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#4 of 2011 for ID community: “Stylus” Computer Program Aims to Bridge Gap Between Real World and Artificial Evolutionary Simulation.

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Every year, Access Research Network publishes a list of the 10 most significant science news stories for the year, for the intelligent design community – in consultation with theorists and writers. For 2011, here’s #4:

Many computer simulations that purport to simulate Darwinian evolution have deficiencies: Pro-ID scientists like William Dembski or Robert Marks have shown how programs smuggle in information such that they are pre-directed to evolve their targets. Doug Axe’s work demonstrates that such programs typically evolve solutions to artificial, rather than real-world problems. A new peer-reviewed paper in BIO-Complexity by Axe, Philip Lu, and Stephanie Flatau explains that the “functions” of the digital organisms in these simulations are often divorced from real-world meaning. According to Axe they designed Stylus to present a more accurate picture of what evolution might be able to accomplish in the real world: “The motivation for Stylus was the recognition that prior models used to study evolutionary innovation did not adequately represent the complex causal connection between genotypes and phenotypes.”

Basic to life is an information conversion, where the information carried in genes (the genotype) is converted into an organism’s observable traits (the phenotype). Those biological structures then perform various functions.

Stylus uses Chinese characters as digital objects as explained in the paper: “These translation products, called vector proteins, are functionless unless they form legible Chinese characters, in which case they serve the real function of writing. This coupling of artificial genetic causation to the real world of language makes evolutionary experimentation possible in a context where innovation can have a richness of variety and a depth of causal complexity that at least hints at what is needed to explain the complexity of bacterial proteomes.” There probably will never be a perfect computer simulation of biological evolution, but the free Stylus software brings new and improved methods to the field of evolutionary modeling. This tool will help those interested in testing the viability of Darwinian claims to assess whether complex features can be created by random mutations at the molecular level.

See also:

#1 of 2011 for ID community: 50th Peer-Reviewed Pro-ID Scientific Paper Published.

#2 of 2011 for ID community: The Design of the Butterfly Continues to Inspire and Amaze.

#3 of 2011 for ID community: Woodpecker Drumming Inspires Shock-Absorbing System.

#5 of 2011 for ID community: Explosive Radiation of Flowering Plants Confirmed

#6 of 2011 for ID community: Golden Orb-Weaver Fossil Spider Provides New Evidence for Stasis.

#7 of 2011 for ID community: Complexity in the Universe Appears Earlier Than Thought.

#8 of 2011 for ID community: An Identity Crisis for Human Ancestors.

#9 of 2011 for ID community: DNA Repair Mechanisms Reveal a Contradiction in Evolutionary Theory.

#10 of 2011 for ID community: Limits to self-organization of life identified

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Comments
What evidence for design have you brought to the table?Petrushka
January 11, 2012
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Suppose I can't. what's your point?Petrushka
January 11, 2012
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1) Because its science. 2) Because its the way we find it. 3) Because you yourself keep bringing it up (eg "no evidence for design"). 4) Because you'd rather have your spleen removed with a fork than to acknowledge the evidence in front of you. - - - - - Now, how are you going to enciode the information in your knots without physical representations and physical protocols acting together in a dynamic semiotic system?Upright BiPed
January 11, 2012
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Abstract representations and protocols are a formal system, Petrushka – a formal system. A system which must arise PRIOR to genetic heredity – prior to the onset of evolution by means of mutable genetic information.
You seem to be bringing origin of life into a discussion of evolution. My question is why?Petrushka
January 11, 2012
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I don’t understand why you are asking the question.
Petrushka, I find that very hard to believe. I have been rather consistent in my dealings with you for the very reason that you have (in turn) been rather consistent in repeatedly taking for granted what must be explained, while at the same time voicing over and over and over again that ‘no evidence whatsoever exist for design’. Above, you suggest the idea of modeling evolution by means of encoding knots, and you give your reasons for the suggestion – fine. My first question to you is how are you going to encode the information without a formal system of representations and protocols - that is, (as you seem to acknowledge) by abstracting the state of the knots into physical representations which must in turn be coordinated to specific protocols for decoding those representations back in to the state of the knot. In other words, without the rise of the abstractions and rules (which are the critical requirements of any and all recorded information). Abstract representations and protocols are a formal system, Petrushka – a formal system. A system which must arise PRIOR to genetic heredity – prior to the onset of evolution by means of mutable genetic information. And it is also a sterling example of irreducibly complex (a physical representation and a physical protocol operating in a precise dynamic relationship, how could it be any other way, either object is useless without the other). To any rational person, information is the organizing force behind all living systems. And its very existence is entirely dependent on a formal semiotic system of representations and protocols. Look at your own language that you used… where you talk of abstractions, rules, and procedures. These are the things you simply take for granted, and under the scenario of materialism, these are the very things which must be organically produced (prior to genetic evolution) from nothing but the very simplest of chemical structures. Materialism promotes proto-life chemistry as being the source of the observed formalities in biology; creating abstractions and establishing rules. Gimme a break. You should seek to be more accurate in your apprasal of the evidence.Upright BiPed
January 11, 2012
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I don't understand why you are asking the question. There has to be some equivalent of DNA and some procedural language for describing the process of moving the string ends. So what is your point? My point is that knots can be abstracted, and so can the movements required to form them. And unlike dictionary lists, there is no arbitrary limit to the number of different knots. And like protein folds, any possible configuration can be classified as belonging or not belonging to the set of knots. One does not need a list, just a few rules.Petrushka
January 10, 2012
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So what is it going to be Petrushka? How are you going to record the state of your knots in information without a formal system of physical representations and physical protocols (just like any other form of encoded information). Be upfront about it.Upright BiPed
January 10, 2012
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So you say that you want to model evolution by the encoding of knots. (Evolution, obviously being driven by variation in the encoded information used for replication, unless you now wish to claim that evolution can occur without replication). But when asked how you intend to encode the information, you first respond that you don't understand the question about "encoding", and now you respond that you don't understand what is meant by "replication". Did you not say:
So why not Model evolution as knot tying? There are ways of coding them digitally. I’m sure there’s a way to code them.
So the question is rather basic; How do you plan to encode them into information without a formal system of representations and protocols? Again, if Step One is a cause for problem, then you are very obviously over your head. (Yet, you are the first to claim that there is no evidence of design in nature).Upright BiPed
January 10, 2012
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I'm not sure what you mean by a means of replication. Do Chinese characters replicate? The process being modeled is incremental change. In order to have evolution there must exist a landscape having connected regions of function, as defined by some definition of fitness. I don't know about Stylus,so I asked if it supports incremental, selectable change. But I also think any model of evolution should have the capacity to create objects not in the dictionary used by the selection function. Which is to say, it should support the creation of novelty and novel functionality. Arrangements of strings can be modelled in a way that allows determining whether they form a knot, even if the knot takes a form never seen before. One could even classify them and sort them by complexity.Petrushka
January 10, 2012
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You've repeated the statement that you can record knots as encoded information. I assume you mean to encode these as a means of replication. Among other things, I am asking how you plan to do that without a formal system of representations and protocols. If that question trips you up, then perhaps you are in over your head. It happens.Upright BiPed
January 10, 2012
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I'm not sure what you are asking. Knots are definitely functional. They also exhibit a continuum of functionality. They can be described in a way that allows new forms that have never existed before. That makes them more like proteins, which might be viewed as a subset of knots. Ckinese characters are a limited set, and evolving them is just a variation ova the Weasel program. I find my Itatsi.com program slightly more interesting, because it is not limited todictionary words. It can create new words that are not in any dictionary, but which could be useful to people looking for new tradenames. I've already seen it produce some existing drug names -- words that are not in its dictionary. It can do this because its definition of fitness is based on pronouncability rather than on inclusion in a dictionary.Petrushka
January 10, 2012
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Encode them? As information? For what effect, or purpose? Can they be encoded without the use of abstractions, and rules to actualize those abstractions, or are representations and protocols (a formal system) required for the encoding itself?Upright BiPed
January 10, 2012
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Really? What is that ratio? What is your source? Does Stylus support selection of incremental improvements? Does it have populations with individuals having selectable differences in fitness? My question about knots is a question about whether an objectively definable function can occur without being designed. There's an entire branch of mathematics dealing with knots. I'm sure there's a way to code them.Petrushka
January 9, 2012
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One reason they chose Chinese is because the ratio of the number of Chinese characters to the universe of possible characters is roughly equal to the ratio of the number of actual functional proteins to the number of possible proteins. Can you say the same thing about knots?EndoplasmicMessenger
January 9, 2012
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Why does the program have to produce existing words in order to demonstrate evolotion? The other day I was thinking about knots and whether they are similar to protein folds. Certainly knots represent specified functional information. There are ways of coding them digitally. Their existence is objective in a way that human languages are not. They do not require a dictionary of targets. So why not Model evolution as knot tying?Petrushka
January 9, 2012
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