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Computer Simulations and Darwinism

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Okay dudes, no more talk about my abandonment of atheism. Here’s some science and engineering talk.

I know something about computer simulations. In fact, I know a lot about them, and their limitations.

Search algorithms (and especially AI-related search algorithms) are a specialty of mine, as is combinatorial mathematics.

The branching factor (the average number of moves per side) in chess yields approximately 10^120 possible outcomes, but the number of legally achievable positions is approximately 10^80 — the estimated number of elementary particles (protons and neutrons) in the entire known universe. Compare this to the branching factor of nucleotide sequences in the DNA molecule. Do the math.

Finite element analysis (FEA) of nonlinear, transient, dynamic systems, with the use of the most sophisticated, powerful computer program ever devised for such purposes (LS-DYNA, originally conceived at Lawrence Livermore National Laboratory in the mid-1970s for the development of variable-yield nuclear weapons) is another of my computer-simulation specialties.

Dyna has been used heavily in the automotive industry for simulating car crashes, so that cars can be designed to produce the least damage to occupants.

In these simulations everything is precisely known and empirically quantified (the material properties of the components — modulus of elasticity, mass density, shear modulus, precisely calibrated failure modes, etc.).

In addition, the explicit FEA time step (the minimal integration time step determined by the software based on the speed on sound in the smallest finite element and its mass density, which is required to avoid numerical instability) is critical. In my simulations the time step is approximately a ten-millionth of second, during which partial differential equations, based on the laws of physics (F=ma in particular) are solved to compute the physical distortion of the system and the propagation of the forces throughout the system in question.

One learns very quickly with FEA simulations that even with all of this knowledge and sophistication one must empirically justify the results of the simulation incrementally by comparing the results with the reality it attempts to simulate.

One false assumption about a material property or any of the other aspects of a simulation can completely invalidate it. Worse yet, it can produce results that seem reasonable, but are completely wrong.

So, the next time someone tries to convince you that a computer simulation has validated the creative power of the Darwinian mechanism of random errors filtered by natural selection in biology, you should tell them to go back to school and learn something about legitimate computer simulations, and how difficult it is to produce reliable results, even when the details are well known.

Comments
DrBot
But is not just features of a system, like gravity, aerodynamic characteristics, etc. The solution it looks to prove is programmed in from the beginning. That is the the question-begging circularity that Eric speaks of.
No it isn’t.
What isn’t? The solution being programmed in from the beginning, or that being the question-begging circularity that Eric speaks of?uoflcard
October 5, 2011
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DrBot
But is not just features of a system, like gravity, aerodynamic characteristics, etc. The solution it looks to prove is programmed in from the beginning. That is the the question-begging circularity that Eric speaks of.
No it isn’t.
What isn't? The solution being programmed in from the beginning, or that being the question-begging circularity that Eric speaks of?uoflcard
October 5, 2011
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DrBot
You mean more substantial than “seems to have been designed”? Can ID offer any evidence beyond this?
Observation: Functional, complex, specified information Proven causes of Observation: Intelligence/Design, none others Inference to best explanation: Intelligence/Design That is why it "seems" to have been designed. How much evidence could you possibly want that this fCSI can be generated by intelligence? Every word you type is further evidence of this. The evidence that is lacking is that anything besides intelligence is capable of generating fCSI. That's all this debate boils down to, really. Can you offer evidence rather than assertions and apriori assumptions? Your view was accepted as fact long before this problem was ever known, and we still are not to the bottom of the complexity of life.uoflcard
October 5, 2011
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DrBot, Have I made an ID-related claim regarding the mammalian inner ear? If I don't have anything substantial then I won't make a claim. That's good advice for anyone. I'm still free to point out that someone else's claim that the mammalian inner ear "seems to have evolved" is insubstantial, which it still is, just in case anyone got distracted.ScottAndrews
October 5, 2011
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If there is something more substantial than “seems to have evolved,” use that to establish the premise.
You mean more substantial than "seems to have been designed"? Can ID offer any evidence beyond this?DrBot
October 5, 2011
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But is not just features of a system, like gravity, aerodynamic characteristics, etc. The solution it looks to prove is programmed in from the beginning. That is the the question-begging circularity that Eric speaks of.
No it isn't.DrBot
October 5, 2011
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Elizabeth, since you apparently have very little understanding/experience with computer programs and the problem of circularity, let's step back a bit. Please just answer my question from 2.1.1.1. Would such a program prove that Darwinian evolution is false, or would it be an example of circular reasoning?Eric Anderson
October 5, 2011
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Petrushka, After mentioning the mammalian inner ear, you say, "We can easily demonstrate the adequacy of that kind of change. Breeders exploit it all the time." Are you saying that one could breed a new type of inner ear or some similar change? You are saying that. Perhaps it's the difference between the length of legs and having legs in the first place and knowing how to use them that we need to focus on. By your own words you indicate great uncertainty about how the mammalian ear might have evolved. If there is something more substantial than "seems to have evolved," use that to establish the premise. Right now the assertion that no such pathway has ever been observed stands unchallenged. It's what we know, and it carries far more weight than what someone things might have happened but can't explain in any specific detail.ScottAndrews
October 5, 2011
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Not a single person here doubts that the Darwinian mechanism works when this pathway is present. But we have no evidence that such a pathway has ever existed for any complex, specified, functional feature/mechanism/object/information that has ever been observed. None.
There are two major categories of change. Those that affect protein coding and those that affect developmental pathways. The mammalian middle ear seems to have evolved purely by the route that changes development, things like leg length in dogs. In the case of the ear, it appears to have affected the size and timing of bone development. We have fossil evidence that it was incremental. We can easily demonstrate the adequacy of that kind of change. Breeders exploit it all the time, and did so long before Darwin.Petrushka
October 5, 2011
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DrBot
You appear to be arguing that it is wrong to include features of a system in a simulation of that system if you are attempting to establish what effect those features have on the system.
But is not just features of a system, like gravity, aerodynamic characteristics, etc. The solution it looks to prove is programmed in from the beginning. That is the the question-begging circularity that Eric speaks of. Taking your analogous simulation, let's say I want to run a simulation to see if a freely falling object's flight path (let's say, a feather) can spell out the word "Hello" in cursive. Would it be misleading to program in a powerful jet stream that just happened to spell out the word "Hello" in cursive? Seems obvious to me, and it also seems that this is exactly what Avida does. It is programmed to succeed.uoflcard
October 5, 2011
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But Eric, the whole point of the AVIDA simulation is to show that if a feature is “rewarded” it will evolve! That’s the Darwinian mechanism! And it works! It’s not circular to demonstrate that the mechanism you propose works, works! It’s just successful!
But it entirely misses the point of the primary challenge to Darwinism, which is the question "IS there a bit-by-bit, functionally increasing pathway to any complex, specified, functional system?" This pathway is guided every step of the way in these "simulations". Not a single person here doubts that the Darwinian mechanism works when this pathway is present. But we have no evidence that such a pathway has ever existed for any complex, specified, functional feature/mechanism/object/information that has ever been observed. None. That is the point. I have personally seen it described to you on this website dozens and dozens of times, and have done so myself many times (three times in this thread, in fact) and have never seen an evidence-based reply. Great, AVIDA proves that the Darwinian mechanism works (as long as we figure out the one challenge ID has been talking about for the last 10+ years). Similarly, I will run a one-step simulation to show that I am rich: uoflcard's Bank account = $50,000,000 See, I'm rich! (Once I actually get the $50,000,000)uoflcard
October 5, 2011
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you’ve got a neutral sequence hanging around (from duplication or whatever your preferred approach is). Even if you have complete and total freedom to tweak the sequence all you want, you simply are not likely to stumble upon a functional protein sequence.
I think you are wrong. What Axe did was start with modern functional sequences and explore the possibility of finding adjacent functional sequences, without breaking functionality. What others have done is start with completely novel sequences, ones having nothing in common with living things, and explore the possibility that they might have function. And some do. So the issue is not whether you can improve on existing proteins, but whether you can find new, minimally functional proteins. It matters that duplication and other genomic changes provide sequences that are "off line" so to speak. Mutations in non-necessary genes are neutral, so it is possible to cross to other islands. But the really interesting thing being revealed by sequencing technology is that genes are very old, and most predate multi-celled organisms.Petrushka
October 5, 2011
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The existence proof is down to you, guys. ID claims a big enough increase in complexity cannot be done spontaneously simply *because it has not been observed*. I would like to ask you a few things. 1. Do you acknowledge the fact that between System A that has vision of any kind (no matter rudimentary or not) and System B which doesn't there is a complexity gap. 2. Do you appreciate how big this complexity gap is? 3. Do you appreciate the likelihood of such a spontaneous advantageous complexity increase given our universe?Eugene S
October 5, 2011
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Elizabeth- what is this alleged "Darwinian hypothesis"? Also there isn't any evidence that all mutations/ genetic changes are Darwinian processes- that is the point of what Eric said. Scientists just ASSUME all changes are Darwinian. That said ID is NOT anti-evolution and is OK with reproduction, heritable variation and an envirnment. ID just posits the variation is directed via internal programming. Geez you anti-ID types are so clueless it is painful.Joseph
October 5, 2011
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Dr Liddle: Kindly cf my current discussion of the underlying issues here in an update post. GEM of TKIkairosfocus
October 5, 2011
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All the key issues about the Darwinian mechanism are *assumed* as premises and programmed into the system. It is entirely circular, 100%.
No, all the key observations are modelled in the simulation - all the mechanisms that are observed to exist. The output of the simulation confirms the hypothesis - that given heritable variation in reproductive success within an environment, adaptation will occur. If not then which of the following aspects of the simulation are not observed to exist in reality: >> Reproduction. >> heritable variation. >> an environment.DrBot
October 5, 2011
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And that is the wrong answer. Enough has been said here at UD and elsewhere that there are. But that obviously does not count…
No it doesn't - you need evidence, not just claims.DrBot
October 5, 2011
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No, they are not "assumed as premises", Eric. You really are confused! It tests the Darwinian hypothesis that given heritable variation in reproductive success within an environment, adaptation will occur. And it does. The "solutions" to the "problems" posed by the environment are not assumed at the outset, either in nature or in AVIDA. But in both, the problems are given as survival problems, and the evolving populations finds solutions that are, a priori, unknown. The reason it may seem "circular" to you is that it is so self-evidently true. That was the beauty of Darwin's insight.Elizabeth Liddle
October 5, 2011
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Eric, I'm not sure you have understood. You appear to be arguing that it is wrong to include features of a system in a simulation of that system if you are attempting to establish what effect those features have on the system.
Is there a route from point a, to b, to c to get to our final function? Avida is programmed to assume that there is. (2) ...
Let me paraphrase the argument. I want to study the effect of an aerodynamic feature on a free falling object and hypothesize that the feature will allow the object to drift a given distance in relation to the drop altitude. So I create a simulation that includes gravity, air, and the aerodynamic feature I am studying. You are claiming that it is circular to include these features? Can you tell us how you would create an experiment to test the hypotheses that AVIDA was created to test without the circularity you allege?
In other words, if I assume all of the key points about my theory, then I can demonstrate the veracity of my theory.
Then you create a model and see how well the model matches observed data. . . If you propose pixies as a feature then you need to demonstrate that they exist and how they operate, not just claim that they do.DrBot
October 5, 2011
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Liz, I'll just leave you with these thoughts: Do you ever marvel at the beauty of the laws of physics which govern the universe and that appear to be fine-tuned for the emergence of life? Do you think about the fact that these laws can be represented by equally elegant and beautiful mathematical equations, and that the human mind has uncovered these profound relationships? Do you ever think, deep in your soul, about the profound discontinuity between human and animal life, and where that might have come from in a geological instant? Are you completely convinced that your materialistic worldview can account for Chopin's piano concerto? If your worldview is correct (and I find it superbly irrational) then nothing ultimately matters. We are just meat-machines, and all of the discussion on this forum is a completely pointless waste of time, as is your life, and as is mine.GilDodgen
October 4, 2011
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Elizabeth, see my comment above. All the key issues about the Darwinian mechanism are *assumed* as premises and programmed into the system. It is entirely circular, 100%. If you doubt this, then please answer the following question: I have a theory that there is no indirect Darwinian pathway from point x to y. I write a computer program, *building in the fact that there is no possible indirect pathway from x to y.* I run the program, and sure enough, none of my fake "organisms" make it from x to y through an indirect pathway. Would you say that the program has demonstrated the veracity of my theory? Or would you say that the program is an exercise in circular reasoning?Eric Anderson
October 4, 2011
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Elizabeth: “But Eric, the whole point of the AVIDA simulation is to show that if a feature is “rewarded” it will evolve! That’s the Darwinian mechanism! And it works! It’s not circular to demonstrate that the mechanism you propose works, works! It’s just successful!” Well, I posted a long comment earlier today, but apparently it went into the ether. Briefly, the Avida paper demonstrates purely circular question-begging reasoning. Let’s look at some of the key questions about the alleged Darwinian mechanism. (1) Is there a route from point a, to b, to c to get to our final function? Avida is programmed to assume that there is. (2) Does each point along the route confer a functional advantage? Avida is programmed to provide such advantage. (3) Is there an end-looking goal to the progress? Avida supplies the end “goal”. (4) Would organisms be rewarded more for getting closer to the goal? Avida includes an increasing award along the way. (5) Does it only take a small number of changes to get from point x to y? Avida is programmed with a short, simplistic path. (6) Is it easy for mutations to achieve each step along the way? Avida is programmed with that assumption. Those are off the top of my head, and we could probably think of others if we took a few minutes. In other words, if I assume all of the key points about my theory, then I can demonstrate the veracity of my theory. Congratulations. Guess what, I can prove my theory about pixies creating all the trees in the forest too. All I have to do is assume that pixies exist and regularly create trees in the forest and, voila, I have shown my theory! Let’s be very clear, in addition to all the problems that arise from the fact that Avida doesn’t mimic anything close to biotic reality, the primary Avida paper Darwinists love to point to as a demonstration of Darwinian principles in action is nothing but question-begging circularity. As a demonstration of Darwinian evolution having the ability to evolve irreducibly complex features (which was the point of the exercise), it is fatally flawed and logically invalid. Please take some time to think through this issue before jumping on the Avida bandwagon. Darwinism isn’t proven wrong just because of the Avida circularity, so it’s OK for you to acknowledge that Avida is circular. :)Eric Anderson
October 4, 2011
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"The Darwinian answer is "no"." And that is the wrong answer. Enough has been said here at UD and elsewhere that there are. But that obviously does not count...Eugene S
October 4, 2011
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This really does betray a complete misunderstanding of both AVIDA and evolution on both your parts! The reasoning is not "circular" at all. The hypothesis is that if you have self-replicating critters that reproduce with variance, and that the variance results in differential reproduction in a given environment, the population will tend to adapt to that environment, meaning that its members will tend to have features that enhance its chances of surviving and reproducing in that environment. All the AVIDA simulation does is specify the environmental constraints on survival. In nature, these simply exist. Thus, AVIDA simulates a toy version of nature, in which populations evolve to survive environmental hazards and exploit resources. In AVIDA the environmental resources are exploited by critters that can perform logic functions. In life they are exploited by critters that can perform foraging functions. No circularity at all.Elizabeth Liddle
October 4, 2011
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But Eric, the whole point of the AVIDA simulation is to show that if a feature is "rewarded" it will evolve! That's the Darwinian mechanism! And it works! It's not circular to demonstrate that the mechanism you propose works, works! It's just successful!Elizabeth Liddle
October 4, 2011
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Indeed. So the issue is: are there islands? The Darwinian answer is "no".Elizabeth Liddle
October 4, 2011
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would hope you would appreciate this by now, but it bears repeating. First, bad design is not a valid argument against design.
No, it isn't, but it would be an argument against a good designer.
Second, the bad design nonsense, from Darwin to modern times, enjoys an extremely poor track record — nearly 100% negative.
I didn't say the giraffe's neck was "badly" designed (although I would say our own backs were, also female pelvises). I said it looked incrementally designed - retrofitted from an earlier model. Why else would the recurrent laryngeal nerve take such a hugely circuitous route? But the point about incremental retrofitting is that however successful the result (and incremental modification is often an excellent way to proceed), it tends to leave a "paper trail", as in the recurrent laryngeal nerve. Or what are called "skiamorphs" in human design.Elizabeth Liddle
October 4, 2011
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gene duplication and fusion seem to always pop-up when i read about new genes.Starbuck
October 4, 2011
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Uoflcard, It is so clear and obvious, isn't it? Trouble is they will never agree with this, maybe some individuals will, but not the entire cohort. They will keep on repeating that Windows 7 bit by bit can come spontaneously out of "Hello, world!" or that long messages can appear by chance as a result of letters spontaneously sticking together in words and then in sentences. And that meaning can emerge out of chaos by itself...Eugene S
October 4, 2011
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Elizabeth: “But Gil, the range of “existing” information in any given population that is “mixed and matched” is itself the result of mutations!” If you simply mean that mutations are happening and changing existing information, then sure (although they wouldn’t be changing it for the better, see below). If you mean that mutations are responsible for the functional complex specified information that is in organisms in the first place, then your statement is an unsupported article of faith.
Well, we need a clear definition of information in order to continue with this conversation. If a mutation results in a viable phenotype that nonetheless bears brand new alleles, we can say there is "new" information - we now have a DNA sequence that "tells" the other molecule in the cell to do something new. There is no reason to think that this wouldn't be something "better", but more likely it is something that is neither better nor worse, simply slightly different. If it is disastrously worse, it probably won't get passed on to many offspring, if any, and will quickly drop right out of the gene pool. If neutral, it may propagate through the population, and if better, it is more likely to do so. Once it has become prevalent, and most members of the population bear it, to their advantage, we say that the population has "adapted", in that it now mostly consists of individuals that have a new feature that fits it better for the current environment. So in this sense the population genome, and the prevalence of the new allele represents population-level "information" about what works in the current environment. As for "the functional complex specified information that is in organisms in the first place" then it depends what you mean by "in the first place". Why should we assume that "in the first place" the "information" was particularly complex? We know that Darwinian processes (heritable variance in reproductive success) results in information, on at least two levels (the organism and the population), and that this information tends to accumulate. What 's to prevent it starting simple and becoming more complex?
“Mutations – novel sequences – are constantly being drip-fed into the population . . .” Again, if you mean that mutations can change sequences, sure. If you mean that mutations bring about new functional complex specified information, then this statement is unsupported.
I mean that mutations result in brand new alleles. These represent new information in the sense that they build and/or maintain an organism in a new, if tiny, way. They also represent variety in the population gene pool. This means that the population can adapt, as you would agree it does, which means that it represents "information" from which "nature" "selects" what "works" in the current, or changing environment. If you mean something else by "new functional specified information" then please say what. I have just supported my own statement.
“Especially as we know from simulations that this is exactly what happens!” Not clear what you mean by “this.” What is it you think is happening in computer simulations? If you are referring to the fact that simulations are programmed to keep the “helpful” changes and cull the bad ones, then we are simply talking about a circular programming logic.
Computer imulations of evolutionary processes simulate the natural process by which "helpful" changes are bred from and the poorer ones are "culled" by hazard. That's not "circular programming logic" it's simply the implementation of the very mechanism that Darwin proposed, and it works.
If you are suggesting that simulations produce new functional complex specified information, that is simply false. No computer simulation has ever done so.
Lots of simulations have done so. That's why we use them - to gain "new functional, complex, specified information" about how to solve a problem. Quite literally. Sometimes the information is a piece of computer code; sometimes it is a novel design (antennae, for instance); sometimes it is a classifying algorithm. All are new (they didn't exist at the beginning of the run); functional (they do a useful job); complex (in the sense of being highly unlikely to be generated by a random draw of components, although sometimes more elegantly simple than human designs); and specified (one of a sub set of possible patterns), and they tell us something we didn't know (so they contain information).Elizabeth Liddle
October 4, 2011
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