Actually, DNA is location addressable. DNA is composed of nucleotides with a specific sequence. The sequence itself is the "address" of a site on the DNA. LOTS of proteins specifically bind ONLY to certain sites on DNA, making them "location addressable".
Look up Cre/LoxP, V(D)J recombination, transcriptional operators, and the list goes on and on..
DNA and RNA will also hybridize only to specific sequences, or undergo homologous recombination with partially homologous regions. This is what the researchers are using to "control" their grid.
It's viscous, it's a psuedoliquid! It can migrate down gravitational potentials! It can replicate itself by splitting (and even ostracize OTHER forms of polymers who try to get in between)! It vibrates, oh it vibrates! It absorbs water, it's drinking, it's drinking!
MY GOD, IT'S ALIVE!... (Yes, this is a joke)
Physics itself produces some amazing phenomenom. While it might be cutesy that some plasma is splitting and vibrating synchronously (everything vibrates, sigh. Lasers vibrate synchronously), it is not 'Alive'.
Ok, there's anecdotal evidence. But if someone did a poll and asked this question:
"Which news story would you believe more? One from Fox News and one from CNN."
I wonder what the outcome would be.
IMO, CNN is a little left slanted, but that's mostly because they cater to the "world" audience and, surprisingly, I'd say Americans are more conservative about a lot of things than many other nations in the world. (Especially Europe)
But...do the majority of Arabs believe that Al Jazeera is the unbiased story? I bet the majority of Americans know that FOX is purposely biased.
(At least roughly 1/2 of Americans would never watch FOX because FOX specifically caters to their opposing idealogy. Of the other half, I bet the majority still doesn't watch FOX because they know it's all bs.)
How many Arabs are against Arab Nationalism?:) There's very few differing (substantially different) viewpoints in the Arab Middle East. Even the "moderates" have to check their talk of reform for _fear_ of a fundamentalist calling them an American-lackey and declaring jihad against them. How does that encourage free speech, free thought, and useful discussion? It doesn't!
You're very correct in saying that Fox News is just about the same as Al Jazeera. The important question is whether the viewers of Al Jazeera recognize the difference between a 'CNN' and a 'Al Jazeera'. (Not like CNN is perfect, but I digress.) In the Arab media environment, There is no relatively objective news source. We have CBS, NBC, ABC, along with the CNN and other cable news. We can tell the difference between Fox News and CNN, because we have a CNN to show us the difference.
In the U.S, we recognize that Fox news is biased. In the Middle East, do viewers of Al Jazeera recognize the same thing? I think that's the real question.
I know they can watch CNN by satellite. I wonder if they believe that Al Jazeera is the truth and that CNN is the biased version. (By truth, I mean closer to the truth. By biased, I mean farther from the truth.) If so, that's a giant idealogical gap between us and them.
It's also possible that Al Jazeera cut and pasted from SpaceDaily.com. (See Slashdot original link.)
(I read SpaceDaily.com's article and you just quoted it back to me verbatim saying it was from Al Jazeera.)
Soo....I know you didn't know that, of course, but you have to admit that Al Jazeera doesn't have the objective standards that other newspapers try to adhere to.
I won't deny that some stories within the U.S are very politically charged and may not receive the objective view that they deserve, but there is a difference between stating the exceptions and stating the Norm.
The Norm for Al Jazeera is Arab Nationalism. They're catering to their viewers, of course, but they're doing so at the cost of objectivity. It's more like a circus than a news show. More entertainment than news. Have you ever watched it?
Whether or not you agree with his prediction that human employees will be replaced with robots, the guy's suggestions as to what the consequences could (or should) be are poorly thought out.
The author suggests that the government extract sources of income (and he gives some far-fetched examples) that would provide every consumer in the U.S with a salary of $25,000 a year...for doing nothing.
The author's main suggestion is that the U.S government should sell advertisement space on every possible surface it owns (dollar bills, road surfaces, etc etc). While he purports capitalism, he doesn't really understand it. As the supply of "Advertisement space" rises, the price of it will drop. If the U.S govt. made it so readily available, advertisers would no longer pay as much for it.
Additionally, the very idea of supplying every consumer with a fixed income check is not capitalism...it's socialism! There is never any free lunch in this world. See the Soviet Union, Cultural Revolution China, North Korea, etc, etc. With no incentive for work, no one will work. Having not earned the money, people will hate it. With so much assured money in the system, prices will rise. The money won't go far enough...people will become poor. The only rich people will be people who produce things and sell them. People who get the checks in the mail will remain poor forever.
So, I don't think that's the answer, although it's been suggested before (Marx, Mao, etc, etc).
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...
It's amazing how much you miss it when you move away from the Garden state. People drive like idiots where I'm living...slow idiots. Fast idiots, I can deal with.
Re:Some Non-Sci-Fi Picks for the real Thinker
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I've read 'The Prince' and I agree it's a great one. I haven't read 'The Art of War' yet, but it's probably more relevant to current conflicts than Clausewitz's...now that asymmetric warfare and precision bombing are two major themes to new military conflicts.
Some Non-Sci-Fi Picks for the real Thinker
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Science Fiction/Fantasy might be great to let your brain relax, but it won't leave you educated beyond the superficial themes most fiction writers insert. There are always exceptions, but once you've read the good ones, it's all down hill from there...
If you want TRUE stories that are much better than the fiction some fantasy writers dream up, then try some History. Truth is much more interesting than fiction... Here's my picks:
_Ancient History_
Gates of Fire (Steven Pressfield)
About the Persian-Greek war and the Spartan's stand at the Thermopylae gates.
The Peloponnesian War (Donald Kagan)
About the title Greek war, with an indepth description of the tactics, the decision making process, the culture war, and analogies to the Cold War and other conflicts
Caesar's War Commentaries (Julius Caesar)
Read his exploits written by the man himself. Look around for a good translation, though. If you're interested in literature, get an exact one. If not, there's translations that convert to the first person/etc that make it a much more fluid story. Play Praetorians (PC game) while reading for the best experience.
Guns, Germs, and Steel (Jared Diamond, I think)
An anthropological explanation of why the Western World has (so far) dominated the world in culture, prosperity, and technology. Condemns racist rationales and explains the causes by reason of resources available on the different continents and differences in political states
_American History_
John Adams (David McCullough)
Extremely well written biography about our 2nd President
_Classics_ (classic fiction, I should say)
Anything by Alexander Dumas is a great read. Count of Monte Cristo, Three Musketeers, Man in the Iron Mask. Quite different from the movies (more sex, hah) and better pick up lines.
Anything by Oscar Wilde. Very funny plays (in a British way, I guess). 'The Importance of Being Earnest' is his most famous one, I guess. The movie was well done, if you saw it, liked it, and wanted to read the play itself...
_Contemporary_
Anything by Kurt Vonnegut. Read Slaughterhouse-Five and I bet you'll get hooked. Mother Night is especially Vonnegut-esque (dark sarcasm) and his short stories are very good.
Yes, I will say it: Atlas Shrugged and/or The Fountainhead. It will give you that good American "I want to be rich and I won't feel bad when I am" feeling. Jokes aside, Atlas Shrugged is a good story and, excepting a certain 80 page monologue, not _too_ preachy. I mean, Who is John Galt, anyways?;)
Ok, I'll stop.
It's amazing how enjoyable a good book can be when you don't have a teacher telling you to read it.
Words are just words. Just because you can think of some (what you call) new idea doesn't mean it's doable or practical or that _you_ can actually do it.
The Space Elevator was imagined by Arthur C. Clark a while back. Did he patent it because he thought of it? No. He didn't create one, nor design one (ie. detailed schematics), nor prove that he could build one.
The first person to be able to build long lengths of carbon nanotubes will surely get a patent for their TECHNIQUE. It will be priceless. It will be genius. But saying "I imagine that one could build " does not earn one a patent.
If you want to protect something that you imagined up..then it's called a copyright. If you want to protect something that you physically created, it's called a patent.
Big difference.
(Actual definitions may differ. I am not a lawyer. I'm an Engineer. Thank God.)
This guy may be an engineer (so am I), but he sure doesn't act like it. There are a million obstacles to creating a _working_ prototype of something versus theorizing about the existence of such an object. REAL engineers do actual work to create such objects. Only then does someone deserve to hold the patent on the object..after they've proven that they can build it.
Until then, it's all bullshit hype.
For an example of a real engineer, read this .
Of course, it's the USPTO that mistakes hype for substance...at the cost of the true innovators in this country.
The game chants "death" every time one of your villagers died. My roommate freaked out (Junior year of college) because he kept hearing someone chant "death". This is a guy who regularly kept a collection of swords, katanas, and knives in the room as well as some pistols (mock or not).
The developers of B&W definately wanted to freak ppl out with random easter eggs. If you used a name that was on B&W's list of common names, it would randomly chant your name within the game. Now that was weird.
One thing they didn't mention is that Gene circuits can not only exhibit bistable behavior (bits), but multistable behavior (trinary, etc). Because chemical species exist in concentrations and not 'on' or 'off, there's quite a bit of additional complexity that can be utilized to perform added functions.
Differentiating stem cells in the body take a signal (concentration of a chemical species) and differentiate into different cell types (more than two different cell types).
Sometimes, it's like an 'if then' statement => If received X signal, differentiate into cell type A, else B. If received signal Y (after having received X), differentiate into cell type C, else D.
Or, it might receive a 'low' signal of X and go A. Medium => B. High => C. None => D.
There's different mechanisms that can be employed to give the gene this behavior. But, the cell must be able to effectively distinguish between 'none', 'low', 'medium', and 'high'..even in a highly fluctuating environment. So it's not simple nor has it ever been studied rigorously before.
Yes, scientists have played with gene circuits and have created some interesting designs. But, it's becoming an engineering discipline whereby the engineer should know _exactly_ what will happen if the microbiologist assembles the specific components together in a cell. That'll take a decade or more, but it's getting there.
Howard Salis Chemical Engineer University of Minnesota
If you want to read a great paper, read Adam Arkin's paper on the Stochastic simulation of Lambda-Phage infection of E. coli. It's from 1998 (I think). The fact that one can simulate exactly what occurs inside cells is amazing. The next step is to _predict_ what will happen. This is what engineers do.
How many times do you see buildings spontaneously collapse?:)
I think scientists grossly overexaggerate the usefulness of the Human genome sequencing project. So you know the sequence of the genome.
We still have to find all of the coding portions of the genome and separate them from non-coding portions.
We still have to find a way to infer the structure and function of a protein from its sequence.
We still have to find a method to engineer proteins systematically and by design. (No guess and check..)
We still have to find a method to model and simulate how multiple proteins and genes interact in order to give us the behavior of the entire system. There are no genes that do one thing or provide one attribute. They all contribute to the behavior of the system, but not linearly and usually unpredictably.
We still have to find a way to alter human DNA successfully, without triggering the immune response too much, and without causing cancer.
We still have a LONG way to go before we see genetically modified humans.
I'd say we'll see many more GM foods and animals long before some guy feels he can get it right on the first try. But that's what engineering is all about...knowing exactly what is going to happen when you create something so that it _will_ work on the first try. (How many buildings collapse spontaneously?)
Not until we understand the complex interactions (and there's a LOT of them) in the body will we be able to engineer biological systems with a supremely high degree of aforeknowledge.
80% of all the scientific articles in the WORLD are published by people either living in the U.S or studying here.
The U.S has the most universities in the world and the most prestigious/highest quality ones.
And..here's a causation vs. correlation difference for you...to illustrate the point.
People are not stupid if they disagree with you. I find that most protesters/ranters fail to see this.
On the Topic of Determinism vs. Stochasticity...
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Genome Surprise
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The assumption that each gene codes for one protein is usually false. But, regardless of that, there exists an additional "degree of freedom" that biological organisms can utilize in order to allow themselves to assume as many "states" of gene expression as possible.
The topic of stochastic gene expression is becoming more interesting recently because of further advances in studying single-cell gene expression and the design of genetic regulatory networks.
Because the concentrations of many gene regulatory proteins are so dilute/low, there exists significant fluctuations in the number of molecules that actually regulate the gene's expression. These fluctuations vary from time to time and from cell to cell, producing non-deterministic levels of gene expression. The non-determinism (called stochasticity) can cause some very interesting behavior that leads to numerous potential 'states' of gene expression versus a single, deterministic state.
So, on a very real basis, probability has a lot to do with how certain genes are expressed. Successful biological systems, however, hate random chance unless it's advantageous. These certain genes that utilize the internal noise of a "small" biological system do so because it gives some sort of advantage to them..either coding for numerous possible states with the least number of genes or for allowing the cell to randomly pick between possible states in order to create a heterogeneous cell population.
If you're interested in some scientific articles, try Adam Arkin's paper from 1998, detailing a stochastic simulation of a virus that attacks E. coli cells. The virus randomly selects whether it will replicate itself quickly and burst the cell open or integrate itself into the bacteria's genome and sit dormant. The probability of each event depends on the state of the bacteria at the time of infection. If the bacteria is starved, the virus goes dormant. If it's healthy, the virus goes into replication mode.
Because the concentrations of many gene regulatory proteins are so dilute/low, there exists significant fluctuations in the number of molecules that actually regulate the gene's expression. These fluctuations vary from time to time and from cell to cell, producing non-deterministic levels of gene expression. The non-determinism (called stochasticity) can cause some very interesting behavior that leads to numerous potential 'states' of gene expression versus a single, deterministic state.
So, on a very real basis, probability has a lot to do with how certain genes are expressed. Successful biological systems, however, hate random chance unless it's advantageous. These certain genes that utilize the internal noise of a "small" biological system do so because it gives some sort of advantage to them..either coding for numerous possible states with the least number of genes or for allowing the cell to randomly pick between possible states in order to create a heterogeneous cell population.
If you're interested in some scientific articles, try Adam Arkin's paper from 1998, detailing a stochastic simulation of a virus that attacks E. coli cells. The virus randomly selects whether it will replicate itself quickly and burst the cell open or integrate itself into the bacteria's genome and sit dormant. The probability of each event depends on the state of the bacteria at the time of infection. If the bacteria is starved, the virus goes dormant. If it's healthy, the virus goes into replication mode.
Is it ethical to genetically modify food using biotechnological techniques? Are there unseen side effects to the introduction of trans-species genes? This issue is real big in Europe, but not as controversial in the U.S. Why? If it tastes better and doesn't hurt you (or anyone else), can it really be that bad?:)
Stem Cell Research...this issue is extremely controversial right now. Is it ethical to use embryonic stem cells in order to find treatments for numerous diseases, including diabetes, cancer, Alzeihmer's (sp?), etc.
Or..if you're more interested in public policy & technology...
How about the privacy of information regarding one's genomic attributes. Can a health insurance company be allowed to examine your genome and determine whether you are more likely to have heart disease, cancer, etc? Should such information be stored in public databases (to be accessible by hospitals, insurance companies, and the government)?
I completely agree. A lot of the episodes of TNG didn't need to happen in space or with aliens. It was just damned good drama (but with serious conflict..not soap opera). Hell, even my sister watched TNG and she hated Sci-fi shows.
I don't even bother watching Enterprise. It has none of the campy 60s feel of TOS, none of the fine acting or writing of TNG, and none of the interesting characters of DS9.
They need to stop poorly imitating Voyager (why would you imitate crap?) and start coming up with NEW ideas that are relevant to our current events. But, of course, there's ABSOLUTELY nothing happening in the world right now that could _ever_ be explored in a sci-fi setting...
Maybe I misread, but what's so wrong about using the 2nd Law of Thermodynamics to prove or disprove the validity of a claim?
Any system may not decrease its entropy without an input of work.
In fact, the laws of thermodynamics and physics should be emblazoned on the walls of the US Patent Office. I bet they'd reduce the workload of faulty patents by tenfold.
I'll explain how someone can earn a billion dollars...
Produce a product that everyone wants. Make a profit. Do that over and over again, in finitum.
And the only way to do that is through innovation and engineering because there's a thousand other people out there who see the product, mimic it, and try to sell it for less.
Better products come from better technology. Better technology fuels overall growth of the nation (and the world). Better technology relieves the scarcity of resources that defines the state of an economy.
People who keep making better products do more for the world than people who whine about how current products are distributed or shared.
Slashdot Mirror
Actually, DNA is location addressable. DNA is composed of nucleotides with a specific sequence. The sequence itself is the "address" of a site on the DNA. LOTS of proteins specifically bind ONLY to certain sites on DNA, making them "location addressable".
Look up Cre/LoxP, V(D)J recombination, transcriptional operators, and the list goes on and on..
DNA and RNA will also hybridize only to specific sequences, or undergo homologous recombination with partially homologous regions. This is what the researchers are using to "control" their grid.
It's viscous, it's a psuedoliquid! It can migrate down gravitational potentials! It can replicate itself by splitting (and even ostracize OTHER forms of polymers who try to get in between)! It vibrates, oh it vibrates! It absorbs water, it's drinking, it's drinking!
...
MY GOD, IT'S ALIVE!
(Yes, this is a joke)
Physics itself produces some amazing phenomenom. While it might be cutesy that some plasma is splitting and vibrating synchronously (everything vibrates, sigh. Lasers vibrate synchronously), it is not 'Alive'.
Ok, there's anecdotal evidence. But if someone did a poll and asked this question:
:) There's very few differing (substantially different) viewpoints in the Arab Middle East. Even the "moderates" have to check their talk of reform for _fear_ of a fundamentalist calling them an American-lackey and declaring jihad against them. How does that encourage free speech, free thought, and useful discussion? It doesn't!
"Which news story would you believe more? One from Fox News and one from CNN."
I wonder what the outcome would be.
IMO, CNN is a little left slanted, but that's mostly because they cater to the "world" audience and, surprisingly, I'd say Americans are more conservative about a lot of things than many other nations in the world. (Especially Europe)
But...do the majority of Arabs believe that Al Jazeera is the unbiased story? I bet the majority of Americans know that FOX is purposely biased.
(At least roughly 1/2 of Americans would never watch FOX because FOX specifically caters to their opposing idealogy. Of the other half, I bet the majority still doesn't watch FOX because they know it's all bs.)
How many Arabs are against Arab Nationalism?
You're very correct in saying that Fox News is just about the same as Al Jazeera. The important question is whether the viewers of Al Jazeera recognize the difference between a 'CNN' and a 'Al Jazeera'. (Not like CNN is perfect, but I digress.) In the Arab media environment, There is no relatively objective news source. We have CBS, NBC, ABC, along with the CNN and other cable news. We can tell the difference between Fox News and CNN, because we have a CNN to show us the difference.
In the U.S, we recognize that Fox news is biased. In the Middle East, do viewers of Al Jazeera recognize the same thing? I think that's the real question.
I know they can watch CNN by satellite. I wonder if they believe that Al Jazeera is the truth and that CNN is the biased version. (By truth, I mean closer to the truth. By biased, I mean farther from the truth.) If so, that's a giant idealogical gap between us and them.
It's also possible that Al Jazeera cut and pasted from SpaceDaily.com. (See Slashdot original link.)
(I read SpaceDaily.com's article and you just quoted it back to me verbatim saying it was from Al Jazeera.)
Soo....I know you didn't know that, of course, but you have to admit that Al Jazeera doesn't have the objective standards that other newspapers try to adhere to.
I won't deny that some stories within the U.S are very politically charged and may not receive the objective view that they deserve, but there is a difference between stating the exceptions and stating the Norm.
The Norm for Al Jazeera is Arab Nationalism. They're catering to their viewers, of course, but they're doing so at the cost of objectivity. It's more like a circus than a news show. More entertainment than news. Have you ever watched it?
"You can read more on Al Jazeera and USA Today".
Wow. Is that a first? Is Al Jazeera to be considered a reputable media outlet? Does it deserve linking from a Slashdot site?
I don't know how well their technology coverage is, but I do know that their "World news" is highly skewed and biased.
Yeah, USA Today is certainly not #1, but compared to Al Jazeera, it's superbly honest.
When was the last time Slashdot linked to the Inquirer?
Whether or not you agree with his prediction that human employees will be replaced with robots, the guy's suggestions as to what the consequences could (or should) be are poorly thought out.
The author suggests that the government extract sources of income (and he gives some far-fetched examples) that would provide every consumer in the U.S with a salary of $25,000 a year...for doing nothing.
The author's main suggestion is that the U.S government should sell advertisement space on every possible surface it owns (dollar bills, road surfaces, etc etc). While he purports capitalism, he doesn't really understand it. As the supply of "Advertisement space" rises, the price of it will drop. If the U.S govt. made it so readily available, advertisers would no longer pay as much for it.
Additionally, the very idea of supplying every consumer with a fixed income check is not capitalism...it's socialism! There is never any free lunch in this world. See the Soviet Union, Cultural Revolution China, North Korea, etc, etc. With no incentive for work, no one will work. Having not earned the money, people will hate it.
With so much assured money in the system, prices will rise. The money won't go far enough...people will become poor. The only rich people will be people who produce things and sell them. People who get the checks in the mail will remain poor forever.
So, I don't think that's the answer, although it's been suggested before (Marx, Mao, etc, etc).
Oh, it's fast, booyah!
Computational biology just sucks up those FLOPS!
It's like budda.
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
...then I don't ever want to be Right!
It's amazing how much you miss it when you move away from the Garden state. People drive like idiots where I'm living...slow idiots.
Fast idiots, I can deal with.
I've read 'The Prince' and I agree it's a great one. I haven't read 'The Art of War' yet, but it's probably more relevant to current conflicts than Clausewitz's...now that asymmetric warfare and precision bombing are two major themes to new military conflicts.
Science Fiction/Fantasy might be great to let your brain relax, but it won't leave you educated beyond the superficial themes most fiction writers insert. There are always exceptions, but once you've read the good ones, it's all down hill from there...
;)
If you want TRUE stories that are much better than the fiction some fantasy writers dream up, then try some History. Truth is much more interesting than fiction... Here's my picks:
_Ancient History_
Gates of Fire (Steven Pressfield)
About the Persian-Greek war and the Spartan's stand at the Thermopylae gates.
The Peloponnesian War (Donald Kagan)
About the title Greek war, with an indepth description of the tactics, the decision making process, the culture war, and analogies to the Cold War and other conflicts
Caesar's War Commentaries (Julius Caesar)
Read his exploits written by the man himself. Look around for a good translation, though. If you're interested in literature, get an exact one. If not, there's translations that convert to the first person/etc that make it a much more fluid story. Play Praetorians (PC game) while reading for the best experience.
Guns, Germs, and Steel (Jared Diamond, I think)
An anthropological explanation of why the Western World has (so far) dominated the world in culture, prosperity, and technology. Condemns racist rationales and explains the causes by reason of resources available on the different continents and differences in political states
_American History_
John Adams (David McCullough)
Extremely well written biography about our 2nd President
_Classics_ (classic fiction, I should say)
Anything by Alexander Dumas is a great read. Count of Monte Cristo, Three Musketeers, Man in the Iron Mask. Quite different from the movies (more sex, hah) and better pick up lines.
Anything by Oscar Wilde. Very funny plays (in a British way, I guess). 'The Importance of Being Earnest' is his most famous one, I guess. The movie was well done, if you saw it, liked it, and wanted to read the play itself...
_Contemporary_
Anything by Kurt Vonnegut. Read Slaughterhouse-Five and I bet you'll get hooked. Mother Night is especially Vonnegut-esque (dark sarcasm) and his short stories are very good.
Yes, I will say it: Atlas Shrugged and/or The Fountainhead. It will give you that good American "I want to be rich and I won't feel bad when I am" feeling. Jokes aside, Atlas Shrugged is a good story and, excepting a certain 80 page monologue, not _too_ preachy. I mean, Who is John Galt, anyways?
Ok, I'll stop.
It's amazing how enjoyable a good book can be when you don't have a teacher telling you to read it.
Salis
Words are just words. Just because you can think of some (what you call) new idea doesn't mean it's doable or practical or that _you_ can actually do it.
The Space Elevator was imagined by Arthur C. Clark a while back. Did he patent it because he thought of it? No. He didn't create one, nor design one (ie. detailed schematics), nor prove that he could build one.
The first person to be able to build long lengths of carbon nanotubes will surely get a patent for their TECHNIQUE. It will be priceless. It will be genius. But saying "I imagine that one could build " does not earn one a patent.
If you want to protect something that you imagined up..then it's called a copyright. If you want to protect something that you physically created, it's called a patent.
Big difference.
(Actual definitions may differ. I am not a lawyer. I'm an Engineer. Thank God.)
Until then, it's all bullshit hype.
For an example of a real engineer, read this . Of course, it's the USPTO that mistakes hype for substance...at the cost of the true innovators in this country.
Howard Salis
Black & White
The game chants "death" every time one of your villagers died. My roommate freaked out (Junior year of college) because he kept hearing someone chant "death". This is a guy who regularly kept a collection of swords, katanas, and knives in the room as well as some pistols (mock or not).
The developers of B&W definately wanted to freak ppl out with random easter eggs. If you used a name that was on B&W's list of common names, it would randomly chant your name within the game. Now that was weird.
One thing they didn't mention is that Gene circuits can not only exhibit bistable behavior (bits), but multistable behavior (trinary, etc). Because chemical species exist in concentrations and not 'on' or 'off, there's quite a bit of additional complexity that can be utilized to perform added functions.
:)
Differentiating stem cells in the body take a signal (concentration of a chemical species) and differentiate into different cell types (more than two different cell types).
Sometimes, it's like an 'if then' statement => If received X signal, differentiate into cell type A, else B. If received signal Y (after having received X), differentiate into cell type C, else D.
Or, it might receive a 'low' signal of X and go A. Medium => B. High => C. None => D.
There's different mechanisms that can be employed to give the gene this behavior. But, the cell must be able to effectively distinguish between 'none', 'low', 'medium', and 'high'..even in a highly fluctuating environment. So it's not simple nor has it ever been studied rigorously before.
Yes, scientists have played with gene circuits and have created some interesting designs. But, it's becoming an engineering discipline whereby the engineer should know _exactly_ what will happen if the microbiologist assembles the specific components together in a cell.
That'll take a decade or more, but it's getting there.
Howard Salis
Chemical Engineer
University of Minnesota
If you want to read a great paper, read Adam Arkin's paper on the Stochastic simulation of Lambda-Phage infection of E. coli. It's from 1998 (I think). The fact that one can simulate exactly what occurs inside cells is amazing. The next step is to _predict_ what will happen. This is what engineers do.
How many times do you see buildings spontaneously collapse?
I think scientists grossly overexaggerate the usefulness of the Human genome sequencing project. So you know the sequence of the genome.
We still have to find all of the coding portions of the genome and separate them from non-coding portions.
We still have to find a way to infer the structure and function of a protein from its sequence.
We still have to find a method to engineer proteins systematically and by design. (No guess and check..)
We still have to find a method to model and simulate how multiple proteins and genes interact in order to give us the behavior of the entire system. There are no genes that do one thing or provide one attribute. They all contribute to the behavior of the system, but not linearly and usually unpredictably.
We still have to find a way to alter human DNA successfully, without triggering the immune response too much, and without causing cancer.
We still have a LONG way to go before we see genetically modified humans.
I'd say we'll see many more GM foods and animals long before some guy feels he can get it right on the first try. But that's what engineering is all about...knowing exactly what is going to happen when you create something so that it _will_ work on the first try. (How many buildings collapse spontaneously?)
Not until we understand the complex interactions (and there's a LOT of them) in the body will we be able to engineer biological systems with a supremely high degree of aforeknowledge.
Salis
80% of all the scientific articles in the WORLD are published by people either living in the U.S or studying here.
The U.S has the most universities in the world and the most prestigious/highest quality ones.
And..here's a causation vs. correlation difference for you...to illustrate the point.
People are not stupid if they disagree with you. I find that most protesters/ranters fail to see this.
The assumption that each gene codes for one protein is usually false. But, regardless of that, there exists an additional "degree of freedom" that biological organisms can utilize in order to allow themselves to assume as many "states" of gene expression as possible.
The topic of stochastic gene expression is becoming more interesting recently because of further advances in studying single-cell gene expression and the design of genetic regulatory networks.
Because the concentrations of many gene regulatory proteins are so dilute/low, there exists significant fluctuations in the number of molecules that actually regulate the gene's expression. These fluctuations vary from time to time and from cell to cell, producing non-deterministic levels of gene expression. The non-determinism (called stochasticity) can cause some very interesting behavior that leads to numerous potential 'states' of gene expression versus a single, deterministic state.
So, on a very real basis, probability has a lot to do with how certain genes are expressed. Successful biological systems, however, hate random chance unless it's advantageous. These certain genes that utilize the internal noise of a "small" biological system do so because it gives some sort of advantage to them..either coding for numerous possible states with the least number of genes or for allowing the cell to randomly pick between possible states in order to create a heterogeneous cell population.
If you're interested in some scientific articles, try Adam Arkin's paper from 1998, detailing a stochastic simulation of a virus that attacks E. coli cells. The virus randomly selects whether it will replicate itself quickly and burst the cell open or integrate itself into the bacteria's genome and sit dormant. The probability of each event depends on the state of the bacteria at the time of infection. If the bacteria is starved, the virus goes dormant. If it's healthy, the virus goes into replication mode.
Salis
This topic is actually a focus of much research.
Because the concentrations of many gene regulatory proteins are so dilute/low, there exists significant fluctuations in the number of molecules that actually regulate the gene's expression. These fluctuations vary from time to time and from cell to cell, producing non-deterministic levels of gene expression. The non-determinism (called stochasticity) can cause some very interesting behavior that leads to numerous potential 'states' of gene expression versus a single, deterministic state.
So, on a very real basis, probability has a lot to do with how certain genes are expressed. Successful biological systems, however, hate random chance unless it's advantageous. These certain genes that utilize the internal noise of a "small" biological system do so because it gives some sort of advantage to them..either coding for numerous possible states with the least number of genes or for allowing the cell to randomly pick between possible states in order to create a heterogeneous cell population.
If you're interested in some scientific articles, try Adam Arkin's paper from 1998, detailing a stochastic simulation of a virus that attacks E. coli cells. The virus randomly selects whether it will replicate itself quickly and burst the cell open or integrate itself into the bacteria's genome and sit dormant. The probability of each event depends on the state of the bacteria at the time of infection. If the bacteria is starved, the virus goes dormant. If it's healthy, the virus goes into replication mode.
Salis
Is it ethical to genetically modify food using biotechnological techniques? Are there unseen side effects to the introduction of trans-species genes? This issue is real big in Europe, but not as controversial in the U.S. Why? If it tastes better and doesn't hurt you (or anyone else), can it really be that bad? :)
Stem Cell Research...this issue is extremely controversial right now. Is it ethical to use embryonic stem cells in order to find treatments for numerous diseases, including diabetes, cancer, Alzeihmer's (sp?), etc.
Or..if you're more interested in public policy & technology...
How about the privacy of information regarding one's genomic attributes. Can a health insurance company be allowed to examine your genome and determine whether you are more likely to have heart disease, cancer, etc? Should such information be stored in public databases (to be accessible by hospitals, insurance companies, and the government)?
Talk amongst yourselves.
Yes, Captain Obvious! :)
I completely agree. A lot of the episodes of TNG didn't need to happen in space or with aliens. It was just damned good drama (but with serious conflict..not soap opera). Hell, even my sister watched TNG and she hated Sci-fi shows.
I don't even bother watching Enterprise. It has none of the campy 60s feel of TOS, none of the fine acting or writing of TNG, and none of the interesting characters of DS9.
They need to stop poorly imitating Voyager (why would you imitate crap?) and start coming up with NEW ideas that are relevant to our current events. But, of course, there's ABSOLUTELY nothing happening in the world right now that could _ever_ be explored in a sci-fi setting...
Maybe I misread, but what's so wrong about using the 2nd Law of Thermodynamics to prove or disprove the validity of a claim?
Any system may not decrease its entropy without an input of work.
In fact, the laws of thermodynamics and physics should be emblazoned on the walls of the US Patent Office. I bet they'd reduce the workload of faulty patents by tenfold.
I'll explain how someone can earn a billion dollars...
Produce a product that everyone wants. Make a profit. Do that over and over again, in finitum.
And the only way to do that is through innovation and engineering because there's a thousand other people out there who see the product, mimic it, and try to sell it for less.
Better products come from better technology. Better technology fuels overall growth of the nation (and the world). Better technology relieves the scarcity of resources that defines the state of an economy.
People who keep making better products do more for the world than people who whine about how current products are distributed or shared.