Limiting the Designer
by MikeGeneTo what degree is the design of a designer constrained by his/her building material? For example, imagine that we enlisted the service of the worlds most creative and brilliant engineers and tasked them to design a space craft that will carry men to Mars and back. Now, let's add one constraint "“ the only material available to the designers is concrete. Would these brilliant designers be able to meet the design objective?
Or consider the computer. Today's computers are more sophisticated than computers from the 1950s, allowing people to design programs that allow you and me to communicate with great ease and little cost. Why is it that programmers seem to be able to do more with computers today than they could in the 1950s? Is it because today's designers are smarter than yesterday? Have new laws of nature been discovered? Or does it have something to do with an observation from Hartwell et al.?
An early stored-program computer (left), built around 1950, used vacuum tubes in logic circuits, whereas modern computers use transistors and silicon wafers (right), but both are based on the same principles.
So again, to what degree is the design of a designer constrained by his/her building material? Furthermore, since natural selection can act as a designer-mimic, wouldn't it too be subject to similar limitations?
May 13th, 2008 at 12:41 am
Good question. The constraint is defined by properties of the building material and its sufficiency to bring about an outcome.
Yes. This brings up an interesting point. Catalytic properties of RNA are cited as a basis for the supposition that inital enzymes were ribonucleic acids rather than proteins. The idea being that RNA could fulfill the dual role of information storage and catalyst and at the same time be more likely to have arisen in an extracellular environment. But that necessitates a switch in buidling materials midway through a project. Proteins would take over most catalytic functions and DNA become the storage nucleic acid. This transformation would have to occur without compromising an organism's viability. So what are the limitations? The final word is not in.
Comment by Bradford — May 13, 2008 @ 12:41 am
May 13th, 2008 at 1:14 am
I think the problem of evil is such a limit; our world is perfect in many respects, but without the possibility of evil (that may challenge us) then our world would be impossible. Likewise, the mistakes of the blind watchmaker are needed too, otherwise the watchmaker would not know of that which gives sight. The limits are brought to us by a necessary blind spot that sources a self-referral condition. But the felt tension tells us that the blind spot is not really blind, as our sight sources the innate feeling that has no reason for its being. The tension subsides, in sublimates itself and is replaced by a love of life. And this remains until we fall into the blind stupor again, and then learn from our mistakes again. This has been the basis of spiritual healing, in my view. The "mistake" is often telling us something important about ourselves.
Comment by Stephen — May 13, 2008 @ 1:14 am
May 13th, 2008 at 8:54 am
I do not believe this is correct except for simple changes. I am of the opinion James Shapiro has a better description of the evolution of systems which implies possibly intelligence even down to the cellular level….
To the degree that populations act like the combinatorial immune system, sure, we have examples of selection being used as an adaptive strategy by design, but that is only one part of the repertoire and a small part of evolutionary adaptive strategies….
There is an ongoing thread at PandasThumb about Gambler's Ruin and Kimura's work. I still owe Olegt some revisions to my original simulation, and I hope to get to them this week. I will also be going to Minnesota to talk to Walter ReMine some time in June about population genetics. Walter was very pleased with my discussion on the topic of Gambler's Ruin and had some suggestions to polish my arguments….the bottom line is that we might be able to put some numbers on the role of natural selection's participation in evolution. I have suggested 1% would be extraodinarily generous to attribute to natural selection. I have to also agree with Bill Dembski's interpretation of No Free Lunch postulates that natural selection would be very hard pressed to be a designer mimic.
To make matters worse for the advocates of selection, the problem of Gambler's ruin makes it extremely difficult to defend the assertion of natural selection being a designer-mimic because it becomes almost empirically imperceptible whether a random walk or natural selection was at work for large scale changes at the nucleotide level. I think the question will be interesting because we may want to ask how can we quantify James Shapiro and Barry Hall's work on adaptive mutations?
If it can be shown that mutations have some pre-programmed foresight, that would be suggestive of some front loading, but I think the mechanisms for the major organic changes in the past are no longer in operation (Davison)….that's not to say that we might not be able to reverse engineer some of the front loading of the past. That suggestion was by Behe…that would be an interesting research project, even though the experimental details appear to be staggaring at this time…
Finally, regarding the constraints on the designer. The designer has to put TONS of error correction since we are dealing with nano-molecular systems. At the macroscopic scale, there is a lot of natural cancellation of undesirable quantum effects, but the smaller the systems become, and the faster they operate the more deliberate the error correction has to be.
For example, building a logic gate with macroscopic objects like vacuum tubes and discrete transistors, one is not as concerned with error correction as one would be when one is worried about serious amounts of barrier tunneling and the equivalent of delayed-double slit intereference issues at the quantum level. When I worked briefly in a nano systems department, there was serious investigation into Schrodinger's equation and the problem of ensuring computers would not be plagued by the problems of the delayed choice double-slit problem — since some of the nano-logic gates were small enough that their past computation could be influenced by future observations in an undesirable way….
PS
I'm on travel and I left my bunny book at home. I'll get back to reading it soon. Mike, you were soooooo kind to list me in the acknowledgements section of the book….I'm going to have to finish reading your book someday soon!
By the way, it was nice to see Nobody listed in your book too. Hey, Nobe, you're famous now.
Comment by Salvador T. Cordova — May 13, 2008 @ 8:54 am
May 13th, 2008 at 11:59 am
Yes. You can build one hell of a catapult out of concrete.
No. Titanium, concrete, or rocks would work equally well for the blind watchmakers spacecraft. He's in no hurry.
I'll even wager that the blind watchmaker has already sent many many tons more material to Mars than NASA has.
Rocks! Pioneers of space travel!
Is there anything they can't do?
Comment by chunkdz — May 13, 2008 @ 11:59 am
May 13th, 2008 at 12:55 pm
Sal says:
::::gulp::::
Thanks Mike! Guess I should have had the foresight to select a more intelligent username several years ago.
Comment by nobody — May 13, 2008 @ 12:55 pm
May 13th, 2008 at 1:50 pm
Hi nobody,
I know the feeling. Kidding aside, my gratitude is quite sincere.
Comment by MikeGene — May 13, 2008 @ 1:50 pm
May 13th, 2008 at 2:46 pm
Hi Bradford,
Indeed. So this gets back to proteins as a biological universal and to what extent the blind watchmaker would be a success without the help from proteins.
Is there even a first word?
Also, here is another thought. If we assume a switch-over, it occurred long before the last common universal ancestor. Yet if life, working hand-in-hand with the blind watchmaker, is capable of making such switch-overs, why did such an ability disappear with the last universal common ancestor? If there is a better polymer than proteins, then why haven't the DNA/RNA/protein-based life forms discovered it and facilitated another switch-over during the billions of years since the last universal common ancestor?
Comment by MikeGene — May 13, 2008 @ 2:46 pm
May 13th, 2008 at 3:13 pm
Mike:
Maybe because once a genetic code is in place, it's hard to change it. It would presumably take many intermediary mutational steps with lower fitness to accomplish such a transition. The fitness valley would be too wide and too deep. Hey, one might even call it evolutionary irreducible complexity.
Consider a "mutant codon" (mutant tRNA) that would code for something else than an amino acid, let's call it monomer X. How do you incorporate X into a chain of amino acids if X cannot form a proper peptide bond with amino acids?
Comment by Raevmo — May 13, 2008 @ 3:13 pm
May 13th, 2008 at 3:24 pm
Mike,
What does the blind watchmaker consider a success?
For that matter, what does the blind watchmaker consider?
Comment by chunkdz — May 13, 2008 @ 3:24 pm
May 13th, 2008 at 4:13 pm
Hi Raevmo,
But I am not talking about changing the genetic code. I'm thinking in terms of the hypothetical take-overs, where minerals were supposedly supplanted by nucleic acids and then later the RNA world was supposedly supplanted by the RNA-protein world.
All livings things use four basic biological molecules "“ lipids, proteins, nucleic acids, and proteins. That was something that was established billions of years ago. But what's wrong with superimposing a fifth type of biological molecules during these vast spans of deep time? The blind watchmaker could use the RNA/DNA/protein-based cells to spawn this new molecule (like the hypothetical ribo-organisms supposedly spawned proteins) to play a helping role at first and then, like the RNA-to-protein transition, a better molecule takes over. In other words, since proponents of the RNA world see the cell as a protein world superimposed on an RNA world, why hasn't another layer been added by the blind watchmaker?
Maybe it's "proteins: as good as it gets."
Comment by MikeGene — May 13, 2008 @ 4:13 pm
May 13th, 2008 at 4:16 pm
Hi chunkdz,
As Dawkins would say, the blind watchmaker has no mind and no foresight.
Comment by MikeGene — May 13, 2008 @ 4:16 pm
May 13th, 2008 at 4:36 pm
Comment by Bilbo — May 13, 2008 @ 4:36 pm
May 13th, 2008 at 4:37 pm
Mike:
But you wrote this before:
That sounds to me a lot like you were asking why the genetic code wasn't replaced, since as you pointed out yourself the LUCA already had the current genetic code. But OK, I see what you mean. Maybe the word "addition" would have captured your meaning better than "switch".
Nothing wrong with that. Are you sure there are just four? Lots of other good stuff is synthesized. I'm thinking ethanol, THC, opiates.
Comment by Raevmo — May 13, 2008 @ 4:37 pm
May 13th, 2008 at 4:52 pm
Very interesting that Dawkins would admit that. Or is he forced to say that, based on his beliefs?
Comment by nobody — May 13, 2008 @ 4:52 pm
May 13th, 2008 at 5:09 pm
Mike:
Finally, the proteins-are-optimal-conjecture that we were all waiting for. In the next episode: how this increases the plausibility of front-loading.
Comment by Raevmo — May 13, 2008 @ 5:09 pm
May 13th, 2008 at 5:32 pm
Then he's already a success - proteins or no proteins.
Mike, the limits you are asking about are not imposed by the design material. They are imposed by expectations. Expectations come from will. Will comes from mind.
Comment by chunkdz — May 13, 2008 @ 5:32 pm
May 13th, 2008 at 5:38 pm
That's IF you believe the blind watchmaker hypothesis.
Comment by nobody — May 13, 2008 @ 5:38 pm
May 13th, 2008 at 5:56 pm
Hi nobody,
I don't reject the hypothesis as much as I reject the metaphor. It implies that watchmaking is something that blind, mindless idiots do.
It would have been more honest if Dawkins had named the book "The Blind Mindless Idiot Who Made A Watch", but I guess that would not have been as catchy.
Comment by chunkdz — May 13, 2008 @ 5:56 pm
May 13th, 2008 at 6:03 pm
It would be more honest if Dawkins admitted that life is high technology.
Comment by nobody — May 13, 2008 @ 6:03 pm
May 13th, 2008 at 6:30 pm
A "blind watchmaker" sounds plausible. Sure it would be difficult for a blind person, and time consuming, but it could be done. Nice title for a book. Feels good to know the handicapped can accomplish great things.
But open the book and you see that Dawkins' watchmaker is no watchmaker at all. And he's not just blind. He's a blind, mindless, purposeless idiot with no higher brain function beyond wiggling his fingers. He is little different from the proverbial box of watch parts being shaken for a billion years.
It's a terrible metaphor, and intellectually dishonest, in my opinion. A lame attempt to anthropomorphize the "pitiless indifference" that Dawkins' universe is built upon. I do wish that Mike would cease to perpetuate it through his writings in support of the blind watchmaker hypothesis.
Comment by chunkdz — May 13, 2008 @ 6:30 pm
May 13th, 2008 at 6:44 pm
chunkdz:
Come on, it's a play on Paley's watch, nothing more. He's blind as in not having foresight. It's not that bad. In fact, it's a highly effective meme, seeing as even you are using it.
Comment by Raevmo — May 13, 2008 @ 6:44 pm
May 13th, 2008 at 7:23 pm
That Dawkins fellow and those other evolutionists. Why don't they just admit it. I mean, seriously, they know they are wrong. They know they have been lying and hiding the truth. Why don't they just admit it.
Comment by hrun — May 13, 2008 @ 7:23 pm
May 13th, 2008 at 7:33 pm
Old habits die slowly.
Comment by nobody — May 13, 2008 @ 7:33 pm
May 13th, 2008 at 7:50 pm
But you'd think by now. I mean it's been generations of scientists and they just keep on lying, hiding, obfuscating and denying.
Ah well. Maybe the next generation…
Comment by hrun — May 13, 2008 @ 7:50 pm
May 13th, 2008 at 8:17 pm
We could start a movement.
Comment by Zachriel — May 13, 2008 @ 8:17 pm
May 13th, 2008 at 8:23 pm
Next Official Generation Of Dedicated Scientists?
Comment by Raevmo — May 13, 2008 @ 8:23 pm
May 13th, 2008 at 8:47 pm
Hi Raevmo,
I am talking about the four universal macromolecules. Here's a fairly standard presentation of them.
You may be correct, as this is a new idea that I am currently fleshing out. But it would be an addition that is analogous to the addition of proteins to the hypothetical ribo-organism. As Bradford noted, the RNA world hypothesis entails the notion that proteins took over most of the catalytic roles and DNA took over the information storage roles. So why hasn't 3.5 billion years of the blind watchmaker's meandering stumbled upon something that would similarly take over some/many of the roles that proteins play?
LOL. Still trying to play chess with me, eh? No, I'm not ready to make that conjecture, as I'm still feeling things out. As for front-loading, as far as I see it, its plausibility is now on solid enough ground that this type of analysis is not needed for such purposes. But then again…..
Anyway, I'm currently looking at things from a different angle.
Instead of trying to anticipate where I am going so you can properly posture yourself in opposition (surprise, surprise), why not simply focus on the questions that I have laid on the table?
Comment by MikeGene — May 13, 2008 @ 8:47 pm
May 13th, 2008 at 8:51 pm
Hi chunkdz,
I like the metaphor because it helps to distinguish a designer from a designer-mimic. Let me [gag] quote from WikiLand:
I'm afraid I don't agree with you or Salvador about the relative impotence of the blind watchmaker. However, I realize for a lot of people, that is the very fulcrum of the debate. But for me, I focus on intelligent design not as a substitute for RM &NS, but as something that can recruit and exploit RM & NS to help carry out design objectives. My current line of inquiry with proteins and the limitations on designers suggests that RM & NS have been propped up.
Comment by MikeGene — May 13, 2008 @ 8:51 pm
May 13th, 2008 at 8:56 pm
Raevmo,
Blind people can make watches. Blind people with no mind cannot. It's classic question begging, and it's lame.
Comment by chunkdz — May 13, 2008 @ 8:56 pm
May 13th, 2008 at 9:10 pm
Mike:
Raevmo:
Mike:
Hrun: As far as I can tell Raevmo was not anticipating but 'post'icipating. Seems like you made pretty clear in your assay that you suspect proteins were designed to help evolution along. If proteins were specifically designed to help evolution along, how could that not be taken as an 'increase the plausibility of front-loading'. I guess the only place where Raevmo went wrong was calling it the 'next' chapter when it was already in the last chapter.
Comment by hrun — May 13, 2008 @ 9:10 pm
May 13th, 2008 at 9:39 pm
Mikegene,
I actually think the perception of evolution as a creative force rivaling to a designer, rather than as one more tool available to a designer, is one of the biggest difficulties in the entire ID debate. I can understand questioning or explaining all manner of aspects of evolution (I've seen some good articles about that recently, outside the ID camp - funny how anyone who questions the mainstream first had to insist they hate ID more than anyone else), but the certainty that evolution must be roundly false for design to be true is ridiculous.
Just wanted to throw that in there.
Comment by nullasalus — May 13, 2008 @ 9:39 pm
May 13th, 2008 at 11:08 pm
Hi Hrun,
No, Raevmo mentioned that "we" were "waiting for" something. This clearly tipped off the role of anticipation on the part of the group that Raevmo was speaking for.
Indeed. And you think that is the same thing as "proteins-are-optimal?"
What enhances the plausibility of front-loading are the extent and continual discoveries of deep homology (that keep surprising the non-teleologists) and mechanisms that could be used to carry designs into the future (as discussed in the book). The use of proteins as a fundamental building material probably enhances front-loading in a general fashion (overall evolvability), but as I mentioned, given the other evidence, doesn't strike me as something that adds much to that case (of course, it doesn't hurt). What proteins-as-building-material add is the suspicion that the blind watchmaker has been propped up. It's either that or life cannot exist without proteins (a viable hypothesis). Of course, these are subtle differences that are still being sorted out in the tiny bits of gray matter I possess.
Proteins-as-optimal material is an intriguing possibility to explore, but Raevmo jumped the gun, as that argument is not on the table. Proteins as a class of molecules as something that increases the plausibility of front-loading? I wasn't looking at it from that angle, but maybe there is something there.
Comment by MikeGene — May 13, 2008 @ 11:08 pm
May 13th, 2008 at 11:25 pm
Hi nullasalus,
Exactly. And it seems to me that mainstream ID focuses on eliminating the rival (the "˜Duck hunt'). But I came to this debate as a theistic evolutionist. Instead of seeing evolution as a rival creative force that must be eliminated, I suspect the creative force could be recruited and employed by a designer. And that's my focus. To what extent can we design through evolution? To what extent is evolution designed?
And thanks for throwing that in. Yes, this is a central theme of my book. Design and evolution are not contradictory concepts. And evolution by natural selection does not equate with non-teleology. There are too many unexplored options out there.
Comment by MikeGene — May 13, 2008 @ 11:25 pm
May 13th, 2008 at 11:39 pm
Mike, it is hard to believe that you would say that you were not looking at proteins from the angle that they might increase the plausibility of front-loading if in your assay you write that "[y]ou can almost think of proteins are a form of tech material designed to exploit and prop up the blind watchmaker." You suggest that proteins were designed for the goal of helping evolution along.
But just because something is hard to believe, it certainly does not prove it wrong. Maybe it just makes it less plausible.
Comment by hrun — May 13, 2008 @ 11:39 pm
May 14th, 2008 at 12:03 am
I still absolutely don't get the protein argument. Sorry.
We know that RNA can be used for longterm information storage (e.g. RNA viruses, telomere templates). We know that RNA can have catalytic function (e.g. splicing). We know that RNA can be used as short term information transmission (e.g. mRNA). We know that RNA can even be used to regulate gene expression (RNAi).
Some of these functions are now predominantly performed by other molecules (protein and DNA).
So the argument now appears to be that the because proteins have not been replaced by another biomolecule (with potentially even better stability and functional variety) that this is an indication of design.
Yet, what if there had been such a replacement (like from RNA to protein)? You would still be able to make the same argument. What if there had been no such replacements? Well, I guess in the RNA world without proteins you wouldn't be making any arguments, but theoretically your argument would be just as valid.
So we find ourselves in a situation where whatever happens, your argument remains equally valid. Or, it boils down to: Because we know of exactly ONE case where catalytic biomolecules were replaced with other catalytic biomolecules the plausibility of front-loading is increased? Strange.
And I'm still wondering about this one: Do non-teleologists actually think that there should be no such deep homologies or do they merely profess surprise at the specific ones they find. Or, in other words, do the teleologists actually make predictions about which 'deep homologies' will be found where? And which structures are actually novel developments?
Because I have honestly not seen a single specific prediction along these lines. All I have seen are comments like: "Hahaha, silly non-teleologists. They are surprised at their results they just found out as the first people on the planet, while teleologists would not have been surprised." I think if there actually were such predictions, they would be so easily testable.
And I can tell you one thing: If, for example, a couple of years ago, a teleological researcher would have predicted that comb jelly fish and not sponges were the older group of metazoans, then about two months ago all of a sudden the world of biological researchers would have perked their ears up and everybody would have wanted one of those teleologists on their groups to help them guide their research.
Comment by hrun — May 14, 2008 @ 12:03 am
May 14th, 2008 at 12:06 am
hrun:
Patience, patience hrun. Did you ever watch a good boxer set up his opponent with jabs and feints and movement so that he can land the desired blow at the opportune time? You're telling the other guy to throw his reknown left hook and he is biding his time waiting until the right moment.
Comment by Bradford — May 14, 2008 @ 12:06 am
May 14th, 2008 at 12:14 am
Hi hrun,
LOL. If I was looking at proteins from the angle that they might increase the plausibility of front-loading, I would just say so. But front-loading is about designing the future through the present. That is, one attempts to reach a future objective by somehow channeling the process of evolution. It's about rigging evolution to increase the odds that certain trajectories might be explored. "Helping evolution along" does not entail such an objective, as "helping evolution along" is just "helping evolution along." Are you under the impression that front-loading is simply about making sure that evolution happens? Do you even know what I mean when I speak of the increasing plausibility of front-loading? Or do you tune out at that point?
What's your problem, hrun? Are you just trying to score some silly debate point?
Comment by MikeGene — May 14, 2008 @ 12:14 am
May 14th, 2008 at 12:16 am
What does this have to do with patience?
Mike says that he was not looking at proteins from that angle, yet his assay indicates otherwise. Mike writes in his assay that it proteins could have been DESIGNED to ACHIEVE a goal effectively. And shortly after he says that he did not look at the optimality of proteins as increasing the plausibility of front-loading. I must have poor reading comprehension.
Comment by hrun — May 14, 2008 @ 12:16 am
May 14th, 2008 at 12:17 am
hrun:
That Nature developed a functional tool (RNA) right at the outset. That's the supposition but we know (no suppositions needed) that proteins enable a diversity unattainable with RNA alone. There is a gradation and FL cites progressions.
Why? Front loading explains a rich diversity not possible without proteins. My questions relate to the theorized transition from RNA catalysts to protein catalysts. Details would be very revealing and could be supportive of or in opposition to FL or a non-FL view.
Comment by Bradford — May 14, 2008 @ 12:17 am
May 14th, 2008 at 12:20 am
I think Mike wants to lay out his case step by step and not have to rush to conclusions without laying down the complete foundation.
Comment by Bradford — May 14, 2008 @ 12:20 am
May 14th, 2008 at 12:24 am
My problems are too plentiful to enumerate.
I know. That's exactly why I quoted your assay:
When you write "designed to exploit" one (or at least I) assumes that this being who did the designing tried to exploited the blind watchmaker to achieve a certain goal. And that goal can't just be "to prop up evolution" since you explicitly connect the "exploit" and the "prop up" with "and", indicating that these are two very separate points.
So, as I said before, in your assay you are already pointing at the phenomenal properties of proteins as increasing the plausibility of front loading. Not that there is anything wrong with that. I just don't understand why you would chide Raevmo for suggesting that you will do something in the future if you actually already have done it.
Comment by hrun — May 14, 2008 @ 12:24 am
May 14th, 2008 at 12:40 am
But exploiting and propping up are generic functions that, by themselves, don't entail a future goal. It simply means an enhanced evolvability which, in turn, may be necessary for front-loading, but not sufficient (unless the objective of front-loading is just to make sure evolution happens). I mentioned these are subtle differences.
Comment by MikeGene — May 14, 2008 @ 12:40 am
May 14th, 2008 at 12:41 am
Mike asks:
Individual programmer productivity hasn't budged much since the advent of the first high level languages like Fortran, Lisp, BASIC, and COBOL. However, there are many more programmers today than in the 1950's and programming frameworks or libraries allow programmers to work at an ever higher level of abstraction. Consequently, when a programmer writes a program today, he is in effect stitching together other programs rather than writing a program from scratch. This is commonly referred to as modular programming, and if there has ever been a silver bullet in software engineering, it was the invention (discovery?) of the function call.
Faster hardware is another factor. Programmers don't have to wait nearly as long for feedback regarding their programs. So, instead of waiting say 60 minutes for their 1000 line program to compile, they are able to compile a 10,000 line program in seconds.
What programming language did God use? DNA is the tip of the iceberg.
Comment by David — May 14, 2008 @ 12:41 am
May 14th, 2008 at 12:45 am
One problem - there is no case. I'm simply thinking out loud and raising questions as they come to me. I'm exploring, feeling things out, moving in general directions, etc. A case may or may not materialize as a consequence.
I often liken my thinking to an intellectual crockpot. I throw in facts, questions, various proposed explanations, etc. Then sometimes, I wake up one morning, maybe weeks or months later, and presto, a delicious case is waiting for me. Of course, sometimes it's just a stinky mess that I toss into the garbage.
Comment by MikeGene — May 14, 2008 @ 12:45 am
May 14th, 2008 at 1:19 am
hrun says:
In previous generations, some design denial can be excused because of ignorance. However, there's no excuse now. It's clear that life is very high technology. People like Dawkins need to wake up. We've had massive increases in our knowledge within the past few years. Here's a multi-billion dollar example: The Human Genome Project was "completed" in 2003. Did that end the investigation into DNA? No. The HGP only scratched the surface.
Comment by nobody — May 14, 2008 @ 1:19 am
May 14th, 2008 at 7:28 am
No way, nobody. Paley wrote his book on how design is self-evident decades before Darwin. Nobody (not even nobody) can claim ignorance on this matter.
Comment by hrun — May 14, 2008 @ 7:28 am
May 14th, 2008 at 7:28 am
MG
I think that if a convincing case is to be made for frontloading serious attention needs to be given to the question of what the goal is. And the answer needs to be more specific. Simply pointing to a feature and pointing out that it makes "what we see today" more likely seems backwards. It's sort of like when Mr. Bean stumbles through an unlikely adventure and then looks smug as if to say "that was my plan all along".
The goal of the frontloading would constrain the evidence that is seen as supporting. Right now it just seems unnecessarily sloppy
Here are some off the cup ideas for possible Goals
Consciousness entity Frontloading
Evolution enhancing Frontloading
Diversity enchaining Frontloading
Discovery enhancing Frontloading
Rational thinker ensuring Frontloading
Maybe you should pick one or two and run with it if it turns out to be a dead end you can just move back grab another goal and start over.
Just my two cents
Peace
Comment by fifth monarchy man — May 14, 2008 @ 7:28 am
May 14th, 2008 at 7:34 am
Ah, come on Mike. You were talking about a designer doing the exploiting. I don't know any meaning of 'exploit' that does entail an actual goal. Things are exploited for a reason.
In any case. I will leave it at that. I just have to say that I find this rather silly. But I honestly can not think of any reading of a sentence like "proteins were designed to exploit evolution" that does not imply a goal by the being that did the designing. But, as I said, I have numerous problems, and reading comprehension could be one of them.
Comment by hrun — May 14, 2008 @ 7:34 am
May 14th, 2008 at 9:08 am
Recalling that the "Blind Watchmaker" is not Darwin's metaphor. Quite the opposite: Darwin has natural selection assiduously scrutinizing ever detail of life and making rational decisions on the basis of foresight, invariably acting to benefit its creations.
One might suspect that Dawkins was motivated to radically recast Darwin's metaphor to avoid its "quasi-divine" aspect. Turning Darwin's god-like natural selection into an absurd parody"”a physically and mentally disabled piece-worker.
Avoiding Darwin's theomorphic and Dawkins' anthropomorphic conception, natural selection is simply an identifiable set of conditions effecting some measure of the performance of life forms, traditionally the relative growth rate.
And, of course, natural selection doesn't do anything an intelligent designer wouldn't do, assuming the same objective.
But Dawkins' metaphor does highlight that the principal limitations upon design are not material but mental: knowledge and imagination, and I suspect more than latter than the former.
Comment by Rock — May 14, 2008 @ 9:08 am
May 14th, 2008 at 9:25 am
*** self edited ***
Comment by hrun — May 14, 2008 @ 9:25 am
May 14th, 2008 at 9:36 am
Sorry to come in on this discussion so late (final exams, grades, and Mothers' Day intervened).
The underlying concept being obliquely addressed in this thread is a combination of what Ernst Mayr called "emergence" and Stephen J. Gould called "contingency", which together seem to me to be what Mike refers to as "front loading".
"Emergence" is the appearance of new properties from combinations of entities that lack such properties in and of themselves. Mayr points out repeatedly that emergence is a fundamental property of biological systems, not only because of evolution but because of the hierarchy of structures and functions that characterize all biological systems. For starters we could identify six major emergent levels of biological organization: biomolecules (carbohydrates, lipids, proteins, and nucleic acids), cells, metacellular organisms (i.e. organisms composed of aggregates of specialized cells in which not all cells retain the ability to reproduce independently), populations, communities, and ecosystems. At each level of organization there are phenomena that do not occur at the "lower" (i.e. constituent) levels of organization. Cells do things that biomolecules do not, multicellular organisms do things that cells do not, etc.
Emergent properties are essentially combinatorial; they depend upon the relationships between the constituent parts. Clearly, such relationships have adaptive consequences; some combinations persist and proliferate more effectively than others. These become the emergent properties that we observe in the various levels of biological organization.
Once again, the question before both EBers and IDers is, where do the various emergent properties come from? They clearly do not come from natural selection, as it can only preserve properties, it cannot originate them. So the real question is, does the emergence of new properties exhibit qualities that support the observed properties of their predecessors, or do they seem to come out of "left field"
IMO, this is still an open question. One approach to the answer would be a mathematical model that would exhibit the same kinds of saltational changes that we observe in the fossil and genomic records of macroevolution. This is difficult, because most of the mathematical tools available to us now are gradualistic and continuous, rather than punctuational.
Related to the foregoing is the phenomenon of "contingency", as most fully worked out by Stephen J. Gould. Macroevolution exhibits massive contingency: that is, what is possible in the future is almost entirely constrained by what has happened in the past. The emergence of various properties at different levels of biological organization is apparently almost completely dependent on the events that have preceded them. This means that true "optimality" is an illusion in biological systems.
This idea was captured well by Sewall Wright's "shifting balance" theory of evolution, in which he pointed out mathematically that optimality is an "accidental" outcome of changes in adaptive regimes (what he metaphorically referred to as adaptive "landscapes"). It is easy to find adaptations that exhibit "sub-optimality", and virtually all of these are the result of some kind of historical contingency. That is, the existing "design" is the result of various historical compromises, in the same way that the physical location of codes on hard drives are the result of historical processes. Unlike our hard drives, our genomes and phenomes cannot be "defragged" or "optimized", as such processes require passing through "valleys" of suboptimality which natural selection prohibits (i.e. you can't use "magic" to get from here to there).
I hope it is clear how these two phenomena "“ emergence and contingency "“ are intertwined in evolutionary biology. From my perspective as a biologist, they are inescapable features of the natural world and any theory of origins and evolution, be it "classical" EB or some form of ID, must somehow incorporate them. IMO those of us who use EB as our dominant research paradigm are closer to having a comprehensive theory that incorporates them both, and that is compatible with the other natural sciences, such as physics and chemistry, which do not depend on "magic" (i.e. the production of complex emergent properties out of nothing, rather than out of simpler properties present at lower levels of organization).
IMO it is time to reconsider the work of D'Arcy Thompson and Gregory Bateson (and perhaps his illustrious ancestor), whose work on the science of form and the power of cybernetics provide a new way to approach these problems.
Comment by Allen_MacNeill — May 14, 2008 @ 9:36 am
May 14th, 2008 at 9:44 am
I would also add the ongoing work of Lynn Margulis, who is both a dedicated EBer and an iconoclast who works from a completely different overall paradigm than most EBers. Her theories of serial endosymbiosis and symbiotic genome acquisition provide compelling models for major evolutionary transitions that have the "saltational" characteristics upon which Eldredge and Gould based their theory of punctuated equilibrium.
However, we are still waiting for a theoretician who will formulate the mathematical models that can capture these processes in ways that can then be tested and refined by comparison with empirical studies. I was very intrigued at first by William Dembski's mathematical analyses of complexity, but upon further examination it is clear that they do not even begin to capture the properties I have outlined above, and have recently become so contaminated with ad hoc requirements as to be virtually useless for any formal application to the empirical record.
Comment by Allen_MacNeill — May 14, 2008 @ 9:44 am
May 14th, 2008 at 9:53 am
Hi Mike,
Seems to me that mainstream ID is an oxymoron. ID is a fringe movement. And if you are positioning yourself to be on the margin of the fringe, it's a dangerous place to be: as John Wheeler famously quipped, the boundary of a boundary is zero.
Comment by olegt — May 14, 2008 @ 9:53 am
May 14th, 2008 at 10:00 am
Allen_MacNeill, that was a good description of emergence and emergent properties. Is there any way though that emergence is not tied to underlying genetic changes? Can emergent properties be causally decoupled from alterations of genomic sequencing or are they really more complex expressions of genetic change? In the more recent post a view is put forth which discounts selection as a factor. Could you link events together so as to explain emergence, at least on a theoretical level, through a concrete albeit hypothetical example?
Comment by Bradford — May 14, 2008 @ 10:00 am
May 14th, 2008 at 10:05 am
That seems quite contrary to the original definition of Natural Selection put forth by Darwin in Origin of Species:
Darwin clearly says it must be of benefit to the individual and its reproductive potential. Do you have a cite which indicates otherwise?
Comment by Zachriel — May 14, 2008 @ 10:05 am
May 14th, 2008 at 10:05 am
moderation help please.
Comment by Zachriel — May 14, 2008 @ 10:05 am
May 14th, 2008 at 10:19 am
Bradford: Good questions all, and especially the first one. As we learn more about how gene expression is regulated, it is becoming clear that phenotypes are only indirectly tied to genotypes. Indeed, there appears to be a continuum of interaction between genotypes and phenotypes, from tight correlation in prokaryotes through looser correlation in unicellular eukaryotes to very loose correlation in metacellular eukaryotes (especially animals). That is, variations in nucleotide sequence can be closely tied to variations in phenotype in prokaryotes, but not in metacellular animals.
Instead, what seems to play the most important role in phenotypic variation in metacellular eukaryotes is developmental plasticity, which is in turn a function of homeotic gene regulation and cybernetic feedback processes during development that connect changes in structure and function with feedback from the environment. If this sounds suspiciously like "lamarckian" evolution, this is not an accident. The year 2009 marks not only the bicentennial of Darwin's birth, it also marks the bicentennial of the publication of Lamarck's Philosophie Zoologique, and the reemergence of lamarckian ideas in evolutionary biology.
I hope it is clear that lamarckian processes (such as epigenetic imprinting, etc. - see Jablonka and Lamb for a full description) can be exactly the kinds of processes that produce emergent properties, as the result of feedback between developing organisms and their environments. As M. West-Eberhard has strongly argued, genetic changes often follow, rather than cause phenotypic variations in eukaryotes (especially animals), and so the "engines of variation" in animals do indeed "decouple" genetic variation from phenotypic variation.
As to how important selection is in evolution, it is becoming clear that "selection" (which I would prefer to call "preservation", following Darwin's expressed desire in his letter to Charles Lyell), is only one of several important factors in evolution. Selection limits variation; ergo, it cannot possibly fully explain the origin of new phenotypic variations, nor is it necessary to produce such variations. On the contrary, it now appears that much of the variation (especially at the biomolecular level) is almost entirely neutral with respect to selection. Comparative genomic analysis, such as is just getting started now, will eventually show what fractions of the genomes of different organisms can be explained by selection. At this early stage in such analysis it appears that the answer is "not much." I would be surprised if this conclusion were eventually changed to "most of it."
This should be very cold comfort to IDers, as it indicates that even less of the biological diversity we observe in the world around us "makes sense" from a teleological viewpoint. To paraphrase J.B.S. Haldane, evolution is not only stranger than we imagine, it is stranger than we can imagine.
Comment by Allen_MacNeill — May 14, 2008 @ 10:19 am
May 14th, 2008 at 11:46 am
Allen MacNeill:
How strange, Allen. You've just described the thrust of EAM quite well (down to the decidedly Lamarckian proposition that adaptation occurs first in the organism responding in real-time to its environment and only later encoded if it proves useful). This is precisely what I predicted years ago biological science would do if it really wanted to be science and not metaphysics. Follow the evidence where it leads and all that.
This prediction wasn't hard to make, as the evidence has been coming in fast and furious. Straightforward "this is where the evidence looks to be leading," from the standpoint of EAM - the notion that there are multiple designers at work in the biosphere. Billions of them. All doing what their ancestors designed them to do - adapt, survive, thrive. To which each successful organism adds its own tweaks to the system or merely contributes to the deep-time process by producing lots of offspring.
Truth is that science can't speak to ultimate origin. That's just dueling metaphysics - creationists and religiously-motivated IDers versus metaphysical materialists. It's not science and shouldn't govern the science or anybody working in science. Remove the metaphysical fight and what do we have? Modern Evolutionary biology moving steadily towards an understanding of evolutionary process that includes processes originated in the ID camp.
I can imagine some strange things, but among them is not EAM or Front-Loading. These seem quite evident to me even though they seem to be very revolutionary to you. I am not surprised, nor am I shocked or suffering any cognitive dissonance. If your science is now becoming aware of these concepts let me be among the first to welcome you to the fold.
Comment by Joy — May 14, 2008 @ 11:46 am
May 14th, 2008 at 11:57 am
This seems to be correct. It's one of the things that piques our interest in front-loading.
In light of Gould's observations on contingency this couldn't be more wrong.
Comment by chunkdz — May 14, 2008 @ 11:57 am
May 14th, 2008 at 12:29 pm
Sorry, what's "EAM"
Comment by Allen_MacNeill — May 14, 2008 @ 12:29 pm
May 14th, 2008 at 12:50 pm
You're not the first to ask.
ISCID blurbs "Endogenous Adaptive Mutagenesis refers to an approach to evolutionary theory which finds its mechanism, (that is, the causal explanation for biological evolution), within the organism itself, not in any external agent."
Comment by Zachriel — May 14, 2008 @ 12:50 pm
May 14th, 2008 at 1:03 pm
Hi hrun,
Yes, it's just a communication glitch. As I have clarified, "exploiting and propping up" speak to evolvability. Simply consider the context of these recent points by surveying what I have laid on the table.
1. The entire Tree of a Life is a protein-dependent output. Evidence for evolutionary processes is evidence for a protein-dependent phenomenon.
2. Proteins are amazingly diverse building material, capable of performing an immense array of functions. We know of no other building material that is as versatile.
3. The immense versatility of proteins is coupled to a single manufacturing process. Elegant.
4. There is very little-to-no evidence to support the notion that protein-less evolution would be as successful as protein-dependent evolution.
5. Since designers are limited by their building material; evolution (as designer-mimic) is likewise limited by its building material.
Does this all enhance the plausibility of front-loading? Yes, as laying down a particular substratum, it would seem so in a more general fashion. But my focus is more along the lines of the original questions that remain unanswered:
Comment by MikeGene — May 14, 2008 @ 1:03 pm
May 14th, 2008 at 1:08 pm
Hi olegt,
I hear ya loud and clear. The danger is indeed quite dangerous "“ I'm about two inches away from talking to myself. I am quite aware of this.
Human beings are naturally social and this shapes our approach to reality (although I don't think many realize the extent). Thus, the social pressure gives me a choice: "get with the program or shut up." The ID movement is upset with me because I don't think ID is science and also (I suspect) because I think evolution/natural selection is a good designer-mimic. Their opponents are upset with me because I don't judge ID to be pure nonsense and seriously entertain a fairly aggressive teleological perspective.
As for getting with the program, what are my choices? I can't get with the ID program for the reasons we both know: ID is not science and attempts to disprove evolution or the efficacy of RM & NS are doomed. But I can't get with the critics' program because of something else I know: the non-teleological perspective on evolution is just that "“ a perspective. It's just the Duck; more culture/metaphysics than scientific fact. The are too many haunting clues and unanswered questions for me to buy into that perspective.
So this leaves me with the following option: to shut up or not to shut up? And this is indeed a question that has occupied my mind for the last month or so. I'd like to tie up some loose ends, but this is probably my last summer posting here.
Comment by MikeGene — May 14, 2008 @ 1:08 pm
May 14th, 2008 at 1:25 pm
Hi Mike,
Whatever else you do - DON'T SHUT UP! Never let your curiosity and exploration die.
If you need to take a break, to recharge your batteries, that's completely understandable. Take care. Hope to see you again soon.
Comment by nobody — May 14, 2008 @ 1:25 pm
May 14th, 2008 at 2:54 pm
Episodic or punctuated dynamics has been observed in simple but exact models of RNA and protein evolution and is attributed to the "degeneracy," "redundancy," or "neutrality" of the genetic code (the genotype -> phenotype map). This discovery has inspired research in evodevo (where it is also observed in far more complex maps), bioengineering, search & optimization theory, evolutionary computing, machine learning and artificial intelligence, and theories of technological evolution.
Over the years, try as I might, I have been unable to garner little interest in these developments. I think I know why that is: The participants have little interest in current, vibrant, theoretical and empirical developments and are basically stuck in a mid-19th to early-20th century rut. Arguing over defunct theories of evolution.
Comment by Rock — May 14, 2008 @ 2:54 pm
May 14th, 2008 at 3:56 pm
Can you provide an example of episodic or punctuated dynamics?
Comment by Bradford — May 14, 2008 @ 3:56 pm
May 14th, 2008 at 4:28 pm
Mike's original questions:
You seem to think that the "blind watchmaker" didn't make the proteins. Why is that? I realize that if she did make them it would sort of ruin your nice story, but surely you must have better reasons than that.
Comment by Raevmo — May 14, 2008 @ 4:28 pm
May 14th, 2008 at 4:47 pm
What evidence do you have that the "blind watchmaker" made proteins?
Comment by Bradford — May 14, 2008 @ 4:47 pm
May 14th, 2008 at 4:52 pm
Allen MacNeill:
Sure, much variation at the molecular level might well be neutral. But how much of that variation maps to phenotypic variation anyway? I guess not too much. The most striking phenotypic variation, the variation in adaptations to the environment, are you saying they are not the result of natural selection?
Comment by Raevmo — May 14, 2008 @ 4:52 pm
May 14th, 2008 at 5:01 pm
MikeGene,
I'd encourage you to continue with your efforts. The effects of what you say and propose are real, but not immediately seen - after your book came out, I heard a lot more conversation about 'front-loading' in the context of ID, and continue to hear it. Over at UD, I see more and more people who either accept evolution with the same conditions as you do (naturally, there will be other differences of opinion) or people who easily could if they got past what really is an artificial cultural hump.
Hell, if there were a way for you to retain your anonymity (I completely understand your desire to let your ideas be the central topic), I'd suggest you approach a group like Templeton's. While I think there's a lot of interesting developments among ID proponents, I also think there's a natural relation to be had with TEs - the terms are not necessarily exclusive. And Templeton in particular seems very friendly to your manner of.. call it intellectual synthesis.
Comment by nullasalus — May 14, 2008 @ 5:01 pm
May 14th, 2008 at 5:08 pm
Bradford:
Hey, I asked first. Mike simply assumes that proteins didn't evolve without magic intervention, and then declares the "blind watchmaker" impotent. That seems a bit unfair. He should explain his reasons for such a strong assumption.
But there is evidence that the genetic code evolved from a simpler version with fewer amino acids and two-nucleotide codons to the more complicated version we have now. If that is correct, one wonders why the designer didn't front-load the final version from the start.
Comment by Raevmo — May 14, 2008 @ 5:08 pm
May 14th, 2008 at 5:38 pm
It was an informal idea promoted by mturner of ARN. It drew a lot of inspiration from:
1. the work of James Shapiro on cellular intelligence and self-evolution
2. adaptive mutations (such as evidence by the work of Barry Hall)
3. occasional forays into life-force vitalism
"Adaptive Mutations" presume that mutations are not random but have some degree of foresight ranther than being blind like "random mutations".
I do not know if EAM devled into the work of geneticist John-Jo McFadden and quantum evolution. I read McFadden book Quantum Evolution.
McFadden's work was referenced by Behe on the topic of adaptive mutations.here: A True Acid Test. I am skeptical that McFadden's ideas of retrocausality can work in biological evolution. We have hints of retrocausality in delayed-choice experiments and quantum computers, but the time frames involved in some of these experiments are probably on the order of femto seconds as far as being able to create a retrocausal event….quantum retrocausality would not be favorable to biological evolution (as we know it) since biological evolution happens in time frames much larger than femto seconds.
Comment by Salvador T. Cordova — May 14, 2008 @ 5:38 pm
May 14th, 2008 at 5:56 pm
An alarming thought. We — both critics and proponents — would be much the poorer without you.
Comment by Bilbo — May 14, 2008 @ 5:56 pm
May 14th, 2008 at 6:20 pm
Salvador T. Cordova wrote:
Neither delayed-choice experiments, nor quantum computers violate causality—not even on the femtosecond scale—as long as the results are consistent with the orthodox quantum mechanics (within which these ideas were conceived). Standard QM respects causality and so far there is no indication that any quantum experiments go beyond the standard QM.
Comment by olegt — May 14, 2008 @ 6:20 pm
May 14th, 2008 at 6:26 pm
He read my design matrix evaluation of proteins, which gave them a score of +4.5 if I remember, and was immediately convinced.
If there is such evidence, this would count against ID. Let's assume there is such evidence, and put it through the design matrix:
Analogy Still counts high as resembling our codes: +5
Discontinuity We now have evidence of a precursor to our present code, and might even be able to extrapolate to a simpler code, and eventually to no code. -2
Rationality It seems irrational to start with one code and then change to another. -3
Foresight Apparently the designer didn't see the need for a different code until after designing the first one. -4
New score for genetic code: -1
The genetic code moves from strong evidence for design to weak evidence for non-design.
Comment by Bilbo — May 14, 2008 @ 6:26 pm
May 14th, 2008 at 6:58 pm
Nah, it's a matter of which magic is stronger.:grin:
Comment by Bradford — May 14, 2008 @ 6:58 pm
May 14th, 2008 at 7:21 pm
Sal:
I doubt if mturner was up on JJ McFadden's speculations. I am more familiar with his EM field theory of consciousness, and I found it lacking in several pertinent areas. But he's at least interesting and an independent thinker.
EAM does have adaptation primarily occurring in phenotypes - in the organism, in real-time response to selective stress - and later encoded (by whatever mechanism) into epigenetic inheritance or genomic rearrangements.
Random mutations in genes are known to occur as inherited variations, as accidents during processing, and as individually acquired damage. These, according to the EAM model, are primarily harmful to the organism if they're not neutral. These cause disease or susceptibility to disease.
Selection never could work on anything that's neutral - random or otherwise. That's just a plain fact. That the very earliest (evolutionarily speaking) organisms seem to have the genetic 'tool-kit' necessary to become all that we see around us is a serious indictment of Darwinism (Selection Is All), Mendelism (Genes Are All) and Neodarwinism (We Don't Know but Believe What We Say Anyway).
If life designs itself, it answers a lot of open questions, while at the same time opening avenues of approach that could prove immensely useful to us, FAPP.
The metaphysical position it came from (panentheism) is entirely irrelevant. And it's short on minute detail from a biological standpoint. I don't think mturner or bertvan are biiologists, and I'm not. Metaphysically you can believe whatever you like about ultimate causation, but you could have done that all along. Science can't 'prove' anybody's metaphysics in the real world. Not Richard Dawkins', not yours, not mine. That's not its job, never was.
The critics we get aren't generally on the front lines of biological research. Heck, most of us IDers aren't on the front lines of biological research either. We all think we know what's real. The front lines of biological research have long since moved on. Following the evidence, as *IS* its job.
Comment by Joy — May 14, 2008 @ 7:21 pm
May 14th, 2008 at 9:54 pm
raevmo asked:
Exactly. The persistence and proliferation of those characteristics we refer to by the term "adaptations" are the result of natural selection, but the origin of those characteristics is not. This is not to say that natural selection doesn't canalize the variations that arise via the mechanisms listed at my blog: