Freethought & Rationalism Archive

Principia · 05-12-2003, 05:09 AM

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Albert:
Ah, Principia, that paragraph was the one you cited, not me. Why am I not surprised that it does not articulate my point?
[...]
Note, those 5 were �one-step-prior� mutations. Way prior to them, two mutations, whose reproductive fitness was reduced by a whopping >50%, were the lucky two whose �descendants emerged as eventual winners,� according to my citation.

Are you being honest now, Albert? Because now you are back into the mode of telling me things that you clearly have no earthly clue about.

Read the paper again, Albert. The section you quoted (paragraphs on p. 141) came from one under the heading Case-study population. That was the one where they talked about the lucky two descendants. You are a technical writer, right? What does "case-study" mean to you?

Now, let's look at the section I am talking about. It was under the heading Variations on a theme, which started with the all too important sentence:

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The case-study population was one of 50 that evolved under identical condtions, 23 of which acquired EQU.

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No. But I bet you do. And I bet you won�t tell me, either. You know why? Because in addition to being presumptuous, a lack of honesty tends to induce displays of condescension.

First you call what I wrote �idiotic comments.� So I categorize what I wrote as one paraphrase, two questions, one self-effacing statement and one compliment and ask you for an explanation.

Get over yourself, Albert. It becomes clear that your own "self-effacement" was nothing but a rhetorical show. It is your "paraphrase" that was disingenuous. Here let's revisit what you actually paraphrased in three sentences, from one sentence of Nic's:

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Nic: The only things that I see the mutation rate affecting are the cases where they had a detrimental mutation that was "rescued" by a later mutation such that the two had a net benefit.
Albert: The article made a point of stressing the fact that detrimental mutations preceded the evolution of EQU, that without the detrimental mutations, EQU may not have evolved. In the real world, those deleterious mutations would not have been rescued immediately by the artificially high mutation rate. They�d have had to wait for many generations for another mutation to snatch success from the jaws of defeat, and in that timeframe, been swallowed up by death.

The premise, as I have demonstrated, is incorrect. In no way could any reasonable reader have concluded that the authors said "without the detrimental mutations, EQU may not have evolved." And despite two opportunities now to read the paper, Albert, you continue to assert it. This is not what an honest person calls paraphrasing. It is distortion. Here, let's look at what a dictionary defines as paraphrase:

Code:

1 : a restatement of a text, passage, or work giving the meaning in another form

"Giving the meaning in another form." The irony of it all is that by your own admission, you have no clue what the meaning is. So why call it paraphrasing, Albert -- especially when several posts later, you told me that it was an argument.

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I�ve happily asserted at every turn that my knowledge of evolution is sparse.

Finally, something I can agree with.

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That�s why I�m here, to learn.

But then your posture as a deeply concerned close-minded skeptic betrays your innocence. Your having an agenda, like starting a multi-page discussion on the evolution of morality is as absurd as a schoolboy questioning the wisdom of his arithmetic teacher because there are frauds in the world. No, I think the image you want to project is incongruous with the one you are projecting.

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What's your excuse? To display how engaging and winsome you can be in an honest give and take dialogue with your inferiors?

Give it a break, Albert. I am calling it as I see it and I see no indications that you are open-minded enough to be learning. For someone who says things like:

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You guys are celebrating the proof of evolution here based upon virtual mutations that deviate by many many orders of magnitude from the biological facts. [...] At a million virtual replications per second, the Avida program could run that many replications in just 304 days, not �thousands or millions of years� as you say. [...]Because evolution, as a theory that explains the process by which complexity extant today may have developed from the simplicity of yesterday, is a time-contingent process. Speeding up the mutation rate is functionally equivalent to extending the amount of time organisms had to evolve. But in reality, the time evolution had to do its magic is fixed, perhaps 3 � billion years max. So increasing the mutation rate seems like cheating, seems like pretending evolution had more time than it did to produce what it did. [...] Evolutionists should show some compassion on us and not make it any more difficult than it already is to believe their theory.

I'll let the readers judge if you are displaying open-mindedness and a willingness to learn; or if you are the one here with an anti-evolutionary agenda. But, I nearly forget this sentence, which I love best:

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Albert Cipriani: This I cannot understand.

As a technical writer, you have chosen an interesting way of phrasing this supposed "self-effacement." You cannot, rather than you do not, understand. Tell us, Albert. Who forbids you to understand evolution? Is it your ownself, with all your preconceptions, or is it some Higher calling?

pz · 05-12-2003, 01:21 PM

Cool it down a bit, Principia. You can make the same points without the testosterone, and be a bit more likely to get a reply from Albert...which I would like to see.

Oh, and Albert -- your post just before this one wasn't exactly a model of delicate decorum, either.

Captn Kidd · 05-13-2003, 02:09 PM

I think Albert has a point about the elevated mutation rate improving the odds of a deleterious mutation being rescued.

If a mutation decreases fitness by 50% (rather extreme), it will be weeded from the gene pool ruthlessly. If it doesn't get rescued in the next few generations, it will disappear. A high mutation rate increases the odds that it will be rescued before it disappears. So yes, Albert, you are correct in your assertion.

On the other hand, small genomes, small population sizes and small numbers of generations decrease the odds of us seeing these "rescue" events. If the experimenters had gone with "realistic" mutation rates, they would also have needed to go with populations "realistic" genome sizes, and populations that approximate the number of bacteria on the planet, for untold millions of generations. That is far beyond any conceivable computing power in the coming decades.

I look at the high mutation rate in the experiment as a computational shortcut to get around our limited hardware. Somebody earlier posted the an approximation for the number of generations of bacteria...but that underestimates the total by an immense amount. The more valid comparison would be the number of bacterial generations times the size of the bacterial genome in base pairs times the bacterial population of the earth...and that get's into some impossibly big numbers for computer simulation.

The high mutation rate in this experiment makes it possible to see the types of mutations that would happen in a larger population of more complex organisms over a longer period of time.

Did that help explain it?

Principia · 05-13-2003, 02:30 PM

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Captn Kidd: The high mutation rate in this experiment makes it possible to see the types of mutations that would happen in a larger population of more complex organisms over a longer period of time.

A masterfully diplomatic post. But if Albert, or for that matter any other like-minded people, has an issue with the relevance of the computer model towards simulating every detail of biotic reality, then they are barking up the wrong tree. Once again, quoting directly from the paper:

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To examine the evolutionary origin of a complex feature in much greater detail than has previously been possible, we have performed experiments with digital organisms -- computer programs that self-replicate, mutate and compete [17-26]. As Daniel Dennett [27] has emphasized, "...evolution will occur whenever and wherever three conditions are met: replication, variation (mutation), and differential fitness (competition)." By using this tractable system, we aim to shed light on principles relevant to any evolving system.

"...principles relevant to any evolving system," that possesses the 3 criteria. Nowhere did the authors imply that they were out to model actual evolutionary history. But, what principles are they talking about? Look again at the paper:

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Our experiments demonstrate the validity of the hypothesis, first articulated by Darwin [1] and supported today by comarative and experimental evidence [2-16], that complex features generally evolve by modifying existing structures and fucntions. Some readers might suggest that we 'stacked the deck' by studying the evolution of a complex feature that could be built on simpler functions that were also useful. However, that is precisely what evolutionary theory requires, and indeed, our experiments showed that the complex feature never evolved when simpler functions were not rewarded. Our experiments also show that many different genomic solutions produce the samae complex function. Following any particular path is extremely unlikely, but the complex function evolved with a high probability, implying a very large number of potential paths [32]. Although the complex feature first appeared as the immediate result of only one or two mutations, its function invariably depended on many instructions that had previously evolved to perform other functions, such that their removal would eliminate the new feature.

My emphasis of only the last sentence is not meant to imply that this is in fact the only evolutionary principle illustrated by Avida. But it is this last sentence that eviscerates many of the Creato and IDiot arguments. In particular, the inference that if a function requires multiple interacting parts (e.g. instructions) then the function could not have evolved, is patently untenable. It also reinforces the counterargument that one cannot merely dismiss a function's evolutionary history merely by inspection.

But, here's a suggestion to the critics: Rather than complain about the inaccuracy of the model wrt to biotic reality, DO SOMETHING about it, namely research. Arm-chair philosophizing has a dismally poor track record of helping increase the practical knowledge of mankind.

PS: quotes of course from Lenski et al.

Principia · 05-14-2003, 06:24 AM

As I suggested earlier, the threads over at the IDiot strongholds might become really interesting as they struggle to save their pet theories. Take a look at some of the recent whinings:

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IDiot #1: In other words, what I'm saying is that this program appears to impose an entirely artifical selective pressure to promote a complex result that would never fly out in the real world. In the real world, the only thing that matters is how many offspring you produce. That's it. There's no extra benefit from doing fancy logical calculations or analysis on your own environment (what the heck is the EQU function supposed to contribute towards fitness in the computer simulation anyway???). The bottom line is, the authors of this study introduced this totally arbitrary selection for "computational merit" which has absolutely no tie-in with real fitness and actually rewards organisms which are less fit, in a reproductive sense, than their peers.

"In the real world, the only thing that matters is how many offspring your produce," coming from a biology graduate student at your local secular university...

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IDiot #2: Probably I have not made myself clear. It appears to me that EQU can be computed by acting on using the original NAND function to different part of the problem subspace, a number of times. One part can be when A=B=1, related to (A^B), the other part can be when A=B=0, related to (~A^~B). The third operation combine the results using another NAND operation. If this is the case, then EQU is just another expression of NAND, acting on transformed and partitioned problem subspaces. There is no novelty in the new EQU function. It is the old NAND function. So rather than showing the power of a Darwinian process, surprisingly the experiment has shown its limit.

Um, why does he feel the need to repeat a factual error? EQU requires 5 NAND and other instructions to manipulate registers. The authors came up with 19 instructions at a minimum.

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IDiot #3: In fact, no doubt EQU itself only requires very little instructions, this has no equivalent with any of the IC systems that design theorists study. In fact, the bacterial flagellum cannot be reduced so drastically and still retain function, which explains why EQU is so plastic and the flagellum is not. It is universal among eubacteria. [...] There are many ways to achieve motility. I get along just fine without flagella, as a matter of fact. But we're not talking about just motility, especially with the bacterial flagellum. We are talking about motility via bi-directional rotor motor-driven propeller, there is no such thing as a simpler way to do that. On the other hand, there is a simpler (as admitted by the authors of the paper)ways to do EQU , and which is why there might be plasticity there, there is no plasticity among the parts that are required to attain the function in bacterial flagella. You need all 20 parts, or there is no motility via bidirectional rotor motor-driven propeller. All the parts are conserved and universal.

Besides committing the same fallacy as IDiot #2, this guy moves the goal posts around too. "Simpler" ways to achieve EQU (at a minimum of 19 instructions), but no simpler ways to achieve "bidirectional rotor motor-driven propeller" (at a minimum, according to him, of 20 parts)? Right...

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IDiot #4: That being pointed out, however, charlie d.'s contention is that the paper may show that IC can be achieved through natural processes, modelled by the program in question and mentioned in the paper. My response is that I'm not sure that it does. A system is not IC if the informational gap is so small that it can be jumped by random processes. In spite of the fact that the virtual mutations are simulated to be random, both the jump to the intermediate NAND function and then the jump to the EQU function have a probability approaching 1, given the way the simulation is designed and the number of generations executed. One does not need ID to achieve such results, nor do the results appear to qualify as IC for the reason I have just laid out.

"A system is not IC if the informational gap is so small that it can be jumped by random processes." As expected, another qualification to the IC definition. What the hell is an informational gap, and how do you measure it? I bet we won't find out any time soon.

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IDiot #5: Well, if they are instructions critical to the EQU function, you will no longer have EQU. But that's not sufficient to call it IC. Knock out one of the letters that produced METHINKS IT IS LIKE A WEASEL, and you no longer have that. Like EQU, it either is or isn't, by definition. But like Micah points out, how does this translate to the biological world? Is METHINKS IT ID LIKE A WEASEL good enough to provide some functionality or not? Is a function that matches EQU on a 32 bit string for 31 of the 32 positions good enough to provide a selective advantage? Note that the simulation does indeed reward some of the component functions used to build EQU, and that puts them reasonably "close by" in an evolutionary sense, for some of the reasons John points out.

Any more explicit, and this would've been a major concession. But he punts off to the nearest IDiot before getting nailed...

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IDiot #5 again:
The parts are "well matched" to the function via ID. The designers of the program picked a limited set of components conducive to the goal of EQU. That isn't anything like a bacterial flagellum in the real world.

Hmm... there was only one logical primitive in the entire experiment: NAND. But, here he parrots IDiots #1 and IDiots #3.

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IDiot #6: All this talk of moving goalposts is bull*&^$ as far as I'm concerned. Truly... has a theory ever been put forth that hasn't been modified to deal with new data sets? Isn't it the practice of science to generalize originally specific theories onto larger domains? The people moving the goalposts of this entire conversation are the ones who are demanding of IC and Behe something that is not demanded of any other scientific theory in the history of the world. It is exceedingly frustrating. This is why it is important to remember the context in which Behe proposed his theory. It certainly was not in the context of logic primitives which can be slapped together in a sequential 2 dimensions to achieve new functions. Personally, I think that those who get wrapped up in this "moving the goalposts" tactic have very little interest in really finding out how relevant this project is to Behe's original conception of IC. Blindly defending any research that comes out which seems to have implications against ID is cheap cognition. As the friendly moderator often says: this is the mindset of people fighting a battle and not of people engaging in dialogue. Unchartiable standards are the signs of closed minds.

"Behe didn't consider logical primitives when he made up his Bull#&^$ thesis about IC. Therefore this experiment doesn't apply. Mommirator!!!" LOL

These people are pathetic.

Principia · 05-14-2003, 06:35 AM

Note that the essence of what the IDiots are saying is that there are no experimental setups which would convince them their theories are wrong. If anyone devises an experimental system that produces IC, then by "definition" that IC state was "front-loaded" into the system teleologically. If anyone devises an experimental system that evolves within human lifespans, then it is not biologically realistic or relevant. If an evolved system appears IC and was not originally considered by Behe or Dembski, then it is unfair to apply a different domain of inquiry.

So, short of God appearing with his lab notebook, or someone discovering time travel, ID is obviously an untestable thesis. If they complain otherwise, just point to these threads. The irony in all of this is that, once again, it is the Darwinian atheist materialist scientistssss who did the experiments, and yet we find the IDiots sitting on the sidelines.

PS: Can't sign off for the day, without putting up this favorite of mine:

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IDiot Jack: The only value to this study that I can see is in propaganda value, which I guess is why Robert Pennock was involved. And it's suceeding to some degree, clearly.

*Laugh*

pangloss · 05-14-2003, 08:12 AM

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PS: Can't sign off for the day, without putting up this favorite of mine: *Laugh*

I've always considered Jackie boy to be basically worthless....

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05-12-2003, 01:21 PM	#32
pz Veteran Member Join Date: Aug 2001 Location: Morris, MN Posts: 3,341	Cool it down a bit, Principia. You can make the same points without the testosterone, and be a bit more likely to get a reply from Albert...which I would like to see. Oh, and Albert -- your post just before this one wasn't exactly a model of delicate decorum, either.

05-13-2003, 02:09 PM	#33
Captn Kidd Regular Member Join Date: Aug 2002 Location: Texas Posts: 166	I think Albert has a point about the elevated mutation rate improving the odds of a deleterious mutation being rescued. If a mutation decreases fitness by 50% (rather extreme), it will be weeded from the gene pool ruthlessly. If it doesn't get rescued in the next few generations, it will disappear. A high mutation rate increases the odds that it will be rescued before it disappears. So yes, Albert, you are correct in your assertion. On the other hand, small genomes, small population sizes and small numbers of generations decrease the odds of us seeing these "rescue" events. If the experimenters had gone with "realistic" mutation rates, they would also have needed to go with populations "realistic" genome sizes, and populations that approximate the number of bacteria on the planet, for untold millions of generations. That is far beyond any conceivable computing power in the coming decades. I look at the high mutation rate in the experiment as a computational shortcut to get around our limited hardware. Somebody earlier posted the an approximation for the number of generations of bacteria...but that underestimates the total by an immense amount. The more valid comparison would be the number of bacterial generations times the size of the bacterial genome in base pairs times the bacterial population of the earth...and that get's into some impossibly big numbers for computer simulation. The high mutation rate in this experiment makes it possible to see the types of mutations that would happen in a larger population of more complex organisms over a longer period of time. Did that help explain it?

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