Refutation Of Evolutionary Algorithms    

Atheist's logic 101

"If I can only create life here in the lab (or in my computer), it will prove that no intelligence was necessary to create life in the beginning"

http://legacy-cdn-assets.answersingenesis.org/assets/images/articles/ee/v2/life-by-chance.jpg                 

“The computer is not going to generate anything realistic if it uses Darwinian mechanisms.”

Dr. David Berlinski: Accounting for Variations - video

http://www.youtube.com/watch?v=aW2GkDkimkE 

"Darwin or Design" with Dr. Tom Woodward with guest Dr. Robert J. Marks II - video

http://www.youtube.com/watch?v=Yoj9xo0YsOQ 

Digital Irreducible Complexity: A Survey of Irreducible Complexity in Computer Simulations - Winston Ewert - April 2014

Abstract: Irreducible complexity is a concept developed by Michael Behe to describe certain biological systems. Behe claims that irreducible complexity poses a challenge to Darwinian evolution. Irreducibly complex systems, he argues, are highly unlikely to evolve because they have no direct series of selectable intermediates. Various computer models have been published that attempt to demonstrate the evolution of irreducibly complex systems and thus falsify this claim. However, closer inspection of these models shows that they fail to meet the definition of irreducible complexity in a number of ways. In this paper we demonstrate how these models fail. In addition, we present another designed digital system that does exhibit designed irreducible complexity, but that has not been shown to be able to evolve. Taken together, these examples indicate that Behe’s concept of irreducible complexity has not been falsified by computer models. – Cite as: Ewert W (2014) Digital irreducible complexity: A survey of irreducible complexity in computer simulations. BIO-Complexity 2014 (1):1–10. doi:10.5048/BIO-C.2014.1.

http://www.uncommondescent.com/intelligent-design/paper-irreducible-complexity-ic-not-falsified-as-claimed/ 

Latest BIO-Complexity Paper Finds that on Irreducible Complexity, Michael Behe Has Not Been Refuted - Casey Luskin April 18, 2014

Excerpt: In a new paper in the journal BIO-Complexity, "Complexity in Computer Simulations," computer scientist Winston Ewert reviews much of the literature claiming to show, including via computer simulations, how irreducible complexity might have evolved by undirected means. He finds that "Behe's concept of irreducible complexity has not been falsified by computer models." The models include Avida, Ev, Steiner trees, geometric models, digital ears, and Tierra. Ewert reports that in many cases, the "parts" that compose the irreducibly complex system are "too simple." The programs are designed such that systems that the programs deem "functional" are very likely to evolve. -

http://www.evolutionnews.org/2014/04/latest_bio-comp084531.html 

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/   

Panda’s Thumb Richard Hoppe forgot about Humpty Zombie - April 15, 2014

Excerpt: I discovered if you crank up Avida’s cosmic radiation parameter to maximum and have the Avida genomes utterly scrambled, the Avidian organisms still kept reproducing. If I recall correctly, they died if the radiation was moderate, but just crank it to the max and the creatures come back to life!

This would be like putting dogs in a microwave oven for 3 days, running it at full blast, and then demanding they reproduce. And guess what, the little Avida critters reproduced. This little discovery in Avida 1.6 was unfortunately not reported in Nature. Why? It was a far more stupendous discovery! Do you think it’s too late for Richard Hoppe and I to co-author a submission?

Hoppe eventually capitulated that there was indeed this feature of Avida. To his credit he sent a letter to Dr. Adami to inform him of the discovery. Dr. Adami sent Evan Dorn to the Access Research Network forum, and Evan confirmed the feature by posting a reply there.

http://www.creationevolutionuniversity.com/idcs/?p=90 

Despite the stubborn reluctance of some Darwinists to admit to the abject failure that is inherent in Dawkins' “Weasel” computer program for providing any support whatsoever for Darwinian claims, I am grateful for what Dawkins’ “Weasel” computer program has personally taught to novices like me. Because of the simplicity of the program and the rather modest result, i.e. “Methinks it is like a weasel”, that the program was trying to achieve by evolutionary processes, it taught me in fairly short order, in an easy to understand way, that,,

“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.”

- William Dembski

In fact so effective was Dawkins’ “Weasel” project at teaching me this basic, ‘brick wall’, limitation for material processes to ever create even trivial levels of functional information, that I highly recommend Wiker & Witt’s book “A Meaningful World” in which they show, using the “Methinks it is like a weasel” phrase that Dawkins’ used from Shakespeare’s play Hamlet, that the problem is much worse for Darwinists than just finding the “Methinks it is like a weasel” phrase by a blind search, since the “Methinks it is like a weasel” phrase doesn't makes any sense at all unless the entire play of Hamlet is taken into consideration so as to give the “Weasel” phrase a proper context. Moreover the context in which the phrase finds its meaning is derived from several different levels of the play. i.e. The ENTIRE play, and even the Elizabethan culture, provides meaning for the individual “Weasel” phrase.

A Meaningful World: How the Arts and Sciences Reveal the Genius of Nature – Book Review

Excerpt: They focus instead on what “Methinks it is like a weasel” really means. In isolation, in fact, it means almost nothing. Who said it? Why? What does the “it” refer to? What does it reveal about the characters? How does it advance the plot? In the context of the entire play, and of Elizabethan culture, this brief line takes on significance of surprising depth. The whole is required to give meaning to the part.

http://www.thinkingchristian.net/C228303755/E20060821202417/ 

In fact it is interesting to note what the overall context is for “Methinks it is like a weasel” that is used in the Hamlet play. The context in which the phrase is used is to illustrate the spineless nature of one of the characters of the play. To illustrate how easily the spineless character can be led to say anything that Hamlet wants him to say:

Ham. Do you see yonder cloud that ’s almost in shape of a camel?

Pol. By the mass, and ’t is like a camel, indeed.

Ham. Methinks it is like a weasel.

Pol. It is backed like a weasel.

Ham. Or like a whale?

Pol. Very like a whale.

http://www.bartleby.com/100/138.32.147.html 

After realizing what the context of ‘Methinks it is like a weasel’ actually was, I remember thinking to myself that it was perhaps the worse possible phrase Dawkins could have possibly chosen to try to illustrate his point, since the phrase, when taken into context, actually illustrates that the person saying it (Hamlet) was manipulating the other character into saying a cloud looked like a weasel. Which I am sure is hardly the idea, i.e. deception and manipulation, that Dawkins was trying to convey with his ‘Weasel’ example.

But is this context dependency that is found in literature also found in life? Yes! Starting at the amino acids of proteins we find context dependency:

Fred Sanger, Protein Sequences and Evolution Versus Science – Are Proteins Random? Cornelius Hunter – November 2013

Excerpt: Standard tests of randomness show that English text, and protein sequences, are not random.,,,

http://darwins-god.blogspot.com/2013/11/fred-sanger-protein-sequences-and.html 

(A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics – 2012

Excerpt (Page 4): The Probabilities Get Worse

This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search.

http://powertochange.com/wp-content/uploads/2012/11/Devious-Distortions-Durston-or-Myers_.pdf 

Moreover, context dependency is found on at least three different levels of the protein structure:

“Why Proteins Aren’t Easily Recombined, Part 2″ – Ann Gauger – May 2012

Excerpt: “So we have context-dependent effects on protein function at the level of primary sequence, secondary structure, and tertiary (domain-level) structure. This does not bode well for successful, random recombination of bits of sequence into functional, stable protein folds, or even for domain-level recombinations where significant interaction is required.”

http://www.biologicinstitute.org/post/23170843182/why-proteins-arent-easily-recombined-part-2 

Moreover, it is interesting to note that many (most?) proteins are now found to be multifunctional depending on the overall context (i.e. position in cell, cell type, tissue type, etc..) that the protein happens to be involved in. Thus, the sheer brick wall that Darwinian processes face in finding ANY novel functional protein to perform any specific single task in a cell in the first place (Axe; Sauer) is only exponentially exasperated by the fact that many proteins are multifunctional and, serendipitously, perform several different ‘context dependent’ functions within the cell:

Human Genes: Alternative Splicing (For Proteins) Far More Common Than Thought:

Excerpt: two different forms of the same protein, known as isoforms, can have different, even completely opposite functions. For example, one protein may activate cell death pathways while its close relative promotes cell survival.

http://www.sciencedaily.com/releases/2008/11/081102134623.htm 

Genes Code For Many Layers of Information – They May Have Just Discovered Another – Cornelius Hunter – January 21, 2013

Excerpt: “protein multifunctionality is more the rule than the exception.” In fact, “Perhaps all proteins perform many different functions by employing as many different mechanisms.”

http://www.fasebj.org/content/23/7/2022.full 

Context dependency, and the problem it presents for ‘bottom up’ Darwinian evolution is perhaps most dramatically illustrated by the following examples in which ‘form’ dictates how the parts are used:

An Electric Face: A Rendering Worth a Thousand Falsifications – Cornelius Hunter – September 2011

Excerpt: The video suggests that bioelectric signals presage the morphological development of the face. It also, in an instant, gives a peak at the phenomenal processes at work in biology. As the lead researcher said, “It’s a jaw dropper.”

https://www.youtube.com/watch?v=wi1Qn306IUU 

What Do Organisms Mean? Stephen L. Talbott – Winter 2011

Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: “Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements … take unique meaning from their context.[3]“,,,

http://www.thenewatlantis.com/publications/what-do-organisms-mean 

I think pastor Joe Boot, although he is talking about the universe as a whole in the following quote, illustrates the insurmountable problem that ‘context dependency’ places on reductive materialism very well:

“If you have no God, then you have no design plan for the universe. You have no prexisting structure to the universe.,, As the ancient Greeks held, like Democritus and others, the universe is flux. It’s just matter in motion. Now on that basis all you are confronted with is innumerable brute facts that are unrelated pieces of data. They have no meaningful connection to each other because there is no overall structure. There’s no design plan. It’s like my kids do ‘join the dots’ puzzles. It’s just dots, but when you join the dots there is a structure, and a picture emerges. Well, the atheists is without that (final picture). There is no preestablished pattern (to connect the facts given atheism).”

Pastor Joe Boot – 13:20 minute mark of the following video

Defending the Christian Faith – Pastor Joe Boot – video

http://www.youtube.com/watch?v=wqE5_ZOAnKo 

Supplemental quote:

‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does not insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’ -

Stephen Meyer – (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate – 2009)

Stephen Meyer – Functional Proteins And Information For Body Plans – video

http://www.metacafe.com/watch/4050681 

Conservation of Information Made Simple - William A. Dembski - August, 2012

Excerpt: Biological configuration spaces of possible genes and proteins, for instance, are immense, and finding a functional gene or protein in such spaces via blind search can be vastly more improbable than finding an arbitrary electron in the known physical universe. ,,,

,,,Given this background discussion and motivation, we are now in a position to give a reasonably precise formulation of conservation of information, namely: raising the probability of success of a search does nothing to make attaining the target easier, and may in fact make it more difficult, once the informational costs involved in raising the probability of success are taken into account. Search is costly, and the cost must be paid in terms of information. Searches achieve success not by creating information but by taking advantage of existing information. The information that leads to successful search admits no bargains, only apparent bargains that must be paid in full elsewhere.

http://www.evolutionnews.org/2012/08/conservation_of063671.html

 

Artificial Intelligence is Law/Mechanism - Winston Ewert - November 2013

http://www.uncommondescent.com/computer-science/dawkins-weasel-vs-blind-search-simplified-illustration-of-no-free-lunch-theorems/ 

The Tragedy of Two CSIs - Winston Ewert - November 25, 2013

http://www.uncommondescent.com/computer-science/the-tragedy-of-two-csis/ 

"Captcha" Breakthrough by AI (Artificial Intelligence) Illustrates Biomimetic Design - November 26, 2013

Excerpt: Since intelligent design presupposes a mental act directed toward a purpose, AI is a misnomer. It should more properly be described as "artificial execution of human-designed algorithms."

This is really a story about biomimetics -- a form of intelligent-design science. The engineers looked to the way a brain solves a problem and tried to imitate it. It took human intelligent design to design the computer. It took intelligent design to write the software. It took human ID to test it, tweak it and perfect it till it succeeded. It requires human intelligence to see a good design. It takes ID to formulate a purpose. Then it requires human intelligence and will to move things in a preferred direction for that purpose. Nothing is left to unguided processes. Even selection from random trials (falsely called "Darwinian" algorithms) employs human purposeful choice.

http://www.evolutionnews.org/2013/11/captcha_breakou079551.html 

A.I. Has Grown Up and Left Home - Dec. 19, 2013

Excerpt: The history of Artificial Intelligence,” said my computer science professor on the first day of class, “is a history of failure.” This harsh judgment summed up 50 years of trying to get computers to think. Sure, they could crunch numbers a billion times faster in 2000 than they could in 1950, but computer science pioneer and genius Alan Turing had predicted in 1950 that machines would be thinking by 2000: Capable of human levels of creativity, problem solving, personality, and adaptive behavior. Maybe they wouldn’t be conscious (that question is for the philosophers), but they would have personalities and motivations, like Robbie the Robot or HAL 9000. Not only did we miss the deadline, but we don’t even seem to be close. And this is a double failure, because it also means that we don’t understand what thinking really is.

http://nautil.us/issue/8/home/ai-has-grown-up-and-left-home 

The Closing of the Scientific Mind - David Gelernter - January 1, 2014

Excerpt: The Flaws.

But the master analogy—between mind and software, brain and computer—is fatally flawed. It falls apart once you mull these simple facts:

1. You can transfer a program easily from one computer to another, but you can’t transfer a mind, ever, from one brain to another.

2. You can run an endless series of different programs on any one computer, but only one “program” runs, or ever can run, on any one human brain.

3. Software is transparent. I can read off the precise state of the entire program at any time. Minds are opaque—there is no way I can know what you are thinking unless you tell me.

4. Computers can be erased; minds cannot.

5. Computers can be made to operate precisely as we choose; minds cannot.

There are more. Come up with them yourself. It’s easy.

http://www.commentarymagazine.com/article/the-closing-of-the-scientific-mind/ 

Complexity by Subtraction Was Weird Enough; Now, Complexity by Harmful Mutations - Sept. 2, 2013

Excerpt:  Naturally, Lenski's lab ignored the critique of Avida published in an IEEE paper in 2009 by Ewert, Dembski and Marks. -

http://www.evolutionnews.org/2013/09/complexity_by_s_1076091.html 

How Information Theory Is Taking Intelligent Design Mainstream - William Dembski - Casey Luskin - podcast/video

http://www.youtube.com/watch?v=8UCLJKLQNbs 

The Evolutionary Informatics Lab: Putting Intelligent Design Predictions to the Test - Casey Luskin - February, 2012

Excerpt: The work of the Evolutionary Informatics Lab demonstrates that ID proponents are capable of producing innovative techniques for tackling questions related to intelligent design and evolution. First, the lab developed a methodology for studying the degree to which information is smuggled into evolutionary algorithms. Then, the researchers applied that methodology to various well-known programs like ev, Avida, and Dawkins' "Weasel Simulation," and successfully identified sources of "active information" in each. As the lab's website promised, their research has shown that even the best efforts of ID-critics cannot escape the fact that intelligence is required to generate new information.

http://www.evolutionnews.org/2012/02/the_evolutionar056061.html

Climbing the Steiner Tree--Sources of Active Information in a Genetic Algorithm for Solving the Euclidean Steiner Tree Problem - 2012 - Winston Ewert, William A Dembski, Robert J Marks II

http://bio-complexity.org/ojs/index.php/main/article/view/50 

Applied Darwinism: A New Paper from Bob Marks (W. Dembski) and His Team, in BIO-Complexity - Doug Axe - 2012

Excerpt: Furthermore, if you dig a bit beyond these papers and look at what kinds of problems this technique (Steiner Tree) is being used for in the engineering world, you quickly find that it is of extremely limited applicability. It works for tasks that are easily accomplished in a huge number of specific ways, but where someone would have to do a lot of mindless fiddling to decide which of these ways is best.,, That's helpful in the sense that we commonly find computers helpful -- they do what we tell them to do very efficiently, without complaining. But in biology we see something altogether different. We see elegant solutions to millions of engineering problems that human ingenuity cannot even begin to solve.

http://www.evolutionnews.org/2012/04/applied_darwini058591.html

Time and Information in Evolution: Winston Ewert, William A. Dembski, Ann K. Gauger, and Robert J. Marks II - December 2012

http://www.biologicinstitute.org/post/37465769739/time-and-information-in-evolution 

Here are all the main publications (which are linked) at evoinfo lab:

http://evoinfo.org/publications/ 

Here is the search for a search paper:

The Search for a Search: Measuring the Information Cost of Higher Level Search William A. Dembski and Robert J. Marks II

Abstract: Needle-in-the-haystack problems look for small targets in large spaces. In such cases, blind search stands no hope of success. Conservation of information dictates any search technique will work, on average, as well as blind search. Success requires an assisted search. But whence the assistance required for a search to be successful? To pose the question this way suggests that successful searches do not emerge spontaneously but need themselves to be discovered via a search. The question then naturally arises whether such a higher-level “search for a search” is any easier than the original search. We prove two results: (1) The Horizontal No Free Lunch Theorem, which shows that average relative performance of searches never exceeds unassisted or blind searches, and (2) The Vertical No Free Lunch Theorem, which shows that the difficulty of searching for a successful search increases exponentially with respect to the minimum allowable active information being sought.

http://evoinfo.org/publications/search-for-a-search/ 

Before They've Even Seen Stephen Meyer's New Book, Darwinists Waste No Time in Criticizing Darwin's Doubt - William A. Dembski - April 4, 2013

Excerpt: In the newer approach to conservation of information, the focus is not on drawing design inferences but on understanding search in general and how information facilitates successful search. The focus is therefore not so much on individual probabilities as on probability distributions and how they change as searches incorporate information. My universal probability bound of 1 in 10^150 (a perennial sticking point for Shallit and Felsenstein) therefore becomes irrelevant in the new form of conservation of information whereas in the earlier it was essential because there a certain probability threshold had to be attained before conservation of information could be said to apply. The new form is more powerful and conceptually elegant. Rather than lead to a design inference, it shows that accounting for the information required for successful search leads to a regress that only intensifies as one backtracks. It therefore suggests an ultimate source of information, which it can reasonably be argued is a designer. I explain all this in a nontechnical way in an article I posted at ENV a few months back titled "Conservation of Information Made Simple" (go here). ,,,

,,, Here are the two seminal papers on conservation of information that I've written with Robert Marks:

"The Search for a Search: Measuring the Information Cost of Higher-Level Search," Journal of Advanced Computational Intelligence and Intelligent Informatics 14(5) (2010): 475-486

"Conservation of Information in Search: Measuring the Cost of Success," IEEE Transactions on Systems, Man and Cybernetics A, Systems & Humans, 5(5) (September 2009): 1051-1061

For other papers that Marks, his students, and I have done to extend the results in these papers, visit the publications page at www.evoinfo.org 

http://www.evolutionnews.org/2013/04/before_theyve_e070821.html   

A.I. Has Grown Up and Left Home - Dec. 19, 2013

For example, genetic approaches represent algorithms with varying parameters as chromosomal “strings,” and “breed” successful algorithms with one another. These approaches do not improve through better understanding of the problem. All that matters is the fitness of the algorithm with respect to its environment—in other words, how the algorithm behaves. This black-box approach has yielded successful applications in everything from bioinformatics to economics, yet one can never give a concise explanation of just why the fittest algorithm is the most fit.

Neural networks are another successful subsymbolic technology, and are used for image, facial, and voice recognition applications. No representation of concepts is hardcoded into them, and the factors that they use to identify a particular subclass of images emerge from the operation of the algorithm itself.

http://nautil.us/issue/8/home/ai-has-grown-up-and-left-home 

Of related note:

"Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source from a mind or personal agent."

(Stephen C. Meyer, "The origin of biological information and the higher taxonomic categories," Proceedings of the Biological Society of Washington, 117(2):213-239 (2004).)

Kurt Gödel - Incompleteness Theorem - video

http://www.metacafe.com/w/8462821 

Alan Turing & Kurt Godel - Incompleteness Theorem and Human Intuition - video (notes in video description)

http://www.metacafe.com/watch/8516356/ 

Here is what Gregory Chaitin, a world-famous mathematician, said about the limits of the computer program he was trying to develop to prove that Darwinian evolution was mathematically feasible:

At last, a Darwinist mathematician tells the truth about evolution - VJT - November 2011

Excerpt: In Chaitin’s own words, “You’re allowed to ask God or someone to give you the answer to some question where you can’t compute the answer, and the oracle will immediately give you the answer, and you go on ahead.”

http://www.uncommondescent.com/intelligent-design/at-last-a-darwinist-mathematician-tells-the-truth-about-evolution/

Here is the video where, at the 30:00 minute mark, you can hear the preceding quote from Chaitin's own mouth in full context:

Life as Evolving Software, Greg Chaitin at PPGC UFRGS

http://www.youtube.com/watch?v=RlYS_GiAnK8 

Moreover, at the 40:00 minute mark of the video Chaitin readily admits that Intelligent Design is the best possible way to get evolution to take place, and at the 43:30 minute mark Chaitin even tells of a friend pointing out that the idea Evolutionary computer model that Chaitin has devised does not have enough time to work. And Chaitin even agreed that his friend had a point, although Chaitin still ends up just 'wanting', and not ever proving, his idea Darwinian mathematical model to be true! In fact the following paper took his toy model apart and found it wanting

Active Information in Metabiology - Winston Ewert, William A. Dembski,  Robert J. Marks II - 2013

Excerpt: Introduction: Chaitin’s description of metabiology [3] is casual, clear, compelling, and mind-bending. Yet in the end, although the mathematics is beautiful, our analysis shows that the metabiology model parallels other attempts to illustrate undirected Darwinian evolution using computer models [10–13]. All of these models depend on the principle of conservation of information [14–21], and all have been shown to incorporate knowledge about the search derived from their designers; this knowledge is measurable as active information [14,22–25].

Except page 9: Chaitin states [3], “For many years I have thought that it is a mathematical scandal that we do not have proof that Darwinian evolution works.” In fact, mathematics has consistently demonstrated that undirected Darwinian evolution does not work.

http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2013.4/BIO-C.2013.4 

Related quotes from Chaitin:

The Limits Of Reason - Gregory Chaitin - 2006

Excerpt: an infinite number of true mathematical theorems exist that cannot be proved from any finite system of axioms.,,,

http://www.umcs.maine.edu/~chaitin/sciamer3.pdf 

“For many years I have thought that it is a mathematical scandal that we do not have a proof that Darwinian evolution works.”

Gregory Chaitin

Dennett on Competence without Comprehension – William A. Dembski – June 2012

Excerpt: As it turns out, there are problems in mathematics that can be proved to be beyond resolution by any algorithm (e.g., the halting problem).

http://www.evolutionnews.org/2012/06/dennett_on_comp061451.html#sthash.pIAPWiRP.dpuf 

 

Dennett on Competence without Comprehension – William A. Dembski – June 2012

Excerpt: In 1936 Turing proposed a universal mechanism for performing any and all computations, since dubbed a Turing machine. In the last seventy-plus years, many other formal systems have been proposed for performing any and all computations (cellular automata, neural nets, unlimited register machines, etc.), and they've all been shown to perform the same -- no less and no more -- computations as Turing's originally proposed machine.,,,

Something is a Turing machine if it has a "tape" that extends infinitely in both directions, with the tape subdivided into identical adjacent squares, each of which can have written on it one of a finite alphabet of symbols (usually just zero and one). In addition, a Turing machine has a "tape head," that can move to the left or right on the tape and erase and rewrite the symbol that's on a current square. Finally, what guides the tape head is a finite set of "states" that, given one state, looks at the current symbol, keeps or changes it, moves the tape head right or left, and then, on the basis of the symbol that was there, makes active another state. In modern terms, the states constitute the program and the symbols on the tape constitute data.

From this it's obvious that a Turing machine can do nothing unless it is properly programmed to do so.,,,

Once a Turing machine is properly programmed, it will produce the solution to any computational problem. But humans -- read "intelligent designers" -- invariably do the programming. Turing, far from having obviated the "trickle-down theory of intelligence," actually underscores its preeminent role in the field of computation.

http://www.evolutionnews.org/2012/06/dennett_on_comp061451.html#sthash.pIAPWiRP.dpuf 

Algorithmic Information Theory, Free Will and the Turing Test – Douglas S. Robertson

Excerpt: For example, the famous “Turing test” for artificial intelligence could be defeated by simply asking for a new axiom in mathematics. Human mathematicians are able to create axioms, but a computer program cannot do this without violating information conservation. Creating new axioms and free will are shown to be different aspects of the same phenomena: the creation of new information.

http://cires.colorado.edu/~doug/philosophy/info8.pdf 

Roberts Marks on Avida and ev - video - 6:00 minute mark

http://www.youtube.com/watch?v=Uc6Ktq0SEBo

Information. What is it? - Robert Marks - lecture video (With special reference to ev, AVIDA, and WEASEL)

http://www.youtube.com/watch?v=d7seCcS_gPk

If Darwinism is true then why can’t we design  ‘super’ programs for computers with it?

Why doesn’t software industry use evolution? - niwrad - Oct. 21, 2013

Excerpt: Computer aided evolution speed:

Consider a single 10^15 flops computer and suppose, for the sake of argument, that a program “mutation” needs an equivalent of 1000 floating-point operations. We get a computer aided evolution speed (CAES) = 10^12 mutations / sec.

Since, according to Darwin, unguided biological evolution was able to spontaneously produce all 500 million species on earth (from bacteria to man) in 3 billion years (biological evolution time = BET), computer aided evolution could automatically produce software containing an equivalent overall amount of functional complex specified information in what we call “computer aided evolution time” (CAET). In other words, we state that the product of “speed x time” is equal for biological evolution and for computer evolution:

CAET x CAES = BET x BES

CAET is then = (BET x BES) / CAES

in numbers:

CAET = (3×10^9 x 1250) / 10^12 = 3.75 years

Evolution applied to software programming would produce software equivalent to the organizational information that present and past organisms contain in less than 4 years. Then, again, why software houses don’t save billion dollars in employers by applying Darwinian evolution to the software creation?

My short answer: because Darwinian evolution works exactly zero, when the goal is to create systems. It is fully incapable to create the least system in principle. If it were capable to do that just a little, software producers would use it. To put it differently, if Charles Darwin was right Bill Gates would be far richer than he is…

http://www.uncommondescent.com/intelligent-design/why-doesnt-software-industry-use-evolution/ 

Dr. David Berlinski: Random Mutations (to computer programs?) - video

http://www.youtube.com/watch?v=DGaUEAkqhMY 

Estimating Active Information in Adaptive Mutagenesis

http://www.blythinstitute.org/images/data/attachments/0000/0005/EstimatingActiveInformationPoster_final.pdf

From David Tyler: How do computer simulations of evolution relate to the real world? - October 2011

Excerpt: These programs ONLY work the way they want because as they admit, it only works because it has pre-designed goals and fitness functions which were breathed into the program by intelligent designers. The only thing truly going on is the misuse and abuse of intelligence itself.

http://www.uncommondescent.com/darwinism/from-david-tyler-how-do-computer-simulations-of-evolution-relate-to-the-real-world/comment-page-1/#comment-401493 

Conservation of Information in Computer Search (COI) - William A. Dembski - Robert J. Marks II - Dec. 2009

Excerpt: COI puts to rest the inflated claims for the information generating power of evolutionary simulations such as Avida and ev.

http://evoinfo.org/publications/bernoullis-principle-of-insufficient-reason/

Evolutionary Synthesis of Nand Logic: Dissecting a Digital Organism - Dembski - Marks - Dec. 2009

Excerpt: The effectiveness of a given algorithm can be measured by the active information introduced to the search. We illustrate this by identifying sources of active information in Avida, a software program designed to search for logic functions using nand gates. Avida uses stair step active information by rewarding logic functions using a smaller number of nands to construct functions requiring more. Removing stair steps deteriorates Avida’s performance while removing deleterious instructions improves it.

http://evoinfo.org/publications/evolutionary-synthesis-of-nand-logic-avida/

New paper using the Avida “evolution” software shows it doesn’t evolve. - May 2011

http://www.uncommondescent.com/evolution/new-paper-using-the-avida-evolution-software-shows/

No evidence that there is enough time for evolution - Lee Spetner - May 2011

Excerpt: Thus their conclusion that “there’s plenty of time for evolution” is unsubstantiated. The probability calculation to justify evolutionary theory remains unaddressed.

http://www.uncommondescent.com/evolution/no-evidence-that-there-is-enough-time-for-evolution/

The effects of low-impact mutations in digital organisms (Testing Avida using realistic biological parameters) - Chase W Nelson and John C Sanford

http://www.tbiomed.com/content/8/1/9

The Problem of Information for the Theory of Evolution – debunking Schneider's ev computer simulation

Excerpt: In several papers genetic binding sites were analyzed using a Shannon information theory approach. It was recently claimed that these regulatory sequences could increase information content through evolutionary processes starting from a random DNA sequence, for which a computer simulation was offered as evidence. However, incorporating neglected cellular realities and using biologically realistic parameter values invalidate this claim. The net effect over time of random mutations spread throughout genomes is an increase in randomness per gene and decreased functional optimality.

http://www.trueorigin.org/schneider.asp

The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective

William DeJong and Hans Degens Open Evolution Journal, February 2011,

Abstract: Both digital codes in computers and nucleotide codes in cells are protected against mutations. Here we explore how mutation protection affects the random change and selection of digital and nucleotide codes. We illustrate our findings with a computer simulation of the evolution of a population of self replicating digital amoebae. We show that evolutionary programming of digital codes is a valid model for the evolution of nucleotide codes by random change within the boundaries of mutation protection, not for evolution by unbounded random change. Our mutation protection perspective enhances the understanding of the evolutionary dynamics of digital and nucleotide codes and its limitations, and reveals a paradox between the necessity of dysfunctioning mutation protection for evolution and its disadvantage for survival. Our mutation protection perspective suggests new directions for research into mutational robustness.

http://benthamscience.com/open/toevolj/articles/V005/1TOEVOLJ.pdf

The following is a short informative video that accompanies the preceding paper

Contradiction in evolutionary theory - video (The contradiction between extensive DNA repair mechanisms and the necessity of 'random mutations/errors' to DNA for Darwinian evolution to be feasible)

http://www.youtube.com/watch?v=dzh6Ct5cg1o

The Capabilities of Chaos and Complexity - David L. Abel

Excerpt: "To stem the growing swell of Intelligent Design intrusions, it is imperative that we provide stand-alone natural process evidence of non trivial self-organization at the edge of chaos. We must demonstrate on sound scientific grounds the formal capabilities of naturally-occurring physicodynamic complexity. Evolutionary algorithms, for example, must be stripped of all artificial selection and the purposeful steering of iterations toward desired products. The latter intrusions into natural process clearly violate sound evolution theory."

http://www.mdpi.com/1422-0067/10/1/247/pdf

Constraints vs. Controls - Abel - 2010

Excerpt: Classic examples of the above confusion are found in the faulty-inference conclusions drawn from many so-called “directed evolution,” “evolutionary algorithm,” and computer-programmed “computational evolutionary” experimentation. All of this research is a form of artificial selection, not natural selection. Choice for potential function at decision nodes, prior to the realization of that function, is always artificial, never natural.

http://www.bentham.org/open/tocsj/articles/V004/14TOCSJ.pdf

Arriving At Intelligence Through The Corridors Of Reason (Part II) - April 2010

Excerpt: Summarizing the status quo, Johnson notes for example how AVIDA uses “an unrealistically small genome, an unrealistically high mutation rate, unrealistic protection of replication instructions, unrealistic energy rewards and no capability for graceful function degradation. It allows for arbitrary experimenter-specified selective advantages”. Not faring any better, the ME THINKS IT IS LIKE A WEASEL algorithm is programmed to direct a sequence of letters towards a pre-specified target.

http://www.uncommondescent.com/intelligent-design/arriving-at-intelligence-through-the-corridors-of-reason-part-ii/

Algorithmic Information Theory, Free Will and the Turing Test - Douglas S. Robertson

Excerpt: Chaitin’s Algorithmic Information Theory shows that information is conserved under formal mathematical operations and, equivalently, under computer operations. This conservation law puts a new perspective on many familiar problems related to artificial intelligence. For example, the famous “Turing test” for artificial intelligence could be defeated by simply asking for a new axiom in mathematics. Human mathematicians are able to create axioms, but a computer program cannot do this without violating information conservation. Creating new axioms and free will are shown to be different aspects of the same phenomena: the creation of new information.

http://cires.colorado.edu/~doug/philosophy/info8.pdf 

The following site has some easy examples of the types of questions that would trip a computer up in a Turing test:

Artificial Intelligence or intelligent artifices? - June 3, 2013

http://www.uncommondescent.com/intelligent-design/artificial-intelligence-or-intelligent-artifices/ 

Algorithmic Information Theory, Free Will and the Turing Test - Douglas S. Robertson

Excerpt: The basic problem concerning the relation between AIT (Algorithmic Information Theory) and free will can be stated succinctly: Since the theorems of mathematics cannot contain more information than is contained in the axioms used to derive those theorems, it follows that no formal operation in mathematics (and equivalently, no operation performed by a computer) can create new information.

http://cires.colorado.edu/~doug/philosophy/info8.pdf 

At last, a Darwinist mathematician tells the truth about evolution - November 2011

Excerpt: 7. Chaitin looks at three kinds of evolution in his toy model: exhaustive search (which stupidly performs a search of all possibilities in its search for a mutation that would make the organism fitter, without even looking at what the organism has already accomplished), Darwinian evolution (which is random but also cumulative, building on what has been accomplished to date) and Intelligent Design (where an Intelligent Being selects the best possible mutation at each step in the evolution of life). All of these – even exhaustive search – require a Turing oracle for them to work – in other words, outside direction by an Intelligent Being. In Chaitin’s own words, “You’re allowed to ask God or someone to give you the answer to some question where you can’t compute the answer, and the oracle will immediately give you the answer, and you go on ahead.”

 8. Of the three kinds of evolution examined by Turing (Chaitin), Intelligent Design is the only one guaranteed to get the job done on time. Darwinian evolution is much better than performing an exhaustive search of all possibilities, but it still seems to take too long to come up with an improved mutation. http://www.uncommondescent.com/intelligent-design/at-last-a-darwinist-mathematician-tells-the-truth-about-evolution/

Also Per Chaitin; Oracle must possess infinite information for ‘unlimited evolution’ of a evolutionary algorithm; i.e. The Oracle must be God!

http://www.uncommondescent.com/intelligent-design/at-last-a-darwinist-mathematician-tells-the-truth-about-evolution/comment-page-1/#comment-408176

"Computer simulations of Darwinian evolution fail when they are honest and succeed only when they are not."

David Berlinski

GAs (Genetic Algorithms) come in different flavours. Some, like the weasel, are only ill inspired propaganda. Others are useful and serious computational tools. But no human made GA says anything about the “spontaneous” GA which is modeled in neo-darwinism. So, if darwinists want to show what their model can really do, they should really analyze the RV (Random variation) + NS (Natural Selection) algorithm, and not others which are completely different.

http://www.uncommondescent.com/intelligent-design/michael-yarus-and-the-thing-that-couldnt-die/#comment-356715

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

Evolutionary Computation: A Perpetual Motion Machine for Design Information? By Robert J. Marks II

Final Thoughts: Search spaces require structuring for search algorithms to be viable. This includes evolutionary search for a targeted design goal. The added structure information needs to be implicitly infused into the search space and is used to guide the process to a desired result. The target can be specific, as is the case with a precisely identified phrase; or it can be general, such as meaningful phrases that will pass, say, a spelling and grammar check. In any case, there is yet no perpetual motion machine for the design of information arising from evolutionary computation.

http://www.idnet.com.au/files/pdf/Evolutionary%20Computer%20Simulations.pdf 

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 J. Marks II - video

http://www.youtube.com/watch?v=Kxv3Q0VaX9E 

How Information Theory Is Taking Intelligent Design Mainstream - William Dembski PhD

http://www.youtube.com/watch?v=8UCLJKLQNbs 

7:00 minute mark

 "For many years I thought that it is a mathematical scandal that we do not have a proof that Darwinian evolution works."

Gregory Chaitin - Proving Darwin 2012 - Highly Respected Mathematician

Darwin as the Pinball Wizard: Talking Probability with Robert Marks - podcast

http://www.idthefuture.com/2010/03/darwin_as_the_pinball_wizard_t.html

Here are a few quotes from Robert Marks from the preceding podcast, as well as link to further quotes by Dr. Marks:

* [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].

Robert J. Marks II - Distinguished Professor of Electrical and Computer Engineering at Baylor University

http://en.wikiquote.org/wiki/Robert_J._Marks_II

Adaptive Robots: Yet More Evidence for Evolution? - November 2010

Excerpt: 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.

http://darwins-god.blogspot.com/2010/11/adaptive-robots-yet-more-evidence-for.html

Do Robots Have Feelings? Dr. Rosalind Picard (MIT) at The Veritas Forum at Rice - video

http://www.youtube.com/watch?v=pz_l34L-tfE

podcast - Dr. Neil Steiner: Comparing Natural and Human-Engineered Systems

http://intelligentdesign.podomatic.com/entry/2013-07-01T17_41_57-07_00 

listen in as Casey Luskin talks with Dr. Neil Steiner, an engineer who works on computer and engineering research with the Information Sciences Institute at University of Southern California. Dr. Steiner offers his expertise to give unique insight into the debate over intelligent design and evolution, comparing natural biological systems to human designed technology.

Can a Computer Think? - Michael Egnor - March 31, 2011

Excerpt: The Turing test isn't a test of a computer. Computers can't take tests, because computers can't think. The Turing test is a test of us. If a computer "passes" it, we fail it. We fail because of our hubris, a delusion that seems to be something original in us. The Turing test is a test of whether human beings have succumbed to the astonishingly naive hubris that we can create souls.,,, It's such irony that the first personal computer was an Apple.

http://www.evolutionnews.org/2011/03/failing_the_turing_test045141.html

 

Modular Biological Complexity - Christof Koch - August 2012

Summary: It has been argued that the technological capability to fully simulate the human brain on digital computers will exist within a decade. This is taken to imply that we will comprehend its functioning, eliminate all diseases, and “upload” ourselves to computers (1). Although such predictions excite the imagination, they are not based on a sound assessment of the complexity of living systems. Such systems are characterized by large numbers of highly heterogeneous components, be they genes, proteins, or cells. These components interact causally in myriad ways across a very large spectrum of space-time, from nanometers to meters and from microseconds to years. A complete understanding of these systems demands that a large fraction of these interactions be experimentally or computationally probed. This is very difficult.,,,

This is bad news. Consider a neuronal synapse -- the presynaptic terminal has an estimated 1000 distinct proteins. Fully analyzing their possible interactions would take about 2000 years. Or consider the task of fully characterizing the visual cortex of the mouse -- about 2 million neurons. Under the extreme assumption that the neurons in these systems can all interact with each other, analyzing the various combinations will take about 10 million years..., even though it is assumed that the underlying technology (in computers used to try to understand the biological interactions) speeds up by an order of magnitude each year. ,,,

Improved technologies for observing and probing biological systems has only led to discoveries of further levels of complexity that need to be dealt with. This process has not yet run its course. We are far away from understanding cell biology, genomes, or brains, and turning this understanding into practical knowledge.

http://www.sciencemag.org/content/337/6094/531.summary 

Mathematicians Offer Elegant Solution to Evolutionary Conundrum

Excerpt: UBC researchers have proffered a new mathematical model that seeks to unravel a key evolutionary riddle–namely what factors underlie the generation of biological diversity both within and between species.,,, existing mathematical models that incorporate these ‘rare type’ advantages tend to have some serious shortcomings,”,,,

http://www.sciencedaily.com/releases/2010/04/100422153931.htm

translation,,, all the calculus level math, that has been taught to intimidated freshman biology students for decades, does not explain the origination of biological information. Thus, massive bandages were applied to the existing evolutionary equations to hide the fact that evolution cannot explain the generation, nor spread, of novel functional information in biological forms. Worse still, this 'new' mathematical model has not even been rigorously tested in the real world though it is offered as a 'elegant solution'.

Here are a few computer programmer articles on the absurdity of Darwinism accounting for programming logic (active information):

Darwinism from an informatics point of view - May 2010

http://www.uncommondescent.com/biology/darwinism-from-an-informatics-point-of-view/

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

The Fairyland of Evolutionary Modeling - May 7, 2013

Excerpt: Salazar-Ciudad and Marín-Riera have shown that not only are suboptimal dead ends an evolutionary possibility, but they are also exceedingly likely to occur in real, developmentally complex structures when fitness is determined by the exact form of the phenotype.

http://www.evolutionnews.org/2013/05/the_fantasy_wor071901.html 

A Darwinian Enigma: Defending The Preposterous After Having Been Informed

Excerpt: I’m thoroughly familiar with Monte Carlo methods. Trial and error can be a useful tool in an intelligently designed computer program, given a limited search space, sufficient computational resources, and a goal in mind.

None of this has anything to do with extrapolating Monte Carlo methods in computation to the origin of information in biological systems.

Unsupported extrapolations such as this are the hallmark of Darwinian speculation, which is the antithesis of rigorous scientific investigation. -

Gil Dodgen - Programmer of 'Perfect Play Checkers'

http://www.uncommondescent.com/intelligent-design/a-darwinian-enigma-defending-the-preposterous-after-having-been-informed/comment-page-1/#comment-410559

World Championship Checkers - Perfect Play - Gil Dodgen

http://www.worldchampionshipcheckers.com/

Another reason why the human mind is not like a computer - June 2012

Excerpt: In computer chess, there is something called the “horizon effect”. It is an effect innate in the algorithms that underpin it. Due to the mathematically staggering number of possibilities, a computer by force has to restrict itself, to establish a fixed search depth. Otherwise the calculations would never end. This fixed search depth means that a ‘horizon’ comes into play, a horizon beyond which the software engine cannot peer.

Anand has shown time and again that he can see beyond this algorithm-imposed barrier, to find new ways, methods of changing the game.

http://www.uncommondescent.com/computer-science/another-reason-why-the-human-mind-is-not-like-a-computer/ 

Evolutionary Algorithms: Are We There Yet? - Ann Gauger

Excerpt: In the recent past, several papers have been published that claim to demonstrate that biological evolution can readily produce new genetic information, using as their evidence the ability of various evolutionary algorithms to find a specific target. This is a rather large claim.,,,,, As perhaps should be no surprise, the authors found that ev uses sources of active information (meaning information added to the search to improve its chances of success compared to a blind search) to help it find its target. Indeed, the algorithm is predisposed toward success because information about the search is built into its very structure.

These same authors have previously reported on the hidden sources of information that allowed another evolutionary algorithm, AVIDA [3-5], to find its target. Once again, active information introduced by the structure of the algorithm was what allowed it to be successful.

 These results confirm that there is no free lunch for evolutionary algorithms. Active information is needed to guide any search that does better than a random walk.

http://biologicinstitute.org/2010/12/17/evolutionary-algorithms-are-we-there-yet/

Here is a far more accurate computer simulation for what we find in life than these severely misleading Evolutionary algorithms::

To Model the Simplest Microbe in the World, You Need 128 Computers - July 23, 2012

Excerpt: Mycoplasma genitalium has one of the smallest genomes of any free-living organism in the world, clocking in at a mere 525 genes. That's a fraction of the size of even another bacterium like E. coli, which has 4,288 genes.,,,

The bioengineers, led by Stanford's Markus Covert, succeeded in modeling the bacterium, and published their work last week in the journal Cell. What's fascinating is how much horsepower they needed to partially simulate this simple organism. It took a cluster of 128 computers running for 9 to 10 hours to actually generate the data on the 25 categories of molecules that are involved in the cell's lifecycle processes.,,,

,,the depth and breadth of cellular complexity has turned out to be nearly unbelievable, and difficult to manage, even given Moore's Law. The M. genitalium model required 28 subsystems to be individually modeled and integrated, and many critics of the work have been complaining on Twitter that's only a fraction of what will eventually be required to consider the simulation realistic.,,,

http://www.theatlantic.com/technology/archive/2012/07/to-model-the-simplest-microbe-in-the-world-you-need-128-computers/260198/ 

Here is the image, from the preceding article, on the integrated processes of M. genitalium

http://cdn.theatlantic.com/static/mt/assets/science/cellmodules.jpg 

Of related interest, although I consider this particular computer simulation to be a far more accurate reflection of reality than Dawkin's weasel program (and other such Evolutionary Algorithms) Gil Dodgen, who works building accurate computer models/simulations for a living, recently posted on the inherent limits, and reliability, of computer simulations:

All Claims Made as the Result of a Computer Simulation Should be Considered BS, Until Proven Otherwise - July 20, 2012 - GilDodgen

Excerpt from comment section: I’ve written software of all kinds for almost 40 years, I’ve taught a range of undergraduate CS and CIS courses, and consulted in many areas including software quality assurance. No non-trivial program is bug-free; no, not one. Two things cause people to earnestly believe that their simulations are reliable – hubris and agreeable results.

http://www.uncommondescent.com/intelligent-design/all-claims-made-as-the-result-of-a-computer-simulation-should-be-considered-bs-until-proven-otherwise/#comment-428243 

In the Physorg write up of this computer simulation study they stated:

Researchers produce first complete computer model of an organism - July 20, 2012

Excerpt: Most biological experiments, however, still take a reductionist approach to this vast array of data: knocking out a single gene and seeing what happens. "Many of the issues we're interested in aren't single-gene problems," said Covert. "They're the complex result of hundreds or thousands of genes interacting.",,,

To integrate these disparate data points into a unified machine, the researchers modeled individual biological processes as 28 separate "modules," each governed by its own algorithm. These modules then communicated to each other after every time step, making for a unified whole that closely matched M. genitalium's real-world behavior.,,,

Consulting the model, the researchers hypothesized that the overall cell cycle's lack of variation was the result of a built-in negative feedback mechanism.

http://phys.org/news/2012-07-researchers-produce-first-complete-computer.html 

And indeed the 'negative feedback' of their 28 separate "modules," each governed by its own algorithm. computer model of the Mycoplasma is due to what can be termed ' the poly-constraint of poly-functionality' they are dealing with in their model of Mycoplasma:

The primary problem that poly-functional complexity presents for neo-Darwinism is this:

To put it plainly, the finding of a severely poly-functional/polyconstrained genome has put the odds, of what was already astronomically impossible for finding a single gene, to what can only be termed fantastically astronomically impossible. To illustrate the monumental brick wall any evolutionary scenario must face when I say genomes are poly-constrained by poly-functionality, I will use a puzzle:

Instead of searching for a single gene/protein, we would actually be encountering something more akin to this illustration found on page 141 of Genetic Entropy by Dr. Sanford.

S A T O R

A R E P O

T E N E T

O P E R A

R O T A S

Which is translated ;

THE SOWER NAMED AREPO HOLDS THE WORKING OF THE WHEELS.

This ancient puzzle, which dates back to 79 AD, reads the same four different ways, Thus, If we change (mutate) any letter we may get a new meaning for a single reading read any one way, as in Dawkins weasel program, but we will consistently destroy the other 3 readings of the message with the new mutation.

This is what is meant when it is said a poly-functional genome is poly-constrained to any random mutations. Thus that is why there is a inherent 'negative feedback' in Mycoplasma as well as, by default, in their model.

Here is a brutally honest admission that neo-Darwinism has no mathematical foundation from a job description from Oxford university, seeking a mathematician to ‘fix’ the ‘mathematical problems’ of neo-Darwinism:  

Oxford University Seeks Mathemagician — May 5th, 2011 by Douglas Axe

Excerpt: Grand theories in physics are usually expressed in mathematics. Newton’s mechanics and Einstein’s theory of special relativity are essentially equations. Words are needed only to interpret the terms. Darwin’s theory of evolution by natural selection has obstinately remained in words since 1859. …

http://biologicinstitute.org/2011/05/05/oxford-university-seeks-mathemagician/

On this following site, a expert computer programmer explains why computers are not truly 'intelligent', as humans are, even though the computers can play (calculate) chess and checkers much better than humans:

Epicycling Through The Materialist Meta-Paradigm Of Consciousness - May 2010

GilDodgen: One of my AI (artificial intelligence) specialties is games of perfect knowledge.

See here:

worldchampionshipcheckers.com

In both checkers and chess humans are no longer competitive against computer programs, because tree-searching techniques have been developed to the point where a human cannot overlook even a single tactical mistake when playing against a state-of-the-art computer program in these games. On the other hand, in the game of Go, played on a 19×19 board with a nominal search space of 19×19 factorial (1.4e+768), the best computer programs are utterly incompetent when playing against even an amateur Go player.,,,

http://www.uncommondescent.com/intelligent-design/epicycling-through-the-materialist-meta-paradigm-of-consciousness/#comment-353454

of related interest:  

Since neo-Darwinists believe that Evolutionary Algorithms, programmed by brilliant engineers, are fully capable of mimicking evolutionary processes, and even eventually reaching the point of ‘self-evolving’ to greater and greater heights of undreamed computational power, then, according to their reasoning, it is entirely plausible that we are now living in some type of gigantic Evolutionary Algorithm computer simulation that was programmed by some future humans???

,,,for a clear example of the absurdity that neo-Darwinism leads to, this following philosophical argument closely parallels what we should expect to see if evolutionary processes were truly unbounded in their information generation capacity, as neo-Darwinists hold, in future computational evolutionary algorithms,,,:

ARE YOU LIVING IN A COMPUTER SIMULATION? BY NICK BOSTROM

Department of Philosophy, Oxford University

VII. CONCLUSION

A technologically mature “posthuman” civilization would have enormous computing power. Based on this empirical fact, the simulation argument shows that at least one of the following propositions is true: (1) The fraction of human-level civilizations that reach a posthuman stage is very close to zero; (2) The fraction of posthuman civilizations that are interested in running ancestor-simulations is very close to zero; (3) The fraction of all people with our kind of experiences that are living in a simulation is very close to one.

If (1) is true, then we will almost certainly go extinct before reaching posthumanity. If (2) is true, then there must be a strong convergence among the courses of advanced civilizations so that virtually none contains any relatively wealthy individuals who desire to run ancestor-simulations and are free to do so. If (3) is true, then we almost certainly live in a simulation. In the dark forest of our current ignorance, it seems sensible to apportion one’s credence roughly evenly between (1), (2), and (3).

Unless we are now living in a simulation, our descendants will almost certainly never run an ancestor-simulation.

http://www.simulation-argument.com/simulation.html

Who'd Have Thought A Man Talking About His Arm Would Be So Interesting? - video

http://www.upworthy.com/whod-have-thought-a-man-talking-about-his-arm-would-be-so-interesting-2 

Refutation of ‘We Are Living In A Computer Simulation’ Argument

http://www.uncommondescent.com/intelligent-design/nyt-columnist-asks-is-intelligent-design-theory-a-form-of-parallel-universes-theory/#comment-490686 

Thus, according to neo-Darwinian reasoning of virtually unlimited computational power in the future for Evolutionary Algorithms, either we are currently living in a computer simulation, or future humanity becomes extinct so as to not run the simulation!!!,,, or, an option that was not mentioned in the above philosophical argument, Evolutionary Algorithms are, in reality, extremely limited in their ability to optimize computer programs above what man has currently programmed them to achieve;

My bet is on the latter,,,  Of related note on the absurdities that neo-Darwinism leads to::

Anthropic Principle – God Created The Universe – Michael Strauss PhD. – video

http://www.metacafe.com/watch/4323661

In the preceding video, at the 6:48 minute mark, Dr. Strauss states:

‘So what are the theological implications of all this? Well Barrow and Tippler wrote this book, ‘The Anthropic Cosmological Principle’, and they saw the design of the universe. But they are atheists basically, there’s no god. And they go through some long arguments to describe why humans are the only intelligent life in the universe. That’s what they believe. And, so they got a problem. If the universe is clearly the product of design, but humans are the only intelligent life in the universe, who creates the universe? So you know what Barrow and Tippler’s solution is? Heh, It makes perfect sense. Humans evolve to a point, someday, where they reach back in time and they create the universe for themselves. (audience laughs) Hey, these guys are respected scientists. So what brings them to that conclusion. It is because the evidence for design is so overwhelming that if you don’t have God, you have humans creating the universe, back in time, for themselves.’

- Michael Strauss PhD. Particle Physics

William Dembski comments on Elizabeth Liddle’s probabilistic objection - Excerpt: Elizabeth Liddle seems stuck with where the discussion over CSI was ten years ago when I published my book NO FREE LUNCH.

She characterizes the Bayesian approach to probabilistic rationality as though that’s what science universally accepts when in fact the scientific community overwhelmingly adopts a Fisherian approach (which, by the way, is not wedded to a frequentist approach — epistemic probabilities, Popper’s propensities, and Bernoulli’s indifference principle all work quite well with it).

Liddle makes off that CSI is a fuzzy concept when her notion of prior probabilities when applied to design inferences is nothing but an exercise in fuzzification.

http://www.uncommondescent.com/intelligent-design/lizzie-joins-the-id-camp-without-even-knowing-it/comment-page-1/#comment-396200

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THE GOD OF THE MATHEMATICIANS – DAVID P. GOLDMAN – August 2010

Excerpt: we cannot construct an ontology that makes God dispensable. Secularists can dismiss this as a mere exercise within predefined rules of the game of mathematical logic, but that is sour grapes, for it was the secular side that hoped to substitute logic for God in the first place. Gödel’s critique of the continuum hypothesis has the same implication as his incompleteness theorems: Mathematics never will create the sort of closed system that sorts reality into neat boxes.

http://www.firstthings.com/article/2010/07/the-god-of-the-mathematicians