Subjects: Evolutionary computation. Information technology–Mathematics.
… the authors establish that their mathematical analysis of search applies to models of evolution.
I have all sorts of fancy stuff to say about the new book by Marks, Dembski, and Ewert. But I wonder whether I should say anything fancy at all. There is a ginormous flaw in evolutionary informatics, quite easy to see when it’s pointed out to you. The authors develop mathematical analysis of apples, and then apply it to oranges. You need not know what apples and oranges are to see that the authors have got some explaining to do. When applying the analysis to an orange, they must identify their assumptions about apples, and show that the assumptions hold also for the orange. Otherwise the results are meaningless.
The authors have proved that there is “conservation of information” in search for a solution to a problem. I have simplified, generalized, and trivialized their results. I have also explained that their measure of “information” is actually a measure of performance. But I see now that the technical points really do not matter. What matters is that the authors have never identified, let alone justified, the assumptions of the math in their studies of evolutionary models.a They have measured “information” in models, and made a big deal of it because “information” is conserved in search for a solution to a problem. What does search for a solution to a problem have to do with modeling of evolution? Search me. In the absence of a demonstration that their “conservation of information” math applies to a model of evolution, their measurement of “information” means nothing. It especially does not mean that the evolutionary process in the model is intelligently designed by the modeler.1
I was going to post an explanation of why the analysis of search does not apply to modeling of evolution. But I realized that it would give the impression that the burden is on me to show that the authors have misapplied the analysis.2 As soon as I raise objections, the “Charles Ingram of active information” will try to turn the issue into what I have said. The issue is what he and his coauthors have never bothered to say, from 2009 to the present. As I indicated above, they must start by stating the assumptions of the math. Then they must establish that the assumptions hold for a particular model that they address. Every one of you recognizes this as a correct description of how mathematical analysis works. I suspect that the authors recognize that they cannot deliver. In the book, they work hard at fostering the misconception that an evolutionary model is essentially the same as an evolutionary search. As I explained in a sidebar to the Evo-Info series, the two are definitely not the same. Most readers will swallow the false conflation, however, and consequently will be incapable of conceiving that analysis of an evolutionary model as search needs justification.
The premise of evolutionary informatics is that evolution requires information. Until the authors demonstrate that the “conservation of information” results for search apply to models of evolution, Introduction to Evolutionary Informatics will be worthless.
1 Joe Felsenstein came up with a striking demonstration that design is not required for “information.” In his GUC Bug model (presented in a post coauthored by me), genotypes are randomly associated with fitnesses. There obviously is no design in the fitness landscape, and yet we measured a substantial quantity of “information” in the model. The “Charles Ingram of active information” twice feigned a response, first ignoring our model entirely, and then silently changing both our model and his measure of active information.
2 Actually, I have already explained why the “conservation of information” math does not apply to models of evolution, including Joe’s GUC Bug. I recently wrote a much shorter and much sweeter explanation, to be posted in my own sweet time.
a ETA: Marks et al. measure the “information” of models developed by others. Basically, they claim to show that evolutionary processes succeed in solving problems only because the modelers supply the processes with information. In Chapter 1, freely available online, they write, “Our work was initially motivated by attempts of others to describe Darwinian evolution by computer simulation or mathematical models. The authors of these papers purport that their work relates to biological evolution. We show repeatedly that the proposed models all require inclusion of significant knowledge about the problem being solved. If a goal of a model is specified in advance, that’s not Darwinian evolution: it’s intelligent design. So ironically, these models of evolution purported to demonstrate Darwinian evolution necessitate an intelligent designer. The programmer’s contribution to success, dubbed active information, is measured in bits.” If you wonder Success at what? then you are on the right track.
The Series
Evo-Info review: Do not buy the book until…
Evo-Info 1: Engineering analysis construed as metaphysics
Evo-Info 2: Teaser for algorithmic specified complexity
Evo-Info sidebar: Conservation of performance in search
Evo-Info 3: Evolution is not search
Evo-Info 4: Non-conservation of algorithmic specified complexity
Evo-Info 4 addendum
Sure. It has more parts that come together to make the whole or contribute to the final function = it is more complex.
No, because you have not increased the number of parts. Assuming by mutations you mean nucleotide substitutions. If you don’t, you’re going to have to tell me the nature of those 600 mutations.
You’re going to have to tell me more about these two cells than their labels (benign tumor vs metastasised cancer cell). They could be equally complex, I don’t know, because their mere labels don’t tell me that.
I get that you ask these questions because you genuinely believe you’ve found something wrong with my defintion. Maybe you should just get to that instead of, again, acting out the part of an inane person who finds the whole thing preposterous.
Have you asked yourself why you come here and interact with me and others? Do you think that the way you “argue”, if one can even call it that, is in any way convincing? Are you here because you believe that the things you say will be found convincing? Or are you just here to point you fingers, mock, and laugh?
🙂
Entire books have been written!
I like the way they put that.
Good thing these guys don’t post here, they’d be crucified. Or worse, labelled ‘ID Creationists.’
Atheists are supposed to be rational. We expose that as a fallacy. They are as idealistic and bigoted as religious believers, if not worse.
What’s the fallacy?
Yes, I know. I said nothing that your comment here refutes. Your claim was that the base organism has to gain energy in order to reproduce. That’s simply false. The organisms don’t have to gain anything in order to reproduce. It’s the default condition, as you admit.
If an organism never gains and more ‘energy’ beyond what it has been given when it is first created it can still reproduce. Even if an organism loses ‘energy’ it can still reproduce.
So your initial statement is just false. Get over it.
Wrong. All organisms are created equal and given the same amount of CPU time. They don’t need to gain anything in order to reproduce. If they “evolve” a logic function they are rewarded with more CPU cycles which means they can reproduce faster relative to other organisms.
It doesn’t have to gain energy so that it can reproduce itself.
Read it.
LoL. A book for “skeptics.”
Did you know that phoodoo?
Just as bigoted as people who stereotype people?
Hilarious. Why don’t you send a note to Gusz Eiben, and ask him about me? (I’ve only been introduced to Jim Smith — can’t say I know him.)
Once again thank you for admitting it. However you’ve yet to show anyone other then you has those characteristics. Perhaps you could provide links to support this claim? Oh, wait, it is you…
Have you read the OP in the last couple weeks?
Plus there are my comments about evolutionary search on the previous page. Have you forgotten about those too?
It’s entirely plausible that you really believe that. But I was asking phoodoo, and if the same is true for him, it really does raise the question why his posts are so consistently and thoroughly inane and void of any substance. If what you say really is phoodoo’s goal with having this particular argument, it makes it all the more perplexing that none of his posts even hint at being constructed to accomplish that.
No, it isn’t.
Yes they do.
I don’t “admit” this, I inform you that it is so. You denied it.
It isn’t “given” any energy to begin with. It is given the ability to gain, as in take in, or obtain it. The particular word they use is obtain. http://www.dictionary.com/browse/obtain
obtain
[uh b-teyn]
verb (used with object)
1. to come into possession of; get, acquire, or procure, as through an effort or by a request: to obtain permission; to obtain a better income.
2. Obsolete. to attain or reach.
http://www.dictionary.com/browse/gain
gain
[geyn]
verb (used with object)
1. to get (something desired), especially as a result of one’s efforts: to gain possession of an object; to gain permission to enter a country.
2. to acquire as an increase or addition: to gain weight; to gain speed.
3. to obtain as a profit: He gained ten dollars by this deal.
The analogy here could be that you were create with arms and hands so you can take food and put it in your mouth. Not that you were created with food already in your digestive tract.
Yes, this analogy isn’t exactly correct in all aspects, since technically if no energy already exists in your body, you wouldn’t be even able to move your arms to grab any food.
But for the avidian, there doesn’t exist any energy “inside” the organism when it is first created. It is created with the ability to take it up and THEN start using it.
It can’t lose energy (it doesn’t store any that can be lost), it can suffer mutations that decrease the rate at which it obtains(aka gains) it.
You know what, if I was wrong I would readily admit it and move on, because I honestly think this is a minor point of little relevance to what the experiment was set up to address. I just happen not to be wrong.
I haven’t denied this so I don’t know what you think I’m wrong about here. Yes, each experimental run was started from an identical, basic organism.
Wrong.
“Experiments began with an ancestor that could replicate but could not perform any logic functions. All organisms were identical and obtained equal energy to execute their genomic programs, including the copy commands by which a genome replicates itself one instruction at a time.”
If they evolve a logic function they are rewarded with more CPU cycles which means they can reproduce faster relative to other organisms.
I read it. It confirmed everything I have been saying. You should get over it.
Rumraket,
It sounds like you don’t even have the faintest idea what you are talking about.
I wonder why you post here.
Please enlighten me then.
Rumraket,
Ok.
Don’t post about things you know nothing about.
Also, its possible there are things you feel you know a lot about. That may also be wrong.
I thank you for being this constructive. What in particular is it I know nothing about?
Yes, it’s possible there are such things. But then I need to find out what those things are. I’m not going to just assume this is one such case on your mere assertion.
I know that I’m very far from having expertise in evolutionary computation. But I still know enough to be able to see what is wrong with what both you and Mung are saying, and I am able to articulate it.
The apparent and obvious fact that this pisses you off and makes you want to shut me up isn’t going to stop me. Just get over it already. Be an adult.
Pot kettle black
Pot kettle black
Are they?
I take atheists to be human. And humans are not rational.
Atheists are supposed to be rational in the same sense that theists are supposed to be ethical. Neither is true, but it advances the self-interests of organizations claiming to represent those groups to say so. In other words, such claims function as ideology.
Atheists aren’t supposed to believe in God.
I’ve never understood that this meant they were supposed to be rational, per se. Unsuprisingly. most of them claim to be rational (and often empirical) about it, but who doesn’t claim that about their “chosen” position?
It’s a matter of judgment whether or not a particular atheist actually is rational, about atheism or other ideas.
Glen Davidson
I’ll name that tune in three.
You think he’ll have better luck when you’ve already dug in your heels and refuse to receive the light you’ve already been given?
What’s the point of creating an initial population if none of them can reproduce?
Nothing would happen. There would be no “evolution.” Reproducing organisms (organisms that reproduce) is the default condition.
How many CPU cycles is each initial organism given so that it can reproduce and what does it have to do in order to be granted those processor cycles?
So it could already replicate. Now let’s follow your logic.
It can replicate, but it can’t replicate because it has to “gain energy” before it can reproduce. And how does it gain energy? By evolving. And how does it evolve without replicating? Beats me.
They would never evolve if they first had to evolve some feature or other that would allow them to gain the energy so that they could evolve.
Not only is this what the paper tells us but it’s basic logic. And you fail.
How do they gain energy?
And yet, when started, they can’t perform any logic functions. So again, following your logic, they cannot “obtain energy” because they can’t reproduce in order to evolve the functions they need so that they can gain the energy they need so that they can reproduce.
Don’t be obtuse.
Mung:
Did Lenski et al. choose the EQU target to suit Avida (with default instruction set)?
I don’t know what they were thinking. It’s difficult even to tell where their paper begins and where Avida ends. Take for example their Figure 1. Was the exclamation point after EQU a mistake?
My belief is they exactly what they were doing and avoid discussing why they made the choices they did even in the Methods portion of their paper. The best clue, imo, regarding their thinking, is in their Table 1.
So to give a direct and unequivocal answer your question, yes. I believe they did.
Now let me ask you a question. If they published a paper proclaim how wonderful it is that Avida could evolve the AND function and that it proves that complexity can evolve, would that have impressed anyone?
Here’s another question. If certain logic functions were no more or less meritorious than any other logic function, would that make it impossible for EQU to evolve, or would it have merely made it more imprabable than it already was.
Because really, what we get down to at the root of all this, is an exercise in probability. Dawkins’ WEASEL program could have hit the target phrase without all the fancy shenanigans given enough time and resources, and the Lenski et al experiment is no different when it comes to EQU.
God, from his heaven above, could have smiled on them and given them an EQU when they didn’t expect one, and no one would have attributed it to a miracle. It might have been seen as a fluke, but one within the bounds of what was theoretically possible within the program.
Why am I wrong?
It would appear that we have found something we can agree on. 🙂
And I don’t just mean when it comes to atheists.
But if the atheists here at TSZ are no more or less rational than the theists, and their declarations of rationality in the face of the irrational is ideology, how do we spread that good news?
Tom, you’re a rare bird here at TSZ. You actually know what you’re talking about
I apologize if it appears that I am gloating at your expense.
But surely you have some sense of the shit I’ve taken over the years here at TSZ for my stance on EAs, GAs and EC and what those fields can contribute to the debate over ID vs “it just happened, that’s all. No reason.”
Hell, if we want to try to draw in the philosophers we could ask why the logic functions used by Avida work at all. Are they applicable in any world, or only this one? Why should they work both in vivo and in silico?
I have been given nothing but assertions.
What’s the point of creating an initial population if none of them can reproduce?
I agree that would be silly. They could reproduce already, by obtaining energy and executing instructions.
From the paper:
“Digital organisms compete for the energy needed to execute instructions. Energy occurs as discrete quanta called ‘single-instruction processing’ units, or SIPs. Each SIP suffices to execute one instruction. By executing instructions, a digital organism can express phenotypes that enable it to obtain more energy and copy its genome. In Avida, organisms can acquire energy by two mechanisms.
First, each organism receives SIPs in proportion to its genome length. Second, an organism can obtain further SIPs by performing one- and two-input logic operations on 32-bit strings (Supplementary Information).”
From the methods section:
“Experimental conditions
Every population started with 3,600 identical copies of an ancestral genotype that could replicate but could not perform any logic functions. Each replicate population that evolved in the same environment was seeded with a different random number. The handwritten ancestral genome was 50 instructions long, of which 15 were required for efficient self-replication; the other 35 were tandem copies of a single no-operation instruction (nop-C) that performed no function when executed.
(…)
Each digital organism obtained ‘energy’ in the form of SIPs at a relative rate (standardized by the total demand of all organisms in the population) equal to the product of its genome length and computational merit, where the latter is the product of rewards for logic functions performed.”
They didn’t have to first evolve to obtain energy, they could this already in the beginning. Obviously, otherwise they would not be able to execute their genomic programs and the commands for replication.
Going back to my arm-with-hand analogy, the avidians essentially were created with an arm that could stuff their mouthes with food. That arm did not require energy of it’s own to run. It just works. That’s analogous to how the Avidian obtains energy by default. It is created with this ability. It obtains a SIP and executes an instruction, obtains one more SIP and executes one more instruction. Or actually, it might obtain all the SIPs required for a full life cycle, and then run the instructions one at a time, not sure which. Regardless of whether it takes in one or all of the required SIPs for a full cycle, before it starts running the instructions(the paper isn’t very clear on this point), it does actually run the instructions one at a time in a serial (as opposed to in parallel) manner.
Evolving to be able to execute logic functions was rewarded with additional energy. As in, if after they replicated a number of times and happened to mutate so they could perform those logic functions, they would be rewarded with even more energy than their base acquisition rate.
Yes, reproducing organisms is the default condition. They can reproduce because they were created with the ability to obtain the energy they need to execute their genomic programs.
I’ve quoted the paper directly several times. It’s not going to stop being what the paper says.
I don’t know the conversion rate between a CPU cycle and a SIP and it doesn’t seem pertinent to what we are arguing about. But by default an organism obtains a number of SIPs “equal to the product of its genome length and computational merit”.
None of what you write following this is my logic.
“Each digital organism obtained ‘energy’ in the form of SIPs at a relative rate (standardized by the total demand of all organisms in the population) equal to the product of its genome length and computational merit”.
I see now that you have confused logic functions with genomic instructions.
Not all the genomic instructions are logic functions. Evolving logic functions is rewarded with more SIPs than are needed to execute all the genomic instructions.
Haha, no it seems what we’re actually doing is following your giant trail of confusion around because you haven’t fathomed that there is a difference between a genomic instruction and a logic function.
And I am supposed to be the one who has no idea what I’m talking about here?
FUCKING LOL.
All of this is wrong, because they don’t need to evolve logic functions in order obtain energy for executing their genomic instructions. They simply obtain SIPs in a number equal to the number of genomic instructions they have (effectively, genome length) and then run those instructions one at a time in a linear manner. Including the copying commands for replication.
Mung,
You were unable to note who is claiming “it just happened, that’s all. No reason.” on the Is ID a reasonable alternative… thread. Would you be able to do so now? Who is claiming what just happened without reason?
And are we still talking about biology? If not, then it still seems to me it is the theists who are the only ones saying “it just happened” (what else is “let there be light” apart from the ultimate “just so story”?). Everyone else is either proposing explanations or saying “I don’t know”.
Once again it’s more projection. You accuse others of what you know only you are guilty of. You can easily demonstrate otherwise just by providing a citation to those people who are claiming “it just happened”.
Atheists don’t appear to have the ability to organise themselves into such an organisation (one that effectively advances their self-interests. The religious right on the other hand…
Do they receive enough SIPs to enable them to reproduce even in the absence of gaining energy through evolving logic functions? The answer is yes.
Do they have to evolve a longer genome in order to gain enough energy to reproduce? The answer is no.
So they don’t have to gain anything in order to reproduce. They don’t have to gain a longer genome and they don’t have to gain the ability to perform logic functions. There is no gain of energy needed for them to reproduce. It’s part of the basic package that they are granted by the platform.
If they never gained a longer genome and if they never gained the ability to perform a logic function they would still reproduce. So you were wrong.
No shit sherlock. Yet you claimed they had to gain energy in order to reproduce. They don’t have to gain anything in order to reproduce. They are given everything they need. They can reproduce FASTER if they GAIN more CPU cycles.
But they do not need to GAIN more CPU cycles in order to reproduce. So you were wrong.
Crap. I bought the book. Can I get my money back?
Just in case Rumraket is paying attention.
Why should Avida reward longer genomes that don’t even perform a logic function? Surely there was a point to that feature of Avida.
I know, let’s reward even longer legs on Giraffes.
Why should Avida reward longer genomes that don’t even perform a logic function?
Surely there was a point to that feature of Avida.
Seems like Rumraket finally figured out he had no case.