Artificial Life Experiments Show How Complex Functions Can Evolve

NSF ^ | May 8, 2003 | Staff

[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."

[f.Christian]

Haven't seen the general unified theory of evolution lately ... anymore --- what happened ?

[f.Christian]

I have a very close friend -- family member who I started to tease ...

"stop bucking the system (( truth // reality ))"

(( he's been through a lot recently ))---

at a recent get together ...

we were crashed by one of those chronic complainer (( ranting // raving // drunk )) ---

loser (( evo -- anarch-loon )) type ...

and my only remark was ---

"he wasn't even in the system (( sanity )) " !

[Ichneumon]

AndrewC statement #1: Which, of course, makes my original statement, that a transistor was in a sense two diodes back-to-back, entirely correct.

AndrewC statement #2: I replied that putting two diodes back-to-back did not make a transistor.

Tell you what, as soon as you're done arguing with yourself, get back to us.

Meanwhile:

In the race for smaller and smaller electronic components, Man-Kit Ng, SM'97, PhD'02, and chemistry professor Luping Yu have made a gigantic leap forward. The pair created a molecular diode—an electrical component that conducts electricity in one direction—by chemically bonding two electrically opposed compounds made mostly of hydrogen and carbon, embedding them in a sheet only one molecule thick, and then transferring the sheet to a gold platform. The resulting diode, approximately 12 atoms wide, could be the first in a move toward smaller, simpler, and thus faster transistors—which are made by placing two diodes back to back.

University of Chicago Magazine, December 2002

[Ichneumon]

I think it was a post by g3k, calling someone a liar.

How would that be any different from his other posts?

[jwalsh07]

You might want to google NPN or PNP and Transistors. You're ignoring the base of the transistor.

[gore3000]

It was a post calling me a liar (this seems to be boilerplate). I had responded to a post about the article in "Nature" and got called a liar because my answer wasn't about naturally occuring nuclear reactors.

Still lying (now with the aid of the moderator who lets the evos slime and abuse to their hearts content). The post was #1524 where in response to:

WHERE ARE THE EXAMPLES OF MATTER ASSEMBLING ITSELF WITHOUT HUMAN INTERVENTION????

You responded with:

Even if you have lapsed into cap-shouting, there are examples.

That was the one about the nuclear reactor about which you keep lying about and now say it had nothing to do with the question posed to you. In Post#1617 you tried to say it was about a paper in Nature too. The paper in question in the whole discussion has been the same. What has not changed is your lying to cover up your previous lies.

AND AS YET NOT A SINGLE ONE OF THE EVOLUTIONISTS HAS BEEN ABLE TO SHOW A SINGLE EXAMPLE OF MATTER SELF ASSEMBLING

[PatrickHenry]

Non-shouting PLACEMARKER

[gore3000]

In the race for smaller and smaller electronic components, Man-Kit Ng, SM'97, PhD'02, and chemistry professor Luping Yu have made a gigantic leap forward. The pair created a molecular diode—an electrical component that conducts electricity in one direction—by chemically bonding two electrically opposed compounds made mostly of hydrogen and carbon, embedding them in a sheet only one molecule thick, and then transferring the sheet to a gold platform. The resulting diode, approximately 12 atoms wide, could be the first in a move toward smaller, simpler, and thus faster transistors—which are made by placing two diodes back to back.

Yup, only humans and God can bend the rules of nature to make them do what they wish.

[gore3000]

How would that be any different from his other posts?

Imagine that, evolutionists lie and they get called liars. How awful! I have shown to have told numerous lies in this very thread. But you folk, being totally shameless liars have no compunction to continue with your lies and like the Clintonites, to attack those who call on your lies.

[Ichneumon]

Here is an example of the problem:

Coevolution is often seen in a number of species of flowering plants that coevolved with specific pollinators (insects, bats, etc). The pollinator gets a reward such as nectar for pollinating the plant. Moth-pollinated plants often have spurs or tubes the exact length of a certain moth’s “tongue.” For example, Charles Darwin predicted the existance of a moth in Madagascar based on the size and shape of a flower he saw there. The moth was actually discovered about 40 years later. The common snapdragons that many people plant in their gardens are designed for a bumblebee of just the right weight to trip the opening mechanism.

From: Coevolution and Pollination

Note Darwin's remark that there had to be a specific insect that fed on this plant. Well here we see the problem, the insect could not live without the plant and the plant could not live without the insect.

There you go again, mistaking your shortsightedness for facts.

First, nowhere does it in any way say that the "insect could not live without the plant". You just made that up.

You are invited to explain where, exactly, you got the bizarre idea that the moth is somehow crippled in a way that makes it impossible for it to feed from any other flower in the area. Such an explanation will go a long way towards documenting your flawed reasoning processes.

If you're making the mistake of reading too much into the opening "definition" of coevolution on that page ("evolution of two species totally dependent on each other"), this only shows why a little knowledge is a dangerous thing. Coevolution is *not* limited to "total" dependence, as even a quick Google search for the term (not to mention any Biology text) would make clear. Complete mutual dependence is *one* type of coevolution, but hardly the only type. And there's nothing about the Predicta moth which would preclude it from feeding on other flowers. It just *prefers* the Star of Bethlehem Orchid because, being the only moth able to reach its nectar, it has no competition inter-species competition there.

Second, although the orchid almost certainly is totally dependent upon the moth for pollination, that's no problem for evolution (nor would it be even if the moth *were* completely dependent upon the orchid). See below.

In fact, the plant had to be the correct shape, etc. for the insect to feed on it.

No, again, the moth has a long enough proboscis it could feed on damned near anything it wanted to, including the Star Orchid if it were many other shapes/sizes.

Just saying that flowers coevolved with specific pollinators does not answer the question of how such a thing could occur.

Of course it doesn't. Simple understanding of evolution, however, *does*. Which is why you're left baffled, presumably.

but what has to be taken into account is that it takes time, lots of time, for the proper mutations to arise and plants (like all species) have to continue reproducing throught this long time. Without the insect, and a specific constitution to allow this insect to spread its pollen, the plant would not have survived for a single generation more. This makes the evolutionary explanation of the rise of plants total nonsense.

The only thing that's "total nonsense" is your empty declaration that there is no evolutionary progression by which such symbiosis could arise. You haven't supported that claim, you've simply declared it, based on nothing more than your "I can't think of how it might happen". That's not good enough, that's an "argument from ignorance" fallacy.

First a bit of background. Today, the Star Orchid of Madagascar has a nectar trap that is 10.5 inches deep at the bottom of a twelve-inch tubular flower well. (Amusing side note: The species name in its latin name, "Angraecum sesquipedale", means "foot-and-a-half"). Orchids of the genus Angraecum are pollinated by moths. Thus, it seems that this particular species would only be visited by, and thus pollinated by, a moth with a tongue at least 10.5 inches long! None were known in Darwin's day, but he predicted that one would be found eventually. And it was found many years later, and named Xanthopan morgani praedicta, because it was the "predicted" moth. Its tongue is 11.75 inches long:

*Here's* how it could easily occur (one way out of several):

1. The orchid began pretty much as most other orchids in the area. But something about it (color, shape, time of bloom, whatever) attracted that particular moth (which at the time had a more ordinary proboscis) more strongly than most other insects which also visited the flower.

2. This set up an evolutionary incentive. Plants pollinate each other (i.e., mate and reproduce) more successfully if they can get a particular kind of insect to visit them often, intead of just attracting any insect that comes along. The reason is that an insect that goes feeding more selectively from Star Orchid to Star Orchid passes along the pollen much more directly and often than will an insect that wanders randomly among dozens of different species of flowers.

3. Thus, since the Predicta moth was already at least a little bit more of a selective feeder on Star Orchids than other insects were, any variation/adaptation which allowed an individual Star Orchid to a) attract the moth more strongly, or b) discourage/block other insects from using up the nectar that could be used to attract the Predicta moth, would increase that individual's reproductive success, since its pollen would be passed along to other Star Orchids more often than those that allowed any damned insect to wander off wit hits pollen, and/or wasn't so successful at getting more Predicta moths to visit.

4. This evolutionary pressure would, quite directly and through the usual well-understood processes of evolution, cause the Star Orchid to shape itself more and more specifically for the Predicta moth over generations.

5. Meanwhile, since the Predicta moth found itself after many generations (of Orchids) with a plant that had nectar reserved for the moth's exclusive use, there was evolutionary pressure for the Predicta moth to become more selective in seeking out Star Orchids.

6. Over time, neither species had any reason to bother with other pollinators/food sources, since both were benefiting so successfully from the arrangement.

[Sidebar: Note that at this point, the Orchid and the moth have already evolved into strict exclusivity (although presumably the moth could feed on other flowers if need be, although it had more incentive not to), *without* ever reaching what Gore3000 naively believes would be some sort of impossible reproductive gap. The orchid has simply tailored itself to the moth, and excluded all other insects, while the moth has simply grown preferential to the orchid which is always full of nectar for it. There's absolutely no "prevention" of reproduction here for either species at any point.]

7. But why such a *ridiculously* long flower/tongue? That's where a little arms race between the two species comes into play. Through variation, some Predicta moths will have longer tongues than others. The problem for the orchid is that extra-long-tongued moths can reach the nectar without having to push far enough into the flower itself to pick up any pollen. So some moth visits will result in the orchid "losing out" on a chance at reproduction. Consequently, over generations the orchids which have extra-deep nectar wells will reproduce more often, since even the longer-tongued moths will need to dive in deeply enough to pick up their pollen, and those orchids will outcompete their shallower brethren. As the flowers slowly deepen on average over generations, the moths need to pick up the pace as well, because the shorter-tongued moths now find themselves starting to lose out more often than their longer-tongued moth brethren. So there's an evolutionary pressure for the moths to evolve longer tongues as well. Over countless generations, there's an ever-rising spiral of deeper flowers and longer tongues, to the point of almost silliness.

Thus, there are perfectly ordinary evolutionary pressures which can, contrary to Gore3000's naive belief, produce co-evolved species without ever causing any sort of evolutionary impasse.

Time, there is no infinite time,

There doesn't need to be.

there is no billions of years for a species to go through the necessary mutations to survive.

What are you babbling about here?

Species have to reproduce, eat and survive on a daily basis, and this gives absolutely no time for the changes required for this 'coevolution' or for many other changes postulated by evolutionists.

See above and get back to us when you've caught on.

[AndrewC]

The resulting diode, approximately 12 atoms wide, could be the first in a move toward smaller, simpler, and thus faster transistors—which are made by placing two diodes back to back.

Yeah, right. So place two diodes back to back and see what you get. No amount of wishing is going to make it a transistor despite the incomplete use of words in a "technical" journal such as the University of Chicago magazine. It is a simple demonstration. Go to radio shack. Buy 2 1N4001 diodes. Twist their cathodes or anodes together(or any d*** way you please). Now try to make the contraption amplify a current like a transistor. Good luck.

[PatrickHenry]

Another great post. Long tongue placemarker.

[longshadow]

Long tongue placemarker.

Are you trolling for single women, or just bragging?

[Ichneumon]

You might want to google NPN or PNP and Transistors.

Been there, done that, but frankly the EE courses I took in college were a lot more detailed.

You're ignoring the base of the transistor.

How so?

I think you're misreading the point being made. A transistor is "back-to-back diodes" in the sense of its internal construction at the semi-conductor level. A diode is a single PN junction:

That is, a section of P-doped semiconductor connected in series to a section of N-doped semiconductor.

A transistor is an NPN or PNP sandwich:

If you take two NP junctions (a diode) and join them head-to-head or tail-to-tail, you get a sequence of either NPN or PNP -- the structure a transistor. The middle of the semi-conductor "sandwich" is the Base of the transistor.

Note that this is very different from AndrewC's attempts to divert the discussion to the straw man version of "soldering the leads of two diodes together", which of course is quite another thing.

[Ichneumon]

It is a simple demonstration. Go to radio shack. Buy 2 1N4001 diodes. Twist their cathodes or anodes together(or any d*** way you please). Now try to make the contraption amplify a current like a transistor. Good luck.

Why are you dishonestly trying to change the subject to "twisting" leads together, when you know full well that the discussion concerns mating the semiconductor layers?

In any case, does this mean that you're now retracting your original claim that, "Which, of course, makes my original statement, that a transistor was in a sense two diodes back-to-back, entirely correct"?

[Ichneumon]

Another great post. Long tongue placemarker.

[Ichneumon]

AND AS YET NOT A SINGLE ONE OF THE EVOLUTIONISTS HAS BEEN ABLE TO SHOW A SINGLE EXAMPLE OF MATTER SELF ASSEMBLING

Butterfly eggs self-assemble into butterflies.

In any case, you keep shifting the goalposts -- every time someone provides a good example, you say, "*That's* not what I meant..." Okay, fine -- so define "self-assemble" as you are using here. Be precise and specific. We'll wait.

And while you're at it, self-assemble into *what*? Raindrops self-assemble into lakes, for example. Chaotic water droplets self-assemble into highly organized snowflakes.

In short, just what in the *world* are you babbling about?

[Ichneumon]

Yup, only humans and God can bend the rules of nature to make them do what they wish.

Does not follow from the example given, but thanks for sharing your philosophical prejudices with us.

[Ichneumon]

Imagine that, evolutionists lie and they get called liars.

I think the readers are perfectly capable of judging for themselves who exactly has been most dishonest on these threads.

How awful!

I didn't say that such frequent accusations were awful of you -- just typical.

I have shown to have told numerous lies in this very thread.

Why yes, yes you have indeed. Thanks for admitting it.

[Ichneumon]

[The simulation did punish unneeded and useless functions by having these useless functions consume limited resources.]

Another bald faced lie from you. It says no such thing in the article above and that is why you cannot give a quote which says that. It is a completely a figment of your imagination. A totally made up statement with no basis in fact. Since it was completely concocted out of thin air, it is legitimate to call it a lie and not an error.

Ahem:

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.

That's from "the article above", you bile-spewing Troll.

Don't you get tired of being wrong all the time? Don't you get tired of calling people liars when in fact it is you yourself who is most guilty?