## Thursday, November 4, 2010

### Adaptive Robots: Yet More Evidence for Evolution

Not only do biological organisms adapt before our eyes, but in recent years researchers have developed robots that adapt via Darwinian selection. As one recent research paper explained:

Darwin suggested that adaptation and complexity could evolve by natural selection acting successively on numerous small, heritable modifications. But is this enough? Here, we describe selected studies of experimental evolution with robots to illustrate how the process of natural selection can lead to the evolution of complex traits such as adaptive behaviours. Just a few hundred generations of selection are sufficient to allow robots to evolve collision-free movement, homing, sophisticated predator versus prey strategies, coadaptation of brains and bodies, cooperation, and even altruism.

Can robots illustrate how complex traits evolved? Yes they certainly can, the paper concludes. According to the authors, such experiments provide “a spectacular demonstration of the power of natural selection.” Is that true?

Joseph Raphson was a seventeenth century English mathematician who is most famous for devising a numerical method that was also devised, independently, by Isaac Newton. Newton derived the method years earlier but it, as with so much of his work, went unpublished for decades. Therefore Raphson’s work was his own and he rightly is credited alongside the great Newton. Of course standing alongside a giant often means one is overlooked. Today the method is usually referred to simply as Newton’s method, sometimes as the Newton-Raphson method, but never as Raphson’s Method.

The Newton-Raphson method is a relatively simple iteration for finding where a curve has a value of zero. This root finding algorithm is a handy way of calculating difficult formulas, such as the square root of a number. The idea is to temporarily replace the complex curve with a simple straight line. The straight line, which approximates the curve but is far easier to work with, takes you closer to the answer and allows you to generate a new, better, straight line approximation. After only a few iterations you have a an answer that is good to a few decimal places.

An important property of the Newton-Raphson method is that it works with no knowledge of the overall curve. It needs to know only the shape of the curve locally, at the current approximate answer.

Today’s numerical methods are more complex and sophisticated, but the Newton-Raphson method remains an excellent pedagogical tool as well as a useful method in many practical applications. It is also a simple example of the connection between numerical methods and evolutionary theory.

The Newton-Raphson method’s ignorance of the overall curve is analogous to evolution’s ignorance of a population’s overall fitness surface. The Newton-Raphson method nicely converges to a mathematical solution just as evolution is proposed to nicely find biological solutions. Neither knows anything more than the local shape of the curve, but this is sufficient to locate the roots.

In fact certain branches of numerical methods have used biological and evolutionary concepts to explore new approaches. Genetic algorithms and neural networks are computational methods that use concepts such as fitness, genes, chromosomes and selection.

Not surprisingly evolutionists have interpreted the success of these numerical methods as yet more compelling evidence for evolution. Do not these computational algorithms demonstrate the underlying feasibility of Darwin’s idea?

Of course not. Such fallacious logic has it backwards. Clearly Darwin’s idea is mathematically tractable. That is, if fitness landscapes are relatively smooth and reasonably shaped, and if an initial population just happens to appear, and if biological variation just happens to arise and accumulate, and if populations do not resist such change, then of course species can evolve to new designs. Indeed evolutionists often refer to Darwin’s idea as a truism. It necessarily follows from the premises.

And so it is hardly surprising that we can develop numerical methods that solve problems in this manner. Indeed, Newton and Raphson’s work predates Darwin by almost two centuries. By the nineteenth century there was no question that, given the right properties, iterative numerical solutions could move toward a solution in a stepwise manner. And today our methods are all the more sophisticated. But none of this justifies the evolutionary premises.

Consider the robot research in the paper referenced above. The evolutionary robot experiments took place in an engineered environment. Most of the experiments were computer simulations. That is, the experiments took place in computers created by people, developed in programming languages developed by people, running on electricity provided by people, and interpreted by people. Some of the experiments used actual robots in a testing environment that reflected the computer simulations.

Furthermore, the robot’s capabilities were pre arranged and provided. The algorithms that provided the instructions for the robots, as well as the robot configurations, evolved. But such evolution was within the context of the provided capabilities.

For instance, the algorithms that provided the instructions for the robots are controlled by weighting factors and these weighting factors are varied in the experiments to “evolve” the robot behavior. The weighting factors alone do nothing. They rely on the advanced algorithms and software to have their effect.

And sophisticated sensors were supplied that provided the inputs to the algorithms. In turn, the algorithm outputs controlled electronic motors that set the robot into motion. Then the experimenters provided simple criteria (which they referred to as the robot fitness) to select the best designs at each iteration. Just as the Newton-Raphson method iterates toward a solution, the robots were iterated toward their solutions. Here is how the paper described one experiment:

The sensors were connected to eight input neurons that were connected to two output neurons, which each controlled the direction and speed of rotation of one of the wheels. The genome of the robots consisted of a sequence of bits encoding the connection weights between input and output neurons. Mutations allowed the strengths of connections between neurons to change over generations. Experimental selection was conducted in three independent populations each consisting of 80 individuals. The performance of each robot was evaluated with a fitness function describing the ability of the robot to efficiently move in the maze.

It may have been a nifty bit of engineering work, but this is hardly evolution in action. If you randomize aspects of pre supplied functionality, and select for certain outcomes, then you will end up with those outcomes. Here is how the authors described one outcome:

the best evolved individuals across all replicates moved in the direction corresponding to the side with the highest number of sensors. This was because individuals initially moving in the direction with fewer sensors had higher probability of colliding into corners and thus had lower probability of being selected for reproduction.

It seems to have been a fine piece of work, and such approaches are undoubtedly useful in robot design, training and control. But this has very little in common with biological evolution.

And the experimenters even solved the problem of large-scale change by designing a “gene” to supply different algorithmic topologies:

The genome of each robot consisted of two chromosomes, one encoding the topology of a neural network and the other encoding the shape of a body composed of rigid blocks linked by controllable articulations. This led to the coevolution of different types of robots capable of moving towards the cube and preventing access to its opponent. For example, some robots consisted of a cubic block with two articulated, arm-like structures, which were used for moving on the ground and holding the cube. Other robots were composed of only two articulated worm-like segments where one segment was so large and heavy that, once placed over the cube, it prevented the opponent from displacing it.

Given these engineering heroics it is hardly surprising that the experiments worked so well:

Just a few hundred generations of selection are sufficient to allow robots to evolve collision-free movement, homing, sophisticated predator versus prey strategies, coadaptation of brains and bodies, cooperation, and even altruism.

Yes the robots evolved in this engineered environment, but it is simply a misrepresentation to claim this is evidence of biological evolution. Nonetheless this is precisely what the authors claimed:

these experiments revealed how the coevolution between brain and body morphologies can produce various types of adaptive behaviour and morphologies. … These examples of experimental evolution with robots verify the power of evolution by mutation, recombination, and natural selection.

Verify the power of evolution? A spectacular demonstration of the power of natural selection? This is, to put it diplomatically, a non scientific misrepresentation. Unfortunately this is what we can expect from evolutionists. If there is anything spectacular here, it is the steady stream of myth-like claims made by evolutionists. When not overtly religious, the evidence they produce for their theory is, frankly, absurd. Religion drives science and it matters.

1. "If you randomize aspects of pre supplied functionality, and select for certain outcomes, then you will end up with those outcomes."

So if we start with an existing organism, make some random changes to some of their offspring's DNA, let the new organisms try to make a living and some of the new organisms turn out to be better at making a living than their parents, it's not evolution?

You really don't understand evolution at all, do you?

2. In computer science we recognize the algorithmic principle described by Darwin - the linear accumulation of small changes through random variation - as hill climbing, more specifically random mutation hill climbing. However, we also recognize that hill climbing is the simplest possible form of optimization and is known to work well only on a limited class of problems.
Watson R.A. - 2006 - Compositional Evolution - MIT Press - Pg. 272

In the following podcast, Robert Marks gives a very informative talk as to the strict limits we can expect from any evolutionary computer program (evolutionary algorithm):

Darwin as the Pinball Wizard: Talking Probability with Robert Marks - podcast
http://www.idthefuture.com/2010/03/darwin_as_the_pinball_wizard_t.html

3. The authors are quite clear that the robotics studies are models of evolution, with certain advantages over purely mathematical/numerical models:

"In comparison to theoretical and numerical models of biological phenomena, the embodiment and behavioural features of robot models can result in stronger testing of hypotheses and in higher predictive power [71]–[73]."

These models provide important proofs of principle: the mechanisms of evolution (random mutation, selection, recombination, drift) can generate complex adaptive behavior.

On a related note: here is a study of experimental evolution in phages. An important phage gene is replaced by a random sequence, and after 20 rounds of random mutation and selection, the phage's infectivity (proxy for fitness) increased >10,000-fold.

4. Cornelius:

"Consider the robot research in the paper referenced above. The evolutionary robot experiments took place in an engineered environment. Most of the experiments were computer simulations. That is, the experiments took place in computers created by people, developed in programming languages developed by people, running on electricity provided by people, and interpreted by people."

I didn't read that in the paper. For all we know the electricity was provided by lightning.

Yes, scientists are people! By some bizarre "reasoning" IDCers loooove to imply that it is therefore in principle impossible to model evolution without "intelligent" intervention.

Which is dumb. Very dumb.

5. bornagain77: "In computer science we recognize the algorithmic principle described by Darwin - the linear accumulation of small changes through random variation - as hill climbing, more specifically random mutation hill climbing. However, we also recognize that hill climbing is the simplest possible form of optimization and is known to work well only on a limited class of problems." Watson R.A.

Quote-mine much?

Point-mutations are very limited because they tend towards local maxima. However, recombination and point-mutation are not so limited.

6. bornagain77: "Darwin as the Pinball Wizard: Talking Probability with Robert Marks"

If there is a transcript, we will consider his remarks.

7. troy: By some bizarre "reasoning" IDCers loooove to imply that it is therefore in principle impossible to model evolution without "intelligent" intervention. Which is dumb. Very dumb.

The weather simultion experiments took place in an engineered environment. Most of the experiments were computer simulations. That is, the experiments took place in computers created by people, developed in programming languages developed by people, running on electricity provided by people, and interpreted by people.

Weather is designed! Long reign Æolus!

8. I thought it was a hallmark of ID creationism that randomization plus selection cannot yield novel, useful information.

When faced with a paper (which I suggest people actually read-it is free-rather than taking this as a true summary of the work) that states:

"In the beginning, robots have random values for their genes, leading to completely random behaviours. The process of Darwinian selection is then imitated by selectively choosing the genomes of robots with highest fitness to produce a new generation of robots. "

Cornelius: "Clearly Darwin’s idea is mathematically tractable."

I appreciate the concession. Do your colleagues share this view? I thought otherwise. Are novel, genetically encoded behaviors not information?

"That is, if fitness landscapes are relatively smooth and reasonably shaped,"

Some are, some lead to extinction. The counter that all fitness landscapes are too rugged and 'unreasonably' shaped is false.

"and if an initial population just happens to appear"

Leaving abiogenesis aside, lets say life exists, shall we?

"and if biological variation just happens to arise and accumulate"

We know it does, and by what mechanisms. We can measure it directly by genomic approaches, even in an evolving population. The counter hypothesis-that biological variation never arises or accumulates is false.

"and if populations do not resist such change"

Do you have evidence all populations resist 'such change'? We have direct observations of substantial plasticity in adapting populations.

"then of course species can evolve to new designs."

Cool. Except for the superfluous "new designs"

BTW, is the 'moderate' in moderate empiricism the allowance for assertion against data? Interesting logic in this paragraph.

9. * From an interview with Robert Crowther of the pro-intelligent design Discovery Institute (March 03, 2010). "Darwin as the Pinball Wizard: Talking Probability with Robert Marks,". Retrieved on 2010-05-03.

* [Computer] programs to demonstrate Darwinian evolution are akin to a pinball machine. The steel ball bounces around differently every time but eventually falls down the little hole behind the flippers.
* It's a lot easier to play pinball than it is to make a pinball machine.

* Computer programs, including all of the models of Darwinian evolution of which I am aware, perform the way their programmers intended. Doing so requires the programmer infuse information about the program's goal. You can't write a good program without [doing so].
* Your chances of winning the lottery are about the same whether or not you buy a ticket. It's better ... if you give your money to me and I'll decide whether or not to give it back.
* From the viewpoint of computer simulation, our universe does not contain the probabilistic resources to get a meaningful result for even a moderately sized unassisted [Darwinian] search. In fact, if you take ten to the one thousand of our universes in what is sometimes referred to as the multiverse, the probabilistic resources don't exist there either.
* Let's abandon labels and pursue the truth no matter where it leads. Don't entrench yourself in a paradigm and claim a corner on truth. Many who have done so in history have been shown to be foolish.

further note:

The Genius Behind the Ingenious - Evolutionary Computing
Excerpt: The field dedicated to this undertaking is known as evolutionary computing, and the results are not altogether encouraging for evolutionary biology.
http://biologicinstitute.org/2008/10/17/the-genius-behind-the-ingenious/

Signature In The Cell - Review
Excerpt: There is absolutely nothing surprising about the results of these (evolutionary) algorithms. The computer is programmed from the outset to converge on the solution. The programmer designed to do that. What would be surprising is if the program didn't converge on the solution. That would reflect badly on the skill of the programmer. Everything interesting in the output of the program came as a result of the programmer's skill-the information input. There are no mysterious outputs.
Software Engineer - quoted to Stephen Meyer
http://www.scribd.com/full/29346507?access_key=key-1ysrgwzxhb18zn6dtju0

10. Cornelius Hunter said...

Consider the robot research in the paper referenced above. The evolutionary robot experiments took place in an engineered environment. Most of the experiments were computer simulations. That is, the experiments took place in computers created by people, developed in programming languages developed by people, running on electricity provided by people, and interpreted by people. Some of the experiments used actual robots in a testing environment that reflected the computer simulations.

LOL!

Weather scientists at NOAA use models to study hurricanes. The hurricane experiments took place in an engineered environment. Most of the experiments were computer simulations. That is, the experiments took place in computers created by people, developed in programming languages developed by people, running on electricity provided by people, and interpreted by people. Some of the experiments used actual sensors tested in a real hurricane environment that reflected the computer simulations. Therefore these models can't be used to study the processes of real hurricanes

The goofiness that passes for IDC logic is always good for a morning laugh.

11. Dave Mullenix:

"So if we start with an existing organism, make some random changes to some of their offspring's DNA, let the new organisms try to make a living and some of the new organisms turn out to be better at making a living than their parents, it's not evolution?"
======

According to Darwin, evolution was supposed to be unguided, blind without purpose or intent without motivation towards any goals. Unfortunately for evo-world, scientists have discovered that DNA is a complex multi-layered code. Infact it seems every month we are getting more and more reports of codes within a code regarding DNA. It has checksums, redundancy, error correction and repair mechanisms.

It has instructions for building molecular machines and other objects, modular components and changes its structure based on inputs from the environment. How did evolution invent all these goal/purpose driven mechanisms from nothing more than blind pointless indifference ??? Why would you attach evolutionary signage to clearly complex machinery when Metaphysical are supposed to be out of bounds to evolutionary theory ???

------

Dave Mullenix:

"You really don't understand evolution at all, do you?"
======

Why don't you explain it minus the metaphysics. Explain in detail all the undirected, unguided way it operates.

12. Zachriel:

"The weather simultion experiments took place in an engineered environment. Most of the experiments were computer simulations."

Thorton:

"Weather scientists at NOAA use models to study hurricanes. The hurricane experiments took place in an engineered environment. Most of the experiments were computer simulations."
======

Let me guess, I know I've heard this before.

Oh yeah, Hurricanes are a code, right ???

*eyes rolling*

13. Let's be clear:

DNA is a chemical.

RNA is produced using it as a physicochemical template. Proteins are produced using certain RNAs as templates. These processes are chemical-hydrogen bonding and fit are not abstract symbols.

Some proteins go on to repair DNA (by recognizing bulges due to chemical damage). Some regulate DNA (recognizing the physical and chemical properties of the DNA bases).

Seeing this as a literal abstract code within a code takes the analogy and substitutes it for reality.

14. Wonderful, BA77 treats us with his usual barrage of irrelevant links and quote mines, instead of writing his own "arguments". If anyone is living proof that religion rots the brain, it's Mr Bornagain77.

15. Thorton:

"The goofiness that passes for IDC logic is always good for a morning laugh."

It's Insane Troll Logic.

16. Eocene said...

Let me guess, I know I've heard this before.

Oh yeah, Hurricanes are a code, right ???

*eyes rolling*

Eocene, do you ever visit reality? Even momentarily?

17. RobertC:

"Let's be clear:

DNA is a chemical."
======

Sorry Robert, pen and paper are nothing more than actual physical material substrate. The writting on the page is physical. But the information contained on the paper is immaterial, which means it's nothing more than the ideas, thoughts, plans, blueprints, bytes & bits and codes from an intelligent mind.

If you disagree, then provide us an example of how an informational code containing encoded plans and ideas with purpose and intent morphs from nothing more than chemcials and physics ???

18. Thorton:

"Eocene, do you ever visit reality? Even momentarily?"
======

Seriously Don, do you actually believe a Hurricane is a informational code ???

19. Eocene said...

Thorton:

"Eocene, do you ever visit reality? Even momentarily?"
======

Seriously Don, do you actually believe a Hurricane is a informational code ???

So the answer is 'not even momentarily'.

20. Thorton:

"So the answer is 'not even momentarily'."
======

And the answer is 'YES' along with continued deflection.

Thanks for playing there, Don.

21. Why is Eocene calling Thorton "Don"?

22. "Sorry Robert, pen and paper are nothing more than actual physical material substrate. "

Exactly. And DNA is chemical-the stuff of pen and paper.

"But the information contained on the paper is immaterial "

And here's where the analogy breaks down. DNA is material-the A,T,C,G we assign to it represents real chemicals. And it is the properties of these chemicals that act in replication, transcription, translation and repair, NOT any abstraction! There is no immaterial force, no mind, required to recapitulate any of the processes acting on DNA. Throw the right chemicals in a tube, and transcription, translation, etc. run.

"Encoded plans and ideas with purpose"

Neo-Vitalism. What plans, what purpose?

23. RobertC,

since you hold no information exist in the cell perhaps you would care to drop Bill Gates a note:

Bill Gates, in recognizing the superiority found in Genetic Coding, compared to the best computer coding we now have, has now funded research into this area:

Welcome to CoSBi - (Computational and Systems Biology)
Excerpt: Biological systems are the most parallel systems ever studied and we hope to use our better understanding of how living systems handle information to design new computational paradigms, programming languages and software development environments. The net result would be the design and implementation of better applications firmly grounded on new computational, massively parallel paradigms in many different areas.
http://www.cosbi.eu/index.php/component/content/article/171

24. The following video is far more direct in establishing the 'spiritual' link to man's ability to learn new information, in that it shows that the SAT (Scholastic Aptitude Test) scores for students showed a steady decline, for seventeen years from the top spot or near the top spot in the world, after the removal of prayer from the public classroom by the Supreme Court in 1963. Whereas the SAT scores for private Christian schools have consistently remained at the top, or near the top, spot in the world:

The Real Reason American Education Has Slipped – David Barton – video
http://www.metacafe.com/watch/4318930

25. RobertC:

"Throw the right chemicals in a tube, and transcription, translation, etc. run."
=======

By all means Robby, show us. Give us an impirical scientific formula using the "Scientific Method" so we can all create life in that test tube with nothing more than physics and chemcials.
-------

RobertC:

"Neo-Vitalism. What plans, what purpose?"
=======

Hey that's what we want Robby. Show us how undirectedness, no guidance, pointless indifference and the blind intelligent mythical forces of Tinker Bell brought about all the order and complexity in the natural world around us, which unfortunately now is coming to it's end unless there is actually a creator out there to reverse the effects of the clueless ???

Come on Robby, go for it!!! Be the first!!!

26. the preceding was in response to troy's brain 'rot' comment

27. bornagain77 (quoting Stephen Meyer): "There is absolutely nothing surprising about the results of these (evolutionary) algorithms. The computer is programmed from the outset to converge on the solution. The programmer designed to do that. What would be surprising is if the program didn't converge on the solution. That would reflect badly on the skill of the programmer.

Evolutionary algorithms don't have to have a goal. They may simply navigate a search space. And even when there is a goal, they may or may not converge, depending on the search space.

28. "since you hold no information exist in the cell perhaps you would care to drop Bill Gates a note"

I've said no such thing. I've said DNA and RNA are physicochemical templates, as opposed to abstract codes. Of course the RNA contains information, in the form of codons, that act as a template for tRNAs to pair with, in the formation of protein. This is not controversial.

That you see abstract meaning, codes requiring a mind, plans and purpose in such a system is.

That you don't realize information increases naturally, through Darwinian processes is.

Take this paper-where information increases due to Darwinian processes

Even Cornelius says:

"Clearly Darwin’s idea is mathematically tractable. That is, if fitness landscapes are relatively smooth and reasonably shaped, and if an initial population just happens to appear, and if biological variation just happens to arise and accumulate, and if populations do not resist such change, then of course species can evolve to new designs."

So, I await proof that:

1) All fitness landscapes are unreasonably shaped, or
2) Life (a population) does not exist, or
3) Biological variation does not arise and accumulate, or

Seems like we have great data, and no falsification for all 4. I, therefore, accept Cornelius's conclusion: "then of course species can evolve"

29. bornagain77 said...

The following video is far more direct in establishing the 'spiritual' link to man's ability to learn new information, in that it shows that the SAT (Scholastic Aptitude Test) scores for students showed a steady decline, for seventeen years from the top spot or near the top spot in the world, after the removal of prayer from the public classroom by the Supreme Court in 1963. Whereas the SAT scores for private Christian schools have consistently remained at the top, or near the top, spot in the world:

Correlation doesn't equal causation. The main reasons for the SAT slips in U.S. public schools are dumbed down minimum academic standards (since no one wants their kid to fail), along with larger class sizes (= larger student/teacher ratio, less quality time spent on each subject) driven by budget constraints. Neither of which have anything to do with 'spiritual' links.

30. Thorton,

Not that test scores are everything, but the nations that kick our ass in test scores aren't exactly the most religious!

http://4brevard.com/choice/international-test-scores.htm

Top Scores:
Netherlands, Sweeden, Denmark, Iceland, Norway

http://politics.usnews.com/opinion/articles/2009/02/11/5-least-religious-countries-in-the-world.html

Least Religious:
Estonia, Sweeden, Denmark, Norway

Odd.....wonder what the trend in US States is....

Most religious (percent religion in daily life):
85% Mississippi
82% Alabama
80% South Carolina

I suppose these have the best education?

31. Copy from the previous article brought forward here...

Zachriel said,

"No. For clarity, here are the sets:

A = {cats, lions}
B = {dolphins, cats, lions}
C = {fish, dolphins, cats, lions}"

----

Arranging them together with group names like this renders an obvious nested hierarchy. Your previous example: {fish, {dolphin, {cat, lion}}} was NOT because cats and lions have features that are not in dolphins.

Grouping them together first is not simply for luxury or clarity to show a nested hierarchy... it is a necessity. A nested hierarchy structure follows standard rules. Showing abstract elements falls outside of the standard rules.

Cat > Felidae > Mammalia > Chordata > Animalia

This is the standard biological classification and it is a nested hierarchy.

But, I don't think this is what you mean by your example. Your ABC sets above are arbituary from a purely hierarchical view. You see relationships, but technically anything can be grouped together in this ABC manner and then represented by a nested hierarchy.

When you talk about "one reasonable way to biologically classify fish, dolphins, cats and lions" you did not mention which classification system you are using. Linnaeus? Haeckel? Chatton? Copeland? Wittaker? Wosse, Cavalier-Smith? Other?

32. We must be doing something right in the Netherlands! I'm telling you, it's the superb weed.

Unlike the US, the Netherlands has no separation between church and state. The state fully finances religious schools of any stripe (although I'm not aware of any Satanist schools). They may deny evolution and promote creationism all they want (and they do), but the students have to pass national exams that do require some knowledge of proper evolutionary biology.

33. Troy:

I wrote this to Robert:

=======
Secondly, rationalists have a difficult time thinking outside the box of rationalism. When they hear an empiricist, they project their rationalism onto his position. They have very little ability to engage uncertainty, and instead interpret an empiricists objective evaluation of a theory as representing an underlying truth claim. Here it is, straight from the evolutionist:

"Are you NOT saying that because evolution lacks all the answers at present, that it is wrong?"

Of course I'm not saying this. In fact I've taken pains to be crystal clear that I am, in fact, *not* saying this.
=======

Now to further demonstrate my point you write this:

===
Yes, scientists are people! By some bizarre "reasoning" IDCers loooove to imply that it is therefore in principle impossible to model evolution without "intelligent" intervention.
===

Of course I said no such thing. If ever there was an evolutionary experiment aided by experimenter intervention, this one is it. And if ever there were high claims made that are unjustified, they are in this paper. Unfortunately this paper is typical, and the fact that you and the other evolutionists rush to its defense further demonstrates this.

But none of this means modeling evolution with intervention is impossible and I said no such thing. For a professor such as yourself to make these false, rationalistic, charges helps to illustrate how evolutionary thinking works.

34. This comment has been removed by the author.

35. Eocene wrote:

If you disagree, then provide us an example of how an informational code containing encoded plans and ideas with purpose and intent morphs from nothing more than chemcials and physics ???

Here, Eocene gives a perfect example of smuggling in some assumptions not present in the actual theory of ID.

If we truly assume nothing more than an abstract designer, we can't assume the genome remotely contains the encoded plan, ideas or purpose that the actually designer had in mind. Why? Because this would require the assumption that the designer actually has the ability to successfully encode it's plans, ideas or purpose in a particular medium, including "chemicals and physics."

For example, I can't speak, read or write Russian, which means any attempt to express my plans, ideas or purpose would result in gibberish. Of course, I could always take the time to learn Russian, but this is only possible since I the Russian languages is sufficiently developed and defined so I can express my particular plans, ideas and purpose in a reasonably accurate way and I actually exhibit the ability to learn it. However, it's not sufficiently clear this is actually the case with an abstract designer and the genome.

To use another example, there are many solders returning from combat in the middle east with missing limbs. As designers, our purpose is to return this solders to as much of a normal life as possible. This has led us to research on how salamanders exhibit the ability to regrow missing limbs, including skin, bones an even nerves. The problem is, despite being designers, we do not know how to encode this plan into the human genome.

36. Continued:

We can say the same in other domains. We have lofty goals and plans of how we could create organisms from scratch or even nanotechnology to reach important goals in the fields of biology, energy, etc. Again the problem is that we lack the ability to actually encode our goals into these mediums.

Furthermore, if the genome actually represents the designer's plan, ideas or purpose, this would imply that the designer decided to give salamanders the ability to re-grow limbs but not human beings. We simply have no reason to assume that some abstract designer would intentionally design us with more advanced brains, which allow us to perform complex operations with our appendages, yet intentionally exclude the ability to regrow them.

So, for the sake of argument, even if we assume an abstract deigned was involved, it's unclear how you can assume the genome actually contains the encoded plan, ideas or purpose that the designer had in mind. You must smuggle in assumptions about the designer which are absent from the theory that ID is attempting to present as science.

Even if we assume some level of competence, abstract design could be represented by more than one designer. Unless these designers agree, the actual outcome may not represent the plans, ideas or purpose of either of them. Or, as an agent that makes choices, the designer could have chosen to be "hands off" in regards to the particular kind of life we observe, despite being competent enough to bring about a specific result.

Does this mean it's logically impossible a designer was involved? Of course not. But given the lack of an explanation along with the specific observations we've currently made, an objective approach the subject undeniably leads us to the particular conclusion we should discard this theory, even it ended up being true in reality.

In other words, in science, we accept the fact that we might be wrong for the right reasons (due to strictly following the scientific method) rather right for the wrong reasons (making exceptions due to mere intuition, conflicts with religious or personal beliefs, incredulity, etc.)

37. Neal: your problem is assuming you know what the notation Zach originally used means. You don't. The braces show which organisms group together. Everything inside each pair is a group in itself.

This: {cat, lion}

Means: "Cats and lions group together"

This: {dolphin, {cat, lion}}

Means: "The group 'Cats and lions' groups with dolphins" or alternately (and just as accurately): "Cats and lions and dolphins group together"

And this: {fish {dolphin, {cat, lion}}}

Means: "The group 'Dolphins and cats and lions' groups with fish"

Get it? It means and has always meant exactly what Zach has said. Why do it that way? Because each sub-group is NESTED inside another, larger group. The notation is a visual representation of the fundamental relationship.

For some reason, you just decided it didn't mean that. Well, it did.

38. "If ever there was an evolutionary experiment aided by experimenter intervention, this one is it."

I see no intervention beyond the experimental setup. A system is made, and allowed to run. Random input plus selection yielded evolved 'genetically' encoded behaviors. Do you have evidence the results were fixed?

For example, in the altruism in kin vs. non-kin selection experiment, altruism was not a programmed behavior. It evolved out of necessity in kin only.

39. Dave Mullenix:

===
So if we start with an existing organism, make some random changes to some of their offspring's DNA, let the new organisms try to make a living and some of the new organisms turn out to be better at making a living than their parents, it's not evolution?

You really don't understand evolution at all, do you?
===

No, I'm afraid the problem is I do understand evolution. Evolution is not people creating a sophisticated environment with advanced sensors, actuators, neural network software, topology redesign instructions, artificial selection, and so forth. That does not reflect the biological world nor the evolutionary hypothesis that all of biology just happened to arise on its own, somehow. Nothing about this research was an accident or fluke. The results are repeatable and a consequence of a pre arranged environment specifically designed to produce the desired behaviors. I'm sure they have plenty of technical issues and difficulties they had to work through to obtain their results. If those sensors, actuators, computers and hardware were left alone in the lab, I guarantee you nothing interesting would have occurred.

40. didymus said, "Because each sub-group is NESTED inside another, larger group. The notation is a visual representation of the fundamental relationship."

Zachriel represented sets but it wasn't a nested hierarchy. By definition a nested hierarchy means that a subset must be fully contained within the parent. In what meaningful way are lions and cats fully contained within dolphins? If he wants to from groups that's another discussion, but nested hierarchies have rules.

41. "If those sensors, actuators, computers and hardware were left alone in the lab, I guarantee you nothing interesting would have occurred."

If a population mice are shot to Mars without food, air or water, I guarantee you they won't evolve.

Darwin FAIL!

But seriously, this paper shows, in the established systems, that random input plus selection creates useful information in the form of 'genetically' encoded behaviors. No intervention past the setup-just selection based on pre-established criteria.

I do accept your analysis here:

"Clearly Darwin’s idea is mathematically tractable. That is, if fitness landscapes are relatively smooth and reasonably shaped, and if an initial population just happens to appear, and if biological variation just happens to arise and accumulate, and if populations do not resist such change, then of course species can evolve to new designs."

So, I await proof (from a moderate empiricist standpoint?!) that:

1) All fitness landscapes are unreasonably shaped, or
2) Life (a population) does not exist, or
3) Biological variation does not arise and accumulate, or

Seems like we have great data in support of, and no falsification for all 4. I, therefore, accept your conclusion: "then of course species can evolve"

42. They aren't Neal. Why in the hell do you think dolphins are a set? They're an element of a set.

This one:

{dolphins,{cat,lion}}

See the comma? That separates dolphins from {cat,lion}. The comma indicates a branching: dolphins are on one. Cats and lions are on another. The outer braces indicate that they're all mammals (I hope I'm not spoiling the surprise). This is not that hard. Sheesh.

43. Hunter:

Secondly, rationalists have a difficult time thinking outside the box of rationalism. When they hear an empiricist, they project their rationalism onto his position.

“Rationalist” seems to have become the epithet du jour here. The Free Dictionary online defines:

Rationalist - someone who emphasizes observable facts and excludes metaphysical speculation about origins or ultimate causes.

That can't be right. What is your definition of rationalism and rationalist?

44. Thorton will remember our little experiment of few months ago. We should get our hands dirty again:

I have lots of electronic components at home and at my work desk so
lets make computer (or something like that) in the bag.

Lets fill 30% of the bag with tiny logic gates (simple rules for electron flow) and keep them floating. Attach little magnets to gates so they can self assemble (simple rules for self assembly ). Also, let's put small batteries in the bag and attach little magnets to them as well. Put in there tiny memory chip, too( lets not forget little magnets ).

Slosh the bag.

When can we expect computer to self assemble?

45. Zachriel: For clarity, here are the sets:

A = {cats, lions}
B = {dolphins, cats, lions}
C = {fish, dolphins, cats, lions}

Neal Tedford: Arranging them together with group names like this renders an obvious nested hierarchy.

Yes.

Neal Tedford: You see relationships, but technically anything can be grouped together in this ABC manner and then represented by a nested hierarchy.

Of course, but we're not discussing arbitrary groupings.

Neal Tedford: When you talk about "one reasonable way to biologically classify fish, dolphins, cats and lions" you did not mention which classification system you are using.

Yes, we did mention the classification system: the most parsimonious grouping based on observable biological traits.

Neal Tedford: In what meaningful way are lions and cats fully contained within dolphins?

{dolphins, {cats, lions}}

That doesn't mean that cats and lions are contained within dolphins. It means F = {cats, lions} is contained within M = {dolphins, {cats, lions}}. (A pedant would point out that {cats} is not actually an element of set M, but it's a nested hierarchy in either case.)

Please use the wordy version for clarity.

-
Which two of these three group form the most parsimonious grouping based on observable biological traits; fish, dolphin, cat?

Do the leaves on a tree when grouped by branch and stem form a nested hierarchy?

46. Hmm. Are we in the wrong thread?

47. And yet Christian schools remain at the top or near the top,,, Yet despite your dissing of all things 'spiritual,,,

Little known by most people is the fact that almost every, if not every, major branch of modern science has been founded by a scientist who believed in Christ:

Christianity and The Birth of Science - Michael Bumbulis, Ph.D
Excerpt: Furthermore, many of these founders of science lived at a time when others publicly expressed views quite contrary to Christianity - Hume, Hobbes, Darwin, etc. When Boyle argues against Hobbe's materialism or Kelvin argues against Darwin's assumptions, you don't have a case of "closet atheists."
http://ldolphin.org/bumbulis/
http://www.tektonics.org

A Short List Of The Christian Founders Of Modern Science
http://www.creationsafaris.com/wgcs_toc.htm

The Origin of Science
Excerpt: Modern science is not only compatible with Christianity, it in fact finds its origins in Christianity.
http://www.columbia.edu/cu/augustine/a/science_origin.html

In fact science itself is not possible without God:

This following site is a easy to use, and understand, interactive website that takes the user through what is termed 'Presuppositional apologetics'. The website clearly shows that our use of the laws of logic, mathematics, science and morality cannot be accounted for unless we believe in a God who guarantees our perceptions and reasoning are trustworthy in the first place.

Proof That God Exists - easy to use interactive website
http://www.proofthatgodexists.org/index.php

Materialism simply dissolves into absurdity when pushed to extremes and certainly offers no guarantee to us for believing our perceptions and reasoning within science are trustworthy in the first place:

Dr. Bruce Gordon - The Absurdity Of The Multiverse & Materialism in General - video
http://www.metacafe.com/watch/5318486/

,,, perhaps you prefer absurdity to rationality?

48. Pedant:

===
Rationalist - someone who emphasizes observable facts and excludes metaphysical speculation about origins or ultimate causes.

That can't be right. What is your definition of rationalism and rationalist?
===

Right, that is more of a colloqial definition that equates a "rationalist" with rational thinking, as opposed to irrational thinking. And of course any use of metaphysics must be irrational, so a rationalist is one who exludes such speculation. That definition is erroneous--an unfortunate holdover from the failed, yet still influential, positivism of the 20th c.

When I use the term rationalist or rationalism, I am using it to represent thinkers who emphasize and rely on a priori axioms. That is, they think their way through a problem to a considerable extent, and when they incorporate observations it is more typical that they interpret the the observations according to their theoretical framework.

Empiricism, on the other hand, attempts to minimize the committment to a priori assumptions, and instead attempts to be more flexible in following the data. As a consequence, it has a weaker framework, and indeed a weaker philosophy of science, than rationalism.

Rationalists are dead certain of all kinds of things whereas the empiricist is thinking, "well, maybe, but maybe not ..."

Rationalism has a long history in theology and philosophy, but also in science as well. In fact, whenever scientists work with data, issues of rationalism versus empiricism inevitably, if not explicitly, arise.

A confusion that can arise is that movements, and even individuals, can be both rationalists and empiricists, depending on the particular aspect or subject. Hume, for instance, is generally known as an empiricist, yet his promotion of evolutionary thinking was pure rationalism.

In general, evolutionary thought is one long rationalistic argument. Going back centuries, thinkers have made various theological and philosophical claims that mandated a naturalistic origins narrative, regardless of the data. The data have been pigeon-holed into that framework.

49. Eugen said...

When can we expect computer to self assemble?

At approximately the same we find a Creationist who doesn't have his head up his rectum and who understands evolutionary theory well enough to discuss it intelligently .

We have about 5 billion years or so left in the sun's life, so it's gonna be close.

50. bornagain77 said...

Little known by most people is the fact that almost every, if not every, major branch of modern science has been founded by a scientist who believed in Christ:

Well known by most people with even the slightest scientific understanding is the fact that the religious beliefs of those scientists had zero relationship to the technical content of their work.

I suppose if the Wright brothers had been Vegans we'd be getting the BA77 lecture about how heavier-than-air flight disproves the ability to eat meat.

51. Pedant:

Continuing:

===
Rationalist - someone who emphasizes observable facts and excludes metaphysical speculation about origins or ultimate causes.

That can't be right. What is your definition of rationalism and rationalist?
===

So when an empiricist engages the evidence a presents theoretical problems, he thinks he is on solid ground. After all, Theory X predicts Observation Y, and the empirical data contradict Y. Furthermore, reasonable explanations (eg, sensor failure) do not seem to be available. There is nothing particularly heroic or controversial here. The empiricist has made no high claims, just a simple analysis of the data and how it bears on the theory.

But the empiricist is not on solid ground. What he hasn't anticipated is that he has violated the rationalism behind the theory. Rationalism believes the axioms are true, therefore the theory that was necessiated by the axioms is true, therefore all evidence must support the theory. If it appears to be contradictory, then the observation must be interpreted differently, or the theory must be tweaked, or both. But the evidence is never interpreted as contradicting the theory.

In presenting the data in this way, the empiricist has allowed for the possibility that the theory might be false. This in turn, implies that the axioms might be false. And this is unacceptable.

52. CH,

Would you agree that it's possible to create a model of a bank account using either software, pen and paper, an abacus or even simply using your head?

Would you agree that one can update model of the account independent of the particular implementation selected? (example: withdrawing money from an ATM does not necessitate modifying the software running on the ATM or the software used by your bank)

And would you agree that, regardless what implementation used, adding and removing the same amounts to the account would should result in the same balance?

53. Let's be clear that some of these studies are not models of evolution, they _are_ evolution. Evolution is an abstract process, that, as Dr Hunter has shown, happens whenever certain conditions are met. The interesting question is whether those conditions ever happen during the history of the Earth.

It should also be said that evolution is not restricted in the ways that Dr Hunter asserts. The fitness function does not have to be smooth and continuous - his point of contact with the Newton-Raphson method. This is one of the benefits of genetic algorithms over optimization techniques that require continuity. Asexual reproduction does resemble hill climbing, but there is more to evolution than asexual reproduction. David Goldberg's group at the University of Illinois uses "deceptive functions" - the opposite of smooth and continuous, to create hard problems for GA algorithms to solve using sexual recombination and selection.

Do scientists know the solution in advance of running the experiment? No. Toy problems like Weasel have a target encoded in the fitness function, real problems do not. When Alvy Ray Smith programmed Tierra, he didn't know parasites would evolve, or evolve so quickly.

54. LIFE’S CONSERVATION LAW – William Dembski – Robert Marks – Pg. 13
Excerpt: Simulations such as Dawkins’s WEASEL, Adami’s AVIDA, Ray’s Tierra, and Schneider’s ev appear to support Darwinian evolution, but only for lack of clear accounting practices that track the information smuggled into them.,,, Information does not magically materialize. It can be created by intelligence or it can be shunted around by natural forces. But natural forces, and Darwinian processes in particular, do not create information. Active information enables us to see why this is the case.
http://evoinfo.org/publications/lifes-conservation-law/

55. So, ba77, does the natural world, minus life, just have no information in it whatsoever? Are there no non-biological patterns or constraints or energy gradients in and around the world? Like...I don't know..chemistry, physics, geology, climate, all that good stuff? If there is, what makes you think that can't be shunted around?

56. bornagain77-

This paper, and ones on AVIDA are freely available. Perhaps you'd like to let us know where the information was "smuggled in."

The robots start with randomized genomes. Following selection, their coded behaviors are anything but. I think information IS increasing, as a result of the non-random outputs of selection.

What do you think?

57. @ Eugen
http://en.wikipedia.org/wiki/Hoyle's_fallacy

58. didymos,
the second law:

Information and entropy – top-down or bottom-up development in living systems? A.C. McINTOSH
Excerpt: It is proposed in conclusion that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate.
http://journals.witpress.com/pages/papers.asp?iID=47&in=4&vn=4&jID=19

Evolution Vs. Thermodynamics - Open System Refutation - Thomas Kindell - video
http://www.metacafe.com/watch/4143014

"there are no known violations of the second law of thermodynamics. Ordinarily the second law is stated for isolated systems, but the second law applies equally well to open systems."
John Ross, Chemical and Engineering News, 7 July 1980

"The laws of probability apply to open as well as closed systems."
Granville Sewell - Professor Of Mathematics - University Of Texas El Paso
http://www.uncommondescent.com/intelligent-design/eseb-liitle-shop-of-fallacies/#comment-347999

The Capabilities of Chaos and Complexity: David L. Abel -
Null Hypothesis For Information Generation - 2009
To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: "Physicodynamics cannot spontaneously traverse The Cybernetic Cut:
http://www.mdpi.com/1422-0067/10/1/247/pdf
http://mdpi.com/1422-0067/10/1/247/ag

59. RobertC they have a artificial environment from the get go, if you cannot see the inherent problem of your extrapolation to the ability of evolutionary processes to generate programming that far exceeds the capacity of man to do as such, it seems you have let your preconcieved bias blind you to what is so blatantly obvious.

60. Somehow, when Dembski and Marks ran Avida themselves, they didn't see how they were 'smuggling' information in. You'd think that Dembski would have seen Marks frontloading the active information in, and reported the fact clearly in their paper.

"Mutation, fitness, and choosing the fittest of a number of mutated offspring [5] are additional sources of active information in Avida we have not explored in this paper." from http://evoinfo.org/papers/2009_EvolutionarySynthesis.pdf

It will be interesting to see Dembski and Marks prove that all the active information in the mutation process comes from an intelligent agent. Even when connected to random.org.

61. "Perhaps you'd like to let us know where the information was "smuggled in."

Don't you see, Robert, scientifically speaking, the simple fact that the information is there at all is proof that it was smuggled in. Because if it wasn't smuggled in, then it wouldn't be there being smuggled in to there where it was being smuggled into so that it could be there being smuggled into being there...smuggled...there...uh...being...

See! Perfectly logical!

62. Yeah, Didymos - the 2nd Law! Entropy increases! Once you mix stuff, it stays mixed. Go ahead, try mixing water and alcohol in a beaker. Can't separate them can you? Not even in an open system with a flame under the beaker and a condensing coil on top. Oh, wait...

And salt water - another great proof! Pour salt into the water in a beaker, you can't unmix it. Even in an open system, with a flame under the beaker, after the water evaporates, what's left, huh? Oh, wait...

Air, another great proof! Those molecules are mixed, baby! There's no way to separate them, even in an open system that cools the air down until it liquifies. Well, until some of it liquifies, and then cool it some more and then another part liquifies, and then... Oh, wait...

So, Didymos, I hope your convinced.

63. bornagain77 said...

RobertC they have a artificial environment from the get go, if you cannot see the inherent problem of your extrapolation to the ability of evolutionary processes to generate programming that far exceeds the capacity of man to do as such, it seems you have let your preconcieved bias blind you to what is so blatantly obvious.

(rolls eyes and chuckles) I assume you think if scientists were modeling gravity to compute a space probe's trajectory they'd have to launch the computer into space to get valid results too.

64. Since you guys are so gun ho to have this as proof of evolution let's do a true test,,,

A true test would be to start with Robots with a rudimentary ability to navigate through the maze.

Now, randomly mutate and recompile the navigational source code, selecting, of course, only those copies which actually compile, and then select robots, using the new code, that have improved navigational ability..- SCheesman,,,

What do you guys think? You guys are claiming this trivial hill climbing solution is proof that programming that far exceeds man's ability can magically materialize,,, put your money where your mouth is and do it. I'm quite sure that Microsoft is not worried in the least that it will have to lay off even one programmer due to your 'proof' for the almighty power of evolution to generate astonishing levels of information.

65. bornagain77: Now, randomly mutate and recompile the navigational source code, selecting, of course, only those copies which actually compile, and then select robots, using the new code, that have improved navigational ability..- SCheesman

The biological equivalent would be assembling long random chains of amino acids to see if they would fold into the type of complex three-dimensional structure required to be functional.

66. BA77 said...

What do you guys think? You guys are claiming this trivial hill climbing solution is proof that programming that far exceeds man's ability can magically materialize,,, put your money where your mouth is and do it. I'm quite sure that Microsoft is not worried in the least that it will have to lay off even one programmer due to your 'proof' for the almighty power of evolution to generate astonishing levels of information.

NASA used genetic algorithms based on evolutionary processes to create these spacecraft antennas

NASA Automated Antenna Design

Where did the information for the antenna designs come from?

67. You mean like this?
http://www.cs.northwestern.edu/~fjs750/netlogo/final/mazerules.html

68. "A true test would be to start with Robots with a rudimentary ability to navigate through the maze.

Now, randomly mutate and recompile the navigational source code, selecting, of course, only those copies which actually compile, and then select robots, using the new code, that have improved navigational ability..- SCheesman"

Did you READ the paper? I pick publicly available ones for a reason. Generation 0 robots have nearly zero navigational ability, with random 'genomes'. All have their fitness scored, the best 'survive,' have variation/recombination added, and onto the next generation. By generation 100, they are cruising along very nicely.

69. And in the context of these robots, there isn't source code like C+ or something. They have simple I/O neural nets modulated with a 'genome':

"The robot was controlled by a neural network with eight sensory neurons, each assigned to one of the eight infrared distance sensors and two output motor neurons receiving weighted inputs from each of the eight sensory neurons and from the other output neuron. ... The resulting outputs, in the range [0,1], were used to control the rotation of the two wheels so that an output of 1 generated maximum rotation speed (8 cm/s) in one direction, an output of 0 generated maximum rotation speed (8 cm/s) in the opposite direction ....
The genome encoded the weights of the connections between neurons (2 x 9 + 2 = 20 connections) and of the thresholds (2) as binary numbers with eight bits for each value (22 times 8 = 176 genes)."

70. "Mutation, fitness, and choosing the fittest of a number of mutated offspring [5] are additional sources of active information in Avida we have not explored in this paper."

http://evoinfo.org/papers/2009_EvolutionarySynthesis.pdf

WAIT a MINUTE! The survival of fittest mutant offspring is a source of active information? Hmm....isn't there differential survival in nature all the time? So the 'information' intelligent design types are all excited about could really just be the product of non-random survival?

Information increases in natural selection.

Thanks Dembski and Marks!

71. Dr Hunter,

Thanks for taking the trouble to explain your thinking about rationalism vs empiricism.

When I use the term rationalist or rationalism, I am using it to represent thinkers who emphasize and rely on a priori axioms. That is, they think their way through a problem to a considerable extent, and when they incorporate observations it is more typical that they interpret the the observations according to their theoretical framework.

Some of this resembles the scientific method. Except it is my understanding that scientists interpret data in the light of working hypotheses, which can be distinguished from “a priori axioms” by their tentative nature. Interpreting data according to some kind of hypothetical framework seems essential in all aspects of experience. I hypothesize that I am not a brain in a vat and that my sense organs are informing me about a real world. Such a theoretical framework need not and cannot safely be a priori axiomatic or held without any possibility of being abandoned in the light of further experience. Are not all of our hypotheses always at risk of being invalidated by data? Does she love me? How can I tell? Is the defendant guilty? What is the evidence? Live and learn.

Empiricism, on the other hand, attempts to minimize the committment to a priori assumptions, and instead attempts to be more flexible in following the data. As a consequence, it has a weaker framework, and indeed a weaker philosophy of science, than rationalism.

If I am correct that one can’t interpret data without having some kind of hypothesis in mind, your empiricist would be helpless in interpreting data, and must be simply a clueless observer.

Rationalists are dead certain of all kinds of things whereas the empiricist is thinking, "well, maybe, but maybe not ..."

Since all of science is subject to correction, it appears that scientists are not rationalists by this rule.

A confusion that can arise is that movements, and even individuals, can be both rationalists and empiricists, depending on the particular aspect or subject. Hume, for instance, is generally known as an empiricist, yet his promotion of evolutionary thinking was pure rationalism.

That’s an interesting idea. Do you have some examples of Hume’s pro-evolution writings?

In general, evolutionary thought is one long rationalistic argument. Going back centuries, thinkers have made various theological and philosophical claims that mandated a naturalistic origins narrative, regardless of the data. The data have been pigeon-holed into that framework.

Pigeon-holed? That characterization might apply if a framework existed containing pigeon holes which fit the data better. Any suggestions for such a framework? Or does the echtst empiricist maintain inscrutability concerning the possible existence of alternative frameworks?

72. Hunter continued:

So when an empiricist engages the evidence a presents theoretical problems, he thinks he is on solid ground. After all, Theory X predicts Observation Y, and the empirical data contradict Y. Furthermore, reasonable explanations (eg, sensor failure) do not seem to be available. There is nothing particularly heroic or controversial here. The empiricist has made no high claims, just a simple analysis of the data and how it bears on the theory.

So the empiricist functions exclusively as a critic, with nothing constructive to add to the discussion.

In presenting the data in this way, the empiricist has allowed for the possibility that the theory might be false. This in turn, implies that the axioms might be false. And this is unacceptable.

On the contrary, scientific theories, of which evolution is a case in point, are made to be falsified. Informed criticism is welcome. Uninformed criticism is subject to rebuttal and correction, and we thank you for providing this forum for us to state our views.

73. evolution does not qualify for a scientific theory for it refuses to set any standard for falsification:

Michael Behe on Falsifying Intelligent Design - video

A Primer on the Tree of Life - Casey Luskin - 2009
Excerpt: The truth is that common ancestry is merely an assumption that governs interpretation of the data, not an undeniable conclusion, and whenever data contradicts expectations of common descent, evolutionists resort to a variety of different ad hoc rationalizations to save common descent from being falsified.
http://www.discovery.org/a/10651

Seeing Ghosts in the Bushes (Part 2): How Is Common Descent Tested? - Paul Nelson - Feb. 2010
Excerpt: Fig. 6. Multiple possible ad hoc or auxiliary hypotheses are available to explain lack of congruence between the fossil record and cladistic predictions. These may be employed singly or in combination. Common descent (CD) is thus protected from observational challenge.
http://www.evolutionnews.org/2010/02/seeing_ghosts_in_the_bushes_pa.html

This following article reveals how evolutionists avoid falsification from the biogeographical data of finding numerous and highly similar species in widely separated locations:

More Biogeographical Conundrums for Neo-Darwinism - March 2010
http://www.evolutionnews.org/2010/03/sea_monkeys_are_the_tip_of_the.html

74. as far as the Darwinian claim that purely material processes have the ability to generate highly complex logical information, I suggest that, rather than using the trivial and highly argumentative examples that show 'hill climbing' in a well defined search space, just falsifying this one null hypothesis would suffice to silence critics and win a Nobel:

The Capabilities of Chaos and Complexity: David L. Abel - Null Hypothesis For Information Generation - 2009
To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: "Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration." A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
http://www.mdpi.com/1422-0067/10/1/247/pdf
Can We Falsify Any Of The Following Null Hypothesis (For Information Generation)
1) Mathematical Logic
2) Algorithmic Optimization
3) Cybernetic Programming
4) Computational Halting
5) Integrated Circuits
6) Organization (e.g. homeostatic optimization far from equilibrium)
7) Material Symbol Systems (e.g. genetics)
8) Any Goal Oriented bona fide system
9) Language
10) Formal function of any kind
11) Utilitarian work
http://mdpi.com/1422-0067/10/1/247/ag

75. Sorry BA^77, there is no Nobel for responding to word salad.

76. A little simpler for you then David, how about you guys show me just one code originating from material processes?

The DNA Code - Solid Scientific Proof Of Intelligent Design - Perry Marshall - video
http://www.metacafe.com/watch/4060532

"In the last ten years, at least 20 different natural information codes were discovered in life, each operating to arbitrary conventions (not determined by law or physicality). Examples include protein address codes [Ber08B], acetylation codes [Kni06], RNA codes [Fai07], metabolic codes [Bru07], cytoskeleton codes [Gim08], histone codes [Jen01], and alternative splicing codes [Bar10].
Donald E. Johnson – Programming of Life – pg.51 - 2010

"A code system is always the result of a mental process (it requires an intelligent origin or inventor). It should be emphasized that matter as such is unable to generate any code. All experiences indicate that a thinking being voluntarily exercising his own free will, cognition, and creativity, is required. ,,,there is no known law of nature and no known sequence of events which can cause information to originate by itself in matter. Werner Gitt 1997 In The Beginning Was Information pp. 64-67, 79, 107."
(The retired Dr Gitt was a director and professor at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt, Braunschweig), the Head of the Department of Information Technology.)

“Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible” Donald E. Johnson – Bioinformatics: The Information in Life

Biophysicist Hubert Yockey determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the optimal universal genetic code that is found in nature. The maximum amount of time available for it to originate is 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that is optimal. Put simply, natural selection lacks the time necessary to find the optimal universal genetic code we find in nature. (Fazale Rana, -The Cell's Design - 2008 - page 177)

77. It's really quite amusing to watch Darwinists here chasing their tails with their ubiquitous lack of reasoning skills and twisted logic.

The funniest thing is that if Darwinian evol. were true, then all of the evolutionists thoughts are mechanical.
They think what they do because of chance and necessity, i.e. because of electro-chemical action in their brains, given whatever environmental stimuli their brains are being subjected to.

This of course means that, according to their own inane theory, THEY are the robots.

Naturalistic evolution has clear consequences that Charles Darwin understood perfectly. 1) No gods worth having exist; 2) no life after death exists; 3) no ultimate foundation for ethics exists; 4) no ultimate meaning in life exists; and 5) human free will is nonexistent. ~ William Provine

This means of course, that none of these Darwimpers even chose to believe in neoDarwinian evolution.
It was inevitable and cannot be changed without further mutations, perhaps some brain surgery or maybe some further but opposite electro-chemical stimuli in their befuddled brains.

So why are they here anyway? Duh!

Naturalism cuts its own throat.

78. LOL! Gary the little IDiot yap dog crawls out from hiding under the sofa just long enough to piddle on the carpet.

79. I didn't see anything in the articel about "mutations" that are harmfull or fatal to the robots. If the only mutations that were allowed were either neutral or good, then the only direction they could "evolve" is towards more fitness. Please correct me if I'm wrong.

80. bornagain77 said...

A little simpler for you then David, how about you guys show me just one code originating from material processes?

The spectrum of starlight is a code in the same way DNA is a code. The absorption lines in stellar spectra carry coded information about the chemical elements and molecular compounds that make up the stars. In both the starlight and DNA cases, 'code' merely means that inputs at one end are mapped by physical processes onto results at the other end with no intelligent intervention anywhere in the process.

Of course IDiots like to equivocate over the DNA definition of 'code' with the completely different computer software definition of 'code'.

81. Dave Mullenix:

===
So if we start with an existing organism, make some random changes to some of their offspring's DNA, let the new organisms try to make a living and some of the new organisms turn out to be better at making a living than their parents, it's not evolution?

You really don't understand evolution at all, do you?
===

No, I'm afraid the problem is I do understand evolution. Evolution is not people creating a sophisticated environment with advanced sensors, actuators, neural network software, topology redesign instructions, artificial selection, and so forth. That does not reflect the biological world nor the evolutionary hypothesis that all of biology just happened to arise on its own, somehow. Nothing about this research was an accident or fluke. The results are repeatable and a consequence of a pre arranged environment specifically designed to produce the desired behaviors. I'm sure they have plenty of technical issues and difficulties they had to work through to obtain their results. If those sensors, actuators, computers and hardware were left alone in the lab, I guarantee you nothing interesting would have occurred.
===

You don't understand modeling either.

82. natschuster said...

I didn't see anything in the articel about "mutations" that are harmfull or fatal to the robots. If the only mutations that were allowed were either neutral or good, then the only direction they could "evolve" is towards more fitness. Please correct me if I'm wrong.

You are misunderstanding the whole concept. Try reading the paper again

"The corresponding neural network is connected to the sensors and motors of the robot and the resulting behaviour of the robot is measured according to the fitness function. The genomes of the individuals that had the worst performance are discarded from the population (symbolically thrown in a dustbin) whereas the genomes of the best individuals are paired and crossed over with small random mutations to generate new offspring (the process of selective reproduction is symbolically shown to occur in a “mother robot”). After several generations of selective reproductions with mutations, robots display better or novel behaviours."

The mutations in the logic in each generation were completely random with respect to the robot's fitness. Ones with detrimental performance were killed off, i.e not allowed to reproduce. Ones that showed neutral or beneficial results were allowed to live and pass on their genes. That's differential reproductive success, also called natural selection in the real biological world. The whole process allowed the beneficial mutations to accumulate and complex behavior to evolve, just as happens in the real biological world.

83. Dave Mullenix:

"You really don't understand evolution at all, do you?"

and

"You don't understand modeling either."
======

Bold condescending statements like this don't exactly answer the questions Dave.

84. Thorton:

What do the scientists and computer programmers in the picture represent ???

Blind undirected forces or Intelligent design ???

85. “No, I'm afraid the problem is I do understand evolution. Evolution is not people creating a sophisticated environment with advanced sensors, actuators, neural network software, topology redesign instructions, artificial selection, and so forth. That does not reflect the biological world nor the evolutionary hypothesis that all of biology just happened to arise on its own, somehow. Nothing about this research was an accident or fluke. The results are repeatable and a consequence of a pre arranged environment specifically designed to produce the desired behaviors. I'm sure they have plenty of technical issues and difficulties they had to work through to obtain their results. If those sensors, actuators, computers and hardware were left alone in the lab, I guarantee you nothing interesting would have occurred.“

I will presume that this is a sincere objection and not just one of the usual creationist rhetorics and answer it: You should not read into this experiment more than it says. Experiments can always only demonstrate aspects of the ToE. As it would be fair to criticizes the authors for claiming that their research is the ultimate prove of the ToE, as it is equally unjustified to demand any single piece of research to actually do so; a common and extremely silly tactic of creationists.

Thus I am curious how an experiment would need to be set up so that you would accept it as evidence for the ToE.

86. Second Opinion:

"Thus I am curious how an experiment would need to be set up so that you would accept it as evidence for the ToE."
======

That's not his problem. It's yours. Your religious dogma insists there is no guidance, directedness, goals, purpose or intent on anything evolution does. His belief doesn't say this.

Set up an actual honest experiment without rigging the stupid thing to prove that such blind unguided forces accomplish anything even remotely intelligently designed without having to lie and cheat your way through a rigged metaphysical explanation without hard material proofs.

If that's too tough an assignment, then perhaps you should find a new Church that doesn't require blind faith.

87. Thorton and his buddies

Eugen said...

When can we expect computer to self assemble?

At approximately the same we find a Creationist who doesn't have his head up his rectum and who understands evolutionary theory well enough to discuss it intelligently .

We have about 5 billion years or so left in the sun's life, so it's gonna be close.

Obviously you and your buddies have nothing logical to dicsuss about it. You and your friends post a lot but do not say much.

I will not fall into your insulting trap.

88. Eocene

Set up an actual honest experiment without rigging the stupid thing to prove that such blind unguided forces accomplish anything even remotely intelligently designed without having to lie and cheat your way through a rigged metaphysical explanation without hard material proofs.

I offered them simple experiment earlier but what I received was insults. I think it's their level of discussion.

89. Eugen: I offered them simple experiment earlier but what I received was insults.

Computer parts aren't amino acids.

What if we were to assemble long random chains of amino acids? What are the odds they will fold into the complex three-dimensional shapes necessary for biological function?

90. Eugen said...

I offered them a simple minded Creationist strawman with no connection to reality earlier but what I received was insults. I think it's their level of discussion.

Fixed it for you Eugen. Your original posting received exactly the gravitas it deserved.

91. Eugen:

"I offered them simple experiment earlier but what I received was insults. I think it's their level of discussion."
=====

They aren't interested because they know without admitting it, there are embarassing flaws that expose their figurative unterhosen. But as far as the insults and foul language ???, you have to understand this is a major part of their religious beliefs and divine Darwin given right. It's a genuine identifying mark of who and what they are. The sick thing is they are proud of it.
------

Zachriel:

"Computer parts aren't amino acids."
======

So what ??? You find it perfectly acceptable when you think a intelligently designed computer simulation rigged by some of your religious leaders for a specific biased outcome gives the appearance of proving your point. Why can't he use it then ???
------

Zachriel:

"What if we were to assemble long random chains of amino acids?"
======

It's against the rules. You cannot assemble anything. Intelligent design not allowed. Let them self-assemble without purpose or intent and then show us proof that's what they did.
------

Zachriel:

"What are the odds they will fold into the complex three-dimensional shapes necessary for biological function?"
======

I must have missed something here. Isn't that the point ??? What are the odds that raw materials of nothing but chemicals and physics will just self-assemble any code for the driving of controlled molecular machines for biological life function without any intelligent fingerprints like God's or your's ???

92. Eocene: It's against the rules. You cannot assemble anything. Intelligent design not allowed. Let them self-assemble without purpose or intent and then show us proof that's what they did.

Well, there's no complete theory of abiogenesis, if that's your point.

Zachriel: What are the odds they will fold into the complex three-dimensional shapes necessary for biological function?

Eocene: I must have missed something here.

The question concerned the odds of random amino acid chains folding into functional proteins.

93. Eocene said...

I must have missed something here.

Missing scientific points seems to be your major skill set, with mindless ranting being a close second.

What are the odds that raw materials of nothing but chemicals and physics will just self-assemble any code for the driving of controlled molecular machines for biological life function without any intelligent fingerprints like God's or your's ???

Based on all the accumulated evidence to date, the best estimate of the probability is 1.0

94. Oh boy. Thorton you are an angry little elf. Again, you just want to argue so go in front of the mirror and continue.

Zachriel

I think logic gate experiment would be easy to setup. It's easy to visualize and it should work in the similar way as amino acids you mentioned. Assembly of gates would possibly have some function like assembly of amino acids. Magnets would represent chemical bonds and affinities. To be fair we would have to balance magnetic force with forces of dielectric liquid motion where gates with magnets would be floating. That way bonds would stay for a while and hopefully assemble functional group.

Now, our computer needs one bit adder to start.... (first functional protein)

Interesting I would say. Think of these things sometimes.

95. Eocene: I think logic gate experiment would be easy to setup.

Go for it!

Meanwhile, what do you think the odds would be of random amino acid chains folding into functional proteins?

96. Eocene: I think logic gate experiment would be easy to setup. It's easy to visualize and it should work in the similar way as amino acids you mentioned.

Just trying to help.

97. Eugen saidEugen said...

Oh boy. Thorton you are an angry little elf. Again, you just want to argue so go in front of the mirror and continue.

Not at all. I just have little patience for scientifically ignorant yet arrogant nincompoops like you who do drive by preachings.

I think logic gate experiment would be easy to setup. It's easy to visualize and it should work in the similar way as amino acids you mentioned. Assembly of gates would possibly have some function like assembly of amino acids. Magnets would represent chemical bonds and affinities. To be fair we would have to balance magnetic force with forces of dielectric liquid motion where gates with magnets would be floating. That way bonds would stay for a while and hopefully assemble functional group.

Why do you think that bit of stupidity would accurately model evolution?

First off, populations evolve, not individuals.

Where is the selection - differential reproductive success - in your model?

Where is the imperfect reproduction process that introduces variation for selection to act on?

Where are the heritable traits maintained from generation to generation?

IDiots like you don't even know enough about the actual science to make up a half-decent strawman, let alone an actual scientific model.

98. Zachriel:

"Well, there's no complete theory of abiogenesis, if that's your point."
=====

So evolution has no foundational leg to stand on other than blind faith.

Thanks
-----

Zachriel:

"The question concerned the odds of random amino acid chains folding into functional proteins."
=====

But isn't that the point, minus a biasedly rigged computer simulation ??? The problem is those mythical proteins need instructions to assemble into logical purposed goal driven functions. Thus far you have all outlawed Crick's "Central Dogma of Molecular Biology" on this. Guess we all know why!!!
-----

Thorton:

"Based on all the accumulated evidence to date, the best estimate of the probability is 1.0"
=====

We don't want probability, you folks hate that anyway unless you deem it to be in your favour. Just show us the pre-biotic Test Tube facts of that code magic just happening.

99. Zachriel:

"Eocene: I think logic gate experiment would be easy to setup.

Go for it!

Meanwhile, what do you think the odds would be of random amino acid chains folding into functional proteins?"

and

"Eocene: I think logic gate experiment would be easy to setup. It's easy to visualize and it should work in the similar way as amino acids you mentioned.

Just trying to help."
=====

I think you meant to quote Eugen. I never said that.

100. BA^77,

Read up on the stereochemical hypothesis and the papers of Michael Yarus in this area. RNA triples map to amino acids directly in some cases. The basics of the code is just the chemistry, the shapes of these different molecules.

(BTW, you can call me 'Nak' if it is more familiar.)

101. Eocene: So evolution has no foundational leg to stand on other than blind faith.

That's like saying Newton can't propose a theory of how matter interacts without knowing the origin of matter. We know how life evolves, even if we still have questions about its origin.

Zachriel: The question concerned the odds of random amino acid chains folding into functional proteins.

Eocene: The problem is those mythical proteins need instructions to assemble into logical purposed goal driven functions.

You didn't answer the question, but it might be better directed at Eugen.

102. Eocene said...

Thorton: "Based on all the accumulated evidence to date, the best estimate of the probability is 1.0"
=====

We don't want probability,

Then why did you specifically ask for it?

Eocene: "What are the odds that raw materials of nothing but chemicals and physics will just self-assemble any code for the driving of controlled molecular machines for biological life function without any intelligent fingerprints like God's or your's ???"

'Odds' and 'probability' aren't the identical number BTW, but they both are mathematical representations of the the same thing.

103. Zachriel:

"That's like saying Newton can't propose a theory of how matter interacts without knowing the origin of matter."
======

Maybe you should go back, read and study what Newton revealed about many major religious doctrinal beliefs he requested be publised after his death. He wrote more about religious matters than he did with science, many of which agree with things you no doubt believe.
-------

Zachriel:

" We know how life evolves, even if we still have questions about its origin."
=====

No you don't. You've never once proven how mechanisms are undirected, lucky, chanced and magically by nothing with purpose or intent the way your original Dogma demands. Instead you hijack intelligent informational systems purposely directing molecular machines towards goal driven outcomes which is nothing more than evolutionary heresy to your Church leaders.

104. Thorton:

"'Odds' and 'probability' aren't the identical number BTW, but they both are mathematical representations of the the same thing."
=====

Facts Thorton, not probability of a myth/fable coming true.

105. Go for it!

November 5, 2010 7:45 AM
---
Zach

I'm probably one of few "IDiots" (to use name Thorton gave me) to take up on Miller's evolving mouse trap example in his attempt to refute Behe's irreducibly complex trap. Miller said mouse trap started as a simple bent wire. He gives nice pictures and goes on how it evolved step by step into more complex mouse trap. Guess what: while Thorton was probably throwing tantrums I found piece of solid wire, took hammer and started to make Miller's trap from his first example. You would not believe how hard is to make bent wire trap even with all of my precise hits. I learned that you have to make lots of excuses to your wife if you are going to hammer for hours in the garage. Also, I learned that if you just need bent wire not much is critical. OTOH many things are critical if you need simplest bent wire that will function as a mouse trap. Material, radius, gap, force applied….

I think Miller should've picked different example.

---
Meanwhile, what do you think the odds would be of random amino acid chains folding into functional proteins?
---

Excellent question!
What do you think the odds would be of random gates forming one bit adder?

Maybe we'll answer it in one of the future posts.

106. Eugen said...

I'm probably one of few "IDiots" (to use name Thorton gave me) to take up on Miller's evolving mouse trap example in his attempt to refute Behe's irreducibly complex trap. Miller said mouse trap started as a simple bent wire. He gives nice pictures and goes on how it evolved step by step into more complex mouse trap.

Anyone clueless enough to not understand a simple analogy like Miller used deserves the title of IDiot. Anyone who thinks a good test of evolution is "put a bunch of electronic components in a bag, shake it, and see if a computer spontaneously assembles" might as well be wearing a big sign saying CAUTION! MORON NOT WORTH TRYING TO CONVERSE WITH.

107. Zachriel

ME: "When you talk about "one reasonable way to biologically classify fish, dolphins, cats and lions" you did not mention which classification system you are using. "

---

Zachriel said, "Yes, we did mention the classification system: the most parsimonious grouping based on observable biological traits."

-----

That's basically what the various biological classification systems do, with the newer ones taking on an evolutionary view rather than the Linnaeus method.

So what classification system do you favor?

... Linnaeus? Haeckel? Chatton? Copeland? Wittaker? Wosse?, Cavalier-Smith? Other?

A cladogram is not a nested hierarchy. When you sum up the elements (leaves, nodes, species) you have a nested hierarchy, but technically you can do that with anything. Such a nested hierarchy in itself confirms nothing about evolution. So bring out your next point on nested hierarchies already.

Different algorithms build their cladograms based on their different definitions of what is best. The results are not singular and unique.

Looking at the panoply of characteristics of a Ford F450 Truck, is it best to group it with a Chevy Impala or a Ford F350 Truck?

108. Zachriel: That's like saying Newton can't propose a theory of how matter interacts without knowing the origin of matter.

Eocene: Maybe you should go back, read and study what Newton revealed about many major religious doctrinal beliefs he requested be publised after his death.

You didn't answer the objection. We can have a workable scientific theory of how matter interacts without knowing the origin of matter. Similarly, we can have a workable scientific theory of how life evolves without knowing the origin of life.

Eocene: No you don't. You've never once proven how mechanisms are undirected, lucky, chanced and magically by nothing with purpose or intent the way your original Dogma demands.

That would require looking at the scientific evidence, something you have repeatedly refused to do.

109. Eugen: Do not encourage me ,please.

No, really. Go for it. Take a few mole of electronic components and see what happens. Let us know what you find.

110. Neal Tedford: So what classification system do you favor?

You've been answered: the most parsimonious grouping based on observable biological traits.

Neal Tedford: A cladogram is not a nested hierarchy.

Neal Tedford: When you sum up the elements (leaves, nodes, species) you have a nested hierarchy, ...

Yes. Now you have it. The leaves on a tree form a nested hierarchy when grouped by branch and stem.

Neal Tedford: ... but technically you can do that with anything.

You can arbitrarily arrange things into trees or nested hierarchies, but we're not talking about an arbitrary arrangement.

Neal Tedford: Such a nested hierarchy in itself confirms nothing about evolution.

We'll get to that. But so far we haven't agreed on the most parsimonious grouping based on observable biological traits of fish, cat and dolphin.

Neal Tedford: Different algorithms build their cladograms based on their different definitions of what is best. The results are not singular and unique.

Resolution can be a problem, especially for very ancient or very rapid divergences. This is not unexpected, but we're not up to discussing theory yet. You still won't admit that there is only one reasonable way to group fish, dolphins and cats based on biological traits.

Neal Tedford: Looking at the panoply of characteristics of a Ford F450 Truck, is it best to group it with a Chevy Impala or a Ford F350 Truck?

Good example to show the difference between grouping artifacts and organisms. We might group automobiles first by maker. Or we might group by type first; truck, car, motorcycle. These are each reasonable ways to categorize automobiles.

With organisms, though, we have a different story. We might group fish, dolphins and cats by swimming or walking, but a closer look reveals that these differences are overwhelmed by the vast majority traits shared by dolphins and cats, with fish in the out-group. And no one with even a rudimentary knowledge of biology would disagree. Yet you can't bring yourself to say so.

111. Poof! Oh oh here comes adder ! What the heck do we do with it now?

Let me translate it for you.

Poof! Oh oh here comes protein ! What the heck do we do with it now?

112. Zachriel said, "You can arbitrarily arrange things into trees or nested hierarchies, but we're not talking about an arbitrary arrangement."

That's not the point. When you sum the elements together, it is what it is and such an arrangement in itself shows nothing about similarity or not.

---

You said, "You still won't admit that there is only one reasonable way to group fish, dolphins and cats based on biological traits."

--

You need to be more specific about what kind of grouping you mean for fish, dolphins and cats. Just clarify what grouping you would call them under your classification system. You don't need to be elusive to bring out your point as I already know where you are headed with it. I'm interested in the specifics of your hypothesis.

You said, "With organisms, though, we have a different story. We might group fish, dolphins and cats by swimming or walking, but a closer look reveals that these differences are overwhelmed by the vast majority traits shared by dolphins and cats, with fish in the out-group. And no one with even a rudimentary knowledge of biology would disagree. Yet you can't bring yourself to say so. "

---

I think you feel this way because you have been fully immersed into evolutionary thinking. If you can categorize a Truck by maker, why not categorize life by biomes? They do. Categorizing a truck by maker is not looking at the parts or function of the truck. Look at similarity of parts and just answer the question, "Looking at the panoply of characteristics of a Ford F450 Truck, is it best to group it with a Chevy Impala or a Ford F350 Truck?"

You've gone down this unique nested hierarchy track for so long that you can't see the contradictions in what you said.

113. Eugen,
"Poof! Oh oh here comes adder ! What the heck do we do with it now?"

I think this point out a problem with your experimental design. A bag of floating circuit elements is cool, but if you are demanding a computer, or even an adder, you're adding the Designer element.

114. Cornelius:

"If ever there was an evolutionary experiment aided by experimenter intervention, this one is it."

So what? The experimenters mimicked the processes (selection and random mutation) thought to be important according to evolutionary theory. How is that different in principle from simulating the process in silico in an individual-based simulation, or from doing a numerical approximation of a stochastic differential equation?

You clearly implied the usual creationist canard that the involvement of intelligent designers in the experiment automatically rules out that the experiment can model a process without outside intervention.

You also ignored my quote from the paper demonstrating that the authors see their work as a modelling exercise demonstrating the capabilities of evolutionary processes - and not as direct evidence for biological evolution.

Disclosure: I collaborate with one of the authors on evolving neural networks.

115. you are demanding a computer, or even an adder

David

Yes ,looks like you understand where I 'm going. Even adder would be hard to see out of this. Another thing is what would decide this is adder and put it aside for whatever later. This "from ground up" system seems limited in creativity. It sucks in creativity.
I wonder what would be the difference if we would setup chemical bag ( I like to play with my bags as you can see).

Thorton did you calm down?

116. Eugen said...

E: Yes ,looks like you understand where I 'm going. Even adder would be hard to see out of this. Another thing is what would decide this is adder and put it aside for whatever later. This "from ground up" system seems limited in creativity. It sucks in creativity.
I wonder what would be the difference if we would setup chemical bag ( I like to play with my bags as you can see).

T: Anyone who thinks a good test of evolution is "put a bunch of electronic components in a bag, shake it, and see if a computer spontaneously assembles" might as well be wearing a big sign saying CAUTION! MORON NOT WORTH TRYING TO CONVERSE WITH.

Eugen, did you get your sign yet?

117. To wrap things up in posts like:

“Lets fill 30% of the bag with tiny logic gates (simple rules for electron flow) and keep them floating. Attach little magnets to gates so they can self assemble (simple rules for self assembly ). Also, let's put small batteries in the bag and attach little magnets to them as well. Put in there tiny memory chip, too( lets not forget little magnets ).

Slosh the bag.

When can we expect computer to self assemble?”

or

“That does not reflect the biological world nor the evolutionary hypothesis that all of biology just happened to arise on its own, somehow. Nothing about this research was an accident or fluke. The results are repeatable and a consequence of a pre arranged environment specifically designed to produce the desired behaviors. I'm sure they have plenty of technical issues and difficulties they had to work through to obtain their results. If those sensors, actuators, computers and hardware were left alone in the lab, I guarantee you nothing interesting would have occurred.“

if you are familiar with the topic you can immediately spot Hoyle's fallcay.

http://en.wikipedia.org/wiki/Hoyle's_fallacy

If someone uses Hoyle's fallacy there are two possibilities: Either you don't know enough about the theory of evolution. This can be solved by consulting a biology textbook or internet resources like http://www.talkorigins.org/indexcc/CF/CF002_1.html (talkorigins.org is usually helpful). If you have done so and still use Hoyle's fallacy you are either a moron or dishonest (a liar).

118. second opinion said

you are either a moron or dishonest (a liar).

Here we go again. You and Thorton will make a good team.
BTW me and Thorton always had this love-hate relationship…....except there was no love. I don't know what went wrong.

You see in my simple mind I can not jump from step 1 to step 765.I need to understand steps 2-10 first. So right now I'm stuck on step 2(or 3) and you guys can help me.

Therefore:

Step 2

what would decide this is adder and put it aside for whatever later

or translated for you

what would decide this is protein and put it aside for whatever later

119. Eugen,

I think there is value in understanding your experiment and in comparing it to what we know about the real world.

First, by going back to the level of elctronic components, it seems to me that your back in the world of abiogenesis vs evolution. I'm fine with that, as long as we know it. The discussion of robots and evolution leading from the OP assumes an initial population upon which traditionally understood evolution can operate.

As I understand your experiment, an intelligent agent is providing two different inputs. One is the design of the experiment, the floating gates, what are the magnetic strengths, etc. The other input is the act of sloshing.

Since this is your experiment, I assume these inputs don't bother you. This strikes me as essentially the fine tuning, TE position.

The comparisons are instructive. The energy coming in to the surface of the earth causes the growth of nucleotide chains. It does this by destroying short chains more often than longer chains. Therefore long chains survive and grow over time.

It is not clear that your sloshing will have a similar effect. It might, but I don't know enough about the design to say. If the components are down around the size where Brownian motion is important, then size will affect survival. So there are flavors of your experiment that might mimic biological chemistry, but other flavors would not.

So differential rates of survival gets you a little bit, when the differential survival is based on just physical principles. It isn't clear to me that the electrical activity of these linked components in your experiment can effect their differential survival. If the experiment is designed to allow these electrical interactions, I would say it is closer to modeling biological reality.

My earlier point about demanding an adder really is that if your experiment came to be dominated by op-amps, or low pass filters, it might still be demonstrating evolution. A soup of components doesn't have a goal of 'adder' or 'computer' unless you put it there. If you just mean adder and computer just as examples of circuits of a certain complexity, fine, but that is not clear to me.

120. second opinion said...

If someone uses Hoyle's fallacy there are two possibilities: Either you don't know enough about the theory of evolution. This can be solved by consulting a biology textbook or internet resources like http://www.talkorigins.org/indexcc/CF/CF002_1.html (talkorigins.org is usually helpful). If you have done so and still use Hoyle's fallacy you are either a moron or dishonest (a liar).

Or both. Don't underestimate Creationists' ability to multi-task.

121. Eugen said...

You see in my simple mind I can not jump from step 1 to step 765.I need to understand steps 2-10 first. So right now I'm stuck on step 2(or 3) and you guys can help me.

We can fix ignorance, but we can't fix stupid.

There are plenty of good reference sites online to help with the ignorance part.

UC Berkley: Understanding Evolution

Try reading and learning, then you'll understand why ideas like

First off, populations evolve, not individuals.

Where is the selection - differential reproductive success - in your model?

Where is the imperfect reproduction process that introduces variation for selection to act on?

Where are the heritable traits maintained from generation to generation?

Or stay an ignorant git. You'll certainly have plenty of company with the other IDCer posting here.

122. Neal Tedford: You need to be more specific about what kind of grouping you mean for fish, dolphins and cats.

Remember, we're looking for the most parsimonious grouping based on objective biological traits.

Neal Tedford: Just clarify what grouping you would call them under your classification system.

The group could be any of these:

{fish, dolphins}
{dolphins, cats}
{fish, cats}

You can call them anything you want, but let's call them A, B, C. Let's say D is none of the above, as Eocene has said. It's multiple choice (though you should be able to explain your answer).

Neal Tedford: If you can categorize a Truck by maker, why not categorize life by biomes?

You can certainly do so, but we're looking at biological traits.

Neal Tedford: Looking at the panoply of characteristics of a Ford F450 Truck, is it best to group it with a Chevy Impala or a Ford F350 Truck?

Do they have air conditioning and DVD? Because those traits are independent of many other traits. But let's go with tentatively grouping the Fords together.

Now let's try another example; Ford pickup with the full package (AC, DVD, gps, power steering, brakes, windows, locks, etc.), Chevy pickup with the full package, and a Ford sedan with no extras. Which two group better now? What if the two Fords share a power train?

Do you see the problem? When we start looking at traits, there are several equally consistent nested hierarchies. With organisms, we don't see this pervasive borrowing across lineages. There are no feathers on bats or lions with human heads.

123. Thorton

You finally calmed down….I checked link you posted. This is interesting:

http://evolution.berkeley.edu/evosite/misconceps/IAorigintheory.shtml

Evolutionary theory deals mainly with how life changed after its origin. Science does try to investigate how life started (e.g., whether or not it happened near a deep-sea vent, which organic molecules came first, etc.), but these considerations are not the central focus of evolutionary theory.

David you said

A soup of components doesn't have a goal of 'adder' or 'computer' unless you put it there.

My experiment is obviously not dealing with chemicals. I have no other intention except to see if a soup of components or in a similar way chemicals can produce something functional. There will be more questions than answers.
I think logic points that at step 2 some decisions must be made. Whether it is first adder or protein it's still not alive so there are no "heritable traits , selective pressures, fitness" etc .. It just floats there. What could possibly happen to it next? It will break up the way it was assembled or maybe stick around and wait for next assembly to arrive? What do you think?

Just an honest question, no need to freak out now! ( Thorton)

124. Eugen: Evolutionary theory deals mainly with how life changed after its origin. Science does try to investigate how life started (e.g., whether or not it happened near a deep-sea vent, which organic molecules came first, etc.), but these considerations are not the central focus of evolutionary theory.

That's right. And the evidence suggests that, however life started, it has evolved via natural mechanisms since then.

Eugen: My experiment is obviously not dealing with chemicals.

Chemistry works quite a bit differently.

Eugen: Whether it is first adder or protein it's still not alive so there are no "heritable traits , selective pressures, fitness" etc .. It just floats there. What could possibly happen to it next? It will break up the way it was assembled or maybe stick around and wait for next assembly to arrive? What do you think?

It has to be relatively stable and capable of replication. Because of the delicate structures involved, it is thought that the original replicators had to be segregated from the ambient environment, probably by some sort of lipid membrane. That's one of the many things you don't have available in your simulation.

Also, as mentioned above, you need a large number of components in the soup, possibly moles worth. You may be better off with a software simulation.

125. Thorton:

This paper only demonstrates "evolution" is possible if every mutation can confer some benefit. But what about "adaptations" that require a large number of mutations before a there is some benefit.

126. And the paper only talks about mutations that are harmful in the that they don't confer a benefit relative to another mutations. The robots that are less fit are killed off. But in real life, harmful or fatal mutations that actually destroy the organism happen.

127. This comment has been removed by the author.

128. Eugen said...

I think logic points that at step 2 some decisions must be made. Whether it is first adder or protein it's still not alive so there are no "heritable traits , selective pressures, fitness" etc .. It just floats there. What could possibly happen to it next? It will break up the way it was assembled or maybe stick around and wait for next assembly to arrive? What do you think?

I think you're still pretty ignorant on the actual theory. ToE doesn't expect or require individual pieces of more complex cells to form and just 'sit there' until more pieces form and the whole thing self assembles. That's another stupid IDCer strawman. The only 'function' of the earliest pre-biotic molecules required was the ability to self-replicate with variation. Once you get imperfect self-replication and competition for resources (differential reproductive success), you get evolution. You get the ability to carry forward heritable traits, you get selection, you get the ability to increase complexity. Only much later after the self sustaining chemical reaction has kicked off do you get the evolution of more complex molecules with 'functions' like proteins and ribosomes that we see today.

The science of abiogenesis is looking for the conditions that would allow those most basic pre-biotic self-replicators to form and begin that self sustaining chemical reaction, the one we now call 'life'.

129. natschuster said...

Thorton:

This paper only demonstrates "evolution" is possible if every mutation can confer some benefit. But what about "adaptations" that require a large number of mutations before a there is some benefit.

The experiment wasn't designed or allowed to run near long enough to model complicated morphological adaptations. The experiment was designed to investigate the evolution of behavioral patterns like predator-prey relationships, and it successfully did.

And the paper only talks about mutations that are harmful in the that they don't confer a benefit relative to another mutations.

That's what differential reproductive success is nat: out-competing your neighbor.

The robots that are less fit are killed off. But in real life, harmful or fatal mutations that actually destroy the organism happen.

So you don't you think being 'killed off' due to selection is harmful or fatal to the organisms? Seriously nat, try reading the paper for comprehension.

130. Some mutations will kill an organism even if there are no competitors. Those where left out. That makes the experiment unrealistic.

And, to the bets of my knowledge, nobody questions the ability of natural selection to create adaptations that can be made in small increments. Its the complex adaptations that create the problems.

131. natschuster said...

Some mutations will kill an organism even if there are no competitors. Those where left out. That makes the experiment unrealistic.

No nat, it wasn't left out. Those were the mutations that resulted in the poor performing robots being 'killed'. As in the real world anything that kills you before you reproduce is selection. You just can't seem to grasps the basics, not that you're trying that hard.

And, to the bets of my knowledge, nobody questions the ability of natural selection to create adaptations that can be made in small increments. Its the complex adaptations that create the problems.

Why do you think it's a problem? Science uses Genetic Algorithms with the identical evolutionary processes to produce complex adaptations (including the IDC mantra 'irreducibly complex' things) every day.

132. I didn't see amnything in the article about mutations that rendered the robots inoperable. Mutations lke that doo exist in the real world. I only saw mention of mutations that mkae the robots less fit compared to other robots.

And do have the algorithms that pthat produce complex algorithms been tested in anyway. Or are they still just speculation. I'm just asking.

133. natschuster:

"I didn't see amnything in the article about mutations that rendered the robots inoperable. Mutations lke that doo exist in the real world. I only saw mention of mutations that mkae the robots less fit compared to other robots.

And do have the algorithms that pthat produce complex algorithms been tested in anyway. Or are they still just speculation. I'm just asking.
======

Your going to have to slow it down and take your time in the typing department and not be in such a hurry. Your giving your opponants (who no doubt are vacant in the answers treasure chest) an excuse for deflection from the subject at hand by magnifying spelling errors and perceived literary flaws. Unless of course you were purposely illustrating mutations problems on purpose. *wink*

Well, you know how it is ???

134. natschuster said...

I didn't see amnything in the article about mutations that rendered the robots inoperable. Mutations lke that doo exist in the real world. I only saw mention of mutations that mkae the robots less fit compared to other robots.

Some robots had mutations that led to them being immediately killed. Being killed makes them inoperable. It's still selection, and doesn't alter the outcome of the experiment. You're trying to make distinctions between degrees of 'dead' when none exist.

And do have the algorithms that pthat produce complex algorithms been tested in anyway. Or are they still just speculation. I'm just asking.

They're real and they work. Genetic algorithms are actively being used by science and industry every day. NASA has a whole Evolvable Systems Group that uses them to design complex analog circuits and antennas better and faster than a human could.

135. Here's a fun evolutionary simulation: Darwin Pond.

136. There aren't different degrees of death, true, but there are different causes. An organism can die because it can't run as fast as another organism. Or it can die because it has a defect that is fatal due to a mutation. I didn't see any evidence of the latter kind in the article. In that sense it is unrealistic.

137. And I didn't see any mention in the articles linked about an "adaptation" that requires multiple mutations before there is any advantage can "evolve."

138. natschuster said...

There aren't different degrees of death, true, but there are different causes. An organism can die because it can't run as fast as another organism. Or it can die because it has a defect that is fatal due to a mutation.

The overall cause is the same - a mutation that eventually led to death. The overall result is the same - the animal died before the it could reproduce. When the mutation killed the animal makes not one bit of difference to the validity of the results.

I didn't see any evidence of the latter kind in the article. In that sense it is unrealistic.

It's a model nat. Of course it's not going to reproduce every aspect of reality down to the gnat's behind. But it did reproduce evolutionary processes well enough to validate the hypotheses for the evolution of behavioral patterns.

And I didn't see any mention in the articles linked about an "adaptation" that requires multiple mutations before there is any advantage can "evolve."

That wasn't what was being modeled nat. If you are too lazy to read the paper and the articles on genetic algorithms or do the slightest bit of research on your own I can't help you. You seem to be consciously trying to not 'get' the scientific stuff.

139. Zachriel said, "But let's go with tentatively grouping the Fords together.

Now let's try another example; Ford pickup with the full package (AC, DVD, gps, power steering, brakes, windows, locks, etc.), Chevy pickup with the full package, and a Ford sedan with no extras. Which two group better now? What if the two Fords share a power train?

Do you see the problem? When we start looking at traits, there are several equally consistent nested hierarchies. With organisms, we don't see this pervasive borrowing across lineages. There are no feathers on bats or lions with human heads."

------

"What if the two Fords share a power train?"

Indeed. The same maker could account for the same power train. Perhaps this is why we see similarity across species... same designer. If only ONE automaker and parts supplier manufactured all the vehicles then wouldn't there would be much more similarity shared by automobiles?

As you said, "With organisms, we don't see this pervasive borrowing across lineages."

One designer. We do see borrowing, but apparently evolutionists don't see it as pervasive. "Pervasive" is surely a word that has a precise scientific meaning.

You said, "There are no feathers on bats or lions with human heads."

If there were, would that falsify evolution then? No, it would be explained as examples of convergent evolution. So your statement is true, except when it isn't.

Evolutionists are like Burger King customers, they like to have the evidence "their way".

Consider another issue about automobiles vs. life.... Every human is unique... unique finger print, voice print, etc. Genetically no two people are 100% the same. There are vehicles, however, that are identical (other than serial numbers). When you get down to the most fundamental characters, it is possible to find identical automobiles, but not identical people.

Dolphins and cats are mammals, but this classification was noticed by creationists long before Darwin. Now evolutionists claim it as their own. It's like someone in 1980 claiming they discovered the light blub. Perhaps evolutionists invented the internet also.

140. Tedford the Lying Pastor:

"Dolphins and cats are mammals, but this classification was noticed by creationists long before Darwin."

Aristotle was the first to classify dolphins as mammals rather than fish. He also believed that matter was eternal.

You fail again.

"Now evolutionists claim it as their own."

Pants on fire.

141. This comment has been removed by the author.

142. This comment has been removed by the author.

143. Troy:

"Aristotle was the first to classify dolphins as mammals rather than fish. He also believed that matter was eternal."
=====

Further proof of Evolution being a major part of Greek Mythology, thus religious. Though their religious beliefs were simple in this regard, they never the less believe life oozed out of oceans from fish to animals to humans. The Egyptian and Babylonian ancient pagan civilizations preceeded them in these religious myths centuries before.

Thanks for sharing.

144. Troy,

Aristotle was NOT an evolutionist or creationist. Furthermore, he had general categories of species and genus, but his system became mostly obsolete. He had a general category for live-bearing animals, but Linnaeus, a creationist, was the first to coin the word "mammal" directly from latin in 1758.

Some evolutionists are uncomfortable with giving creationists, like Linneaus, their respect. It is a matter of historical record that creationists founded nearly every branch of modern science. Evolutionists down play this in one way or another, but the fathers of science did not need Darwin to do their great work. Hitler and Stalin did, but not Linneaus and Pasteur, etc.

More on this later.

145. Tedford the idiot said...

Some evolutionists are uncomfortable with giving creationists, like Linneaus, their respect.

Respect for Linneaus is given due to his scientific work. It doesn't comes from him being a creationist.

It is a matter of historical record that creationists founded nearly every branch of modern science.

It's also a matter of historical record that in every case the scientific findings had absolutely nothing to do with their personal religious creationist beliefs.

I really don't know why idiot creationists like Tedford keep using this non-sequitur as 'evidence' for Creationism, except possibly desperation.

"I think logic points that at step 2 some decisions must be made. Whether it is first adder or protein it's still not alive so there are no "heritable traits , selective pressures, fitness" etc .. It just floats there. What could possibly happen to it next? It will break up the way it was assembled or maybe stick around and wait for next assembly to arrive? What do you think?"

Well, as we saw earlier, there are selective pressures that arise just from your choice of component size, magnet strength, and sloshing activity.

Let's say for the sake of definiteness that the only component you are using in your experiment is the NAND gate. This won't stop your experiment from evolving adders or computer CPUs, NAND is all that is necessary.

A full adder built out of NAND only takes 9 components. If you start as Zachriel suggested with a mole of NAND, and your sloshing allows components to connect according to some power law distribution (a reasonable assumption), your experiment is going to contain a very large number of 9-NAND blocks from the very beginning.

How many of these are full adders? I haven't done the math, but there are not that many 9-NAND truth tables, so I think you'll have multiple copies of a full adder right away.

As other posters have pointed out, nothing more is going to happen unless your experiment gets more sophisticated in at least two ways.

You can add an impoerfect copy mechanism easily. Say your magnets connect the components strongly in 2 dimensions and weakly in the third. Then you'll get sheets of NAND that can copy themselves by component sheets making a new layer above and/or below an existing sheet. These components link strongly to each other, forming a new sheet, but only weakly to the sheet next to them. So a bit more powerful sloshing will separate the sheets from each other.

So now your experiment has imperfectly replicating 2D sheets of NAND. Yay! But the sloshing by itself is only driving a the creation of a physical property (2D sheets) that has nothing to do with the component. The only "selection pressure" that exists is only selecting based on magnet strengths, not on component activity.

Just the process of imperfect replication is going to give the experiment some interesting population dynamics over time. Variety of sheets will gradually decrease even if the sloshing keeps the distribution of sizes the same. But there is no driver towards adders or anything else. Adders might exist at the start and then go extinct, or they might come to dominate the 9-NAND size group. Sloshing by itself isn't going to push the population either direction.

So if you want to see more interesting dynamics, perhaps even evolution, you'll need to add some kind of feedback loop into the experiment that involves the NAND. As an analogy in real chemistry, RNA nucleotides can stack together into chains, and these chains can extend and replicate easily. It is the fact that some sequences (even short ones) can fold, twist and then perform some enzymatic activity that creates a preference for some sequences over others. That is the selection pressure of molecular evolution. Your experiment is only a partial model of reality as long as it lacks similar mechanisms.

147. Thorton said,
"It's also a matter of historical record that in every case the scientific findings had absolutely nothing to do with their personal religious creationist beliefs."

The only counter-example is Maxwell's Demon. Before the Fall, it was an Angel! ;-p

148. Neal Tedford: The same maker could account for the same power train.

Perhaps, but at this point, we're just discussing classification.

Zachriel: There are no feathers on bats or lions with human heads.

Neal Tedford: If there were, would that falsify evolution then? No, it would be explained as examples of convergent evolution.

Nope.

Convergent evolution doesn't result in perfect equivalence of complex forms (Darwin 1859). Nor is there any plausible ancestor. Furthermore, we have reports of sphinxes, but scientific investigation has strongly indicated that they are the result of human imagination (design). We can predict with scientific confidence that you will never find a sphinx or a fossil of a sphinx.

Neal Tedford: Dolphins and cats are mammals, but this classification was noticed by creationists long before Darwin.

So can we agree that if we classify fish, dolphins and cats by the panoply of objective biological traits that we would group dolphins and cats?

149. Zachriel said, "So can we agree that if we classify fish, dolphins and cats by the panoply of objective biological traits that we would group dolphins and cats? "

How many times do I have to say yes to this question. Linnaeus grouped these over 200 years ago as mammals.

150. Zachriel So can we agree that if we classify fish, dolphins and cats by the panoply of objective biological traits that we would group dolphins and cats?

Cornelius Hunter: How many times do I have to say yes to this question.

Did you? You kept pointing out how others had reached that conclusion, but didn't say you agree with it. But good. There is only one reasonable way to classify fish, dolphins and cats by biological traits, that is, by grouping dolphins and cats.

Similarly, if we classify dolphin, cats and lions, we would group cats and lions. With these four organisms, we now have an objective nested hierarchy! As we continue to add more organisms, we observe a very strong nested hierarchy (esp. with regards to eukaryotes). If you don't agree, then we can go through the process of adding organisms to our classification to see what is what; frogs, butterflies, beetles, bears, snails, humans, etc.

On a side-note, when we classify vehicles, we do not get this singular nested hierarchy. Rather, we can form many different and equally consistent nested hierarchies. We saw this with the classification of a Ford pickup with the full package (AC, DVD, GPS, power steering, brakes, windows, locks, etc.), Chevy pickup with the full package, and a Ford sedan with no extras. Are we okay here, too?

Now, as we already know, the leaves on a tree form a nested hierarchy when grouped by branch and stem.

So, let's *posit* uncrossed lines of descent, that is, a tree. Let's also assume that at each point of divergence we modify a trait, and for starters, the trait we modify is different at each branch.

It's easy to see that the leaves of such a tree would form a nested hierarchy when arranged by traits, and that this nested hierarchy would exactly match the nested hierarchy formed when we group by branch and stem! In other words, we can reconstruct the pattern of branching from the traits of the individual leaves.

Okay so far?

151. The quote in the previous comment should have been attributed to Neal Tedford.

Here's a fun evolutionary simulation: Darwin Pond.

I played with it and must say gets addictive. Another interesting simulation is

http://golly.sourceforge.net/

This is cellular automata – game of life type simulation.

Thorton said

The only 'function' of the earliest pre-biotic molecules required was the ability to self-replicate with variation. Once you get imperfect self-replication and

Again, I think you jump too many steps forward. You are talking about complete replicating assembly that produce variation and I'm wondering about first component of the future replicating assembly. What is the purpose of this first component? Remember, step 2 comes before step 858.

David

You went into more details than I expected. To be honest I didn't think that far with my simple setup. It could be a Star Trek episode. You would be Spock and Thorton can be Romulan. Cornelius understandably - captain Kirk.

You also said

You can add an impoerfect copy mechanism easily.

Any copy mechanism would not be simple at all. When I tested Miller's wire as a mouse trap I realized how many things are critical for this experiment. I fully understand it's just analogy but Ph.D. in science should have picked something harder to test for BS .Also you may notice I 'm constantly switching between analogies in mechanical, electrical and chemical domains. Reason is (correct me if I'm wrong) that logic should follow from one to another.

Live long and prosper. \\ //

153. Eugen wrote:
"Any copy mechanism would not be simple at all."

I disagree. My example of magnets that are stronger in two dimensions than the third is an example of a copy mechanism.

I was thinking further about the experiment, and realized that you could either use piezo-electric effects to generate electricity from stresses induced by the sloshing, or you could try having the magnets move along conducting wires to induce electricity. This is an opportunity to create the electricity you'll need to get the circuits involved in the activity of the ensembles of components.

I also realized that these little component chips will need to be able to store some small amount of charge if you want any kind of memory to evolve, so add that to the specification of the components.

154. David

I disagree. My example of magnets that are stronger in two dimensions than the third is an example of a copy mechanism.

Hmm, I don't see this being easy.

OK if we use magnets we have to make sure their force of attraction is perfectly balanced with mechanical force of suspending liquid. Fine tuning of these forces will give us physical conditions by which we can get as many connection as disconnections. Slightly too much attracting force will clump everything into a ball. Too little will not allow connections to last long enough. That is engineering problem no.1.
We have to somehow isolate (with membrane ?) those desirable assemblies as soon as they are recognized. If we let them float around for too long random forces will take them apart or add something we do not need. It is very dynamic environment so recognition and isolation has to happen quickly.
That is problem no.2.
I can not even envision recognizing process that would be simple ,reliable and posses filtering abilities. It would be engineering set of problems on its own but we can just call it problem no.3.
I did not want to go into encapsulation system - membrane. Again that would be another set of many critical issues.

This is just a beginning and if we go into more details we'll find constraints and need for optimization and careful fine tuning at every little step.

Simple solution which some posters prefer is to jump to step 886. I don't blame them.