Slashdot Mirror
Convergence of Biology and Computers?
Pankaj Arora asks: "This summer I am working on both Bioinformatics and Molecular Biology research projects at the Mayo Clinic Rochester. Being an MIS major with a heavy CS background, I've been learning about biochemistry performing polymerase chain reactions (PCRs) and RNA retranslation among other things. I've learned biology works a lot like computers; binary has 1s and 0s, DNA has nucleotides: A, T, C, and G. Binary has 8 bits to a byte, DNA has 3 nucleotides to a codon. Computers and biology seem to have a natural fit; information is encoded and represented 'digitally' in a sense. I was wondering what people thought about the future of biology-based and genetics-based computing due to the immense efficiencies that lie in nature. This has been discussed to an extent here, but there were some specific aspects that I feel are quite important and were not discussed thoroughly, thus I have a few questions to pose to the Slashdot community."
"The aspects I would like discussed are as follows:
- In the long run, will biology rewrite computing or will modern day technology concepts and theory be integrated into biology? If both are true, which will have the greater effect? I understand long run is ambiguous in this question, but Iâ(TM)m interested in all thoughts using any applicable definition.
- Tied to the first question: How will the nature of computing, and how we perceive it, change due to biology integration? More to the point, how much of the theory we learn today may change?
- What will be the biggest issue determining the success of the adoption of biology-integrated computing? Will it be technology factors or will it be societal factors (e.g., rebellion by the Right Wing), or something else? What things must hold true to make the idea succeed?
- And perhaps the hottest issue of all: Is there anything inherently wrong with pursuing this avenue? What may be some of the consequences?
(I have an insulin pump) It really hasn't changed my life much yet. Still have to program the thing, refill it, etc. Maybe one day when it's internal and self-regulating, but for now, it's a fancy needle/pda.
it all boils down to this:
;)
binary + DNA = phi
(try and figure that one out
We're like rats, in some experiment! -- George Costanza
The major advantage and disadvantage to biological computing right now is speed. While it can solve some problems much faster than normal computers (due to it's massive parallel computing capabilities), making the DNA to solve the problem, and finding the answer take a long time as well. While both those are speeding up, it will be sometime before it is economically sound to do DNA calculations in anything other than a laboratory environment.
Modular Redundancy--Because 4 out of 5 Nodes agree
Godel, Escher, Bach talks all about the overlaps and comparisons between biology and computers. In particular, Hofstadter details a one-to-one correspondence from the Central Dogma to Godel's Incompleteness Theorem. It's dense, but it's great stuff.
GET YOUR WEAPONS READY! --DR.LIGHT
In the long run, will biology rewrite computing or will modern day technology concepts and theory be integrated into biology?
Where did all that modern day technology come from? Biology has already written computing as our biology lead to our intelligence that lead to our computers.
As one of the chosen few attempting to understand the fundamentals of protein folding, I can say that we are still a long way off from understanding how these "few" 20 amino acids fold into highly-specific structures. There are people with access to super computing centers (ala: UCSD super computing center, IBM's Gene Blue) who still cannot devise a simulation that accurately reproduces biological systems. The amount of atomic and subatomic properties that must be taken into account is just overwhelming. It can take a 64cpu cluster of computers a week to reproduce what nature does in 1 nanosecond!
So how can we restructure our current computing system to a model that is based upon something that we understand only at basic level? We can't. While I agree that a biologically-derived computing architecture could be quite powerful indeed, we are still a LONG way off from the level of understanding needed to even put this idea on the drawing board.
In biology the past 50 years have seen both revolutions and evolutions that have brought biology to an even par with physics, which had been the "queen of science" up through the first half of this century.
If I can do a slightly different interpretation of the questions being asked - can biology inspire changes in computing? The answer is yes - it already has. Many of our ideas of aritificial intelligence or computer learning have come from neural network-type studies of brain structures. At some point, the equivalent circuit in silicon may precisely reproduce what the neuron is doing. Aside from the time issue (nerve conduction is blazingly fast), you would serve your function staying in silicon.
I'm an aspiring computational ecologist, majoring in biology, minoring in CS. (for the uninformed- ecology != environmentalism or anything of that sort) I'm in Minnesota, although at the other end of the state.
I don't think biology will rewrite CS. It will influence it, for sure, but there isn't anything fundamentally different between a biological solution and a technological one. I think as we learn more of the bigger picture in various biological fields, when we truly understand it, we will integrate that knowledge into applied CS. We've been reading the book for some time now, but we really don't know enough about the subject matter to really apply it.
I think there is a lot of use for biomimicry in computing. I think integration of biological elements into our computers is quite a bit far off and perhaps a bit sci-fi-ish for now, but taking ideas (algorithm would often be an understatement) that work well in biological systems and using them in computing is something we can do now with some success.
Working toward a usable PDA environment in the spirit of Newton OS: Dynapad
What I'm listening to now on Pandora...
The mere speed and size of biological communication and information storage gives modern computing technology much to reach for. We are talking about nanometer size particles that store an incomparable amount of information, and when something needs to be done it isn't more than a phosphorylation (occurring in what, 10^-14 seconds) seconds away.
Everything technology attempts to mimic everything natural, like your monitor for example. It is a visual representation of the world and the information therein. The ultimate monitor would be in fact one that lays over your whole visual system giving you endless possiblities as far as resolution and "frames per second" type things.
A keyboard is just the liason between your brain and the computer. If your brain talked directly to your computer, now that would be fast and much less labor intensive. That is what we are all aiming for, thus the "wearable computers" and things like Dasher (pretty cool IMO). Input needs to be faster because our brains are fast.
What will be the biggest issue determining the success of the adoption of biology-integrated computing?
Well, lifeforms have certain weaknesses that rocks and electrons alone do not. Among them are:
-A lifespan
-Virus vulnerability (no pun intended)
-Nutrition requirements
(your typical cell needs things that are harder
to mass-transport than electrons. Water comes to mind)
-Amalcon
Q. In the long run, will biology rewrite computing or will modern day technology concepts and theory be integrated into biology? If both are true, which will have the greater effect? I understand long run is ambiguous in this question, but Iâ(TM)m interested in all thoughts using any applicable definition.
;o) If we jumped forward a hundred years - what we know now would be seen as primitive and childlike dabblings at it. Look at how old fashioned 1903 seems now (when cars were "modern technology").
;o)
Biology will (extremely slowly) be integrated into modern day technology. There will be some technology ---> biology transition too. However biology is far more adaptable. It's not a case of rewriting - it's just a case of historical progression.
In answer to your second question - technology concepts, computing etc as they're designed by biology are already in mainstream use eg:-
computer
phone
automobile etc
Biology affecting technology has had less of an effect eg Velcro - however the balance will change over the next few decades. Biotech is already advancing in great strides.
There isn't any definition as such - predicting the future is all guesswork. You can use statistics - all kinds of methods - in the end it comes down to a gut reaction.
Q. How will the nature of computing, and how we perceive it, change due to biology integration?
It'll become easier for biology to use eg:-
handwriting recognition
voice recognition
etc etc etc (all fifth-generation tasks - read up on sixth-generation if you like)
This is due to technology "evolving" to become more link biology though. The change'll happen too slowly to perceive.
Q. More to the point, how much of the theory we learn today may change?
The fundamentals still remain the same - like mathematics though - it just gets more complicated.
Q. What will be the biggest issue determining the success of the adoption of biology-integrated computing?
Economics. When computers cost millions of dollars only governments and large organisations could afford them. The second problem is marketing (read persuading people they need them). It'd take years though - look at the computer mouse as an example.
Q. Will it be technology factors or will it be societal factors (e.g., rebellion by the Right Wing), or something else?
It'll just happen - although factors will influence how slowly/ quickly certain parts of it do. Technology in the end comes down to ideas + money.
Q. What things must hold true to make the idea succeed?
That we can understand biology & manipulate it to serve us (probably other things too).
Q. And perhaps the hottest issue of all: Is there anything inherently wrong with pursuing this avenue?
Not in my opinion - although all technological advances bring ethical dilemnas - who do you sell it to etc? What (out of many) uses do you put it to?
Q. What may be some of the consequences?
A lot of them have already happened or are in the process of happening.
A society that suffers from greater obesity, global communication, increasing reliance on power production etc etc etc
Video Game cheats, hints a
I have to think that both technologies will come to a point where they can't advance without the other, at least in the medium-term. We know (or think we know) that silicon will reach barriers it can't overcome. And at this point, we don't have a way to create complex biological computers without using existing complex organisms and therefore shooting ourselves in the foot politically. Before real-world interfaces to biological computers can be developed, we need an efficient way to interface with the biology at a low level. Traditional computers will have to provide this for us.
We may even see a true, permanent mesh of the technologies. Silicon is extremely good at some things (communications; providing an interface to mechanical items -- keyboards & mice, monitors, speakers, solar panels, servos, etc.), while it's hard to imagine really good natural language processing, learning, and nonlinear problem solving, much less a modicum of emotion to enhance usability, occuring without biology.
Who knows? My prediction is as follows:
Just a little fantastic speculation...
--Jasin Natael
True science means that when you re-evaluate the evidence, you re-evaluate your faith.
I think that biology will push computing into interesting directions, not through application of any biological principals we discover, but through the demands of biological investigation. Biological systems are too interconnected to be adapted to building software or computers. I take that back, the details of biological systems are too interconnected to be adapated to building software or computers, but the gross principals (e.g. the immune system: T-cells, B-cells etc.) will be increasingly copied in software and computer design.
I believe that eventually we will be able to write complex organisms from scratch. These may not be as robust as what nature produces, but will be useful to us in many fields. Starting with the medical and spreading through the agricultural and even industrial area. I dream of trees which produce a sap, which is easily refined into methane or natural gas. But it's going to take much longer than most people seem to think.
There is no trap so deadly as the trap you set for yourself
-Raymond Chandler, The Long Goodbye
As a medical student with an undergraduate degree in Mathematics, I'm really pleased to see that other scientists are getting excited about the convergence of Mathematics/Compuation and molecular genetics.
First let me correct the slight error in your Ask Slashdot submission: we say that there are three nucleotide bases in an mRNA codon (not DNA codon). If you want a review of how DNA becomes RNA becomes proteins, you can check out the intro to my undergraduate thesis paper (link below).
In fact, I would encourage you to read through my paper in any case, as it may stimulate your thinking or open you up to new areas of bioinformatics research. The paper focuses mostly on a survey of analytic techniques of gene-expression microarrays, but is highly accessible to well-read / intelligent persons (it is light on technical mathematics by design).
Please let me know what you think of it (my email address should be easily inferrable from my website address), and you get a high-five from me if you can find the glaring mathematical error that I didn't get fixed before my defense.
http://blachly.net/james/documents/thesis.html
The best,
James
To hell the luddites. Hack the genome.
With apologies to Steven Levy:
1) Access to the genome, and anything which might teach you something about the way life works, should be unlimited and total. Always yield to the Hands-On Imperative.
2) All information should be free.
3) Mistrust authority- promote de-centralization.
4) Hackers should be judged by their Hacking, not bogus criteria such as degrees, age, race, or position.
5) You can create art, beauty and even life by hacking DNA.
6) Genetic hacking can change your life for the better.
--In the long run, will biology rewrite computing or will modern day technology concepts and theory be integrated into biology? If both are true, which will have the greater effect? I understand long run is ambiguous in this question, but Iâ(TM)m interested in all thoughts using any applicable definition.--
The likelihood that "modern day technology concepts and theory" will be integrated into biology seems unlikely to me, but I think you're really asking the following question-- Will we be able to use technology to design life, based on our ability to manipulate the code? I suspect so, though it will never be possible to escape the reality that what we would be doing was more biology than computer science. For the first part, will biology affect technology? Definitely. Rewrite it completely? I doubt it. It's more likely that biological computing systems will work well for certain tasks but not others (based on factors like complexities or huge numbers of variables).
--Tied to the first question: How will the nature of computing, and how we perceive it, change due to biology integration? More to the point, how much of the theory we learn today may change?--
I don't think anyone can even begin to answer this question, because the possibilites are practically infinite. If I had to guess though, I would say this -- most computer theory (I think not all, but I'm not sure) these days is based solidly on the binary system you mention, things are either one thing or another, a 1 or a 0. I think biological systems may someday be able to solve problems based on "fuzzier" logic, simply because the complexity that could be managed by DNA is very large.
--What will be the biggest issue determining the success of the adoption of biology-integrated computing? Will it be technology factors or will it be societal factors (e.g., rebellion by the Right Wing), or something else? What things must hold true to make the idea succeed?--
Like most things, I think the biggest issue determining the adoption of biology-integrated computing will be the rise of a company that can make a viable product that serves people either better than before or in a new way. Reality has shown that no matter how good an idea is, there are many other factors that can govern what is adopted and what isn't, just look at Betamax vs. VCR. Everybody knows betamax was better, but it didn't matter in the long run.
--And perhaps the hottest issue of all: Is there anything inherently wrong with pursuing this avenue? What may be some of the consequences?--
As in all things, there is nothing inherently wrong with pursuing knowledge. It's how we acquire that knowledge and what we do with it that can lead to moral dilemmas.
They figured out the code segments in DNA. Now they need to figure out the data segments and maybe in time they can figure out how datasegments in DNA manage to make their way into a creatures memory. Thats a few levels of indirctions that have to be figure out.
DNA decoding is starting to pick up on some of the debugging concepts that have been in the digial world for 50 years. There are ways to iterating over code so it looks like the single steping is going places. Its just hard to pull off on a multithreaded cluster and understand whats going on.
Of course what they are having a real problem is with the DRM stuff thats making it hard to build replacement brains out of stem cells.
I think the largest factor in biological computing will be acceptance of society in its use. I believe there is no doubt it will be one of the largest transitions in computing we have seen thus far. Simular to the transition from analog computing to digital, but with a much larger twist.
More and more people seem to accept the roles which computers play in every day lives, but it has taken time. There is still much debate in the use of genetic engineering, but it has become more common practice today than it was a decade ago. Today almost all the foods we eat are genetically engineered to be better, more resilient to pests, yielding larger quantities, whatever the case might be (although I am not a fan of genetically engineered foods).
I think eventually we might be using computers which is some sort of brain (ie vaugely resembling a humans), and this will frighten some people tremendousaly. The moral aspects will most definitely be hindered by the government (whos job seems to be determining morality), thereby extending the process by generations. However ethical computing is not something which Computer Scientists or Biological Engineers should regard as a formality, because I feel it does deserve some very deep thought.
The possibilities are endless, and with all technologies it can be used for Good or Evil. The only thing we can really hope for is that humanity will extend itself rather than drive itself to extinction. So far so good though right?
- To those people at the Mayo Clinic... Keep up the good work! We need more people actively seeking these types of technologies and questions!
A1: No. The informational aspects of DNA have been known for 50 years, only slightly longer than computers and failed to influence computer development. Nor does the computer science theory of information help biologists because they don't understand the intermediate mechanisms thoroughly (like precisely how a cell works).
Q2:Tied to the first question: How will the nature of computing, and how we perceive it, change due to biology integration? More to the point, how much of the theory we learn today may change?
A2: The underlying theory, which is essentially irrelevant, will not change.
Q3: What will be the biggest issue determining the success of the adoption of biology-integrated computing? Will it be technology factors or will it be societal factors (e.g., rebellion by the Right Wing), or something else? What things must hold true to make the idea succeed?
A3: Digital computers will always be better computers than biological based systems, that is why biological computational systems are going to be relegated to university labs and academic papers.
Q4: And perhaps the hottest issue of all: Is there anything inherently wrong with pursuing this avenue? What may be some of the consequences?
A4: If society declares such research forbidden, some other society will pursue it, if it has any value. Ethics only apply in a closed system, which world science is not.
A5: Biological systems and engineered systems are as different as a dog and an engine. Either can pull a sled, but it easy to pick out the engineered version and the biological version. Ask a mechanical engineer how much animal anatomy affects his craft or how much mechanical engineering affects a dog breeder. The questions are as relevant as the ones you asked.
It's still a practical application, despite the trivialness of it.
Yes, maybe a travelling salesperson problem with something on the order of a million possible answers would be solvable using DNA. Right now, it's probably 100 times more capable (speed- and memory-wise) than our conventional computers.
However, DNA doesn't get any smaller or more efficient. It simply cannot advance. As problems get more complex the margin of error gets too large to ignore, and reactions take too long. In the long run (10-20+ years), DNA will not be as fast or accurate as other solutions.
If I had 10 years to collaborate with other scientists to produce the best travelling-salesperson-solving computer, I'd look long and hard at Quantum computing; it's the opposite: it solves more complex problems just as easily as simple ones.
From my original post: "The debate on its usefulness centers around the other physical implications of the existance of such DNA, and where it might have come from, but 'computationally' (in biological terms 'is it ever used to produce a protein?') it is indeed junk."
Nothing you say contradicts that.
Also, don't forget Nature is not purposeful. Putting useful stuff in the junk is not useful, because you're no more likely to mutate such that the formerly useful code is expressed then you are to mutate such that a truly useless portion is expressed. We can "comment out" code; there is no equivalent operation for nature, because "commenting out" is a purposeful act to preserve code for later. And the odds of "uncommenting" are too small to affect anything (the genome is huge).
Also, natural selection only works on expressed genes. For every generation that a formerly-useful gene is not expressed, it is increasingly likely to be corrupted in an increasing portion of the gene pool until it effectively disappears, so the theory that the junk genes are "code libraries" on the long term is effectively twice debunked. On evolutionary scales, completely unexpressed genes are relatively quickly flushed completely out of the pool.
Like I said, the other implications of junk genes are being explored and they are almost certainly not truly useless, but the consensus of the science is that the genes are not useful in what I am calling "computational" ways for the purposes of this discussion. It's really past the time for skepticism on this point, unless you really want to re-write modern genetics. (Which you may, but I doubt.)
Here are a few issues I wanted to address in this discussion.
1. DNA computers â" There has been a lot of hype about DNA computing and how it will revolutionize everything. I think this is never going to happen for several reasons. DNA is a fragile molecule and requires active maintenance by cells to retain its fidelity. Components made out of plastic, metal, and composite inorganic materials are much stronger, tougher, and long-lasting. Also, there has been a big trend towards solid-state electronics (of all kinds) because they are so much more reliable and sturdy. A DNA-based computer belies this trend and is therefore unlikely.
2. Genetic Algorithms â" The concept of using evolutionary principles to find solutions to complex problems is a good one. Generating a random array of solutions is not difficult, and optimizing through successive rounds of competition, selection, and mutation is feasible
3. Manipulating the environment â" You asked how biology will affect computing. The realization that biology works so well because it has evolved precise, molecular control of virtually every biochemical variable has profound implications for technology. Nanoscience is trying to realize this level of molecular control in technology. Computers will obviously be needed to realize this goal, and will also be profoundly affected by it.
4. The bottom line â" systems theory. Biology and bioinformatics have given us a lot to think about, especially in the context of complicated, self-referencing systems. I believe that the major effects of both disciplines on each other will be theoretical and âoebig pictureâ in scale. The fact is that microchips and enzymes have vastly different operating parameters and wonâ(TM)t likely be integrated directly. However, the concepts illuminated by studying biology (massively parallel processing, highly redundant systems, programmed mutation) have had and will continue to have a big effect on how we design computers.
5. Ethical implications â" I envision some big ethical issues as biology and technology become further integrated. As it stands, there is a fairly well-defined dividing line between what is biological and what is technological. When we are able to design cybernetic dogs that actually act like dogs, or when people can replace their eyes with broad-spectrum CCD detectors then that line will begin to blur. As nanotechnology and biotechnology advance, we will likely gain complete control over all life processes. Obviously, that has some wonderful and frightening implications. I guess weâ(TM)ll just have to keep our eyes and minds openâ¦.
I'm a graduate student in chemical engineering at the University of Minnesota and this is my field of research...
(Sorta strange how Minnesota is a big center for medical devices / chemical engineering)
I'm in the process of designing systems of genes that interact to perform specific functions, like switches, oscillators, filters, etc. I won't go into a long harange over how it's done or the detailed specifics, because if you're really interested you can read my paper to be published in 'Computers in Chemical Engineering' that will be published sometime in November/December. (Yes, shameless self-promotion.)
Very briefly, systems of biological reactions occur in such small volumes and in such small concentrations that the traditional mathematics of describing chemical reactions breaks down. One requires probability theory and the usage of Markov processes, a type of stochastic process, to accurate describe what's really going on inside cells. One does this with a very handy algorithm developed by a guy named Daniel Gillespie (search the literature if you're interested) and big freakin computers. (I'm going to gloat: I'm getting access to the 54th fastest computer in the world. Oh, fellow Slashdotters, it brings a tear to my eyes...)
Here's my two bits on the subject of integrating biology and computers...
You have two distinct areas of computational biology (as Slashdotters know it) that will probably go into different directions. One can use computers to design biological systems in order to perform certain functions (medical, industrial, etc). This is entirely analogous to an engineer using a computer to design a factory before building it...and knowing exactly (or almost) how it will all turn out _prior_ to building it. This is also why buildings don't regularly fall down.
Then you have the Cyborg fantasy... Ie. Putting computers in your body to somehow enhance performance. Well, I would say that is numerous decades away because we currently lack the understanding of our brains...and the enhancement of our brains' computational speed is the only area in which digital computers can enhance human performance significantly (I discount super strength as novelty rather than enhancement.)
But, there is a useful aspect to the 'cyborg' fantasy: Using designed cells to enhance the performance of humans. Cures to many of our current diseases require significant changes to our DNA and/or microscopic structure of our cells. Currently, the approach has been to design (or discover randomly...) molecules that interact with our cells in a way that improves our health.
Now extend that thinking further... What about designing whole cells to interact with our cells in order to improve health. Here's some examples that may come true in the next twenty years:
A cell (of human origin) that lives benignly in one's body until it detects a protein that is only produced (in large quantity) by a cancerous cell. When it detects large numbers of that protein, it may do the following actions:
--Replicate itself quickly (in a controlled fashion, unlike cancerous cells, however)
--Warn the person by producing a visible indicator (ie. make the person urinate blue (har har))
--Recruit the person's immune system to attack the cancerous cell
--Attack the cancerous cell itself (phagocytosis, etc)
--Produce a molecule (a drug) that is known to kill that cancerous cell
Here's another example:
Someone designs a microbe that detects one or more specific chemicals in order to alert humans of its presence...a biosensor.
When the microbe (or its ten+ million neighbors) detects a specific chemical (Anthrax, ricin, smallpox, influenza, etc, etc), it produces a green fluorescent protein (GFP)..and tells all of its neighbors to produce GFP too. Thus one has a very sensitive, very specific biosensor. Place 'em in every airport and seaport in the world and one now has an (almost) instant indicator of the presence of such toxins...
So, to answer one o
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