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Digital Biology
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.
At least to some programmers....
Writing a living, breathing program would be the goal of many of us, not just AI programmers
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.
> 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.
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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/06718723
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.
"Old man yells at systemd"
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?'
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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".
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
Probable impossibilities are to be preferred to improbable possibilities.
Aristotele
I love this comment
People with open minds may want to avoid this book
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It's the end of my comment as I know it and I feel fine.
http://www.digitalbiology.com/
Plenty of good stuff. Anyone have other good links?
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
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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.
You can never equivocate too much.
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.
"What is freedom of expression? Without the freedom to offend, it ceases to exist." Salman Rushdie
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.
Please donate your spare CPU cycles to help fight cancer and other diseases
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.
'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?
"What is freedom of expression? Without the freedom to offend, it ceases to exist." Salman Rushdie
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.
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- - You can't take something off the Internet! That's like trying to take pee out of a swimming pool.
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.
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- - You can't take something off the Internet! That's like trying to take pee out of a swimming pool.
He was offered an exclusive patent by the Governor of Pennsylvania. He refused.
You can never equivocate too much.
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.
Darned tropical millipede! What's it doing in our apartment?
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.
"Beware he who would deny you access to information, for in his heart he deems himself your master."
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.
4-star general in a one-man army.
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?
4-star general in a one-man army.
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.
Two of the four diseases the author mentions, ie anthrax and tuberculosis, are caused by bacteria and not viruses.
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.
4-star general in a one-man army.