Comment #15028

Posted by Engineer-Poet on February 5, 2005 07:28 PM (e) (s)

How delicious:  creationism, slain by an example of evolution which can be demonstrated convincingly by anyone who can play the Sims.  It won’t be long (in generational terms) before there is nothing left of it.

The real problem for the supporters of creationism is that they need the origin tale as one of the supports of their traditions and morality.  Problem for them and us is that the morality may be justifiable even if the creation myth is bogus.  It would be a pity to lose that baby with the bathwater.

Perhaps it’s time to work on evolutionary models of morality.

Comment #15029

Posted by RBH on February 5, 2005 08:19 PM (e) (s)

I had a Thumb posting on the Avida simulations here  last year.  It ain’t a bad introduction, if I do say it meself.

RBH

Comment #15031

Posted by Charlie Wagner on February 5, 2005 08:53 PM (e) (s)

Carl Zimmer wrote:

The Avida team makes their software freely available on the Internet, and creationists have downloaded it over and over again in hopes of finding a fatal flaw. While they’ve uncovered a few minor glitches, Ofria says they have yet to find anything serious. “We literally have an army of thousands of unpaid bug testers,” he says. “What more could you want?”

  The fatal flaw is that this simulation bears absolutely no resemblance to what actually goes on in nature. It’s an exercise in nothing. It’s no different than when Ptolemy proposed a theory for the motions of the bodies in the universe that placed the earth at the center and then derived a complex system of epicycles and built mechanical orreries to simulate these proposed motions and to *prove* that this is what was really happening.
  It seems self-evident to me, and it should to all other observers that living organisms are far more technologically advanced and organized than any machine that humans can build. It stands to reason that an intelligence greater than human intelligence was required to construct them. In what dimension can random chance and accidental occurrences produce what the human mind is incapable of producing?
  It just seems so incredibly simple to me.

Christopher Zeeman quoted by Ian Stewart in "Does God Play Dice? wrote:

First came the astronomers observing the motions of the heavenly bodies and collecting data. Secondly came the mathematicians inventing mathematical notation to describe the motions and fit the data. Thirdly came the technicians making mechanical models to simulate those mathematical constructions. Fourthly came generations of students who learned their astronomy from these machines. Fifthly came scientists whose imagination had been so blinkered by generations of such learning that they actually believed that this was how the heavens worked. Sixthly came the authorities who insisted upon the, received dogma. And so the human race was fooled into accepting the Ptolemaic System for a thousand years.

Charlie Wagner
http://enigma.charliewagner.com…

Comment #15032

Posted by PvM on February 5, 2005 09:03 PM (e) (s)

Charlie, Charlie, Charlie. Has it ever occurred to you that your ‘argument’ could benefit from some… uh … logic or supporting evidence. In fact Avida contains many of the essential aspects of evolution such as limited resources, fitness, variation.
Until you familiarize yourself with evolutionary theory, please try to refrain from sounding a bit silly.
Most creationists who oppose Avida, try to reject it on far better ‘reasons’ that Charlie. Come on Charlie, provide at least a challenging review of the article and Avida beyond your usual rejection without much reasoning?

‘it stands to reason’, ‘it seems self evident’, ‘it just seems so incredibly simple to me’ do not bode well in any discussion.

Sigh… If your next posting does not clean up its act, it will be removed to a more fitting place on the bathroom wall of PT.

Comment #15033

Posted by Bob Maurus on February 5, 2005 09:14 PM (e) (s)

Charlie,

“It seems self-evident to me, and it should to all other observers that living organisms are far more technologically advanced and organized than any machine that humans can build. It stands to reason that an intelligence greater than human intelligence was required to construct them.”

You seem like a scratched record stuck in a time warp. Over and over, you offer the same unsupported opinion and demand that others bow to your incredulity - or is it arrogance.

What seems self-evident to you obviously doesn’t seem self-evident to most of the rest of us. It does not stand to reason that “an intelligence greater than human intelligence was required to construct them.”

I tried to explain to you at least once before that Nelson’s Law proves that humans designed biological organisms. You still haven’t accepted that.

Comment #15034

Posted by Joel on February 5, 2005 09:41 PM (e) (s)

Pulling the plug on Avida certainly places this evolutionary simulation in a thermodynamically unfavorable position.

Comment #15035

Posted by Jeff Low on February 5, 2005 11:21 PM (e) (s)

The most well-known intersection of evolutionary biology with computer science is the genetic algorithm or its many variants (genetic programming, evolutionary strategies, and so on). All these variants boil down to the same basic recipe: (1) create random potential solutions, (2) evaluate each solution assigning it a fitness value to represent its quality, (3) select a subset of solutions using fitness as a key criterion, (4) vary these solutions by making random changes or recombining portions of them, (5) repeat from step 2 until you find a solution that is sufficiently good.

We make random mutations and then intelligently select those that fit what we’re looking for.  The program is intelligently selecting those progams that are more fit according to its fitness value.  So, of course, we end up with programs that fulfill exactly what we were looking for.  This is like generating programs that produce a random colors and then selecting those programs that generate only blue, and then we turn around and are amazed that we have programs that produce only blue.  How exactly does this support evolution?

Comment #15037

Posted by steve on February 5, 2005 11:58 PM (e) (s)

Jeff: First learn what evolution is, then learn how Avida works. That should answer your question.

Pim: Sysiphus is an old legend. Over time it has been distorted and altered. For instance, in the version we have, it says he was condemned to push a boulder up a hill for eternity. But in the original, it said he was condemned to explain evolution to Charlie Wagner. Basically the same thing.

Comment #15038

Posted by Great White Wonder on February 6, 2005 12:10 AM (e) (s)

Charlie writes

It seems self-evident to me, and it should to all other observers that living organisms are far more technologically advanced and organized than any machine that humans can build. It stands to reason that an intelligence greater than human intelligence was required to construct them.

Whoa, it seems to me that your thinking must have “evolved” Charlie.  I seem to recall sometime last year arguing with you about whether “ID theory” made any claims about the nature of the designer other than mere “intelligence”.

Now it seems that you have something to say about the intelligence of the designers.  Were the mysterious aliens smarter than any human being who ever lived?  Or were they just super smart, like Einstein?

Any other insights into the designers that you’ve recently acquired?

As always, I’m not really interested in your answers to these questions.

Comment #15041

Posted by Frank J on February 6, 2005 07:35 AM (e) (s)

Charlie Wagner wrote:

It seems self-evident to me, and it should to all other observers that living organisms are far more technologically advanced and organized than any machine that humans can build.

So far. But given how much more “technologically advanced” these autocatalytic systems we call cells are, one could reasonably expect that, even though they, at a casual glance, and in the ridiculuously short time intervals in which they have been observed by humans, seem to evolve only within poorly defined “kinds,” their long range evolutionary potential is almost boundless.

Comment #15042

Posted by Marcus Good on February 6, 2005 08:17 AM (e) (s)

Charlie said:

“It seems self-evident to me, and it should to all other observers that living organisms are far more technologically advanced and organized than any machine that humans can build.”

Please elaborate on exactly what these “technologically advanced” structures within organisms are. I mean, how are you defining “technology” here? Don’t you need to prove they *are* technologically advanced, or a form of technology, in order to point out where they’re advanced?

Also, “It seems self-evident to me, and it should to all other observers”

- ah, the mating cry of the wandering martyrbird. “I can see it, why can’t anyone else?”

Comment #15044

Posted by Charlie Wagner on February 6, 2005 09:46 AM (e) (s)

Marcus Good wrote:

Please elaborate on exactly what these “technologically advanced” structures within organisms are. I mean, how are you defining “technology” here? Don’t you need to prove they *are* technologically advanced, or a form of technology, in order to point out where they’re advanced?

  They are more highly organized and they perform more operations, employ more processes and structures, and are integrated together in more complex ways.
  Take the human brain, for example. It’s far more advanced than any computer that humans have built. Were it not, all of the artificial intelligence people would be folding their tents and going home. They aspire to duplicate what living brains already easily accomplish. Take the cell for another example. It is nothing less than a universal automaton. It’s protein synthetic apparatus can construct any biochemical machine and if given the raw materials, has almost unlimited potential to construct every living thing that ever existed on earth. It can also replicate itself and construct all of its components in a matter of minutes, and a complete organism in a matter of months from a piece of DNA that is millions of times smaller than any functional machine produced by humans.

- ah, the mating cry of the wandering martyrbird. “I can see it, why can’t anyone else?”

  Better than the blind followmebird who flies in ever decreasing concentric circles until it disappears up its own a**hole, all the while shrieking “mountain of evidence…mountain of evidence…”

Comment #15046

Posted by ThisIsPainful on February 6, 2005 10:06 AM (e) (s)

…so, why not refute some of the mountain of evidence?  “I think…” doesn’t cut it.

Comment #15047

Posted by Charlie Wagner on February 6, 2005 11:17 AM (e) (s)

ThisisPainful wrote:

…so, why not refute some of the mountain of evidence?  “I think…” doesn’t cut it.

  When it comes to evidence, I somehow feel like I’m on the Great Plains…

http://www.greydragon.org/trips/Kansas/kansas-countryside082…

Charlie Wagner
http://enigma.charliewagner.com…

Comment #15049

Posted by ThisIsPainful on February 6, 2005 11:45 AM (e) (s)

Are you saying that picture shows explicit evidence that grass was specially created?  Go to talkorigins.org, pick something, and lets discuss your misunderstandings about life.

Comment #15053

Posted by Charlie Wagner on February 6, 2005 12:16 PM (e) (s)

ThisisPainful wrote:

Are you saying that picture shows explicit evidence that grass was specially created?

  No. It’s a metaphor .
The flatness of the plain represents the absence of evidence, just as the mountain represents a large amount of evidence.

Go to talkorigins.org, pick something, and lets discuss your misunderstandings about life.

  I’ve read almost everything in the t.o archive and I’ve been discussing it for over 10 years, having posted thousands of articles.
Just Google on my name (I use both Charlie Wagner and Charles Wagner) and read some of them.
  You can also visit my website at:
http://www.charliewagner.com…
or my blog at:
http://enigma.charliewagner.com…
for more information about me.

Comment #15056

Posted by PvM on February 6, 2005 12:38 PM (e) (s)

Jeff wrote:

We make random mutations and then intelligently select those that fit what we’re looking for.

Not really. Have you looked at the program? It selects according to fitness

Jeff wrote:

The program is intelligently selecting those progams that are more fit according to its fitness value.  So, of course, we end up with programs that fulfill exactly what we were looking for.  This is like generating programs that produce a random colors and then selecting those programs that generate only blue, and then we turn around and are amazed that we have programs that produce only blue.  How exactly does this support evolution?

The program’s fitness function is as ‘intelligently’ designed as nature’s fitness function which selects based on ‘what it’s looking for’. Why do you not have a look at the program and how it works and how it was used before making such strawman arguments.

How does the program supports evolution? Because it is an instance of evolution with variation, selection and competition for resources and helps us understand many issues confronting us when it comes to evolution. Such as: Can evolution increase the information/complexity of the genome? The answer is yes (see Adami or Schneider). Can evolution explain irreducibly complex systems? And the answer once again is yes.
As such it not only helps reject poorly founded assertions (often found amongst creationists) but it also helps researcher with many other issues such as ‘stasis/punk eek’, speciation, ecology, adaptation, robustness/evolvability, dynamics.

For those who want to familiarize themselves with the program and join the countless creationists who seem to be ‘bug testing’ see Avida homepage

I am sure the researchers are looking forward to a well reasoned discussion. I would… And I still am… but sigh…

For instance: Robustness and evolvability are very interesting concepts. Theoretical research has shown how the ability of evolution to evolve itself (evolvability) is also linked to robustness. And what is essential for evolvability? A level of neutrality… Found in the degeneracy of the genetic code for instance.
So in short, what has Avida helped us resolve?

1. Evolution cannot explain the information in the genome. False…
2. Evolution cannot explain the complexity of life such as irreducibly complex systems. False…

Not bad for starters. Even if Avida were limited to disproving creationist assertions, it would have been highly successful.

Charlie. other than mumbling ‘it appears to me that’, ‘it seems self evident that’ has failed to address the issues here. In the thousands of postings on TO, Charlie has not fared much better either.

Comment #15057

Posted by Charlie Wagner on February 6, 2005 01:02 PM (e) (s)

Pim wrote:

Charlie. other than mumbling ‘it appears to me that’, ‘it seems self evident that’ has failed to address the issues here. In the thousands of postings on TO, Charlie has not fared much better either.

  On the contrary, I have addressed the validity of computer simulations many times. You want more? Here it is:
  Computer simulation models of evolution are not valid because there is no way to demonstrate that they model what actually happens in nature. They only model your belief about what happens in nature. So trying to find ‘flaws’ is useless because the simulation is not being judged against what actually is happening, it’s being judged against your belief in what’s happening, which can always be ‘adjusted’ to compensate for any problems.
In general, the value of computer simulations is heuristic, they strengthen what has already been established through other means. The evolutionary mechanism of mutation and natural selection has not been established as the mechanism of evolution. There has been no empirical support for the notion that changes in gene frequency can result in the emergence of highly organized structures, processes and adaptations without the help of intelligent input, so any simulation models based on this mechanism are fictions, and they can never be a representation of the real world because there may be factors at work of which we are unaware.

Charlie Wagner
http://enigma.charliewagner.com…

Comment #15059

Posted by PvM on February 6, 2005 01:19 PM (e) (s)

Computer simulation models of evolution are not valid because there is no way to demonstrate that they model what actually happens in nature. They only model your  belief  about what happens in nature. So trying to find ‘flaws’ is useless because the simulation is not being judged against what actually is happening, it’s being judged against your belief in what’s happening, which can always be ‘adjusted’ to compensate for any problems.

The evolutionary mechanism of mutation and natural selection has not been established as the mechanism of evolution.

FIrst of all we know that mutations happen and that natural selection happen so the next step is to figure out if these mechanisms are of any importance/relevance. Additionally, based on these facts, science can start formulating theoretical foundations and simulations to establish how variation and selection affect the temporal behavior of populations. Computer simulations are not meant to mimick in every detail what happens in nature, they model relevant concepts in nature to see their effect. Such is how science works. If Charlie objects that science is studying evolution because he disagrees with the relevance of variation and selection then fine, let him so argue. But for science, who has found significant evidence supporting their viewpoints, the findings based on Avida help understand in even more intricate detail how evolution has shaped populations. In addition Avida has helped establish that creationist arguments that mutationa and variation cannot explain X, are based on flawed reasoning.

As I said, even if we were to limit Avida to disproving the claims of creationists, it has been highly successful but Avida is doing much more than that. That Avida’s simulations end up strengthening the hypothesis that variation and selection are an important evolutionary mechanism should hardly be seen as an objection. That’s how science works.

Comment #15062

Posted by Charlie Wagner on February 6, 2005 01:49 PM (e) (s)

Pim wrote:

FIrst of all we know that mutations happen and that natural selection happen so the next step is to figure out if these mechanisms are of any importance/relevance.

I agree.
Mutations and natural selection do occur and the goal of evolutionary science is to prove that these effects can result in the emergence of highly organized structures, like the eye and processes like the biochemical pathways in vision, and integrate these into functional, living systems without the help of intelligent input. Therefore, I’m not opposed to using these simulations because I think they can prove that this is not what happens in nature. I could argue that these simulations are not free of intelligent input, but let me put that aside for a moment. I’ll concede for arguments sake that they are. That being the case:
1) is Avida capable of demonstrating that unguided processes of mutation and natural selection can result in greater organization? and
2) has this been accomplished?
What exactly does the computer simulation produce when it is run? Obviously, not a three-dimensional entity or a biochemical process. So what evidence has it actually generated? Is this merely an increase in complexity, which I concede can be generated by non-intelligent, random processes or an increase in information, which I also concede can be generated by non-intelligent, random processes, or does it demonstarte an increase in organization, which is essential to the evolution of living organisms?

Comment #15065

Posted by PvM on February 6, 2005 02:21 PM (e) (s)

Charlie wrote:

Mutations and natural selection do occur and the goal of evolutionary science is to prove that these effects can result in the emergence of highly organized structures, like the eye and processes like the biochemical pathways in vision, and integrate these into functional, living systems without the help of intelligent input. Therefore, I’m not opposed to using these simulations because I think they can prove that this is not what happens in nature.

You are free to think whatever you want Charlie but that’s not relevant to the issue. YOu seem to be intent on moving the discussion towards an irrelevant area namely

1) is Avida capable of demonstrating that unguided processes of mutation and natural selection can result in greater organization? and
2) has this been accomplished?

Describe ‘greater organization’ in a scientific manner that could be tested using Avida.

I am glad that you agree however that creationist claims about information and complexity are misguided and I encourage you to develop your own ideas in a scientific manner. PT has an open submission policy for relevant ideas.

This thread however is about Avida and its relevance. I hope you can accept this and abide by my suggestions to focus on the topic of the thread instead.

Comment #15066

Posted by PvM on February 6, 2005 02:23 PM (e) (s)

Charlie wrote:

Mutations and natural selection do occur and the goal of evolutionary science is to prove that these effects can result in the emergence of highly organized structures, like the eye and processes like the biochemical pathways in vision, and integrate these into functional, living systems without the help of intelligent input.

We have some pretty good evidence that it can.

When evolution skeptics want to attack Darwin’s theory, they often point to the human eye. How could something so complex, they argue, have developed through random mutations and natural selection, even over millions of years?

read more Here

See also

The eye is too complex to have evolved for more relevant research

Comment #15067

Posted by PvM on February 6, 2005 02:36 PM (e) (s)

Some Avida relevant papers

Chris Adami, Learning and Complexity in Genetic Auto-Adaptive Systems Physica D, volume 80 p154 (PDF)

We describe and investigate the learning capabilities displayed by a population of self-replicating segments of computer code subject to random mutation: the tierra environment. We find that learning is achieved through phase transitions that adapt the population to the environment it encounters, with a learning rate characterized by external parameters such as mutation rate and population size. Our results suggest that most effective learning is achieved close to the transition to disorder, and that learning curves of evolutionary systems are fractal.

Many papers by Chris Adami can be found here
and here

Avida’s homepage also has many links as to how Avida has been used in evolutionary research

Comment #15068

Posted by Ginger Yellow on February 6, 2005 02:43 PM (e) (s)

So you can cope with increased complexity and increased information, but not increased organisation? How do you deal with snowflakes then?

Charlie, even if you don’t accept that it’s a valid simulation of nature, Avida shows that an entirely algorithmic process of mutation, reproduction and selection can evolve “irreducibly complex” operations from simple commands.  Given that the central, indeed only, substantial claim of ID is that irreducibly complex things can’t evolve, but must be created fully formed, do you not think that is relevant? And bringing the discussion back to nature simulation, if a system based solely on mutation and selection can create such remarkably “lifelike” products as diversity, complexity, punctuated equilibrium

Comment #15069

Posted by Ginger Yellow on February 6, 2005 02:54 PM (e) (s)

As I was saying:

… (in Dennett’s synthesis-compatible sense), does this not provide at least circumstantial evidence that a similar process might cause such features in nature?

Comment #15070

Posted by FredMcX on February 6, 2005 03:13 PM (e) (s)

Charlie,

Isn’t a logical conclusion of ID that something must have created the intelligence that created us? And so on?

Further, you stated:

> and they can never be a representation of the real world because there may be factors at work of which we are unaware.

This may be true but surely the same argument can be applied to so-called irreducible complexity. As the demolishing of the mousetrap example has shown, just because you cannot conceive something doesn’t mean that it cannot be conceived or implemented. The factors of which “we are unaware” might, quite literally, be factors of which the ID people are unaware because they are seeking evidence for what is, to them, a foregone conclusion.

Put differently, if we are here because invisible pink unicorns that live on Pluto created us then no simulation can ever capture that. However, to the extent that Avida has predictive power than to that extent it is a valid simulation. It is no different than using a computer to predict weather, orbits of planets or through the use of genetic algorithms to design things (circuits, antennas etc) which are not the direct result of traditional “logical” design.

Essentially ID has zero predictive power whereas evolution has - e.g., it predicts that diseases will become resistant to anti-biotics etc. Evolution is not here because it exists to make the point that God does not exist or that God did not craete us. It is here and important because it is actually a useful concept as opposed to ID.

Charlie - do you actually want medical research to proceed based on the notion that we were created and that evolution is wrong?

Fred

Comment #15071

Posted by Joe Shelby on February 6, 2005 03:21 PM (e) (s)

How does the program supports evolution? Because it is an instance of evolution with variation, selection and competition for resources and helps us understand many issues confronting us when it comes to evolution. Such as: Can evolution increase the information/complexity of the genome? The answer is yes (see Adami or Schneider). Can evolution explain irreducibly complex systems? And the answer once again is yes.

actually, my favorite implication of the examples in the article would be: Can evolution explain how competing species in a world of limited resources achieve an equilibrium of existence, rather than the most adaptable species taking over the entire system?  To which, the answer is yes.

its not a common discussion now, but when Darwin first published, the assumption up to that point was that God created the animals specifically to fit their niches in the balance we see them as.  Of course, such a balance couldn’t explain away “casual” extinction (which also happened, and more often than catastrophic (asteroid) or man-induced extinctions). 

Misinterpreted, natural selection, and the social-darwinistic attitudes that came from it, implied that one species must reign supreme.  Avida shows otherwise, as does Darwin and most post-Darwin evolutionary research.

Comment #15093

Posted by DaveScot on February 7, 2005 01:32 AM (e) (s)

Pardon me, but I do believe these digital organisms were created by an intelligent agent called a “computer software engineer”. 

I’d also remind you that the universe hosting these digital organisms was also created by an intellegent agent called a “computer hardware engineer”.

Let me know when you boys get some organisms going that do not require an intelligent agent to get the ball rolling in the first place.

Thanks in advance.

Comment #15096

Posted by Ginger Yellow on February 7, 2005 02:12 AM (e) (s)

“Let me know when you boys get some organisms going that do not require an intelligent agent to get the ball rolling in the first place.”

Spot the logical error in this sentence.

Comment #15097

Posted by Marek14 on February 7, 2005 02:13 AM (e) (s)

You’re missing the point here, DaveScot. Although the program and computer were created by humans, the individual organisms weren’t. Moreover, genetic algorithms frequently lead to solutions that are extremely hard to grasp with human understanding, as they don’t follow rules we usually use when designing something (like having a hiearchy of units and tasks). This would translate into “impotent God”, one who doesn’t understand his creation in full, who can’t predict what effects his miracles would have, and who therefore prefers to sit watching the world in wonder of its marvels.

In other words, the part of “creator” in Avida is limited to creating the universe and its rules and letting it run its course. But this is NOT contrary to evolution! An evolutionist can accept such view of his own universe (and indeed, many Christian evolutionists did), since evolution is not an universal theory - it doesn’t deal with origin of life, it deals with its diversity.

Avida contradicts special creation and ID in that it shows that evolution mechanisms WORK and CAN produce complexity those theories claim it can’t. It won’t contradict theistic evolution or Christianity or most of reasonable religious systems.

Comment #15098

Posted by DaveScot on February 7, 2005 02:19 AM (e) (s)

I wonder if the little digital organisms are arguing amongst themselves whether they were created or are the result of mutation + natural selection.

Should we tell them truth?

ROFLMAO

I find it difficult to take this seriously.

Comment #15099

Posted by DaveScot on February 7, 2005 02:53 AM (e) (s)

Ok Marek, seriously now.

You’re saying that if I offer a hypothesis that the original cell which was ancestor to all contained all the genetic information required to build all the major body plans and that, like ontogeny, phylogeny unfolded by the gradual expression (derepression) of genetic information that was already there, you wouldn’t have a problem with it?

I’m sorry Marek, but neo-Darwinists DO take issue with the origin of life.  The scenario I gave you above easily fits all the observed evidence of evolution much better than mutation/selection.  But it begs the question of how the information was preformed in that first cell.  Neo-Darwinists won’t tolerate that because if the information was preformed that means anticipation and anticipation is the hallmark of intelligence.

Richard Dawkins was absolutely correct when he said that Darwin made it possible for atheists to be intellectually fulfilled.  This is all about ideology, not science.  Science is about the truth.  Science is about following the evidence wherever it leads.

Here’s just such an evolutionary hypothesis given by a guy that’s had a PhD in biology for 50 years and is emeritus professor of biology at University of Vermont.

Comment #15102

Posted by Marek14 on February 7, 2005 06:33 AM (e) (s)

No, I’m not saying anything like that. What you propose, in essence, is a primordial organism that is more complex than anything we see in nature today. But that still won’t give us the answer to question where did complexity come from.

On an aside, the scenario you propose certainly doesn’t fit the evidence. The evidence point to the fact that mutation exist. Parts of genome “destined” to not become expressed until millions of years in the future would mutate beyond recognition very quickly, as nothing would keep the mutations in check.

But there is something more deeply wrong with the argument. And that is the very simple question: can simple things become more complex?
All religious explanations I’ve heard involve a creator with high degree of complexity. He then creates a world with lower complexity. Everything in there is neccessarily (since this the basic reason it’s done) of lower complexity than creator himself.

Does this say anything about origin of complexity? No, it doesn’t. If we ask about origin of the creator of designer - of course that’s usually forbidden - we get three possible answers:

1. Creator rised from something with lower complexity.
In that case, why could he and not us, who are simpler?
2. Creator was created by something else, with even higher complexity.
If this goes ad infinitum, we don’t know anything again.
3. Creator requires no further explanation, he simply is.
In that case, we might say the very same thing about ourselves and get a simpler explanation.

You are right in that science is about the truth. And the truth is that organisms in artifical life environments develop new information and complexity that was not given to them in any form originally. Although the designers of the programs are, in a sense of word, omniscient and omnipotent (as they can get complete information about their world, and they can control it completely), they don’t have intelectual capacity to predict the behaviour of their creation - and indeed, this is one of the best reasons to try out those programs.

Comment #15103

Posted by jonas on February 7, 2005 06:35 AM (e) (s)

DaveScot,

sorry to break it to you, but you are either involutarily or intentionally misrepresenting Marek’s point. He never assumed that phylogeny (either in AVIDA or in real life) comes with all the ‘information’ for new developments already in place. This would be a problematic assumption on several counts not related to the question of who put the information there. To name just two:
- It would make phylogeny a deterministic, easily predictable process (like, as you said, ontogeny), down to every small variation. As nobody so far can predict the exact outcome of AVIDA or real phylogeny, this would clearly be overstating the relevance of original ‘input’ tremendously.
- It would set a clear upper limit on the total amount of  new developments possible - far below the total of possible  expressions allowed by the syntax of the system in question; another feat nobody could find evidence for so far.

What Marek actually seems to have posited is, that even in an environment custom built for phylogeny to take place in,  phylogeny based on generation and selection of genetic information can run in directions not planned for by anybody, thus making evolutionary theory independent of the origins of live or the universe. This is actually something Darwin himself did mention - he was just talking about development, diversification and adaptaion, not about who laid down the ground rules and how.

The knee-jerk reaction you are accusing scientists favouring neo-darwinist theories of, actually stems from the foundational axioms of science. Those people have to accept, as nobody so far has found a way to do meaningful research without them. In my own words they are:
- There is an objective reality shared by everybody.
- This reality can be explained by theories based on observation and measurement.
- Theories based on simpler concepts or already established ones are preferable to those which are not, given a similar expanatory value.
- Factors not observable or testable should not figure prominently in any theory.

The kind of information front-loading (at least in reality)  you are proposing at the very least goes against the third axiom at the moment. Why on earth introduce a hypothetical super-ancestor nobody knows anything about with an unknown information payload and an unknown teleological program, as long as pretty well established and testable mechanisms like gene duplication and subsequent mutation seem to be perfectly able to generate new genes for selection to work upon? When it comes to the ‘intelligence’ behind this ur-being, it is even more clear cut: Nobody has a hypothesis on its nature, what defines its intelligence, the when and how of its working, and nobody seems to have a plan who to test and deduce these details - so why put it into a theory at all, as long as the critiques on better established theories have not gone beyond claims how information can only come from intelligence without backing it up with any positive experimental data or a consitent theory how these two are dependent on each other.
Even worse, if the intelligence in question is attributed features, that would make it per se un-testable, it falls under the even more rigid rejection by the fourth axiom.
To mistake this reluctance of introducing non-observable factors into science for rejection of any philosophical, metaphysical or ethical world-view means misrepresenting the nature of science in a dangerously dogmatic way. That some prominent scientists have commited this fallacy repeatedly and publicly, does not make you doing so any more correct or helpful.

Comment #15104

Posted by Marek14 on February 7, 2005 06:41 AM (e) (s)

Your words are wise, jonas :-) And yes, that’s what I was saying - scientific theories still didn’t say their last word about the origin of life, but evolution works on life no matter where it came from. It’s the same principle as why a geologist doesn’t need a theory of origin of Earth in order to explain many of its features. There are (no doubts) questions in theory of evolution that will require us to know more about the origin of life before they can be answered - but not all questions, not at least.

Comment #15106

Posted by DaveScot on February 7, 2005 07:08 AM (e) (s)

Ontogeny is predictable?  HAR HAR HAR

Only after you watch it happen is it predictable.

What part of the genome codes for instinctual behavior like a newborn baby’s rooting response or its ability to coordinate God only knows how many muscles to nurse and swallow or the autonomic work done by the rest of the digestive tract to get mommy’s milk where it needs to go?  How would you go about predicting that without first seeing it?  Nobody has a clue.

Point mutation exists, sure. That it accumulates to cause the emergence of new phyla is pure unadulterated speculation without a shred of real evidence.  It’s extrapolation most extreme.  It boggles the mind how many people accept that fairy tale with blind faith.  You can’t even demonstrate to me that evolution of new higher taxa is even happening anymore today.  I know, I know, it’s too slow to observe in real time.  Maybe little green men from Mars that control tectonic plate movement are too slow to observe in real time too.  Gimme a break.  Or rather, gimme the facts and keep the guesswork for Discover Magazine subscribers.

Comment #15109

Posted by Marek14 on February 7, 2005 07:45 AM (e) (s)

Ontogeny is predictable exactly as you say it - after you watch it once, ontogeny of all members of the same species is the same. Phylogeny, on the contrary, never repeats.

As for the rest…

You are absolutely right in the account that evolution of new higher taxa can’t be demonstrated to you, I believe. But it says more about yourself than about the evidence. New species were SEEN to arise, for example. Saying that “emergence of new phyla is pure unadulterated speculation” just shows how desperate you are. Why such strong words? Besides, you are wrong - there is plenty of evidence for those who don’t close their eyes to the reality.

Comment #15111

Posted by Ginger Yellow on February 7, 2005 08:01 AM (e) (s)

You’re clearly misinterpreting people for the hell of it. Ontogeny is predictable. What else are we supposed to do but observe it? If you give me a baby human I can tell you it will become an adult human. I can tell you roughly when it will reach various stages of its development, and roughly what it will look like at each stage.

Phylogeny on the other hand, such as in Avida, is not. Even if you observe a particular organism’s historical evolution, there’s no way of predicting what its future evolution will be. Even if you know every single parameter of the environment and all the rules of mutation and selection, there’s no way of predicting how a given organism will evolve. That’s what he means

Comment #15112

Posted by Adam Marczyk on February 7, 2005 08:07 AM (e) (s)

There has been no empirical support for the notion that changes in gene frequency can result in the emergence of highly organized structures, processes and adaptations without the help of intelligent input…

In case you haven’t noticed, Charlie, that is precisely what Avida and other genetic algorithms are intended to show. Genes change in frequency randomly; some of those changes are selected for, and others selected against, by a fitness function that measures whether and how well the individuals achieve whatever the specified goal is, but without specifying how that achievement should be brought about. In other words, the fitness function says what needs to be done, not how to do it. And do we get organized structures and processes out of it?

You’d better believe it. This exact process has been used to design concert halls, airplane wings, load-bearing trusses, voice-recognition circuits, wire antennas with uniform radiation patterns, expert checkers-playing programs, more efficient diesel engines, and far more. Genetic algorithms can pick stocks, design military battle plans, mine patterns from data, schedule airplane landings and assembly lines and identify transmembrane protein segments, all better than humans.

See here for more:
http://www.talkorigins.org/faqs/genalg/genalg.html#examples…

Comment #15113

Posted by Pastor Bentonit on February 7, 2005 08:08 AM (e) (s)

DaveScot trolled:

Point mutation exists, sure. That it accumulates to cause the emergence of new phyla is pure unadulterated speculation without a shred of real evidence.  It’s extrapolation most extreme.

…casually leaving out other mutations such as indels, inversions, transposable element rearrangements as well as horizontal gene transfer. Go figure. Oh, and denominations such as “phyla” are by nature artificial. There currently is intense scientific debate on the species concept per se; higher taxonomical entities are constructions.

Comment #15129

Posted by charlie wagner on February 7, 2005 10:30 AM (e) (s)

Adam wrote:

Genetic algorithms can pick stocks, design military battle plans, mine patterns from data, schedule airplane landings and assembly lines and identify transmembrane protein segments, all better than humans.

  But humans wrote the genetic algorithms. Your claim is no different than saying that computers perform mathematical operations faster and with fewer errors than human minds, so computers are superior to humans. You conveniently forget that humans built the computer. The claim that these genetic algorithms perform their magic without intelligent guidance is incorrect. Intelligent input is required at every step of the way, from writing the code to setting the parameters to evaluating the output. The intelligence is built into the GA by its human authors, just like the intelligence that creates new cells and organisms was built into the DNA by its authors.
  Now if genetic algorithms could be shown to create themselves, then you might be on to something.
 
Charlie Wagner

Comment #15131

Posted by RBH on February 7, 2005 10:44 AM (e) (s)

charlie wagner wrote

But humans wrote the genetic algorithms. Your claim is no different than saying that computers perform mathematical operations faster and with fewer errors than human minds, so computers are superior to humans. You conveniently forget that humans built the computer. The claim that these genetic algorithms perform their magic without intelligent guidance is incorrect. Intelligent input is required at every step of the way, from writing the code to setting the parameters to evaluating the output. The intelligence is built into the GA by its human authors, just like the intelligence that creates new cells and organisms was built into the DNA by its authors.

What charlie conveniently does not mention is that all that intelligent input goes into instantiating the specific unintelligent processes hypothesized to account for the diversity of life on earth, namely random mutations of various sorts, recombination, and selection.  If we took charlie’s complaint seriously, the results of all scientific research would be evidence for intelligent design in the ‘natural’ world.  Even Petri dishes represent intelligent “input”, you know.

RBH

Comment #15135

Posted by charlie wagner on February 7, 2005 10:51 AM (e) (s)

Adam wrote:

In case you haven’t noticed, Charlie, that is precisely what Avida and other genetic algorithms are intended to show.

  Don’t get me wrong about Avida. I think writing Avida was worthwhile and I think using it to test evolutionary mechanisms is also useful. However, to the best of my understanding it has failed to validate mutation and natural selection as the mechanism of evolution because the output is not analogous to what occurs in nature.
  There is no question that mutations occur and natural selection has the power to change the frequency of genes in populations. The problem is to link these effects to the emergence of highly organized structures and processes, such as are found in living organisms.
  So, in order for Avida to validate evolution it must be capable of producing outputs that are analogous to those found in living systems. The key characteristic of living systems, just like human-designed machines, is the use of multiple structures and multiple processes that are integrated into a functional system. This characteristic is called organization, which is different from complexity, information or order. It’s different because not only do the different structures have functions of their own, they also support the functions of the other components and are integrated togather in such a way that all of the components support not only each other, but also the overall function of the system.
  For example, to determine the monthly interest on my mortgage, I have to take the yearly interest rate, divide it by 100 to make it a decimal, divide it by 365 to get the daily rate, multiply this daily rate by the amount of the mortgage and then multiply that by the number of days in a month.
  These calculations are not just faster and less error-prone than human calculations, they are organized in such a way that multiple processes are integrated together in such a way that each step supports the one after it, and all of the steps support the outcome, which is the daily interest that I pay.
  Can any of your GA’s acheive this kind of organization without any intelligent human input?

Comment #15136

Posted by PvM on February 7, 2005 10:55 AM (e) (s)

Now if genetic algorithms could be shown to create themselves, then you might be on to something.

But they do. That’s the beauty of variation and natural selection. The genetic algorithm is nothing more than a correlation between genome and environment. Selection works to increase the information in the genome to ‘match’ the environment.

Adami et al referred to is as a ‘Maxwell-like demon’.

Charlie’s objections, reflect the desperation found among ID proponents having to reject at all cost, Avida’s findings. Abandon all logic and reason and perhaps we can salvage the ID claims… Too bad that Avida shows that most of the ID claims are without ANY merrit.

Combine this with the simple observation that there is no theory or hypothesis of ID and one realizes quickly why more and more people are calling ID scientifically “vacuous”. Charlie’s comments only help to reinforce these findings.

Comment #15137

Posted by Ginger Yellow on February 7, 2005 10:58 AM (e) (s)

The point about genetic algorithms is they prove, given the right starting conditions, that unpredictable, complex, highly efficient evolved algorithms will result. That is exactly what “neo-Darwinism” claims. Evolutionary theory explicitly lays down the necessary conditions for evolution: replication with variation and selection pressure. The whole point is that evolution is substrate neutral - if the conditions apply, in whatever context, you will have evolution.  So you can equally apply a variety of evolutionary theory to memes, for example. Genetic algorithms and their evolution are dramatic empirical proof of the theory. It matters not a jot that intelligent beings set the conditions - their evolution demonstrates that the theory applies, given the conditions. Likewise for biology, it doesn’t matter whether God created DNA or if it self-constructed - as long as you have a starting point of self-replicating proteins, with mutation, and selection pressure from the environment you will get evolution. It’s as much a law of nature as gravity is. Now it’s entirely possible that such evolutionary processes also got us from amino acids to DNA, but the point is it doesn’t matter as far as explaining biodiversity goes. Given DNA, evolutionary theory explains biodiversity.

Comment #15142

Posted by Ginger Yellow on February 7, 2005 11:14 AM (e) (s)

“Can any of your GA’s acheive this kind of organization without any intelligent human input?”

Obviously I don’t personally know if Avida has evolved a directly parallel algorithm. But it certainly has evolved highly complex functions. And I’d gladly bet you $100 that if you created a selection pressure to favour mortgage interest rate calculators, that’s exactly what would evolve. Now you can call that “intelligent human input” if you want, but that’s because you’re asking to evolve something that does what an intelligent human wants it to do. Nature sets its own conditions, and evolution produces organisms that thrive in nature. That’s the way it works.

Comment #15176

Posted by charlie wagner on February 7, 2005 12:42 PM (e) (s)

RBH wrote:

Even Petri dishes represent intelligent “input”, you know.

Well, we agree on one thing at least ;-)

Charlie Wagner
http://enigma.charliewagner.com…

Comment #15177

Posted by PvM on February 7, 2005 12:44 PM (e) (s)

Thanks Charlie. At least your comment shows that you are quick to reject experimental science as relevant. At what cost does Charlie have to reject the obvious findings by Avida… Shudder…

Comment #15205

Posted by Salvador T. Cordova on February 7, 2005 02:03 PM (e) (s)

Avida is well designed system puproting to demonstrate design is not needed.

Thanks to RBH, one my suggested fixes is in the system source code (albeit only a comment fix).  I would have suggested more, but then they’d have to ditch the entire system. 

Avida presumes selection pressures to generate all these wonderful features are even available.

What may well be impossible (selection pressures to create irreducible complexity) are easy givens in Avida.

Royal Truman and I hammered away at Avida at:
Royal Truman and Salvador on Avida

a link at ARN has been renumbered pertaining to my discussion with RBH on Avida:

See : 

http://www.arn.org/cgi-bin/ubb/ultimatebb.cgi/ubb/get_topic/…?

Comment #15222

Posted by Rilke's Grand-daughter on February 7, 2005 02:29 PM (e) (s)

Salvador, a brief review of those threads indicates that you (and Royal) are seriously confused about how Avida works and about the consequences of parameter setting.  RBH demonstrates that quite clearly.

Perhaps you meant these as an excerise in how solidly Avida demonstrates that the key ID objections: the impossiblity of evolving complexity are demolished?

Comment #15240

Posted by John A. Davison on February 7, 2005 03:15 PM (e) (s)

How and especially why would one attempt to model a system that does not now and never did operate in the emergence of organic novelty (evolution)? It boggles my mind that such ventures would even be imagined, less attempted.

With respect to the entire Darwinian scheme, from its mystical beginning to its certain demise, I quote Bertrand Russell:

“It is undesirable to believe a proposition when there is no ground whatsoever for believing it to be true.”

Comment #15265

Posted by Joe Shelby on February 7, 2005 04:37 PM (e) (s)

“chance” is a mis-nomer.  used in this way, it is a word to describe the fact that there are so many unknown variables at play that we can not, with our current abilities to observe, name them all and their specific impacts.

ALL science is based on “chance” — science is the calculation of probabilities (even very precise and accurate ones) and testing to see that they fit within an acceptable margin of error. 

Newton worked *most* of the time, certainly to anything that could be observed at his time and the next 300 years.  but in the end he was wrong beyond a certain margin of error.  Einstein is right except at a certain level of observation (the quantum level), where his calculations break down.

no scientists believes that gravity causes one to fall at precisely 32 ft/sec/sec.  its certainly going to vary based on the mass of the person, their center of mass, the actual center of mass of the earth, wind resistence, the impact of falling through the magnetic field, etc.

the chances of anything falling at *precisely* 32 feet per second are almost inconceivably low,  but its close enough to be *almost* unnoticeable.

and “almost” is the key.  we can *almost* predict exactly how fast something should fall, but that’s still an almost, a “chance”.  We have to choose which variables are negligable in their overall affect compared to which ones are the key.  Mass of the earth is key; almost all other variables are negligable compared to that.  thus, 32 works within that level of abstraction.

(to keep in this direction, try to come up with all the factors that go into throwing a proper curve ball in for a strike.  its impossible.  better to just look at the stats of how often a curve ball gets a strike and work in the probabilities.  its less certain science than classroom exercises in pool balls demonstrating conservation of momentum, but its still science.)

So it is with biology.  we can not predict or calculate or observe the affects of every single quantum-level radiation or electron impact on the DNA molecule or its predecessors.  though philosophically possible, it is utterly unrealistic — the computer/brain to manage keeping track of every free electron or neutrino in the universe would have to effectively be bigger than the universe…and itself would be affected by those very particles.

so we abstract out subsets of those variables and call them “chance”.

and chances are, some of those chances won’t be in the future, which is why the research continues.  but we’ll never be able to entirely abstract out chance, as its reflective of the underlying uncertainty that all of the sciences inherently face.

you want truth, or absolute fact, go to philosophy.  I work with science…its close enough, yet infinitely more accurate.

Comment #15277

Posted by Joe Shelby on February 7, 2005 05:27 PM (e) (s)

for that matter, i still don’t see how you assert that causal reactions are the underlying cause of evolution, and at the same time assert that evolution is finished (at least with regards to us) even though those same reactions that caused evolution up ‘til now are still happening and will continue to happen until the end of the universe…

if i’m mis-reading, feel free to summarize and correct.

Comment #15582

Posted by PvM on February 9, 2005 10:57 AM (e) (s)

A good example of how ID proponents misunderstand Avida can be found in a recent thread at ISCID where RBH has uncovered some major problems with the arguments of Eric Anderson. Too bad the forums is all but dead and responses may be unlikely.

Comment #15660

Posted by Right on February 9, 2005 04:47 PM (e) (s)

John, “gullible” is a term reserved for those on your side of the debate, not the “Darwinists”.  It’s simple: put up some evidence or shut up.

Comment #15819

Posted by DaveScot on February 10, 2005 07:21 PM (e) (s)

PvM wrote:

the genome is ‘exploring’ sequence space

There’s that recurring concept of genes as space explorers.

Does NASA know they have competition?

At least you put ‘exploring’ in quotes to emphasize the anthropomorphizing taking place. 

It’s interesting that while denying intelligent design you can’t help but compare the process to intelligent endeavours like exploration.

So how big is this “sequence space” and how quickly can these explorers “decide” (anthropomorphism intended) decide if they’ve found a beneficial new sequence?  I think one of the points made by Dembski??? was that this space is so incredibly large that undirected exploration of it is an exercise in futility.

Comment #15827

Posted by PvM on February 10, 2005 08:21 PM (e) (s)

So how big is this “sequence space” and how quickly can these explorers “decide” (anthropomorphism intended) decide if they’ve found a beneficial new sequence?  I think one of the points made by Dembski??? was that this space is so incredibly large that undirected exploration of it is an exercise in futility.

One should not believe everything Dembski says. Did you read the article on Promiscuity in Evolution? While Dembski predicted islands of functionality surrounded by oceans of non-functionality (paraphrasing), reality seems to disagree with him once again.

To answer your question about RNA, research (that annoying concept again) has looked into this and found some very fascinating properties of sequence space. (And yes, the genome ‘explores’ sequence space through the mechanism(s) of variation and if applicable selection).

The findings were:

1. More sequences than structures

2. Few common and many rare structures.

3. Common structures are found almost everywhere in sequence space.

4. Neutral networks of common structures extend over whole sequence space.

The concept of scale-free networks and neutrality are fascinating in understanding evolution. For instance, neutrality seems to be essential for evolution to be evolvable and at the same time neutrality provides for robustness.

And the really cool thing is that for scale free networks to arise one requires nothing more than duplication and preferential attachment…

See Here for some more information

It’s time for Dembski to go back to the ‘drawing table’ as his hopeful predictions do not seem to have found much support in reality.
Seems that the position that evolution cannot explain X, seems to have few redeeming qualities when it comes to science. Especially when such argument from ignorance is used to argue ‘Thus Y’.

Comment #15829

Posted by PvM on February 10, 2005 08:34 PM (e) (s)

DaveScott wrote:

It’s interesting that while denying intelligent design you can’t help but compare the process to intelligent endeavours like exploration.

I am not sure what to do with such an ‘argument’. If the use of metaphors is confusing to Dave then he should let me know and I will use more technical terminology. What is worse, using metaphors to facilitate understanding or to confuse metaphors with a need for ID?

For more reading see Metaphors on Trial or, How did the Groundhog Cross the Road? by John Pieret

or DNA, Intelligent Design, and Misleading Metaphors
in (Free Inquiry, Summer 2003)

The popular resurgence of the idea of intelligent design may be a side effect of the extremely productive metaphors used by science.

Synopsis

The discoveries of modern science have led some to reconsider whether the universe is a product of intelligent design.  Hume’s criticism of the design argument, directed at the machine metaphors of his time, still applies today.  Although modern metaphors are more productive, they are, after all, only metaphors.  Sources of the allure of intelligent design are explored.  They include: (1) the nature of the scientific enterprise itself and the disparity between our ability to gain observational knowledge about phenomena and our ability to generate explanations, (2) the fact that intelligent design implies an ultimate purpose that is lacking in the materialistic explanations offered by science, and (3) the psychology of human understanding and the cognitively advantageous but epistemologically misleading tendency to engage in anthropomorphism.

Comment #15847

Posted by DaveScot on February 11, 2005 02:46 AM (e) (s)

PvM

I’m not at all confused when you use metaphors that anthropomorphize evolution and never hinted at confusion.  I completely understand it.  It’s hard to describe a process driven by intelligence without anthropomorphizing.  It’s a dead giveaway - a Freudian slip - that reveals what you really think about evolution.  I’m trying to find a way to get your conscious mind to acknowledge what your unconcious already knows to be true.

Comment #15848

Posted by DaveScot on February 11, 2005 03:29 AM (e) (s)

PvM

So how big is sequence space.

Your answer was about 200 words long and didn’t contain a single numeric value.

When I was in Marine boot camp they taught us that if we didn’t know an answer to a question the proper answer was “SIR, the private does not know the answer but the private will find the answer, SIR.”

Get back to me when you get the answer and keep the dissembling for someone else.

Comment #15849

Posted by DaveScot on February 11, 2005 03:54 AM (e) (s)

PvM

I was skeptical of Dembski’s numbers and double checked them.  I question most of what I read, actually, which handily explains why I don’t buy this all-powerful mutation/selection malarky that’s being sold to 14 year-olds as fact when it’s nothing but a large leap of faith.  The bottom line remains that mutation/selection has not been observed to do anything more than make changes, mostly of scale, without producing any novel new forms.  It requires faith to believe it has greater ability and that means mutation/selection is no longer a theory, it’s a religion.

Common descent I don’t question.  Evolution I don’t question.  It’s the all-powerful mechanism of mutation/selection I take issue with.  Seems like everywhere I turn trying to match that up with the data it’s questionable at best or just plain wrong.  A poor fit here and there I can understand but the fit is poor everywhere except for making small scale changes in rapid fashion - fine tuning a body plan.  It does that well but it doesn’t do changes that add up to novel new body plans.

Copernican Principle of Mediocrity says it ain’t bad for an enlightened thinker to assume that anything about the earth is special.  I know genetic engineers exist on the earth.  Some of them are named Steve.  Therefore it is a valid assumption to think they are common elsewhere.  From there it follows that design is valid option to consider.  If one applies design to the first cell, and the first cell only, supposing that it contained the information required to diversify into myriad basic body plans, then all the data fits like a glove.

While this may not be true, it is certainly on equal ground with mutation/selection in every metric I can think of.  Only a committed secular humanist who believes that in this vast universe mankind is the only designer.  What hubris!

Comment #15869

Posted by PvM on February 11, 2005 10:33 AM (e) (s)

DaveScott wrote:

I was skeptical of Dembski’s numbers and double checked them.  I question most of what I read, actually, which handily explains why I don’t buy this all-powerful mutation/selection malarky that’s being sold to 14 year-olds as fact when it’s nothing but a large leap of faith.

Why is it a leap of faith Dave? Dembski tried to argue that there are reasons why darwinian theory would be unable to find the islands of functionality. His hopes seem to have been shattered by the scientific findings of promiscuity. For instance when looking at the genome, we see how mutation and selection have been responsible for forming the genomes. When using phylogenetic reconstruction, one recovers a (mostly) consistent
picture. That by itself does not PROVE that variation and selection are the only relevant mechanism in evolution but it shows thta it is an important mechanism. Dembski then tried to show that mutation and selection could not increase the information in the genome. Again science showed otherwise. Then there was Behe who hoped that particular structures or pathways could not be explained by variation and selection because, he argued, they are irreducibly complex. When it was shown that patwhays to such systems exist and that such pathways are quite natural, another ‘pillar’ of ID collapsed.

The bottom line remains that mutation/selection has not been observed to do anything more than make changes, mostly of scale, without producing any novel new forms.  It requires faith to believe it has greater ability and that means mutation/selection is no longer a theory, it’s a religion.

Perhaps, it may seem a religion to Dave Scott because his familiarity with what mutations can and cannot produce are limited by his knowledge?

Common descent I don’t question.  Evolution I don’t question.  It’s the all-powerful mechanism of mutation/selection I take issue with.  Seems like everywhere I turn trying to match that up with the data it’s questionable at best or just plain wrong.  A poor fit here and there I can understand but the fit is poor everywhere except for making small scale changes in rapid fashion - fine tuning a body plan.  It does that well but it doesn’t do changes that add up to novel new body plans.

And yet, we see such researchers as Valentine reach the opposite conclusion, namely that the origin of phylum falls well within the Darwinian paradigm. Perhaps scientists are a bit more familiar with the data and understand its limitations as well as its explanatory powers? And mutation/selection is hardly the only mechanism of evolution… As I have shown neutral evolution plays a very important role as well.

ID has raised many objections against (Darwinian) evolution but few if any have shown to be supported by actual evidence. That of course hardly means that Darwinian evolution must be true, science is careful not to make such gap arguments typically found amongst IDists.

So your objection seems to have been reduced to: Evolution works but does not explain the origin of new bodyplans, which I presume you mean new phyla? Is this a correct interpretation of your position? Would you be interested in exploring the evidence?

Copernican Principle of Mediocrity says it ain’t bad for an enlightened thinker to assume that anything about the earth is special.  I know genetic engineers exist on the earth.  Some of them are named Steve.  Therefore it is a valid assumption to think they are common elsewhere.  From there it follows that design is valid option to consider.  If one applies design to the first cell, and the first cell only, supposing that it contained the information required to diversify into myriad basic body plans, then all the data fits like a glove.

While this may not be true, it is certainly on equal ground with mutation/selection in every metric I can think of.  Only a committed secular humanist who believes that in this vast universe mankind is the only designer.  What hubris!

Comment #15873

Posted by PvM on February 11, 2005 10:47 AM (e) (s)

Charlie wrote:

On the contrary, I have addressed the validity of computer simulations many times. You want more? Here it is:
  Computer simulation models of evolution are not valid because there is no way to demonstrate that they model what actually happens in nature. They only model your belief about what happens in nature. So trying to find ‘flaws’ is useless because the simulation is not being judged against what actually is happening, it’s being judged against your belief in what’s happening, which can always be ‘adjusted’ to compensate for any problems.

You have again resorted to ‘it appears to me that’ arguments. But Charlie is correct, models are a simplified view of reality, trying to capture the essential features and see what happens. As such these models show that the simple concepts of mutation and selection are sufficient to explain increase in information and complexity in the genome. Additionally, they show how they are in principle, able to explain IC systems. Models as such are thus essential in understanding that ID arguments are without much merrit.

We know that variation happens, we know that selection happens. Thus models which represent these known mechanisms are useful in testing the limitations and potentials of such mechanisms.

Charlie argues, without much supporting logic or reason beyond ‘it seems to me’, that evolutionary mechanisms can not explain complex interactions. But science once again seems to find that this may be incorrect. For instance a recent finding about promiscuous genes shows that a particular gene can maintain original function and evolve a new function. Combine this with gene duplication and preferential attachment and one recovers a scale free nature found all across biology. What does Charlie’s model predict? Charlie?

Let’s look at the bacterial flagellum, what happened? When, where, how? Care to line up your ‘theory’ against science?

Btw did you address the self assembly of the ribosome? In the end Nelson’s law is as scientifically vacuous as any Gap theory.

Comment #15874

Posted by PvM on February 11, 2005 10:51 AM (e) (s)

I’m not at all confused when you use metaphors that anthropomorphize evolution and never hinted at confusion.  I completely understand it.  It’s hard to describe a process driven by intelligence without anthropomorphizing.  It’s a dead giveaway - a Freudian slip - that reveals what you really think about evolution.  I’m trying to find a way to get your conscious mind to acknowledge what your unconcious already knows to be true.

ROTFL, Dave Scott, your response beautifully shows my point namely that humans are quick to jump to conclusions based on intuition rather than on fact and logic. It’s a well know psychological fact that we are quite succeptible to such. That people thus jump to conclusions that it looks designed thus there must have been an intelligent designer appears to be, according to your argument, a faith based not an evidence based jump.

Have you learned nothing since Hume and Paley? Sigh…

Comment #15878

Posted by PvM on February 11, 2005 11:08 AM (e) (s)

DaveScott wrote:

So how big is sequence space. Your answer was about 200 words long and didn’t contain a single numeric value.

Do you require numerical values to understand my argument namely that common structures extend through sequence space and are ‘close’ to other structures? In other words, yes sequence space is enormous but that is no argument against evolution. Let’s for instance take a ‘typical’ gene of 200 aminoacids, there are 20 amino-acids thus there are 200**20 possible combinations. An enormous number. So yes, by necessity evolution is limited to a sub-space. So yes, exploring all of sequence space is unlikely, but that is not necessarily if common structures are found all through sequence space, close to other sequences.

I understand that science showing your arguments to be without much merrit may be somewhat discomforting but let’s not reject them based on such feelings. As I showed, others (mostly creationists) have argued much of the same and ignored how science addresses them. Now that more and more findings seem to support science, another Gap is closed and ID has to retreat to even darker areas of our ignorance.

I can provide you with numbers about average Hamming distances. Do a google search for “hamming distance RNA” for more

Exploring Phenotype Space Through Neutral Evolution Martijn A. Huynen

Abstract. RNA secondary-structure folding algorithms predict the existence of connected networks of
RNA sequences with identical secondary structures. Fitness landscapes that are based on the mapping between
RNA sequence and RNA secondary structure hence have many neutral paths. A neutral walk on these fitness landscapes gives access to a virtually unlimited number of secondary structures that are a single point mutation from the neutral path. This shows that neutral evolution explores phenotype space and can play a role in adaptation

Read the paper I suggest there are countless papers on this topic.

Comment #15882

Posted by Pastor Bentonit on February 11, 2005 11:58 AM (e) (s)

Über-Troll John A. Davison intoned:

The Ether in Physics, Selection in biology and Phlogiston in chemistry constitute a beautiful demonstration of extrasensory perception since their initial letters spell out ESP. Phlogiston died in the 18th century, the Ether in the 19th and Selection, artificial or natural never existed at all except in the minds of a couple of Victorian naturalists and their thousands of devoted disciples who, for reasons I will never understand, are still with us in the 21st century.

Resorting to cabbalism is definitely going to cut it here, what with all the “Darwinian mysticists” all over the comment pages, sure JAD. Keep on flogging yourself. It is strangely amusing but, in the end, one must feel sorry for you.

Comment #15950

Posted by DaveScot on February 11, 2005 11:08 PM (e) (s)

Joe Shelby

Huxley was on the right track.  Social/cultural factors are sorta right, definitely a part of the equation, but *technologic* evolution I think should be the most apt descriptor.  You boys are able to move genes from plants to animals and vice versa fercrisakes by little more than point & click with a mouse on a workstation.  Okay, more than that, but you get the idea, right?

Stuff that nature might do by accident in a hundred million years you can do in a good week at the office and it’s directed.  I keep tellin’ y’all if evolution didn’t have an intelligent agent mucking with it in the past it certainly has intelligent agents mucking with it now.

But just for the record, there’s an overwhelming appearance that y’all weren’t the first ones in the designer genes business, but if it’s any consolation I believe you’re the first ones in the last few billion years to intelligently interfere with the natural course of events.

Comment #15953

Posted by DaveScot on February 11, 2005 11:40 PM (e) (s)

PvM wrote:

In other words, yes sequence space is enormous but that is no argument against evolution. Let’s for instance take a ‘typical’ gene of 200 aminoacids, there are 20 amino-acids thus there are 200**20 possible combinations. An enormous number.

Ya