Intelligent Design - theory, examples, implications

[Biochemist]

....Quack! Canard at work... Like Bill Bryson said "Its incredibly difficult to become a fossil"...

Sure. But the quantity of fossils is currently large. Large enough that the missing elements look like something more than an accident. And we are missing an uncomfortable number of interphylum links for body morphologies that ought to have fossilised. I think this is a dodge.

[Buffy]

...Complexity theory is a proposed mechanism to quantify the "degree" of chaos. The theorists measure the quantity of computative resource required for resolution of a chaotic system via numerical analysis.

I know. Its an "insider's" thing: the people who want to say they are "not chaos theory" want to make the chaos people into "chaos nuts" and deny that any such work was done by the chaos researchers (See Santa Fe Institute). Unfortunately this is somewhat justified because there is a segment of people who went into Chaos who are seeking links to alien abductions and crop circles. Its been somewhat futile since these same nuts have adopted "complexity theory" too. To those pragmatists among us, this is a tempest in a teapot.

Complexity theory regresses the quantity of chaos into a scalar number.

That's a gross simplification, but its a good basic description. In computer science we define algorithms by the algebraic function that describes their performance as being linear (O(n), prounouced "order n"), logarithmic (O(log n)), exponential (O(n^2) and up), combinatorial (O(n!)). This same idea can be applied to measurement of various things, but when you are describing objects with large numbers of dimensions, this typology is meaningless. The same idea is being applied to "complex" systems, but most of the math is based on information theory which as I mentioned elsewhere does not have the meanings that are typically recognized as "information" and are not "algorithmic" in the CS sense. The way it is used to put it colloquially is to show that there is a direction toward complexity evidenced in these systems, but that does not provide any theories or even guidance into classification of systems as "random" or "designed."

It would be really interesting to contrast the complexity of a prokaryote to the complexity of a mammal. I suspect we would find that the prokaryote and the mammal are actually much closer in complexity than the early primordium was to the prokaryote.

I agree with you completely that its worth a shot if people are interested, but there's absolutely nothing to indicate that the kind of "classification" mechanisms that would be needed by ID are there at all...

 

Cheers,

Buffy

[Biochemist]

...I agree with you completely that its worth a shot if people are interested, but there's absolutely nothing to indicate that the kind of "classification" mechanisms that would be needed by ID are there at all...

Agreed. But this is the avenue that I thought could turn ID into a legitimate science. I think the path is worth pursuit. It would be an egregious trail, but it would be worth it for someone to attempt to characterize the degree of complexity at several points along the evolutionary spectrum. I think the results would be surprising.

[Buffy]

Sure. But the quantity of fossils is currently large. Large enough that the missing elements look like something more than an accident. And we are missing an uncomfortable number of interphylum links for body morphologies that ought to have fossilised. I think this is a dodge.

All bolding added is interpretation of data. Scientists do differ in their support of gradualism versus puctuated equilibrium, but calling Steven Jay Gould an anti-evolutionist is something that he went to his grave railing against. To argue against evolution by arguing that gradualism is not proven is not a necessary or even logical conclusion, since PE posits that there are periods of rapid change, and if rapid enough, the Poisson distribution of fossil capture over time would miss these "blink of a geologic eye" shifts.

 

Cheers,

Buffy

[Buffy]

... it would be worth it for someone to attempt to characterize the degree of complexity at several points along the evolutionary spectrum....

The only argument I make is that characterization would be open to interpretation given what we know now. Given that we never know what we're going to find and given that there's *no* indication that there would be any empirically based method for the "classification", there's a 50/50 chance that the "surprising" result you think will turn out will be the *opposite* of what the ID'ers are looking for! :hihi:

 

Hold 'em,

Buffy

[Biochemist]

All bolding added is interpretation of data.

Agreed.

Scientists do differ in their support of gradualism versus puctuated equilibrium, but calling Steven Jay Gould an anti-evolutionist is something that he went to his grave railing against.

I don't think Gould was an anti-evolutionist. But he certainly was an anti-gradualist.

To argue against evolution by arguing that gradualism is not proven is not a necessary or even logical conclusion, since PE posits that there are periods of rapid change, and if rapid enough, the Poisson distribution of fossil capture over time would miss these "blink of a geologic eye" shifts.

I don't understand the use of the word "evolution" in your sentence. I am arguing against gradualism. If we accept (for the moment) that gradualism is not a common mechanism and that these periods of rapid change are the norm, then we are completely unaware of the mechanism for production of new species/phyla. I suggest that our automatic default to selection-based-on-favorable-mutation is poorly substantiatged, and we ought to be looking for other ways to interpret the data. Specifically, we ought to be envisioning mechanisms for rapid change. The glorious part of the is that it actually might be possible to demonstrate it in the laboratory. Imagine that. It is possible that a single experiemt could overturn 100 years of a presumption of gradualism. THAT would make me chuckle.

 

Perhap more significantly, it would suggest that gradualists were no different that the IDers in thier support of a weak thesis with scant data to underpin the theory.

[Biochemist]

The only argument I make is that characterization would be open to interpretation given what we know now. Given that we never know what we're going to find and given that there's *no* indication that there would be any empirically based method for the "classification", there's a 50/50 chance that the "surprising" result you think will turn out will be the *opposite* of what the ID'ers are looking for!

Sure. But I actually don't know what they are looking for. If they find something new -anything new- it would advance the acceptance of the thinking of this set of folks.

[Buffy]

I don't understand the use of the word "evolution" in your sentence. I am arguing against gradualism.

Yes, but you didn't say so, and when you drop that, your argument is identical to what creationists say to refute evolution, and:

If we accept (for the moment) that gradualism is not a common mechanism and that these periods of rapid change are the norm, then we are completely unaware of the mechanism for production of new species/phyla.

...which is not true, since we are finding out all sorts of things right now (the RNA reverses mutations item I've mentioned a few times here in the last few days is just one), that would cause fits and starts in evolution, and Gould certainly is just one of many not *complaining* about inconsistencies that argue against gradualism, but finding *causes* for it.

I suggest that our automatic default to selection-based-on-favorable-mutation is poorly substantiatged, and we ought to be looking for other ways to interpret the data. Specifically, we ought to be envisioning mechanisms for rapid change. The glorious part of the is that it actually might be possible to demonstrate it in the laboratory. Imagine that.

Over and over you make it sound like the gradualists own the roost, and that's patently *false*. There is still a large group that likes gradualism but it is, shall we say....going the way of the dodo...

It is possible that a single experiemt could overturn 100 years of a presumption of gradualism. THAT would make me chuckle.

Oh my! A whole hundred years! Oh! Its a complete upheaval! You would have chuckled at every scientific discovery then! So what?

Perhap more significantly, it would suggest that gradualists were no different that the IDers in thier support of a weak thesis with scant data to underpin the theory.

...and that's grossly unfair: ID'ers have NO evidence. The argument for gradualism has always in fact been strong, and its only with the rapidly expanding data set that we've been able to see the stair steps in the evolutionary record that argue for punctuated equilibrium. That is NOT turning gradualism on its head, its refining it. Implying that it is--as you are doing here--does nothing but impugn the entire scientific community ("scientists? They're just all a bunch of biased, self-serving a**h**es, just like lawyers and congressmen..."), which is one of our biggest societal problems today, so excuse me for getting hot under the tank top about it...

 

Cheers,

Buffy

[Biochemist]

..since we are finding out all sorts of things right now (the RNA reverses mutations item I've mentioned a few times here in the last few days is just one), that would cause fits and starts in evolution,

I am a little confused. We have known about the action of RNA reverse transcriptase for at least 30 years. I am having a little difficulty seeing how repair of mutations argues for rapid change. It certainly argues for stasis, but provides no foundation for rapid change.

... Gould certainly is just one of many not *complaining* about inconsistencies that argue against gradualism, but finding *causes* for it.Over and over you make it sound like the gradualists own the roost, and that's patently *false*. There is still a large group that likes gradualism but it is, shall we say....going the way of the dodo...

Glad to hear it.

Oh my! A whole hundred years! Oh! Its a complete upheaval! You would have chuckled at every scientific discovery then!

Well, lots of them, yes. I think science is humorous, too. Without a sense of humor, who would appreciate anteaters?

ID'ers have NO evidence. The argument for gradualism has always in fact been strong, and its only with the rapidly expanding data set that we've been able to see the stair steps in the evolutionary record that argue for punctuated equilibrium. That is NOT turning gradualism on its head, its refining it.

Wait a minute. If we believe in stasis and PE, we are not "tuning" gradualism, we are refuting it. Modifying the defintion of gradualism does not improve your argument. And the data was ALWAYS weak. The fact that increased volumes of data made support for the theory weaker is true. But we did not LOSE data that supported gradualism. Gradualism has looked weak since at least the '60s. That is why Gould finally came out and stated the obvious in the early 1970s. And 35 year slater, here we still are, acting like random mutations are preferentially selected in there very posts. I think selection based on mutation is an extremely uncommon cause of speciation. It actually may NEVER have occurred.

[Buffy]

It certainly argues for stasis, but provides no foundation for rapid change.

No it doesn't and its not intended to. Its intended to show that *some* mutation change is reversed, which explains the equilibrium periods, that's *all*.

Wait a minute. If we believe in stasis and PE, we are not "tuning" gradualism, we are refuting it. Modifying the defintion of gradualism does not improve your argument.

Only if you are an absolutist and insist that *any* evidence of reversal of mutation is proof that no mutation has *any* forward movement over time (which is a major false argument in creationism).

And the data was ALWAYS weak.

Huh? Look, the way scientific interpretation of data is that we take our data points and we draw a line that approximates it. With fewer data points its easy to say "its a straight line". You get more and more data points, and a stair step or other more complex shape will emerge. In line with the way that science works, some will get tied to the straight line and continue to argue it, while others push forward on a more complex argument. Your personal feeling that its "always" been weak is not a reasonable or logical conclusion. It would be nice if opinions changed quicker, but the fact is that we are *still* discovering key mechanisms that explain the shifts, and unless those go through the entire validation cycle, you're still going to have sticks in the mud in the community that insist on the older view.

 

The most important thing is that your arguments here basically point to a position of there are no evolutionary changes, ever. That is *exactly* what's implied by saying "gradualism is all wrong, and every element of its formulation is disproven". Quite the contrary, gradualism is built on exactly the same notions of mutation that cause changes in organisms the punctuated equilibrium does. PE does NOT refute mutation as a mechanism, it says that its more complex and there are accelerating and counterveiling effects that are proving to be principally due to non-DNA related effects of RNA, proteins, hormones, etc. The difference between gradualism and PE is ONLY in how fast and how gradual. You of all people should know this! In fact maybe the problem is you're too close to it. You see revolution when its really a tempest in a teapot in the grand scheme of things.

I think selection based on mutation is an extremely uncommon cause of speciation. It actually may NEVER have occurred.

So, since I know you do agree that speciation occurs, do you have an alternate explanation that of necessity both the gradualists and PE folks would disagree with you on?

 

Cheers,

Buffy

[Biochemist]

No it doesn't and its not intended to. Its intended to show that *some* mutation change is reversed, which explains the equilibrium periods, that's *all*.

Thanks.

Only if you are an absolutist and insist that *any* evidence of reversal of mutation is proof that no mutation has *any* forward movement over time (which is a major false argument in creationism).

Wait a minute again. I mistakenly inferred that YOU were suggesting RNA reverse transcriptase supported PE. My suggestion was not that mutations are precluded. My argument is that the affirmative evidence that mutations cause speciation is weak.

... the way scientific interpretation of data is that we take our data points and we draw a line that approximates it. With fewer data points its easy to say "its a straight line". You get more and more data points, and a stair step or other more complex shape will emerge.

Sure, but this is 2005. We are now 40 years post advent of stair-steps, and we are still talking like mutation based speciation is ACCEPTED DOGMA. Look at these posts!!!!!

...Your personal feeling that its "always" been weak is not a reasonable or logical conclusion.

Sorry for the hyperbole. I went to college in the '70s, and I thought it was weak then. For me, this is "'always".

The most important thing is that your arguments here basically point to a position of there are no evolutionary changes, ever.

Let's be specific please. My argument is that there is VERY LITTLE affirmative evidence for GRADUALISM. I have no idea what you men by "evolution" in this context.

...gradualism is built on exactly the same notions of mutation that cause changes in organisms the punctuated equilibrium does. PE does NOT refute mutation as a mechanism

WHAT??? PE has not proffered mechanism, except that it occurs "quickly". This would fundamentally RULE OUT any but the most oxymoronic definitions of gradualism. What do we call it? Not-so-gradual-gradualism????

The difference between gradualism and PE is ONLY in how fast and how gradual.

Are you laughing as you write this?????

I know you do agree that speciation occurs, do you have an alternate explanation that of necessity both the gradualists and PE folks would disagree with you on?

No. In the scientific method, it is NOT mandatory that we have an alternative thesis when we refute a hypothesis. In fact, it is mandatory that we NOT have an alternative for refutation. We need other alternative data for a corresponding affirmation. To my knowledge there is no data set that supports an alternative hypothesis for the PE mechanism.

 

Would you like me to offer a conjecture?

[Buffy]

My argument is that the affirmative evidence that mutations cause speciation is weak....Sure, but this is 2005. We are now 40 years post advent of stair-steps, and we are still talking like mutation based speciation is ACCEPTED DOGMA. Look at these posts!!!!!

"Anticipation is making me late, keeping waiting....."

 

Here's 1996: Score one for Punk Eeek, Sci Am

 

This one's an interesting and brief discussion showing evidence that Darwin himself actually accepted PE: (almost) All you need to know about PE Shows the "evolutionary" acceptance of PE while still faulting Gould and Eldredge for their admitted "hyperbole" (just so you know you're in good company!).

 

And referenced on that page is a good page with a brief description of PE in detail Puncuated Equilibria/TalkOrigins.org which includes this line:

PE is not mutually exclusive of phyletic gradualism. Gould and Eldredge take pains to explicitly point out that PE is an expansive theory, not an exclusive one (1977: Punctuated equilibria: the tempo and mode of evolution reconsidered. Paleobiology, 3, 115-151).

WHAT??? PE has not proffered mechanism, except that it occurs "quickly". This would fundamentally RULE OUT any but the most oxymoronic definitions of gradualism.

No, as referenced above, Gould did not agree with the notion that it was not based on similar mechanisms of speciation via mutation, and specifically that mechanisms for causing the spurts are explainable through selection based on major shifts in environment. Speciation does not happen in a vaccuum, something that the absolutist gradualist position (which note from above *Darwin* did not agree with). This does not mean that speciation does not occur based on mutation and selection, only the rate at which it occurs.

In the scientific method, it is NOT mandatory that we have an alternative thesis when we refute a hypothesis. In fact, it is mandatory that we NOT have an alternative for refutation. ...Would you like me to offer a conjecture?

Tee hee! I know that, silly! I'm just trying to get you to do some weight lifting! Sure, love to hear how speciation occurs without mutation and selection... Got a theory? I won't lose my respect for you if you don't of course... :hihi:

 

Cheers,

Buffy

[Biochemist]

...I'm just trying to get you to do some weight lifting! Sure, love to hear how speciation occurs without mutation and selection... Got a theory? I won't lose my respect for you if you don't of course...

As you might expect, I am not enthusiastic about introducing heretical ideas into a forum of antagonists. Further, I am not a researcher, so I am not likely to be in a position to advance any particular theory by producing serial evidences, or even serial reviews of such. But what the heck.

 

I do think that Gould and Eldridge were being careful. They were not in a position to rule out speciation through mutation. They had to maintain professional decorum (not to mention get more grants). But they certainly did nothing to confirm speciation by mutation. Even in the Sci Am article you linked, there was NO evidence that the morphological changes were driven by mutation, but that was the proffered mechanism in the article. Based on what? The triumph of hope over data?

 

Emperor? clothes? Maybe we can be kind and call it group think.

 

Let me offer the heresy. I am too far away to hear you laugh anyway.

 

I think that production of daughter species is not caused by serial mutation, gradual or otherwise. The intracellular biochemical strictures that keep us in stasis are far too complex and far too successful for a large number of serial mutations to survive long enough to effect a significant morphological change. Therefore, one would have to conclude the that capacity for dramatic change in genotype (reflecting itself in significant change in phenotype) is part of the information load in the parent species. That is, viable genotypical change that is dramatic enough to preclude interbreeding of the daughter species with the parent is maintained in the parental genotype. This sudden expression of genotypical shift tends to express itself when a small isolated population is under environmental stress. I do not believe this is a mutation. It is a feature of the information load in the parent species.

 

This would suggest that the majority of animal and plant kingdom information content was reflected in the first prokaryote. Go figure. But I think this model better reflects our current state of biochemical understanding and our current state of paleontological knowledge than any mutation-based model. Mutations actually might occur, but they have nearly nothing to do with speciation.

 

Doesn't stike me as a whole lot more difficult to swallow that the entire mass of the universe being squashed into a space the size of a Planck length.

 

Feel free to name my theory. I think I like "Biological Big Bang". Do keep in mind that if my heretical theory is true, then the IDers would have to prove an incredible level of CSI in the first prokaryote. Everyting after that would be a natural consequence of that information load, and a fundamentally "natural" process.

[Buffy]

Are you sure you can't hear me laughing? :hihi:

 

We'll call it "Bio's Theory of Non-mutantational, Stress-induced, Pre-programmed, Geno-typic Speciation," or "Bio's Bunny Hop" for short... :hihi:

 

If I follow this, what you're saying is that the information is there and some combination of chemical/hormonal reactions to environmental stress directly cause recoding of DNA sequences. Oddly enough, I think that's sorta kinda what *most* of the community is coming to, except for the fact that they are *not* saying that "mutation is ruled out in all cases" which is the only extremist part of your view, and I don't think there's much evidence of that. There is evidence that various mechanisms do "undo" mutations, but it does not follow that they undo *all* of them, and moreover the more recent models say that RNA, proteins, and other chemicals that have been heretofore ignored (which was *unimaginably* stupid), have a significant impact on how change occurs and becomes permanent. I guess I'd only ask you at this point why you are so vehemently opposed to mutation, for which there's lots of evidence, and why in spite of its existence has *no* effect on change. Again, don't feel compelled to, but I find you just as entertaining as you obviously find me! :) (Fish whistling in the background...STOP it Fish!)

 

Cheers,

Buffy

[Biochemist]

We realy ought to get Fish in on this one. I will PM him if he doesn't find us.

We'll call it "Bio's Theory of Non-mutatational, Stress-induced, Pre-programmed, Geno-typic Speciation," or "Bio's Bunny Hop" for short...

Shorter is better. You will be pleased to know that my real (very secret, and Cajun too) last name is a single syllable name starting with "B" so your last one might become famous with my real name attached. Sure.

If I follow this, what you're saying is that the information is there and some combination of chemical/hormonal reactions to environmental stress directly cause recoding of DNA sequences.

I can't tell if it is hormones (in E Coli?) and I suspect it is not recoding. I suspect it is an outcome that is not a lot different that what we see with trisomy 13. We get a dramatically different, but totally viable species by virture of a macro-level change in DNA structure. It could occur in a VERY small number of generations. Maybe one.

Oddly enough, I think that's sorta kinda what *most* of the community is coming to, except for the fact that they are *not* saying that "mutation is ruled out in all cases" ...There is evidence that various mechanisms do "undo" mutations, but it does not follow that they undo *all* of them

Whoops, back up. I did not suggest that mutations do not occur. I suggested that they have almost nothing to do with speciation. I am pretty sure that the evidence linking mutaion to speciation is nearly nil.

I guess I'd only ask you at this point why you are so vehemently opposed to mutation, for which there's lots of evidence, and why in spite of its existence has *no* effect on change.

Go back and glance at the Scientific American article again. They stated that the E. Coli variant they were using (one that could not use plasmids) suddenly jumped by 30% in volume. You think that is a mutation? It strains credulity to think that all of the intracellular machinery could ramp up 30% nearly overnight (and remain viable) unless it was a very complex alteration in genotype. This probably involved dozens of genes. I think calling that a mutation is a little disingenuous. Complex beneficial changes in genotype are very unlikely to be mutations. Particularly if they happen reproducibly, as that article suggested. Just like trisomy 13. This behavior is much more likely to be a feature of the genetic source code.

[bumab]

The intracellular biochemical strictures that keep us in stasis are far too complex and far too successful for a large number of serial mutations to survive long enough to effect a significant morphological change.

 

Some morphological changes can occur in simple organisms, like insects, with only one mutation. The number of legs is the big, prime example, but coloration is also something that is often changed by a single gene, and has a big effect on fitness.

 

Which brings us to the next point...

 

Therefore, one would have to conclude the that capacity for dramatic change in genotype (reflecting itself in significant change in phenotype) is part of the information load in the parent species.

 

Complexity of the parent species is a major contributor towards speciation time, in the gradualism model. Precisely because of what you have described, it takes many magnitudes of time longer for a horse to potentially speciate then a bacterium. This is related to the genetic complexity and morphological complexity of those genes.

 

An interesting feature of punctuated is that most competitors are wiped out, leaving a lot of niche's open. This allows, in the traditional model, for all (or almost all) mutations to be considered beneficial. This always rubbed me the wrong way a little bit, because most species have anti-mutation features of their genome to guard against agressive mutation (other then bacteria and single celled guys). Why is it that punctuated equilibra seems to occur?

 

I'm starting another thread with my ideas on that...

[Lolic]

Hi Bio,

 

I believe these are the numbers you were asking about:

 

Dembski calculates the outside limit of probability to be 1 in 10^150. He arrives at this number by multiplying:

• the total number of elemental particles estimated to exist in the entire universe (10^80); times

• the number of transitions that each elemental particle can make in a second (10^45); times

• a billion times (10^9) the estimated age of the universe (about fifteen billion years, or 10^16 seconds) which is about 10^25 seconds.

 

I don't believe I referenced a 747. I'm about 20 posts behind at this point. hope to catch up soon.