The Eyes Have It
by MikeGeneFrom here:
The genes that make a fruit fly's eyes red also produce red wing patterns in the Heliconius butterfly found in South and Central America, finds a new study by a UC Irvine entomologist…."We found that evolution is achieved primarily through recycling old genes into new functions, as opposed to evolving entirely new genes from scratch," Reed said.
Yes indeed, evolution is achieved primarily through recycling old genes into new functions, as opposed to evolving entirely new genes from scratch. That's one reason front-loading is plausible.
October 28th, 2007 at 10:03 am
#1 Cooption is exceedingly improbable.
#2 Cooption is rampant.
As we have observed the evolution of cooption, and we have evidence that cooption is an important historical mechanism, indeed, a primary evolutionary mechanism, and as #1 is usually made by some sort of fallacious argument-by-exponent; I'll take #2.
Fins to legs to arms to wings to fins. Cooption.
Comment by Zachriel — October 28, 2007 @ 10:03 am
October 28th, 2007 at 10:14 am
Here is what I wrote: "And co-option, from a non-teleological vantage point, is indeed an appeal to random chance." This is how Zachriel chose to spin it: "Cooption is exceedingly improbable."
What explains the way Zachriel has twisted my words? Is it substandard reading comprehension? Is it that he thinks he has psychic powers? Is it dishonesty?
Comment by MikeGene — October 28, 2007 @ 10:14 am
October 28th, 2007 at 10:34 am
Ah, you didn't have to give me any clues.
"Appeal" means to entreat or to plea. "Random chance" is a catchphrase. "Appeal to random chance" has a clear meaning in context, and it doesn't mean inevitable due to the Law of Large Numbers.
But I will take that as a clarification.
Comment by Zachriel — October 28, 2007 @ 10:34 am
October 28th, 2007 at 10:46 am
I'll answer the question, Zachriel. I think you demonstrated substandard reading comprehension here as a consequence of wanting to score points. When I wrote, "And co-option, from a non-teleological vantage point, is indeed an appeal to random chance," I was NOT making any probability claim. I was correcting Taylor Kessinger's misguided understanding of evolution. He seemed to think that when it came to the origin of the bacterial flagellum, "Such statements demonstrate flagrant ignorance of evolution, whose driving force, natural selection, is the exact opposite of random chance." After noting that he would need to define "driving force" and provide evidence to support this claim, I simply pointed out that "random chance" (his words) is thought to have played a crucial role, at many steps, in the evolution of the flagellum in the form of cooption.
Rather than quote-mine to score rhetorical points, and rather than argue with something you imagine I said, pay attention to what I wrote in the context of where I wrote it.
Comment by MikeGene — October 28, 2007 @ 10:46 am
October 28th, 2007 at 11:12 am
Mike,
Is it possible that "front-loading" is not present in any of the examples you have cited? If so, what would convince you that it's not present?
Comment by Frostman — October 28, 2007 @ 11:12 am
October 28th, 2007 at 11:30 am
Speaking only for myself convincing evidence would be evidence favoring a non-FL option. For example, I've contended that genomic repair mechanisms are an excellent candidate for FL. I've also detailed my reasons why in prior comments.
Comment by Bradford — October 28, 2007 @ 11:30 am
October 28th, 2007 at 11:30 am
There are a lot of unknowns about the evolution of the flagellum; but as it arose more than once, it was probably not mere "random chance" in the sense of being an exceedingly improbable occurrence (over the time-scales and populations involved). Your last sentence reads as an incorrect *generalization* made from the specific case, yet inaccurate even in the instance.
Gamblers may appeal to chance, but the House relies on probability. You can keep all the points. I just wanted a clarification. Thank you.
Comment by Zachriel — October 28, 2007 @ 11:30 am
October 28th, 2007 at 11:48 am
Hi Frostman,
Of coure it's possible. In fact, most of my examples serve to illustrate the plausiblity of front-loading. I'm not, for example, arguing that the wing color of butterflies was indeed front-loaded. I deal with your question in the interview I gave; right now, I have lots of errands to attend to.
Comment by MikeGene — October 28, 2007 @ 11:48 am
October 28th, 2007 at 11:51 am
Hi Zachriel,
Wrong.
I see. Intead of asking for clarification, your tactic is to misrepresent others and see if they respond. Thank you for making it clear that you will misrepresent your opponents to score points.
Comment by MikeGene — October 28, 2007 @ 11:51 am
October 28th, 2007 at 12:00 pm
Was the answer to my first question an implicit yes? Is it possible that front-loading is not present?
You appear to be saying this: Given a new hypothesis X, in order to be convinced that X is not true, evidence must be shown which would rule out X. Is that right?
Comment by Frostman — October 28, 2007 @ 12:00 pm
October 28th, 2007 at 12:05 pm
Frostman:
No. There is no evidence against front loading and there are reasons to believe that standard explanations, attempting to explain the evolution of genomic repair mechanisms, are fundamentally flawed.
Comment by Bradford — October 28, 2007 @ 12:05 pm
October 28th, 2007 at 12:26 pm
Would you explain further? It appears that you are saying that.
It doesn't help to say there is no evidence against X. There is no evidence against the existence of an invisible, silent, odorless, ethereal dragon in my garage (to borrow an example from Carl Sagan).
Comment by Frostman — October 28, 2007 @ 12:26 pm
October 28th, 2007 at 12:36 pm
I disagree. Your statement is wrong on the specifics and an inaccurate generalization. Few if any reseachers in the field think that the flagellum was the result of mere "random chance" in the normal sense of that phrase, but the result of evolutionary processes, including selection pressures. The generalization just compounds the error.
I saw that phrase when you first blogged on Dime-a-Dozen. I initially ignored it as tangential. But then GilDodgen piped up, so I then attempted to engage you directly.
As cooption commonly occurs, it belies the notion that we must "appeal to random chance". There are obviously other important factors involved. After answering a few of your questions, my last statement on that thread was a question directed at you.
Which you didn't answer. (Maybe you were busy.) Then you blogged again on cooption, but apparently taking the opposite tack. So I read, and then reread your statement. I restated it in such a way as to illustrate the apparent contradiction, and was sure to include your original statement including link. By highlighing the apparent contradiction, and turning it into a guessing game, it was clearly a request for clarification.
Then when my motives were questioned, I explained how and why I read your statement that way. And now you repeat the claim that the flagellum is due to "random chance" which leaves me guessing that you are again invoking the term as usually used in Intelligent Design. But you still accuse me of playing rhetorical games.
Comment by Zachriel — October 28, 2007 @ 12:36 pm
October 28th, 2007 at 12:49 pm
Frostman, unless you address the reasons why I think genomic repair mechanisms were front loaded you are wasting time with the Xs.
Comment by Bradford — October 28, 2007 @ 12:49 pm
October 28th, 2007 at 1:12 pm
I did not address it because it was not relevant to the question I asked. I'll ask again: What would convince you that front-loading is not present? Are you sticking with your previous answer?
Comment by Frostman — October 28, 2007 @ 1:12 pm
October 28th, 2007 at 2:11 pm
Frostman:
What sense does it make to ask what would convince me that FL was not present when you have not made an effort to find out why I think it was present. This shows me you are more interested in a dogmatic defense of your position than in learning what the actual position of someone else really is.
Comment by Bradford — October 28, 2007 @ 2:11 pm
October 28th, 2007 at 3:12 pm
Peace.
Comment by Zachriel — October 28, 2007 @ 3:12 pm
October 28th, 2007 at 3:54 pm
Hi Zachriel,
One problem. I never claimed that the flagellum was the result of mere "random chance." In order to prop up your original misrepresentation, you now have to stuff some new words into my mouth. I guess you are just trying to get more "clarification."
Comment by MikeGene — October 28, 2007 @ 3:54 pm
October 28th, 2007 at 4:35 pm
Because if there is nothing which would convince you that FL was not present, then your position on FL is simply dogmatic. If I know that you cannot be convinced otherwise, what sense does it make for me to bother?
The following exchange, which ended with an unanswered question, may become a classic:
I await your reply.
Comment by Frostman — October 28, 2007 @ 4:35 pm
October 28th, 2007 at 4:48 pm
Frostman, contrary to what many think there is no existing model that adaquately explains the causes that brought about initial genomes or the mechanisms by which they control errors and destructive effects of ubiquitous environmental agents. Evolution is viewed as an innovative process but it is more accurately portrayed as a conserving one. In order to induce change there must exist a means of preventing the same. If less than one percent of a genome changes to afford an organism an adaptive advantage (a reasonable figure) this must occur while 99+ % of mutating effects are simultaneously eliminated from a genome. If they are not genomic meltdown occurs along with the demise of the affected organism. In view of biological realities it is my position that a functional cellular genome remains viable only when repair mechanisms exist. Remove them and you induce meltdown. Front load them and you enable life. They cannot evolve through RM + NS because genomic deterioration occurs faster than new information can be fixed.
Comment by Bradford — October 28, 2007 @ 4:48 pm
October 28th, 2007 at 4:59 pm
Frostman
I really appreciate your question and I think it's a valid one to discuss. If you don't mind just so I am sure you are coming at this topic as a honest skeptic would you answer a related question?
What would convince you that in addition to RS/NS a mechanism like frontloading is necessary to account for the origin and/or evolution of life?
Thanks in advance
Peace
Comment by fifth monarchy man — October 28, 2007 @ 4:59 pm
October 28th, 2007 at 6:30 pm
Bradford, my response is contingent upon your answer to my previous question — see the "classic" exchange above.
Comment by Frostman — October 28, 2007 @ 6:30 pm
October 28th, 2007 at 7:32 pm
fmm, there is no RM+NS pathway to life but I assume you are aware of that. For a random mutation to occur there must be an existing genome wherein mutations can occur. What we are really looking at are mainstream arguments from authority or consensus that themselves are based on personal opinion. So the answer to the question about what it would take to to convince one that FL did not occur is to ask for evidence of how life actually arose and what is the evidence upon which that is based? I would assume this evidence would be scientifically sound so where is it?
Comment by Bradford — October 28, 2007 @ 7:32 pm
October 28th, 2007 at 8:00 pm
OK, you have confirmed what you said before, "convincing evidence would be evidence favoring a non-FL option."
I summarized your position as: Given a new hypothesis X, in order to be convinced that X is not true, evidence must be shown which would rule out X. You said no, which appears to be a contradiction unless I misunderstand something. What did you mean by "no"
I think we may yet get somewhere; if we end up with a succinct argument which you accept and I reject, or vice versa, then at least we could understand each other.
Comment by Frostman — October 28, 2007 @ 8:00 pm
October 28th, 2007 at 8:13 pm
I guess I assumed something I should not have assumed. When I mentioned a specific mechanism I claim to be front loaded I thought you would be interested in knowing something about this before continuing. After all how can you present evidence opposed to something when you do not have a clue as to what the affirmative evidence consists of? To convince one that X is untrue by presenting evidence that rules out X appears tautological or did you have something more to add to this?
Comment by Bradford — October 28, 2007 @ 8:13 pm
October 28th, 2007 at 8:34 pm
Frostman
What? huh? I have no clue what that has to do with what I asked
I asked
How about I make it even more simple so we can avoid confusion in the future
What evidence would convince you that RM/NS is insufficient to account for the phenomena that it's supporters claim it explains?
Peace
Comment by fifth monarchy man — October 28, 2007 @ 8:34 pm
October 28th, 2007 at 8:42 pm
[ Confused post deleted; I saw "fmm" and somehow thought it meant "Frostman". ]
Comment by Frostman — October 28, 2007 @ 8:42 pm
October 28th, 2007 at 8:43 pm
FMM, identities are getting mixed up. I'm already convinced of front loading and note that RM/NS is not even a lucid concept unless a genome can be mutated. Since there was a point in time when no genomes existed how do we get past that point when no FL is allowed?
Comment by Bradford — October 28, 2007 @ 8:43 pm
October 28th, 2007 at 8:45 pm
Show me the empirical evidence that indicates my position is flawed. You don't need my permission to do that.
Comment by Bradford — October 28, 2007 @ 8:45 pm
October 28th, 2007 at 8:49 pm
My apologies to Bradford and fifth monarchy man; I saw "fmm" and thought it said "fm" which was an abbreviation for Frostman.
Comment by Frostman — October 28, 2007 @ 8:49 pm
October 28th, 2007 at 9:22 pm
Ditto for a minute I thought I was having a stroke
Peace
Comment by fifth monarchy man — October 28, 2007 @ 9:22 pm
October 28th, 2007 at 9:27 pm
Bradford,
(For those of you just joining us, Bradford quoted something I wrote in a now-deleted post in which I thought he was addressing to me, when in fact he was addressing fifth monarchy man.)
The question was whether it's possible that your position could be flawed. Is that even possible? How would you disprove it? As I mentioned previously, there is no glory in a hypothesis which has no evidence against it. There is no evidence against the existence of an invisible, silent, odorless, ethereal dragon in my garage.
The underlying issue is our understanding of what science is. Unless you can clarify these remarks below, in which you appear to contradict yourself, I can only conclude that your understanding of science itself is fundamentally different. I have asked for a clarification now several times, but you have avoided the issue.
Comment by Frostman — October 28, 2007 @ 9:27 pm
October 28th, 2007 at 11:57 pm
Frostman- forget the confusing exchanges. It's simple. I believe genomic repair functions were front loaded.
Comment by Bradford — October 28, 2007 @ 11:57 pm
October 29th, 2007 at 9:54 am
Bradford, you are quickly losing credibility. I am reminded of Alberto Gonzalez in front of congress. You won't answer the question. Why not? This is important.
As I said, the totality of my response is dependent upon your answer. It appears we cannot even agree on the definition of science. This alone may be the most significant outcome of our conversation.
Comment by Frostman — October 29, 2007 @ 9:54 am
October 29th, 2007 at 10:23 am
Frostman, I've stated my view. It is clear and understandable. I also believe that good science entails the capacity to falsify a hypothesis. If you have input along those lines then come out with it. Don't tell me your response is contingent on my jumping through your hoops. I don't play games.
Comment by Bradford — October 29, 2007 @ 10:23 am
October 29th, 2007 at 10:42 am
I think Frostman is asking for a plausible falsification, a bold empirical prediction that if shown to be false would undermine your claim.
Comment by Zachriel — October 29, 2007 @ 10:42 am
October 29th, 2007 at 12:48 pm
Zachriel:
Is Zachriel correct? If this is what you are seeking I would be glad to comply.
Comment by Bradford — October 29, 2007 @ 12:48 pm
October 29th, 2007 at 1:41 pm
I rather doubt that, as you have not yet complied after many requests, choosing instead to call it a game of jumping through hoops. Previously:
If Zach has somehow nudged you to reply, then by all means do so. Based on your behavior here, my prediction is that you will continue to avoid these questions below. I hope my prediction is incorrect.
This is now the sixth time I have asked for a clarification of the above. Each time you have declined to respond.
Comment by Frostman — October 29, 2007 @ 1:41 pm
October 29th, 2007 at 5:16 pm
Frostman,
Is it possible your position might be flawed? f.m.m. asked the question a little awkwardly, but what would it take to convince you to drop your non-telic position?
Bradford is an experienced veteran of this debate and I'm fairly certain he's answered your question(s) in one guise or another over the years.
For me, it would take an empirically supported elucidation of the origin of self-replicating, information-bearing polypeptides with a reasonable step by step explanation how coding regions for transcription proteins arose to convince me front-loading isn't present. Unguided selection, mutation and adaptation of pre-existing molecules is stipulated and beside the point.
If life did indeed arise unguided from a chance convergence of the right materials in the right environment at the right time, reverse engineering such an event shouldn't be so difficult for clever homo sapiens, no? The raw material must have emergent properties, right?
Unguided and guided and mutually exclusive. Proof of one disproves the other, every time. The origin of genetic information was either caused by intelligence or it was not. There is no in between. To prove newX isn't true would require demonstrating not(newX) is true, because both cannot be true. The first living molecule arose unguided or it did not. There is your X and not(X).
Comment by todd — October 29, 2007 @ 5:16 pm
October 29th, 2007 at 5:21 pm
Frostman:
You're right about differing conceptions of how science works. As much as I disagree with Zachriel on some things we're at least on the same wavelength with respect to how things work. Science is empirical in nature and hypotheses should be supported by experimental evidence or falsified by the same. Convinced that X is true? That's the type of phrase I heard in logic courses. Do you know enough about genomic repair mechanisms to evaluate a related hypothesis and what could falsify it?
Comment by Bradford — October 29, 2007 @ 5:21 pm
October 29th, 2007 at 10:57 pm
Bradford,
Well it looks like I am prescient. Would you just come out and tell us why you won't respond? You've sought to cast the question as jumping through hoops, playing games, and now as an academic question only worthy of logic courses. It is not difficult to see through those spin maneuvers.
Comment by Frostman — October 29, 2007 @ 10:57 pm
October 29th, 2007 at 11:09 pm
todd and fmm,
Your arguments deserve an answer, and I will give my response in due time. At the moment, however, it seems important to prevent the conversation from being sidetracked.
Comment by Frostman — October 29, 2007 @ 11:09 pm
October 30th, 2007 at 12:09 am
Frostman,
Haven't you already sidetracked with all the niggling over X? Or do you refer to the "The Eyes Have It" entry?
Comment by todd — October 30, 2007 @ 12:09 am
October 30th, 2007 at 9:40 am
Aha, but the point about the generic hypothesis X is the most important thing here. It is where Bradford appears to have made a mistake in reasoning, although he refuses to address the issue. Does he stand behind his statements or not? He won't tell us.
I will elaborate with an example. Since I am lazy, I will take Carl Sagan's example I mentioned earlier.
I claim there is a dragon in my garage. Why can't you see it? Well, because it's invisible. And you can't hear it because it is perfectly silent. The dragon is odorless too. Also it is ethereal so you won't notice turbulent air from movement or breathing; a shotgun blast would pass right through it.
You ask me, "What would convince you that the dragon is not present?" I say that convincing evidence would be evidence favoring a non-dragon option. You have no evidence for such a non-dragon option, other than the obvious option that there is no dragon. Furthermore, you are unable to produce evidence which would disprove the existence of the dragon. I win. The dragon hypothesis stays. I remain secure in my belief that a dragon lives in my garage.
What is wrong with the above scenario? Notice I simply replaced the X with the dragon hypothesis. You will probably notice another similarity.
Comment by Frostman — October 30, 2007 @ 9:40 am
October 30th, 2007 at 10:18 am
Frostman,
Thank you for elaborating, although I think your reasoning is fundamentally off. I'd appreciate it if you'd address what I wrote above:
Your analogy fails because your dragon has no visible effect whatsoever. Indeed, one wonders how you know it exists if it cannot be detected in any way! My first question, given the dragon cannot be detected, is what makes you so sure this is a fact?
In the case of FL, we are talking about what appears to be a telic arrangement of molecules! So the FL dragon does express something, er, turbulent, in the natural order. Your dragon leaves no evidence, mine leaves a complex specified program which draws resources from its surroundings to unfold into organism-hood!
I look at molecular biology and genetics and see what looks like an intricate and elegant set of instructions. I have two possible alternatives when evaluating these biological artifacts - they were made or they just happened. There is not a third option so far as I know, please enlighten me if you know otherwise.
Given two mutually exclusive alternatives, I find in the programming analogy a strong inference to teleology - it looks designed. I like to think I'm fair minded so I don't dismiss the naturalist alternative out of hand. But I do ask for an explanation which overcomes stochastic odds for such an arrangement. This would convince me to abandon telic cause.
PS: I hereby name your dragon "Multiverse"
Comment by todd — October 30, 2007 @ 10:18 am
October 30th, 2007 at 10:30 am
Todd:
Telic indeed. Codons of nucleic acids are symbolic representations of the amino acids whose translation enables the synthesis of proteins that afford such codons their selective value. All quantifiable and observable stuff in contrast to the dragon strawman.
Comment by Bradford — October 30, 2007 @ 10:30 am
October 30th, 2007 at 10:54 am
Bradford wrote,
And the proteins required for that translation!! How can that plausibly happen without guidance?
Comment by todd — October 30, 2007 @ 10:54 am
October 30th, 2007 at 11:00 am
Bradford,
The dragon was the extreme example for illustrative purposes. A hypothesis X, in order to be called scientific, must distinguish itself from not-X. The dragon is an uncontroversial example, far-out enough for there to be no disagreement that in this case X is indistinguishable from not-X.
Let us not lose sight of the issue at hand. For the moment I will concede anything you wish about the dragon example. Now, why haven't you clarified your remarks earlier? Honestly I have never been in a discussion where one side will not even address a question one way or the other. This is the seventh request.
Comment by Frostman — October 30, 2007 @ 11:00 am
October 30th, 2007 at 12:01 pm
Frostman:
The front loading of genomic repair mechanisms has no contrasting plausible theory against which it can be compared. You may think that the not FL in this particlular instance is the old RM+NS standby but that has never been experimentally confirmed. Testing the relative merits of the opposing ideas is possible though.
The actual not X dilemna pertains to standard beliefs. How is one to falsify the belief that genomes and their repair mechanisms arose when the pathways by which this would have been accomplished are unspecified and unknown?
Comment by Bradford — October 30, 2007 @ 12:01 pm
October 30th, 2007 at 12:10 pm
The functional value of the proteins lies in their ability to facilitate the synthesis of other proteins, some of which facilitate the synthesis of DNA itself. This type of circular causal chain is not uncommon. It is seen when an observed outcome is the product of a purposeful, intelligent cause.
Comment by Bradford — October 30, 2007 @ 12:10 pm
October 30th, 2007 at 12:42 pm
Bradford,
Your point is moot as I have already said that I will concede anything you wish about the dragon example. Its purpose was to illustrate one aspect of a scientific hypothesis, and it does it well. That is all.
In my previous post I said
You even ignored this. Truly remarkable. Since the original is now getting up in the list, I will quote it yet again.
Bradford, why do you keep ignoring this? You won't say a word about it. Do you stand behind your remarks above? We are left wondering, as you remain mute.
Comment by Frostman — October 30, 2007 @ 12:42 pm
October 30th, 2007 at 1:05 pm
The example was dumb. It illustrated nothing about scientific hypotheses. It was conceived to suit a stereotype and not very cleverly done at that.
The confusion you claim is not shared by others. You asked if when given a new hypothesis X, evidence must be shown which would rule out X to convince me that X is not true right? I correctly responded no and pointed out to you that truth is not what we determine by testing hypotheses. X could be true with no scientific evidence in its favor whatsoever. You also do not have to "rule out" a hypothesis. You can fail to find evidence in its favor or get inconclusive results. I already made this point about the inappropriateness of the truth test when I referenced the distinction between empirical testing and exercises in logic. I'll have to assume you are trolling if you continue along these lines.
Comment by Bradford — October 30, 2007 @ 1:05 pm
October 30th, 2007 at 2:05 pm
Bradford,
Thank you for responding. The answer you just gave was not obvious from your previous comments, all of which clipped my question and went on to something else.
The "classic exchange" does however contain a logical fallacy which the dragon example illustrates. More on this below.
Perhaps the confusion lies here. The "not FL" is in fact not FL. I did not mention RM+NS, and I did not propose comparing FL with RM+NS. The first order of business is to compare FL with not-FL. Compare the dragon exists with the dragon is not there.
What would demonstrate that FL is not there?
Comment by Frostman — October 30, 2007 @ 2:05 pm
October 30th, 2007 at 2:23 pm
Frostman:
Discontinuity.
Comment by Guts — October 30, 2007 @ 2:23 pm
October 30th, 2007 at 2:29 pm
Positive proof of not FL. Keywords: mutual exclusivity.
If FL means purposeful arrangement of genomic data, then not-FL is ANY form of stochastic arrangement of data. RM+NS is the main stochastic contender.
Comment by todd — October 30, 2007 @ 2:29 pm
October 30th, 2007 at 3:15 pm
Frostman:
Guts and Todd already have given you feedback. I'll add Mike's comment that is taken from this blog entry:
You can trace the trail. Since I've begun looking into this I've been surprised by the degree to which precursor gene candidates are buried in deep homology. That's from an evolutionary perspective. From an origins perspective front loading genomic repair mechanisms makes variation possible because it eliminates the natural barrier to it namely, genomic self-destruction.
Comment by Bradford — October 30, 2007 @ 3:15 pm