this to dogs, cats, and animals too. We think of them as little humans with little human feelings. I'm sure concepts like pain or hunger apply to many mammals, but I'm not so sure about heartache and suffering. My cat is sure fussy, but I'm not sure if bitchy is the right word. Maybe it's just a human concept?

Can we get beyond this? I don't think so. We're humans, after all. We only know human things. Maybe licking your fur all day changes your perception of the world. Maybe sniffing butts changes the mind of dogs. Projecting human thoughts may not just be the best way to try to understand this, it may be the only way. (Well, save from licking yourself all day and sniffing butts.)

Abstraction?

[yatest5]

I get the authors point, but I don't think he makes it well..

No one speaks of subroutines that cp themselves through undocumented remote procedure calls because talk of 'computer viruses' carries all of the portent and weight of polio, anthrax, German Measles and tuberculosis.

Yeah, no-one speaks of the exact way all these illness viruses work either since it's easy to abstract it out to a simple term 'virus'/

You screwed up... this is better

[by FortKnox on]

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.tex .uitrc.console .uitrc.vt100 .uitrc.vt102 .uitrc.xterm .urlview .vimrc .xcoralrc .xfm .xim .xinitrc .xserverrc.secure .xsession .xtalkrc.Xdefaults .Xmodmap .Xresources .addressbook .addressbook.lu .bash_history .bashrc .dayplan .dayplan.priv .dvipsrc .emacs .exrc .gimprc .grok .holiday .hotjava .jazz .kde .kermrc .lyxrc .muttrc .nc_keys .pgp .pinerc .profile .seyon .signature .ssh .stonxrc .susephone .tex .uitrc.console .uitrc.vt100 .uitrc.vt102 .uitrc.xterm .urlview .vimrc .xcoralrc .xfm .xim .xinitrc .xserverrc.secure .xsession .xtalkrc.Xdefaults .Xmodmap .Xresources .addressbook .addressbook.lu .bash_history .bashrc .dayplan .dayplan.priv .dvipsrc .emacs .exrc .gimprc .grok .holiday .hotjava .jazz .kde .kermrc .lyxrc .muttrc .nc_keys .pgp .pinerc .profile .seyon .signature .ssh .stonxrc .susephone .tex .uitrc.console .uitrc.vt100 .uitrc.vt102 .uitrc.xterm .urlview .vimrc .xcoralrc .xfm .xim .xinitrc .xserverrc.secure .xsession .xtalkrc.Xdefaults .Xmodmap .Xresources .addressbook 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.seyon .signature .ssh .stonxrc .susephone .tex .uitrc.console .uitrc.vt100 .uitrc.vt102 .uitrc.xterm .urlview .vimrc .xcoralrc .xfm .xim .xinitrc .xserverrc.secure .xsession .xtalkrc.Xdefaults .Xmodmap .Xresources .addressbook .addressbook.lu .bash_history .bashrc .dayplan .dayplan.priv .dvipsrc .emacs .exrc .gimprc .grok .holiday .hotjava .jazz .kde .kermrc .lyxrc .muttrc .nc_keys .pgp .pinerc .profile .seyon .signature .ssh .stonxrc .susephone .tex .uitrc.console .uitrc.vt100 .uitrc.vt102 .uitrc.xterm .urlview .vimrc .xcoralrc .xfm .xim .xinitrc .xserverrc.secure .xsession .xtalkrc.Xdefaults .Xmodmap .Xresources .addressbook .addressbook.lu .bash_history .bashrc .dayplan .dayplan.priv .dvipsrc .emacs .exrc .gimprc .grok .holiday .hotjava .jazz .kde .kermrc .lyxrc .muttrc .nc_keys .pgp .pinerc .profile .seyon .signature .ssh .stonxrc .susephone .tex .uitrc.console .uitrc.vt100 .uitrc.vt102 .uitrc.xterm .urlview .vimrc .xcoralrc .xfm .xim .xinitrc .xserverrc.secure .xsession 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.kermrc .lyxrc .muttrc .nc_keys .pgp .pinerc .profile .seyon .signature .ssh .stonxrc .susephone .tex .uitrc.console .uitrc.vt100 .uitrc.vt102 .uitrc.xterm .urlview .vimrc .xcoralrc .xfm .xim .xinitrc .xserverrc.secure .xsession .xtalkrc.Xdefaults .Xmodmap .Xresources .addressbook .addressbook.lu .bash_history .bashrc .dayplan .dayplan.priv .dvipsrc .emacs .exrc .gimprc .grok .holiday .hotjava .jazz .kde .kermrc .lyxrc .muttrc .nc_keys .pgp .pinerc .profile .seyon .signature .ssh .stonxrc .susephone .tex .uitrc.console .uitrc.vt100 .uitrc.vt102 .uitrc.xterm .urlview .vimrc .xcoralrc .xfm .xim .xinitrc .xserverrc.secure .xsession .xtalkrc.Xdefaults .Xmodmap .Xresources .addressbook .addressbook.lu .bash_history .bashrc .dayplan .dayplan.priv .dvipsrc .emacs .exrc .gimprc .grok .holiday .hotjava .jazz .kde .kermrc .lyxrc .muttrc .nc_keys .pgp .pinerc .profile .seyon .signature .ssh .stonxrc .susephone .tex .uitrc.console .uitrc.vt100 .uitrc.vt102 .uitrc.xterm .urlview .vimrc .xcoralrc .xfm .xim .xinitrc .xserverrc.secure .xsession .xtalkrc.Xdefaults .Xmodmap .Xresources .addressbook .addressbook.lu .bash_history .bashrc .dayplan .dayplan.priv .dvipsrc .emacs .exrc .gimprc .grok .holiday .hotjava .jazz .kde .kermrc .lyxrc .muttrc .nc_keys .pgp .pinerc .profile .seyon .signature .ssh .stonxrc .susephone .tex .uitrc.console .uitrc.vt100 .uitrc.vt102 .uitrc.xterm .urlview .vimrc .xcoralrc .xfm .xim .xinitrc .xserverrc.secure .xsession .xtalkrc.Xdefaults .Xmodmap .Xresources .addressbook .addressbook.lu .bash_history .bashrc .dayplan .dayplan.priv .dvipsrc .emacs .exrc .gimprc .grok .holiday .hotjava .jazz .kde .kermrc .lyxrc .muttrc .nc_keys .pgp .pinerc .profile .seyon .signature .ssh .stonxrc .susephone .tex .uitrc.console .uitrc.vt100 .uitrc.vt102 .uitrc.xterm .urlview .vimrc .xcoralrc .xfm .xim .xinitrc .xserverrc.secure .xsession .xtalkrc.Xdefaults .Xmodmap .Xresources .addressbook .addressbook.lu .bash_history .bashrc .dayplan .dayplan.priv .dvipsrc .emacs .exrc .gimprc .grok .holiday .hotjava .jazz .kde .kermrc .lyxrc .muttrc .nc_keys .pgp .pinerc .profile .seyon .signature .ssh .stonxrc .susephone .tex .uitrc.console .uitrc.vt100 .uitrc.vt102 .uitrc.xterm .urlview .vimrc .xcoralrc .xfm .xim .xinitrc .xserverrc.secure .xsession .xtalkrc.Xdefaults .Xmodmap .Xresources .addressbook .addressbook.lu .bash_history .bashrc .dayplan .dayplan.priv .dvipsrc .emacs .exrc .gimprc .grok .holiday .hotjava .jazz .kde .kermrc .lyxrc .muttrc .nc_keys .pgp .pinerc .profile .seyon .signature .ssh .stonxrc .susephone .tex .uitrc.console .uitrc.vt100 .uitrc.vt102 .uitrc.xterm .urlview .vimrc .xcoralrc .xfm .xim .xinitrc .xserverrc.secure .xsession .xtalkrc.Xdefaults .Xmodmap .Xresources .addressbook .addressbook.lu .bash_history .bashrc .dayplan .dayplan.priv .dvipsrc .emacs .exrc .gimprc .grok .holiday .hotjava .jazz .kde .kermrc .lyxrc .muttrc .nc_keys .pgp .pinerc .profile .seyon .signature .ssh .stonxrc .susephone .tex .uitrc.console .uitrc.vt100 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.susephone .tex .uitrc.console .uitrc.vt100 .uitrc.vt102 .uitrc.xterm .urlview .vimrc .xcoralrc .xfm .xim .xinitrc .xserverrc.secure .xsession .xtalkrc.Xdefaults .Xmodmap .Xresources .addressbook .addressbook.lu .bash_history .bashrc .dayplan .dayplan.priv .dvipsrc .emacs .exrc .gimprc .grok .holiday .hotjava .jazz .kde .kermrc .lyxrc .muttrc .nc_keys .pgp .pinerc .profile .seyon .signature .ssh .stonxrc .susephone .tex .uitrc.console .uitrc.vt100 .uitrc.vt102 .uitrc.xterm .urlview .vimrc .xcoralrc .xfm .xim .xinitrc .xserverrc.secure .xsession .xtalkrc.Xdefaults .Xmodmap .Xresources .addressbook .addressbook.lu .bash_history .bashrc .dayplan .dayplan.priv .dvipsrc .emacs .exrc .gimprc .grok .holiday .hotjava .jazz .kde .kermrc .lyxrc .muttrc .nc_keys .pgp .pinerc .profile .seyon .signature .ssh .stonxrc .susephone .tex .uitrc.console .uitrc.vt100 .uitrc.vt102 .uitrc.xterm .urlview .vimrc .xcoralrc .xfm .xim .xinitrc .xserverrc.secure .xsession .xtalkrc.Xdefaults .Xmodmap .Xresources 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Re:You screwed up... this is better

[Anonymous Coward]

Oh man, Klerck, he got the widening AND lengthening goatse.cx post!! How are you going to top that??

Computers and biology have already merged

[kb3edk]

IIRC it happened a year ago, upon the implementation of RFC 1149.

Please do not feed the hypocrites

[PsiPsiStar]

I love this comment

People with open minds may want to avoid this book

Re:Please do not feed the hypocrites

[Anonymous Coward]

I think the point I was trying to make is that the author of this book very heavily pushes evolution and people who are suceptible to this sort of thing might not want to read it. Those who know the truth about the world's creation might be able to read this book safely. But I am not for sure. The point is that I feel this book is damaging, which is not a point that is going to be well received on slashdot but probably needs to be made anyway.

Re:Please do not feed the hypocrites

[lohen]

OK, I'll bite.

How precisely is belief in evolution 'damaging'? Compared to say: war, plague, famine, injustice, murder, disloyalty, dishonesty, etc, from matters great to little, I struggle to see how I am damaged by my belief (as a best working hypothesis) in evolution or how my belief in evolution could damage others. Even if you disagree with it, I'd suggest that you seriously need a sense of proportion. (This from a man who's posting on slashdot when he should be writing a 2000 word essay on comparative genomics...)

Re:Please do not feed the hypocrites

[JamesOfTheDesert]

Those who know the truth about the world's creation might be able to read this book safely.

Hey, guess what? God just spoke to me, and told me that evolution is real. Feel better?

Re:Please do not feed the hypocrites

[Anonymous Coward]

Please do not suggest such communism

nouns? verbs? help!

[CoffeeJedi]

can anyone navigate the grammatical maze that is this sentence!?:
---No one speaks of subroutines that cp themselves through undocumented remote procedure calls because talk of 'computer viruses' carries all of the portent and weight of polio, anthrax, German Measles and tuberculosis.---

Re:nouns? verbs? help!

[Anonymous Coward]

The two collections of words mean the same thing: "computer virus" and "subroutine that cp's itself through undocumented remote procedure calls". The difference is that virus is sexier. Well, more dangerous and ominous. You don't write an X-Files episode about "undocumented remote procedure calls."

Re:nouns? verbs? help!

[clion999]

You don't write an X-Files episode about "undocumented remote procedure calls."

Yes, there are too many syllables. Scully and Mulder need short phrases like "DAT tape." The biologists are just more poetic. Three letter acronyms sound stupid, but programmers use them all of the time. Programmers love words with plenty of consonants. Biologists love vowels. Vowels are sexier and more ominous too.

Re:nouns? verbs? help!

[Anonymous Coward]

can anyone navigate the grammatical maze that is this sentence!?

Well, I'm no English teaching guy, but here goes:

No one = pronoun
speaks = verb
of = preposition
subroutines = noun
that = pronoun
cp = verb
themselves = pronoun
through = preposition
undocumented = adjective
remote = adjective
procedure = noun
calls = transitive verb
because = conjunction
talk = noun
of = preposition
'computer viruses' = noun
carries = intransitive verb
all = adjective
of = preposition
the = definitive article
portent = noun
and = conjunction
weight = noun
of = preposition
polio, = noun
anthrax, = noun
German Measles = noun
and = conjunction
tuberculosis = noun

Hope that helps.

---------
Visit my tribute to the Teenage Mutant Ninja Turtles Arcade Game at:
http://www.kaejae-worx.com/~don/videogame/tmnt/ind ex.htm

Re:nouns? verbs? help!

[CoffeeJedi]

duh, brain fart! i get it now.... the thing that screwed me up was "...cp themselves through...", it didn't even occur to me that cp was the command for copy, so i was thinking of that as a noun, and the word "through" was just sort of hanging out there by itself then.... thanks

Here's another great link

[westfirst]

http://www.digitalbiology.com/

Plenty of good stuff. Anyone have other good links?

Re:Here's another great link

[payslee]

This one is my favorite. You can watch the flocking boids, and it explains flocking algorithms very clearly and easily.

Plus, it's got links to about 50 other really interesting biological modeling and application sites.

Be careful not to take this too far.

[Yet Another Smith]

I'm a little worried that if this gets too 'faddy' that people could start looking for biological metaphors and ignore other eqeually effective, or perhaps more effective solutions.

For example, from the review above:

genetic algorithms may find patterns of credit card fraud and help us find better jet turbine blades

The genetic algorithm is a great algorithm for optimization problems. However, its not significantly more effective than the simulated annealing algorithm or the less-known controlled random search algorithm.

Each has its advantages and disadvantages, but getting too caught up in the metaphors these algorithms and techniques are based on will unnecessarily shackle your thinking. Of course, the opposite is also true. Refusing to embrace metaphors at all will leave you without the insights that we use metaphors to see, so don't take me too seriously :).

Re:Be careful not to take this too far.

[lukesl]

One comment that complements the previous post is that it is important to distinguish between computational biology and what the book is calling "digital biology." Computational biology is doing biology with computer models. "Digital biology" is doing CS using certain techniques inspired by biological systems. That does not make it biology. The book would be more appropriately titled "biological digitalism."

Re:Be careful not to take this too far.

[Anonymous Coward]

The genetic algorithm is a great algorithm for optimization problems. However, its not significantly more effective than the simulated annealing [sciam.com] algorithm or the less-known controlled random search [dl.ac.uk] algorithm.
This is a great point. Metaphors can limit us. If we want stuff to be too much like evolutionary biology, we fail to see the best solutions. I would bet, for instance, that all of the evolving programs designing turbine blades use pairs of blades to produce the next generation. But why not merge three, four or more? Why can't turbine blades have a digital menage-a-trois? I bet the computer scientists programming these digital versions of evolution are blinded by their adherance to the metaphor.
Take the good, leave the bad. That's what I say.

Re:Be careful not to take this too far.

[clion999]

Yes, we get too amazed and let our enthusiasm outstrip our best judgement. I love the pictures of the fractal ferns, but what the heck does this teach us about biology and computer science? Maybe ferns use the same program again and again in creating fronds, but I doubt it. After a certain point, I think they stop repeating things.

We need to take a few ideas from the natural world, but there's no reason to imitate it slavishly. Why not have strange mating rituals for these digital memes that are supposedly evolving? Why not be a bit more mathematically precise? We might actually prove something for a change instead of talking about how cool it all is.

Re:Be careful not to take this too far.

[Alsee]

I'm familiar with genetic algorithms and simulated annealing, but not with controlled random search. I read the link you gave for it, but it didn't really say how it differed from a genetic algorithm. I spent a while searching on google but still couldn't find the difference.

Could you post a better link, or explain the difference yourself? Thanx.

-

Re:Be careful not to take this too far.

[Yet Another Smith]

sorry, that was the best link I found in a quick google search of my own :P Its not used as much as GA and SA. I'll try to explain, although its hard without pictures.

The CRS is based on the 'Nelder-Mead' simplex method. Here's a better description of that.

It starts with n + 1 points where n is the number of parameters you're optimizing. That's 3 points forming a triangle in 2D space or 4 points forming a tetrahedron in 3D space (the space being the values you're optimizing). Its easiest to think of the 2D situation with the triangle.

Each corner of the triangle is some set of parameters, each of which will have a different 'fitness'. The fitness is the value that you're trying to minimize. Evaluate the fitness at each vertex of teh triangle. Take the largest "least fit" vertex, and 'step the triangle downhill' by reflecting it through the midpoint between the other two points.

This should create a reflected triangle closer to the fitness minimum that you are trying to find. repeat until you get so close to the minimum that you're going in circles.

Now, with the CRS, you use the simplex to take all your steps, but in this case you create a large pool of initial candidates at random, just like you do for the Genetic or Simulated Annealing algorithms. The you create a new simplex by selecting n+1 elements from your initial pool. Step the simplex downhill, and see if your new value is better. IF so, throw away the worst element of the initial population, and replace it with the new one. Then select a new simplex at random from your pool of candidates and repeat the procedure.

This way, you're always producing random steps, so you can't easily get caught in a local minimum, and its a pretty efficient solution. It works well with linear constraints, which seemed to be an advantage over GA and SA when I was working on this myself. I should put a discaimer on here that I'm a geophysicist, not a computer scientist, so I may not use the lingo the same way your average /.er would.

Hope that wasn't too confusing. I'm trying to write this without my boss knowing I'm not working >:)

Re:Be careful not to take this too far.

[Alsee]

Ah, thanx for your explanation. With some thought I was able to picture exactly what you were trying to describe.

It seems like it would only work on a well-behaved search space. SA and CRS are faster with some search spaces, but I still preffer GA. It can attack any problem that SA and CRS can, plus it works on ugly search spaces. In particular CRS and SA seem almost usless for creating a program, one of the coolest tasks for GA.

-

Re:Warning : Ignorance in the name of piety

[gregor_b_dramkin]

I would probably not respond to the above and disregard it if it were not for a recent Sci Am article that showed ~40% of Americans believe in creationism over evolution.

I cannot understand how seemingly intelligent people can ignore overwhelming scientific evidence. Evolution is the most widely explanation for how we came to be. I do not see any inconsistencies with the Genesis *metaphor* for the creation of life. The Bible is written by humans, not God. They may have had divine inspiration, but it was not God's pen in the inkwell. Why do you think there are four "Gospel according to XXXX"?

BTW, God is omniscient. Don't you think He can understand and use a metaphor?

Of all the types of ignorance in the world. Those that perpetuated under the guise of religion are the most virulent and dangerous.

F-word s-word! Expletives!

[Anonymous Coward]

Seeing all this spouting about some fucking lunatics in favor of creationism just make me so fucking sick I'm gonna stop reading /. for today and do something constructive instead in a continent where such wackos won't dwell. Thank you fucking very much.

nouns? verbs? help!

[Anonymous Coward]

Is this an honest request for help from a non-english speaker? Or an engligsh speaker unfamiliar with compound sentance structure? The sentance is fine. Subject="no one". Verb = "speaks of". Object = "subroutines that ... calls". Subject of subordinate clause="talk of 'computer viruses'". Verb of and object subordinate clause="carries" and "all the weight of...". Where is the problem?

Biology vs. Comp. Sci.

[Mannerism]

This area has always interested me because I did my undergraduate degree in molecular biology, and my professional career has been in software engineering.

The first thing that strikes me when biology and computer science are brought together is that although we try to apply principles of the former to the latter, we really have a much firmer grasp of computer science than we do of biology. What we're really doing, I think, is taking some theories and concepts from biology -- evolution and immunology seem to be the big ones -- and adapting those theories to suit digital computers; we're not modelling life per se. It's important to remember, too, that although we can model evolutionary processes like variation and selection in a computer system and produce the anticipated results, we can't thereby prove that evolution applies to life. (I happen to believe that it does, but I have to admit that we have yet to irrefutably prove it). All we're doing is nicely illustrating the theory.

Someone mentioned earlier that everyone claims to be some sort of computer expert these days, and that biologists and psychologists routinely misapply computer concepts. From my perspective, the reverse is true. There seems to be a misconception that biology is straightforward and well-understood, and I just don't know where that comes from. I'm sure I'm not the only biologist who grimaces when "virus" is used to describe software. And the most gaping errors in science fiction always seem to be ones of biology. Computer scientists use words like "genotype" and "phenotype", but genetic algorithms seem to me to be so far removed from the actual complexities of gene expression as to be at best distant cousins. It's more a matter of biology lending ideas and inspiration to computer science than it is some direct translation of life processes to software processes.

Re:Biology vs. Comp. Sci.

[Jonathan]

It's important to remember, too, that although we can model evolutionary processes like variation and selection in a computer system and produce the anticipated results, we can't thereby prove that evolution applies to life. (I happen to believe that it does, but I have to admit that we have yet to irrefutably prove it). All we're doing is nicely illustrating the theory.

But "illustrating the theory" is really everything that ever can be done in science. In math (and CS is really applied math, despite the name) things can be proved. In science, theories can never be proved because it is always possible that someone tomorrow could perform an experiment disproving the theory.

Re:Biology vs. Comp. Sci.

[Joel Ironstone]

I'm not so sure that you cannot prove things in biology as easily as heartily as your prove them in mathematics. Evolution is a triusm. A truism in the sense of philosophy and math is just symbolic philosophy.

Think about it: "Survival of the fittest" That means survival of those that able to survive.

You can't argue with this.

Re:Biology vs. Comp. Sci.

[mOdQuArK!]

Think about it: "Survival of the fittest" That means survival of those that able to survive.

Actually, I revise this for my own personal reference as: "Destruction of the unfit", since the "Survival of the fittest" implies that ONLY the fittest will survive. Your general point, however, is still perfectly valid :-)

Your sig.

[Anonymous Coward]

Ben Franklin refused to patent his stove, lightning rod, bifocals, or anything else. Technology to the people!

Heh. It was the patent office that refused to accept Franklin's patent applications. There's some stupid old rule about "prior art" and having to be the first inventor to get something patented.

The same old rule still applies: in modern history, the Germans invented everything until 1945. After that, Germans living in the USA invented everything.

Re:Your sig.

[gregor_b_dramkin]

He was offered an exclusive patent by the Governor of Pennsylvania. He refused.

Re:Warning - to the wrong book!

[Tungbo]

Even ardent Creationists cannot deny the 'fact' of hereditary mutation, selection, and hence, evolution. Christians have manipulated the genetic stocks of plants and animals for centuries. This is EXACTLY the same thing that Genetic or Evolutionary Programming is doing.

Creationsists only take issue with the scientific theory that Darwinian evolution can explain ALL of the biological phenomena. They cannot deny that evolution exists and works. They have only made arguments that it works too slowly to explain everything. Thus, this warning is extermely misguided.

Re:Warning : Ignorance in the name of piety

[Anonymous Coward]

Of all the types of ignorance in the world. Those that perpetuated under the guise of religion are the most virulent and dangerous.

Many people have used religion as an excuse for their behaviour - but I'd have to say that sadism, greed, and nationalism as sources of ignorance are every bit as dangerous. If anything they may be more dangerous beacuse they lack any core of ethics.

Why is accident and random happening a better explanation than purposeful action by an active intelligence? Belief in Evolution requires as much faith as belief in Creation.

elitism versus morality

[Anonymous Coward]

It's not about elitism, it's about morality. Evolution precludes morality because evolution precludes God and molars come from God. Morality is about humbleness before God, not about holding the door at the store open for a little old lady (which evolutionists often claim to do, as proof that they are moral.)

This does not impress me.

Re:elitism versus morality

[lohen]

'molars' come from God? Fair enough, if you accept creationism, which I don't. It scarcely needs pointing out though ;-)

I still have difficulty with the thought of a god to whom it really matters, if he/she/it has the power to create a universe in which one small part (that we know of) has free will and the capacity to vaguely guess at His nature and receive messages from Him should honestly care what we think of him? Surely it would be gross egoism to imagine that your opinion on its existence could rank so highly with something so vast and incomprehensible?

Re:elitism versus morality

[Anonymous Coward]

he he I meant morals, not molars. Actually both are correct if you think about it.

Re:Warning : Ignorance in the name of piety

[Anonymous Coward]

I know that God understands metaphors and even has used them from time to time. However you must understand that creation is not a metaphor. If the six day creation is not true, then neither is the story of Adam and Eve and the fall from grace. If that is not true, then mankind is not in need of a Savior, then Christianity falls apart, which is a logical impossibility. There are metaphors in the Bible, like where Joshua makes the "sun stand still", clearly this is a metaphor for stopping the spinning of the earth. But creation as a metaphor, let's not go down that road, okay.

By the way you should not so smugly say that evolution has overwheling evidence, I have seen tracks of man and dinosaur side by side. Isn't that sort of hard when science says that they lived millions of years apart. Or maybe those "millions of years" are millions of lies.

damaging

[Anonymous Coward]

If you boil a pot of water and then drop a frog in, he will immediately jump out. On the other hand if you put a frog in a pot of cold water and slowly bring it to a boil, he will quite happily roast to death. This is what evolutionists do to their souls. The lifestyle is damaging because (in MY OPINION) it requires a lifetime of mandated immorality and the worst thing is that by the time people find out that they are wrong it will be too late for them.

Re:damaging

[Anonymous Coward]

Let me get this straight. Your saying that your god is going to punish me for enternity because of my beliefs on evolution. Your god sux man... get a new one.

The truth of the matter is the only reason you believe that your little creation story as the one and only truth is because a couple of heretical gnostics in the 2nd century decided to change the mythos of gnosticism from that of a spritual christ to a flesh and blood christ incarnate. Later when this heresy turned out to be extremely popular with the ignorant and uneducated masses of the mediteranean world, they turned on their gnostic progenitors and deemed them the heretics, even though the spritual christ mythos had existed for several hundred years before the christ 'incarnate' story (which is quite likely a relic of the egyptian mythology of horus and his virgin mother.) Hint - I'm sure you've heard that there were a bunch of other gospels that never made it into the bible... that's because they were written by the gnostics and did not have any reference to an incarnate christ, in fact almost 3/4 of all early gospels were gnostic. Learn the history of christianity and then preach on brother about who has it wrong.

If your fundamentalist version of xtianity is the one truth, then explain to me how it is you have four seperate irreconcilable gospel stories and two seperate irreconcilable creation myths. Something has to give, the bible cannot be 100% fact, the quicker you figure this out, the quicker you will get over your brainwashed upbringing and be able to enter modern society. You fundamentalists make me laugh.

Re:Warning : Ignorance in the name of piety

[Alsee]

I cannot understand how seemingly intelligent people can ignore overwhelming scientific evidence.

Because to most people Science is just as mysterious and magical as Religion.

Millions of children are enrolled in Sunday-School or fulltime religious school learning "You are not supposed to understand this". Truth has nothing to with logic or understanding. "Proof" of truth is not merely meaningless, but rejected as missleading.

Another goal of religious traning is rejecting competing religions. Science seems like just another religion to fight off - a bunch of ideas and beliefs that they don't expect to understand.

-

Re:Warning - to the wrong book!

[Alsee]

Even ardent Creationists cannot deny the 'fact' of hereditary mutation, selection, and hence, evolution... They cannot deny that evolution exists and works.

Sure they can. They do it all the time, hehe.

-

And Then There's Physics...

[strider( corinth )]

Anybody ever notice that the kernel is the core part of a UNIX system, similar to the kernel of an atom, and that the shell is the outer part of each? In each instance the shell is changable, and also the 'interface', as it were, to the whole unit. Seems like this might be a good example of somebody getting cross-field terminology right.

Re:And Then There's Physics...

[zoydoid]

I think you are implying that Unix is like an acorn, not an atom.

Duh

[Whardie Jones]

This guy needs to get a life. Reading books like these are for the computer illiterate.

Boiling Frogs

[tynman]

Just curious-- has anybody actually tried this experiment? I'm sure you'd have to clear channels with the ASPCA, Humane Society and a few others, but I'd really like to see a page devoted to this one. I've heard that analogy so many times, but does it even work?? Surely there must be some French /. reader who would be willing to try boiling frogs immediately and gradually in the name of science. Or at least in the name of gastronomy.

Saying that the frog jumps out immediately from the boiling water assumes: a) the water is suffeciently shallow for the frog to push against the bottom of the pot (I don't know if the pressure exherted against water would be enough to propel a frog out of a pot); b) that the difference in height between the water level and top of the pot is small enough for said amphibious hopper to get out; c) that being submerged in boiling water does not immediately disable the frog's jumping capacities.

I've fried crickets before (yes, I eat strange things), and when you toss them onto a hot pan with some oil (mmm.... butter), they simply don't have time to react before the proteins in their muscles are hydrolized. Not to be morbid about it, but I really don't think our frog has a chance in the boiling water.

Conversely, how dumb do we really think frogs are?? I mean, come on-- if you feel your legs scalding, don't you generally get out of the tub? Admittedly, when the temperature is raised gradually your heat tolerance increases. Indeed, people get so comfortable in saunas that they post warnings about brain damage from being in there too long. But come on. Is the frog really going to sit there and pass on blissfully to oblivion? A fish, I can understand. As the water gets hotter, fewer gasses can be dissolved in it. Since the fish breathes the dissolved gasses, it gradually suffocates. Which is beside the point, since the fish can't jump out of the pot in the first place, but you get the idea.

Somebody, please! Clear up this confusion! In the name of all that is analgous! In the meantime, I'm going to get back to my cricket stir-fry.

p.s. True science and true religion never conflict. To have a complete understanding of science is to understand the universe as it is. True religion is the same. Religion covers the why, science coveres the how. Since our understanding of both is imperfect at best, it's pointless to argue about frivolous details that don't pertain to our salvation. One way or another when we're all dead and sitting around in the waiting room, maybe there will be a documentary video playing in the VCR (DVD? What format do celestial beings use?). Then we can all nod our heads and say, "Oh, duh! Of course." Until then, deal with the fact that currently neither science nor religion has a monopoly on the full truth of "how" things came into being. Let science debate the how of the universe, let religion inspire us with the why, and what our purpose in it is.

Re:Boiling Frogs

[Atrahasis]

Nerves work by a feedback loop, and as you say, the tolerance rises. Frogs don't have the bit that says "wait a minute, its been getting hotter for quite a while now" - while we realise that if something gets hotter for an extended period of time, at the end its going to be considerably warmer than at the start.

Frogs are cold-blooded, and so they don't have a measuring stick to compare temperature. We can tell water is boiling by comparing it to out core temperature - forgs can't - as the water increases in temperature, the frogs core temperature does too. Frogs can't detect specific temperatures (nor can we, but we're certainly better at it), only changes in temperature.

Oh and your cricket thing. Water is never hotter than 100C. Fat can get to much higher temperatures. I don't think it would be true to say boiling water, because the frog would likely be dead from sitting in water at 50C, let alone 100 - hot water would be good enough.

Re:Boiling Frogs

[Hast]

And Google Boy to the rescue:

Next Time, What Say We Boil a Consultant

What is that I hear? Another "Ask Slashdot" question being typed in? Up up and away!

What about differential equations?

[clion999]

I think the reviewer's points about differential equations are good ones. If you check out the link in the bio, one article on AIDS points to the mistakes you can make with choosing the wrong rules for your "metaphors." Differential equations, for instance, require you to be able to take derivatives of the functions and fit the derivatives to some equation. That's great if the functions have derivatives, but it can be misleading if they don't. In one example, an economist hell-bent on using differential equations decides that AIDS can be curtailed if we all have more sex. (I kid you not!).
So are biological metaphors just as suspect? Perhaps. Digital evolution is cool, but I don't see why it is better than any of the other optimization techniques. If anything, the digital bio metaphor forces you to mimic creatures and all of their semi-monogamous, one-on-one reproduction. Equations don't have to conform to such a binary vision.

Re:Warning : Ignorance in the name of piety

[ShavenYak]

By the way you should not so smugly say that evolution has overwheling evidence, I have seen tracks of man and dinosaur side by side.

I thought even the creationists were abandoning this piece of "evidence". See this site for details.

Besides, even if you proved dinosaurs and man did have some overlap in the chronology of life on Earth, it certainly doesn't prove a six-day creation, or a 6000-year-old Earth. Once again, Creationists show their lack of comprehension not only of the scientific process, but also of simple logic.

Why we can't model biology with computers

[Joel Ironstone]

The fundamental reason why we cannot model biology with computers is that biological systems are chaotic. They respond to extremely small fluctuations no floating point processor can handle. In fact the human eye can respond to a single photon. See: http://math.ucr.edu/home/baez/physics/ParticleAndN uclear/see_a_photon.html

Biological systems are sensitive on quantum level and computers certainly cannot be.

Re:Warning [notice to moderators]

[Anonymous Coward]

The above comment, despite apparently looking interesting/insightful to a few moderators already, is absolutely moronic and meaningless. I would be surprised if a human wrote this. It looks like the output from some kind of a science-babble generator.
Please move on.

Give people more credit.

[yardgnome]

What's wrong with the liberal use of a metaphor here and there? The people we're talking about here (biologists and technologists) aren't idiots...they're highly trained and intelligent individuals. As such, most of them can tell when a metaphor is being taken too far.

Let's say I'm trying to explain a concept in molecular biology to a computer scientist. Is it really so bad if I make an analogy connecting something the computer scientist already knows (programming, for example) and something he or she does not know (MAPK pathways, for example)? As long as the analogy holds up on the level that I explain it at, things should work fine.

But because neither the computer scientist nor the biologist are stupid, they won't take the analogy too far. The computer scientist won't immediately think, "I bet obscure programming fact XXXX holds for this biological system he's explaining to me, because he just used programming language YYYY in his metaphor." This won't happen because the computer scientist is a rational person, who knows what a metaphor is and its probable limits.

Yes, it's true that if everyone takes metaphors literally, then we'll run into problems. But the entire reason we can use metaphors for something useful, is that we can also also understand that a metaphor can break down at some point.

I'll admit, I get pissed when popular culture misquotes some arcane (or even general) biological principle. However, that's a totally different thing than using some other subject as a metaphor. Without metaphors, those involved would have to learn these things from scratch, without drawing upon what one already understands. I think it's totally valid to dispense snippets of information through metaphor, since the alternative is working one's way up from ground zero without using metaphor. And that's way too much to ask, considering in biology it takes a PhD for anyone to consider you above zero level.

Re:Why we can't model biology with computers

[yardgnome]

Never say never. When you really get down to it, the only thing that allows organisms to register a single photon is that photon tripping some chromophore into a different conformation. So it's just one particle making an atom switch, thereby making an amino acid twist, thereby making an entire protein move. The subsequent amplification all rely on principles of signal transduction.

So computers must be able to measure single photons, otherwise how did the physicists know that they were emitting a single photon? And to go from single-photon-detection to whole-organism-response only requires a long series of amplification cascades. Why is such a setup so hard to envision in a computer system?

Re:Why we can't model biology with computers

[Joel Ironstone]

Yes, and no. One could design a computer system (electro-optical system) to measure a single photon. and we (not me pesonally) have. The single photon example was simply an example of how sensitive biological systems are to just about everything. To reproduce them, the computer system would have to be as sensitive, and thus would have to be analog for a start. Secondly, any, repeat, any rounding off error would result in different behaviour. I am not saying that we cannot produce a system as complicated as a biological one in a computer, I'm saying we cannot replicate the biological one to any degree of accuracy.

Viruses, biological vs not comparison

[Morannon]

Folks interested in the book might also be interested in a letter to the editor published in the latest issue of the Centers for Disease Control and Prevention (CDC) journal Emerging Infectious Diseases. The journal is a scholarly source about biological diseases. The letter, Contagion on the Internet, compares the biology and evolution of biological viruses to computer viruses.

bio of populations

[Anonymous Coward]

I learned somuch about OO programming through models already present in bio of populations. If you want to emulate complex systems, I recommend that you study the human body's transport mechanisms or ant chemical communication.

There is so much there in teh bio world that is damn cool that we can TRY to use to inspire us to create great subsystems and communicaton mechanisms.

- Zav

Defining (Digital) Life

[Anonymous Coward]

One of the great difficulties in this area -- especially when dealing with the question of Xenobiology -- is the issue of how to define whether something is "alive" or not. No one has yet come up with an acceptable definition that includes everything that humans think of as "life," and that excludes everything that we don't. In addition, we have a human tendency to anthropomorphize "inanimate" objects. Referring to cars, boats, computers, etc "as if" they were alive and had a will of their own.

So the standard way of dealing with it has been a kind of "I know it when I see it" approach to the question of whether or not something is alive. For the most part, this works pretty well. There's almost nothing on Earth that isn't clearly "alive" or "not-alive" and so it's easy to believe that a clear demarcation exists, but that we simply haven't identified the proper criteria yet.

There are some ambiguities, however, which can be controversial. Tom Ray considered his "Tierra" creatures to be alive. Some have claimed that computer viruses are a kind of life form. (Both of these meet the self-replication criteria.) More controversial are the Gaia hypothesis, and the question of whether or not a fetus/embryo/blastocyst qualifies as "human life."

However, it may well be the case that there can be no well-defined demarcation between "life" and "non-life." At one time it was believed that racial distinctions could be biologically defined, yet this turned out not to be true. There is no clear definition that would unambiguously put every single individual into one clear racial category or the other. Some people simply defy such categorization. Even though in most cases, I suspect that most of us feel that we "know it when we see it" what racial category a person belongs to. Also well known to many biologists is that among humans there are certain individuals who do not fall easily into either the category of "male" or "female."

What I suspect is that the concept of whether or not something is "alive" is, in fact, not definable. But that the existence of these categories is merely an artifact of the wiring of human brain. That as humans, our brains evolved to search for patterns and to classify things in categories. These categories often served us well in the environment that we evolved in, where the ambiguous cases may have simply been absent -- or so exceedingly rare as to be unimportant. However, in the larger world of "objective reality", the categories of "alive" and "not-alive" may lose their meaning. We may some day find "things" on Mars or Europa or elsewhere that we simply cannot agree as to whether or not they qualify as "alive."

Something I heard pointed out once with regard to the infamous "Face on Mars" is that humans are genetically programmed/predisposed to "see" faces. It's a part of what has enabled us to survive as social creatures. It allows us to distinguish "human" from "non-human." This can be important for species survival. And so, like many optical illusions, our tendency to recognize a "face" in the rocky patterns of the Martian surface says more about how our brains are wired than it says about life on Mars.

The same may be true of the definition of "life" itself.

Please use metaphors that make sense

[BistroMath]

Two of the four diseases the author mentions, ie anthrax and tuberculosis, are caused by bacteria and not viruses.

viruses??

[bethnewt]

talk of 'computer viruses' carries all of the portent and weight of polio, anthrax, German Measles and tuberculosis. Invoking these mysterious and deadly images is more colorful than tech speak, even if most of the so-called viruses are closer to the common cold than the black plague.

viruses named:
polio
common cold
German Measles

bacteria passed off as viruses:
anthrax
tuberculosis
black plague

*sigh*.

Re:Why we can't model biology with computers

[yardgnome]

Well, I'd personally say that point is arguable. Let's say we're making a system that is capable of responses as complicated as those exhibited as a cell, for example. It's really just a matter of adding in billions of responses. So we'd model a receptor-ligand system by saying "if stimulus X in Y amount then trigger Z." Things get really complicated when you stipulate that stimulus X in Y amount will ONLY trigger Z if your "receptor" is present in the right amount.

When you really get down to it, most biological processes aren't analog. Instead, they're regulated by molecules that can take on a finite number of states. Given, the number of molecules involved is fantastically large, and the number of states they can take is almost always more than 2 (especially since you have to take the effect of things like protein misfolding due to mutation into account).

So yes, it's relatively simple (heh) to produce a computer-based system that's as complicated as a biological one. But to replicate a biological system we'd have to know every X molecule, and all of the resultant Z triggers that can result from Y concentration of X. Then, we'd have to already know how all of the different X molecules connect to eachother (in ways as subtle as "you can't make any more X1 because all of the zinc was used to make X2").

However, while we can't replicate biological systems (and probably never will be able to), we certainly can model them. This is much easier, since we interweave a bunch of different functions in an attempt to arrive at something that generally makes sense. Then try to model some situations where the result is already known. If your model matches reality in almost every case, then you've probably got a winner. Otherwise, Do Not Pass Go.