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Artificial Life Experiments Show How Complex Functions Can Evolve
NSF ^ | May 8, 2003 | Staff

Posted on 05/08/2003 10:11:06 AM PDT by Nebullis

Artificial Life Experiments Show How Complex Functions Can Evolve

Arlington, Va.—If the evolution of complex organisms were a road trip, then the simple country drives are what get you there. And sometimes even potholes along the way are important.

An interdisciplinary team of scientists at Michigan State University and the California Institute of Technology, with the help of powerful computers, has used a kind of artificial life, or ALife, to create a road map detailing the evolution of complex organisms, an old problem in biology.

In an article in the May 8 issue of the international journal Nature, Richard Lenski, Charles Ofria, Robert Pennock, and Christoph Adami report that the path to complex organisms is paved with a long series of simple functions, each unremarkable if viewed in isolation. "This project addresses a fundamental criticism of the theory of evolution, how complex functions arise from mutation and natural selection," said Sam Scheiner, program director in the division of environmental biology at the National Science Foundation (NSF), which funded the research through its Biocomplexity in the Environment initiative. "These simulations will help direct research on living systems and will provide understanding of the origins of biocomplexity."

Some mutations that cause damage in the short term ultimately become a positive force in the genetic pedigree of a complex organism. "The little things, they definitely count," said Lenski of Michigan State, the paper's lead author. "Our work allowed us to see how the most complex functions are built up from simpler and simpler functions. We also saw that some mutations looked like bad events when they happened, but turned out to be really important for the evolution of the population over a long period of time."

In the key phrase, "a long period of time," lies the magic of ALife. Lenski teamed up with Adami, a scientist at Caltech's Jet Propulsion Laboratory and Ofria, a Michigan State computer scientist, to further explore ALife.

Pennock, a Michigan State philosopher, joined the team to study an artificial world inside a computer, a world in which computer programs take the place of living organisms. These computer programs go forth and multiply, they mutate and they adapt by natural selection.

The program, called Avida, is an artificial petri dish in which organisms not only reproduce, but also perform mathematical calculations to obtain rewards. Their reward is more computer time that they can use for making copies of themselves. Avida randomly adds mutations to the copies, thus spurring natural selection and evolution. The research team watched how these "bugs" adapted and evolved in different environments inside their artificial world.

Avida is the biologist's race car - a really souped up one. To watch the evolution of most living organisms would require thousands of years – without blinking. The digital bugs evolve at lightening speed, and they leave tracks for scientists to study.

"The cool thing is that we can trace the line of descent," Lenski said. "Out of a big population of organisms you can work back to see the pivotal mutations that really mattered during the evolutionary history of the population. The human mind can't sort through so much data, but we developed a tool to find these pivotal events."

There are no missing links with this technology.

Evolutionary theory sometimes struggles to explain the most complex features of organisms. Lenski uses the human eye as an example. It's obviously used for seeing, and it has all sorts of parts - like a lens that can be focused at different distances - that make it well suited for that use. But how did something so complicated as the eye come to be?

Since Charles Darwin, biologists have concluded that such features must have arisen through lots of intermediates and, moreover, that these intermediate structures may once have served different functions from what we see today. The crystalline proteins that make up the lens of the eye, for example, are related to those that serve enzymatic functions unrelated to vision. So, the theory goes, evolution borrowed an existing protein and used it for a new function.

"Over time," Lenski said, "an old structure could be tweaked here and there to improve it for its new function, and that's a lot easier than inventing something entirely new."

That's where ALife sheds light.

"Darwinian evolution is a process that doesn't specify exactly how the evolving information is coded," says Adami, who leads the Digital Life Laboratory at Caltech. "It affects DNA and computer code in much the same way, which allows us to study evolution in this electronic medium."

Many computer scientists and engineers are now using processes based on principles of genetics and evolution to solve complex problems, design working robots, and more. Ofria says that "we can then apply these concepts when trying to decide how best to solve computational problems."

"Evolutionary design," says Pennock, "can often solve problems better than we can using our own intelligence."

TOPICS: Culture/Society; Miscellaneous; News/Current Events
KEYWORDS: ai; crevolist
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To: jwalsh07
Sorry, I left off "In that program..."
1,761 posted on 05/21/2003 10:56:49 AM PDT by null and void
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To: null and void
With a bit of practice you could turn out one, maybe two a day...

Hey, you must be pretty good! For a 1 gram carbon resistor you would be precise to around 50 micrograms.(lots of assumptions in your favor) Pretty deft with a file.

1,762 posted on 05/21/2003 10:59:03 AM PDT by AndrewC
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To: AndrewC
Still trying the red herring.

Yes you are. Getting tired of that stale fish yet?

I stated it won't work.

You did, knowing that most people here don't have the background to realize how baldfacedly you're lying.

In a sense, means in a sense.

Nice tautology. Care to make some sort of point?

Junction transistors are not fabricated by putting two diodes back-to-back. They are fabricated by a process of doping(appropriate to you) and redoping(still appropriate to you) a silicon wafer

Sure they are. But that doesn't prove your first sentence, since semiconductor diodes are constructed that way as well. Making a transistor on a semiconductor in that manner is no different than the process of doping an NP junction layer (a diode) followed by another N layer on top of the exposed P layer (which forms a PN junction, a reversed diode). Voila -- a transistor fabricated from two back-to-back diodes.

You *know* this, which is why you have proudly stated:

"Which, of course, makes my original statement, that a transistor was in a sense two diodes back-to-back, entirely correct."
So stop making an ass out of yourself by spending a week attacking *me* for (gasp) agreeing with you on that point. It not only makes you look foolish, it makes you look practically insane.

But hey, don't just take my word for it:

A transistor is formed by placing two diodes back to back in one piece of semiconductor material. This is done by layering N and P material in a sandwich A Brief Review of Transistor Theory

Bipolar Junction Transistors: There are two types of BJT -NPN & PNP – These devices are constructed of two diodes back to back Analog and Digital Electronics - ECET- 329

Transistors are sandwiches of three pieces of semiconductor material. A thin slice of n-type or p-type semiconductor is sandwiched between two layers of the opposite type. This gives two junctions rather than the one found in a diode. [one reversed with respect to the other -- Ich.] If the thin slice is n-type the transistor is called a p-n-p transistor, and if the thin slice is p-type it is called a n-p-n transistor. The middle layer is always called the base, and the outer two layers are called the collector and the emitter. We will consider the (more common) n-p-n transistor here, as used in the MadLab circuits. In a n-p-n transistor electrons are the main current carriers (because n-type material predominates). When no voltage is connected to the base then the transistor is equivalent to two diodes connected back to back. LESSON 4 - SEMICONDUCTORS

Now a transistor is merely a "sandwich" of these devices. A PNP transistor is depicted in figure 2 below. Actually it would be two p-layers with a "thin" n-layer in between. What we have here are two p-n diodes back to back. Transistors

A transistor, which lets the current from source to drain to be controlled by a gate, is a pair of diodes connected back to back. Since a transistor is made of two diodes, the next section will first describe what a diode does and how it works. Logic Diagrams to Transistors, December 10, 1993

BJT has two diodes back-to-back. Lecture 24 - PNP transistor

Bipolar Junction Transistors (BJT) - Consists of two diodes connected back-to-back. ICS217 - Digital Electronics

Question: I see a transistor is like two diodes back to back. How can current flow when one diode is always reversed biased? Answer: The short answer is simply that the two diodes are physically close enough together that they influence each other. The long answer is as follows. A junction diode consists of two regions of silicon-an N-type region doped with an impurity that has an extra electron relative to the silicon atom and a P-type region doped with an impurity that lacks an electron relative to silicon. [...] Now we're in a position to consider the transistor, which has three regions of semiconductor (N-P-N or P-N-P) forming two diode junctions back-to-back. The key to the transistor's operation is the fact that the center region (called the base from the days of the point-contact transistor) is very thin, putting the two diode junctions close together., THE ENGINEER'S TECH-HELP RESOURCE

Now, starting with the bipolar junction transistor (BJT) [...] A BJT comprises two back-to-back diodes, so you can double-check it with an ohmmeter. Troubleshooting at the component level: Understanding component functionality is paramount.

Bipolar junction transistors bipolar junction transistor, a bipolar transistor essentially consists of a pair of PN Junction Diodes that are joined back-to-back The Educational Encyclopedia, Electronic Components

A bipolar junction transistor consists of two back-to-back p-n junctions [a p-n junction is a diode -- Ich.], who share a thin common region with width, wB. Contacts are made to all three regions, the two outer regions called the emitter and collector and the middle region called the base. [...] Since the device consists of two back-to-back diodes, there are depletion regions between the quasi-neutral regions. Chapter 5: Bipolar Junction Transistors

Semiconductor Devices A # 50003: The physical structure of the Bipolar transistor as two back to back diodes. Courses of Aaron Peled, Professor of Electrical Engineering and Photonics

A transistor is two back-to-back diodes, that is alternating layers of either p-type/n-type/p-type (PNP) or n-type/p-type/n-type (NPN). The ‘closeness’ of the two diodes makes it unique, as electrons from one shoot into the other without resistance. Introduction to one of the most important inventions of the 20th Century

Now, are you going to stop trollishly spewing accusations against me of being a "liar" for stating the truth? Or are you going to keep being an a**hole?

Let's cut to the chase and see how fast you try to shift topics again, lest you be nailed down for a change. Is the following an accurate representation of a semiconductor diode, yes or no:

After we've settled *that* question we can move on to the next.

1,763 posted on 05/21/2003 11:32:06 AM PDT by Ichneumon
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To: Ichneumon
Jellyfish... I mean placemarker.
1,764 posted on 05/21/2003 11:37:29 AM PDT by balrog666 (When in doubt, tell the truth. - Mark Twain)
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To: jwalsh07
You don't have the requisite male anatomy to admit when you're wrong.

I admit when I'm wrong, but in this case I'm not. And your childishly making penis references does not constitute proof that I am. On the contrary, it makes it obvious you have nothing else to make your case with.

A battery is the source of potential dipstick, the base or gate of a transistor is an inherent component of same.

No s***, Sherlock. My point exactly. Now are you trolling, or just too stupid to see the parallel I set out for you?

Here it is in words small enough even for you: I described how a semiconductor sandwich of two PN junctions in serial (one reversed) constitutes a transistor. A PN junction, for those of you who get your knowledge from creationist sources, is a diode. Thus a transistor (BJT type, anyway) is formed from two back-to-back diodes. QED.

Then you came along and babbled incoherently about how there has to be a voltage applied to the base of the transistor or it won't work. I pointed out that this was a stupid "point" and in no way invalidated my statement about transistors. Your non sequitur, I pointed out, was as stupid as objecting to the workability of a radio just because it wouldn't do anything without a battery. Well sure, but who'd ever be stupid enough to insist on faulting a radio for not working without a power source? Likewise, what kind of gibbering twit is going to fault a transistor for "not working" unless power is applied to its base (and elsewhere)?

Are we clear *now*, child? Go away and play, the adults are talking.

I repeat, get a refund forthwith.

You can repeat all the cheap unsupported accusations you wish -- it only makes the paucity of your actual contribution to the subject entirely clear.

But if you want to make a stab at acting like a mature grownup for a change, feel free to read post 1763. Then either try to explain how all those other electronics articles are "wrong" also (they must be, since they say what I've said, right?), or take a stab at answering the question at the end. There will be a quiz later, and you *will* be graded on your answers.

1,765 posted on 05/21/2003 11:50:48 AM PDT by Ichneumon
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To: Ichneumon; general_re
After, saying we agree you now attempt to resurrect your lost argument.

Look, the fact that you do not understand the word "like" or understand the meaning of "in a sense" does not make your argument for you. Your links are peppered with words such as "like" or "essentially". Now your initial link states this in context.A transistor is formed by placing two diodes back to back in one piece of semiconductor material. This is done by layering N and P material in a sandwich (Figure 5). In reality a transistor etched into a die would look more like Figure 6.

Notice the author uses "in reality". Blather on, you are not getting anywhere.

I repeat I know that you can use a transistor as a diode in a pinch. After all, it "consists" of back-to-back diodes in a sense.

And you wrote ---Trollish Behavior #9: Not only "in a sense", Troll, but in actuality. Stop squirming, Troll.

1,766 posted on 05/21/2003 11:58:24 AM PDT by AndrewC
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To: All

If you know what I mean. Wink, wink. Hee hee.

1,767 posted on 05/21/2003 12:09:41 PM PDT by PatrickHenry (Felix, qui potuit rerum cognoscere causas.)
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To: AndrewC
The secret is to file a shallow groove. As you get closer to the target value rotate the resistor slightly so you are not filing on the bottom of the groove but at a point on one end of the groove.

It does require a deft touch...
1,768 posted on 05/21/2003 12:14:50 PM PDT by null and void (and a willingness to teach bystanders new words...)
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To: null and void
It does require a deft touch...

A 50 microgram touch on about a 2 watt resistor.

1,769 posted on 05/21/2003 12:16:59 PM PDT by AndrewC
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To: AndrewC
*shrug* I do micromachining for a living.
1,770 posted on 05/21/2003 12:20:29 PM PDT by null and void
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To: null and void
*shrug* I do micromachining for a living.

Using a file!?

1,771 posted on 05/21/2003 12:31:31 PM PDT by AndrewC
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To: null and void
you could post to yourself, junior...

Yes, but then hair would grow on the palms of his hands and he'd go blind......

1,772 posted on 05/21/2003 12:32:58 PM PDT by longshadow
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To: AndrewC
LOL! Not usualy. Using standard lithography and etching mostly.

Seriously, filing in a resistor value is something any lens grinder, diamond cutter or tool maker can learn to do.

Being willing to throw out scores of slightly too high value resistors helps...
1,773 posted on 05/21/2003 12:37:14 PM PDT by null and void
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To: longshadow
I just did it until I needed glasses...
1,774 posted on 05/21/2003 12:37:57 PM PDT by null and void
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To: AndrewC
"actuality" (his word) that a transistor was two diodes back-to-back. I replied that putting two diodes back-to-back did not make a transistor. I gave an actual example of soldering two diodes together,

...So, the question is, is "actuality" the physical black box called a diode by the manufacturers of potted devices, or is "actuality" what occurs on a silicon backplane where the active device actually does it's work?

Just for the record, this is, in your own words, the exact point in this conversation where your habitual jesuistry struck once again.

I will not respond to such a blithering idiot.

You already made and broke this promise once. Perhaps you have a 5 paragraph explanation as to why that didn't occur, as well?

1,775 posted on 05/21/2003 12:37:58 PM PDT by donh (/)
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To: null and void
Not usualy. Using standard lithography and etching mostly.

Well that is more like it.

1,776 posted on 05/21/2003 12:41:59 PM PDT by AndrewC
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To: AndrewC
Nice post Number placemarker.
1,777 posted on 05/21/2003 12:45:42 PM PDT by js1138
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To: js1138
Danger -- beware ... cyber-social virus on the FR --- mad science disease !
1,778 posted on 05/21/2003 12:49:11 PM PDT by f.Christian (( apocalypsis, from Gr. apokalypsis, from apokalyptein to uncover, from apo- + kalyptein to cover))
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To: js1138
It was an accident. I knew it was coming up/

1,779 posted on 05/21/2003 12:49:47 PM PDT by AndrewC
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To: PatrickHenry
If you know what I mean. Wink, wink. Hee hee.

Message received. Wolfpack formation on standby!

1,780 posted on 05/21/2003 1:10:46 PM PDT by balrog666 (When in doubt, tell the truth. - Mark Twain)
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