Skip to comments.Artificial Life Experiments Show How Complex Functions Can Evolve
Posted on 05/08/2003 10:11:06 AM PDT by Nebullis
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."
Not to mention the precision of the temperature, humidity and pressure to maintain same. But hey, no biggie.
No. It means computers can model reality. An iteration in a computer is a model of a generation in life.
Very neighborly of you.
The way to eduacte a novice is to present he or she with false information. Wonderful.
Do you teach in public schools?
:-} Really? What dictionary can I find that bit of wisdom in?
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.
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 TheoryNow, 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?
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. www.chipcenter.com, 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
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.
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.
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.
If you know what I mean. Wink, wink. Hee hee.
A 50 microgram touch on about a 2 watt resistor.
Using a file!?
Yes, but then hair would grow on the palms of his hands and he'd go blind......
...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?
Well that is more like it.
Message received. Wolfpack formation on standby!
What really must twist your panties however is that a blue collar guy like me is at a minimum your "intellectual" equal.
Mind you now, they are "special transistors".
Are you denying that Gould was an atheist? This is the typical doubletalk garbage from you and your friends. That Gould was an atheist is well known and well documented. Like the Clintonites you attack people for telling the truth because you do not like to hear the truth.
Wow, you must be unlucky since you went 0 for 3. Or maybe you're just stupid. Gee, which one would I bet one?
In case you didn't get it, that was a rhetorical question.
Ah, yes, that would the your viewpoint of the world from out of your anal sphincter.
Not only a court jester but an anally fixated one at that.
Any opinion on two diodes back to back equalling a transistor?
Fascinating bit of personal opinion
Excuse me? That water does not self assemble itself into a lake is personal opinion? Your arrogance shows your total dishonesty and idiocy. Only a total fool would think that he can deny obvious facts as above and fool others into believing as he. All the above are created by simple well known forces.
As usual you and your friends dishonestly forget to address the meat of my argument which is (from the post you are supposedly responding to):
The DNA in the simplest organism however, the arrangement of it is not only not due to any natural forces, but it cannot be due to it. Otherwise we would not be able to find all the possible ways in which 3 different bit pairs with 3 possible values (64 in all) appear in the DNA sequences of all species. Such self assembly is totally unknown anywhere in the natural world. For anything even close, one must go and look at humanly designed things.
Let's see you or your friends refute the above.
The slimer gives us another example of his total hypocrisy. It is the evolutionists which EVERY TIME an opponent starts showing that evolution is total bunk that start with the insults. For example, soon after I started posting on this thread (and getting no replies of course as is usual from the evolutionists since they cannot deny the truth but just insult the bearer of it).
I have often challenged you to show a single post from you on this thread which is not an insult. A single post from you discussing the subject at hand. There are none such because you do not discuss, you insult and encourage your friends to do the same and turn threads into shouting matches so that they will be pulled.
Yup, they mark the place to stop discussing and start insulting. They mark the place to start spamming the thread with irrelevancies. They mark the place to start indulging in personal attacks.
They have nothing to do with discussion. They have everything to do with NOT discussing the topic as you are doing right now.