Might As Well Stay Missing . . .

Very nice. I like it a lot.

I had an article on this subject published yesterday. I especially love all the images of Tiktaalik pushing itself up on its "paws" ... when its "paws" are not even tied in to the spine and can't support any weight!

(Besides the fact that Coelacanth had similar bones in its front fins ... was considered a missing link ... but is still alive today. . . .)

In Him,

David S. MacMillan III

That link isn't really a missing one anymore.

David S. MacMillan III: Oh. My. DOG. this was drawn by a cartoonist who is engaging his readers with humor, you dolt! surely you understand humor, right?? by the way, where did that sign come from in the lower left side? did DOG put it there??

David - did you read the AIG response, or come up with all that on your own?

Either way. here's a post that addresses these criticisms - since the author is working on a Ph.D. concerning the evolution of lobe-fin fish, I'm willing to assume he knows a little bit about the subject.

But in this bit from your article: " Tiktaalik was called "the" missing link in the line between land and sea. But if evolution was true, we should find an unbroken path between all "transitions". And we have no transitional form "between land and sea" now, so how can this be "the" missing link? Shouldn't we find hundreds?" you do make a good point. It isn't the missing link, but merely a 'missing link,' if we're even gonna use the term. After all, if you look around the various paleo/evo/sciency blogs, you'll see folks wincing everytime some newspaper article burbles about missing links, especially the missing link. In fact, I was reading someone earlier today who was pointing out that all fossils are transitional fossils - I'll come back and link it if I remember who. Meanwhile, here's another Lancelet quote, with Martin ranting, "Nobody hails anything as "the missing link". "Missing link" is a term that scientists don't use and we even try to ask that the media does not use the term, but they do anyway. We can't stop them, " and one from a comment on this very blog by Dave S., "This is really a terrific discovery. Although I must say I don't care for the cringworthy archaic term "missing link."

I don't understand why you think we don't have a transitional form now, but for the rest of your question, "shouldn't we find hundreds," you have to remember that becoming a fossil is rather like winning the lottery - not something to be counted on, although various factors can make it more or less likely. Then, of course, the fossil not only has to survive for however many millions and millions of years (not get subducted, or eroded, or etc.) but also end up somewhere where we can actually get to it. You might want to read Taxonomy, Transitional Forms,
and the Fossil Record for a look at these and other issues. It's from the American Scientific Affiliation's site (the ASA, founded in 1941, is a"fellowship of men and women in science and disciplines that relate to science who share a common fidelity to the Word of God and a commitment to integrity in the practice of science.")
 

Dan,

I appreciate your politeness. It is much more pleasant to read that kind of writing than someone who calls me a "dolt" when I was referring to illustrations and models in the Times article, not the cartoon. [hint, hint, Grrl]

I really do like that quote "all fossils are transitional fossils." It accurately describes the presupposition that evolution gives you, making it easier for a person to understand the Theory.

The article on Lancelet was laced with ad hominem and irrelevant paragraphs, but it did have a few good points that I took a close look at.

Considering that the AiG article was published hours after the Times article and that no scientist with Creationist leanings has yet been able to examine the specimens, it does not particularly concern me that we do not have all the answers regarding this fossil. Time will tell whether this is a real transitional form or just another fish with certain attributes scaled up.

My post was rather firm. But hey! What's the blogosphere for?

I quote:

I don't understand why you think we don't have a transitional form now. . . .

With Tiktaalik, sufficient time has not yet passed to figure out exactly what it is. Scientists generally wait a little while before classifying a new species because further research always turns up more information.

And I don't know of any other transitional forms. Archeotopterx (did I get that right?) had fully formed wings and feathers. Besides, they found modern birds buried beneath ol' Archie.

And don't feed me that junk about Australopithecus Afarensis. Lucy had flared-out hips (despite Dr. Leakey's attempts to reshape them with a power saw) that would have prevented her from walking upright. And we have found other afarensis fossils that show very ape-like, curved feet which did not make the Laetoli footprints.

But enough about transitional forms. Show me any scientific (repeatable, observable, testable) mechanism that can increase the useable information in the genome along evolutionary lines.

I'm sorry, but evolution is really nothing more than a speculation about what might have happened in the past. Unless you can give me an example of how it happened or when it happened it isn't even a hypothesis, much less a theory.

In Him,

David S. MacMillan III

"I was referring to illustrations and models in theTimes article, not the cartoon"
Well, you have to admit this wasn't particularly clear. Thank you for clearing this up, though.

"Considering that the AiG article was published hours after the Times article"
vs.
"Scientists generally wait a little while before classifying a new species because further research always turns up more information."

Interesting.
Perhaps actual scientists can weigh in on whether sitting back and waiting a little while before classifying a new species is standard operating procedure.

I have to get some sleep, but let me bring up Archaeopteryx for a sec (if I talk about Australopithecus afarensis, I may well stop being polite). You claim that Archaeopteryx isn't a transitional form because it has wings and feathers. However, the definition of transitional form isn't 'exactly in the middle,' but rather something that shows a transition between two groups. That, Archaeopteryx does very nicely. It's certainly a bird, but it's a bird with some very, very dinosaur-looking features. We also have some dinosaurs with somewhat birdlike features, including feathers! Tiktaalik is in fact quite a parallel to Archaeopteryx, if from the other side - a fish, but with some very, very tetrapod looking features.

Think of it this way: imagine you place a camera - set to take pictures at 2 minute intervals - in the kitchen to catch whoever has been stealing cookies out of the coookie jar on top of the fridge. In the morning, the cookies are gone, and you have, out of a stack, two time-dated photos showing 1) your little kid walking towards the fridge with a stepladder, and 2) your little kid walking away, face covered with cookie crumbs. What inference can be reasonably drawn?

In fact, with the fossils we now have - including dinosaurs with 'flight feathers,' and four-winged gliding dinos, it's more like we also have photos of the kid putting the stepladder next to the fridge and climbing up it. But, like parents who can never admit their kid did anything wrong, I believe that even if we were in possession of a sequence of dino->bird transitional fossils beyond a sunstruck paleontologist's most fevered imaginings, many or most creationists would simply ignore or deny it. Perhaps I'll be proven wrong in less extravagent scenarios.

I'm assuming your reference to modern birds under Archie refers to more anatomically modern birds (instead of, say, bluejays), specifically Protoavis. There would seem to be a number of possibilities, including

1) Protoavis is a Triassic bird, and Archaeopteryx is an astonishing but failed example of convergent evolution, a dino 'attempt' to reinvent the wing.
2)Protoavis is a Triassic bird, and Archaeopteryx a bizarre bird offshoot that evolved strangely dinosaurian features.
3)Protoavis is a Triassic bird, and Archaeopteryx a sort of extinct living-fossil bird that shared a even more distant 'eopteryx' ancestor with Proto, and retained various primitive, dinosaurian traits, shedding light on the nature of that transition
4) Protoavis is based on a small quantity of heavily damaged material, and may be misidentified. Archaeopteryx is a bird showing many dinosaurian traits along with bird ones; while probably not a direct ancestor of modern birds, it sheds light on the nature of the dino-bird transition.

It is my understanding that (4) is seen as most likely (and 1&2 essentially impossible), but if anyone's heard differently in terms of actual science, please weigh in.

If you're interested in learning All About Archaeopteryx, this link will take you to a talkorigins page o' Archie.

A few other references:
Archeopteryx (Wikipedia)
Protoavis
Feathered dinosaurs
Archaeopteryx (UC-Berkely Museum of Paleontology)
Are Birds Really Dinosaurs? (UC-Berkely Museum of Paleontology)
Fossil Recod of the Aves (UC-Berkely Museum of Paleontology)
Avian Flight (UC-Berkely Museum of Paleontology)
Maniraptoran dinosaurs (UC-Berkely Museum of Paleontology)
Icons of Evolution: . . . Archaeopteryx (NCSE)
The Protoavis controversy (Evowiki)

And if you're talking transitional fossils, don't forget the one, the only, the it would be nice if they updated it and added graphics . . . the talkorigins Transitional Vertebrate Fossils FAQ by Kathleen Hunt. You might be especially interested in the Introduction which addresses what a transitional fossil is and why gaps exist (or seem to). Also good if slightly dated context for Tiktaalik, I think.

Enjoy

"I'm sorry, but evolution is really nothing more than a speculation about what might have happened in the past. Unless you can give me an example of how it happened or when it happened it isn't even a hypothesis, much less a theory."

Whew! And here I was worrying about antiobiotic-resistant bacteria! Good to know they're not even a hypothesis! Yay! I get to go back to chugging antibiotics at the slightest hint of illness, and simply stopping prescribed treatment regimens as soon as I feel better! And I guess there are no worries about bird flu then, at least i terms of person-to-person transmission . . .

Ok, let's save time: you're going to bring up the standard evolution-denial micro/macro evolution distinction (the one working scientists don't agree with), I'm going to post a link or two something off talkorigins like Microevolution vs. Macroevolution or the giant 29+ Evidences for Macroevolution: The Scientific Case for Common Descent (cuz I'm lazy), you're going to say - well, something, but the gist will be that this is flawed and doesn't show anything. . .

So let's skip all that and make it a little more interesting. What's the criteria for the examples (how, when) that you're asking for? What are you looking for? What sort of thing would you accept?

(Of course, if I misstated or strawmaned one of your potential responses, feel free to correct me . . .)

Hey Dan,

I'll take the TalkOrigins page on micro/macro (I've chopped a few irrelevant parts out for brevity). Then I'll answer your other questions:

Microevolution and macroevolution are different things, but they involve mostly the same processes.

We'll see about that.

Microevolution is defined as the change of allele frequencies (that is, genetic variation due to processes such as selection, mutation, genetic drift, or even migration) within a population.

I wouldn't argue with that necessarily. But I would add this modifier: natural selection eradicates genes that disfavor the organism: genes that change due to selection, mutation, genetic drift, etc.

Macroevolution is defined as evolutionary change at the species level or higher, that is, the formation of new species, new genera, and so forth.

You can define macroevolution in that way if you want to. But their saying so doesn't make it so. All they are talking about is "speciation": the loss of the ability to interbreed with similar organisms. Not macroevolution.

Creationists have created another category for which they use the word "macroevolution." They have no technical definition of it,

I beg to differ. Macroevolution is technically defined as a series of mutations that move an organism upward on the "evolutionary tree" while still affording enough survival advantage for natural selection to favor them. A set of random mutations over millions of years could conceivably (the odds are bad but let's give it to you) change the genes for scales into genes for feathers. But the dysfunctional genes along the way would be removed by natural selection, leaving the reptiles-trying-to-fly back where they started.

Speciation is distinct from microevolution in that speciation usually requires an isolating factor to keep the new species distinct.

Yep. Microevolution slowly alters the gene pool, which with an isolating factor can prevent the two species from being able to interbreed like they could before. But this is not an increase in usable genetic information like I referenced above. Rather there is a specialisation and a loss of now-unnecessary genes.

Supermacroevolution is harder to observe directly. However, there is not the slightest bit of evidence that it requires anything but microevolution.

No, it requires microevolution/natural selection coupled with mutations that increase an organism's survival skills and move it up on the evolutionary scale.

There is no reason to think that small changes over time cannot add up to large changes, and every reason to believe they can.

The "small changes" that microevolution references are a loss of usable, relevant genetic information. The "small changes" that macroevolution requires are an increase of usable, relevant genetic information. Unless you can find an example in nature of the latter than you have no reason to assume that big changes every accumulate.

I don't have time to go further right now (it's 11:15 here) but I will return later. Cheers!

In Him,

David S. MacMillan III

David,How does one determine if an organism has moved 'up' the evolutionary tree? This idea of 'greater evolved-ness' is an artifact of misunderstanding evolutionary theory. Things don't move 'up' so much as they move 'out'.As for mution leading to an increase of genetic information, please read up on gene duplication where by a section of genetic information is copied to an extra location. The copied genes can have a wide range of effects, and will mutate seperatly from their source genes, leading to altered function, and eventually possible irreducibly complex systems.Edward Temptly

I had an article on this subject published yesterday.

It's misleading to refer to a blog post as "having an article published". It sounds like you had to put it through some rigorous process of review. The "publish post" button, however, is not a form of review. I know -- I still have all my typos after I click it.

"I especially love all the images of Tiktaalik pushing itself up on its "paws" ..."

You've used the term "paws" here in quotes. I presume you have a reference for the authors referring to the fins as "paws" in the matter of their texts? They've used "paw" as a verb, but not as a noun. That's a key difference. Still, I'm not talking about the newspaper articles, I'm talking about the original articles in Nature. You have read those, right?

when its "paws" are not even tied in to the spine and can't support any weight!

This is by far my favourite canard circulating about Tiktaalik. You know what, David? This is precisely the same construction found in nearly all early tetrapods, including Ichthyostega and Acanthostega, the next plesions 'up' from Tiktaalik. In fact, it is general for most (if not all) Palaeozoic tetrapods to not have an osseus connection between the shoulder girdle and the spine. It is only once a true sternum develops that can attach to the ribs does such a connection occur. However, a large number of tetrapods seem to manage just fine without such a connection, such as frogs and salamanders.

(Besides the fact that Coelacanth had similar bones in its front fins ... was considered a missing link ... but is still alive today. . . .)

Here you've italicized "coelacanth" as though it were a generic name, this is highly misleading (there is Coelacanthus, but unfortunately, it's extinct). The living genus is Latimeria and it is not represented by fossils. Fossil coelacanths are represented by a variety of different genera, and I suggest that you read up on this.

I suggest that you remove your entry on your website because it is full of absolute falsehoods.

The supposed "footlike" structure is not directly attached to the skeletal system of Tiktaalik which means that it couldn't possibly have used these bones on land. The bones were embedded in the muscle, not in joints attached to the backbone.

You'll have to explain this. I've handled the Tiktaalik material directly. The humerus connects directly to a glenoid in the shoulder girdle, as in all other lobe-finned fishes. The main difference is that the shoulder girdle is made of a big, beefy scapulocoracoid, much more like a tetrapod than any lobe-finned fish (except for, conveniently, another tetrapod-like beast, Panderichthys). As I mentioned above, the shoulder girdle's attachment to the body is quite what we'd expect by comparison to early tetrapods.

Secondly, the animal's status as an intermediate between other lobe-fins and tetrapods is not based on the functional interpreation (rather, the inverse is closer to reality). The authors refer to direct morphological comparisons (i.e. things we can observe) to make two hypotheses in parallel. One is that Tiktaalik stems from a branch that intercalates between Panderichthys and the earliest tetrapods (Acanthostega and Ichthyostega). The other hypothesis is the functional morphological one that makes reference to the robusticity of the elements, their inferred ranges of mobility, and the location of muscle insertion ridges and scars.

To bring up coelacanths as though these people had never considered them is to further point out that you've got some learning to do. The very reason why Tiktaalik is so important is the very fact that it compares in one sense with coelacanths and other lobe-finned fishes, whilst exhibiting striking differences from these forms. Even more significant is that much of what is different about Tiktaalik happens to be that which it shares in common with tetrapods.

Even if Tiktaalik had real limbs attached to its torso, it still would be unable to breathe above water. The lungs operate on an entirely different principle than gills

Can you tell us what you mean by this or why it even matters? Many fishes are known to have lungs and breathe air (cf. lungfishes, bowfin, gar, Arapaima), and by comparison with lungfishes (also lobe-finned fishes) we might infer that Tiktaalik did as well. However, this is neither here nor there. The point is that breathing in amphibians is acheived through the mechanism of buccal pumping In this case, the throat is drawn down and air is essentially "swallowed". Since air has lower viscosity than water, it can be drawn in through the nostrils and so you don't see amphibians "gulping" air the way fishes breathe water.

Interestingly, Tiktaalik and other tetrapodomorph fishes all have an internal nostril, a passage leading from the nasal cavity to the roof of the palate.

As for the "obvious fallacy comes out in the artistic license used to depict the soft tissue around the three "limbs", you've much to learn. The first fin requires absolutely no reconstruction, since none of the silhouette around the fin skeleton is inferred or made of soft tissue. The fan-shaped region is formed of scale-like rays called lepidotrichia and they're quite well preserved in specimens of Eusthenopteron since they're made of bone. In Tiktaalik, there are lepidotrichia as well, but the specimen shows that they did not extend far beyond the limit of the fin endoskeleton. Why they chose to draw a jagged edge is beyond me. However, your inference that this has something to do with the animal's "grip" is false since these elements have nothing to do with fingers and are lost before the earliest known tetrapods. Thirdly, the soft-tissue reconstruction on Ichthyostega is rather modest, since I think it's well-advised to assume that it had muscles in its limbs. What bothers me most is that they didn't use the most current reconstruction of this animal.

David, you're evidently a young guy and at your age and level of experience mistakes are easy for me to forgive. What you have presented, however, borders on lying. I know you were well-intentioned and probably thought you were informing people, but we can see that what you have written is false at even the primary observational level. That is, we can even start by assuming that evolution is wrong, your crticisms are still wrong and not based on fact. A knolwedge of vertebrate anatomy is like learning a very difficult language. You need a lot of the theory and a lot of the practical in order to make sense of it. One needs to have had a broad comparative survey and have done some first-hand dissections. It really helps to log a few 'person-weeks' in a bone room looking at things first-hand and comparing them. The point is, you can't go to newspaper accounts, or to AiG, or even simply trust the papers themselves. You need to look at things first-hand. It is clear that you've had no such experience yet.

Cheers,
Martin

[ps - sorry for the big formatting error on the link, but

David,

The article on Lancelet was laced with ad hominem and irrelevant paragraphs

Could you please point out my ad hominem attacks and irrelevant paragraphs, please? I certainly certainly has many personal attacks on the authors, but I felt that was justified given the depth of their deception. A personal attack is quite different from an ad hominem, where a person avoids a specific argument by attacking the person making it. I can find no such instances in my response.

As for "irrelevant", I hardly think that your record on vertebrate anatomy qualifies you to judge my statements as "irrelevant". However, I will await your explanation.

Considering that the AiG article was published hours after the Times article and that no scientist with Creationist leanings has yet been able to examine the specimens, it does not particularly concern me that we do not have all the answers regarding this fossil.

And the AiG article was a day later than the two Nature articles that are the original reports of this material.

They had all of a few hours to respond to the times, but never even made a mention of the articles except for a link to one of them. No wonder they made such stupid assertions about the fin, we have no evidence that they even read the article that described it! Even if they didn't have a subscription to Nature they could still have access the supplementary data file that contains photographs of the elements for free.

This isn't about AiG having the answers, it's about them having their facts straight before even getting into this. Clearly, they have no intentions on this. They're so sure of themselves that they don't need to see if their statements correspond with reality in any way.

It looks like I'm going to be taking little peck's at David's posts all day.

I really do like that quote "all fossils are transitional fossils." It accurately describes the presupposition that evolution gives you, making it easier for a person to understand the Theory.

That's an interesting way of looking at it, but you seem to have missed the point. The reason why we say "all fossils are transitional" has nothing to do with a preconceived interpretation of them whatsoever. It's actually a little hint to look outside the typological box that has been discredited since Aristotle noted that dolphins have more in common with "beasts of the land than with the fish of the sea".

You see, in the same sense that it is wrong to call a dolphin or a whale a fish, it is wrong to lump all fishes in to one bin as though they are all some sort of imperfect representation of a 'fish ideal'. This goes back to what I was saying about anatomy before.

Consider, for a moment, that we have more in common genetically, morphologically, and embryologically with a trout than either of us does with a shark. However, the overall habitus of a shark and a trout is much more similar. If one considers the distribution of all data, we find that typological boundaries break down.

Even people like Sir Richard Owen (a creationist and a staunch anti-Darwinist) had to wrestle with the classification of the lungfishes, not content to classify them either as a fish or amphibian.

The fact is, the typological categories we had erected in the past ("fish", "amphibian", "reptile") are actually couched in a creationist perception of life as modification of 'essential archetypes' (Linneus was a creationist, let's not forget). These categories began to collapse with the growth of 'gentleman naturalists' who explored the earth's biota found that these boundaries began to collapse. The old Linnean categories grew increasingly insufficient to characterize life's diversity.

The growth of the fossil record only brings that into plainer sight. It offers a new window into animal diversity in the past and its implications are that the lines between categories become increasingly blurred. So, because it has been shown that typological categories don't exist and because the fossil record destroys any doubt of this, all fossils can be considered transitional.

This is only my second day of reading this blog after I chanced upon it while scanning the Internet for Tiktaalic information. It is really fascinating and I admire the knowledge of Dan and Martin who reply to posts by those who misunderstand evolution. I am amazed that I can read the first-hand comments of someone who has actually handled Tiktaalik (isn't that a great name!) fossil material.
One topic I'd like to see replied to at more length is David S. MacMillan III's assertion that microevolution only results in "a loss of usable, relevant genetic information." But doesn't microevolution through natural selection also select for favorable traits so that it can result in a GAIN of "usable, relevant information?" Please correct me if I have misunderstood something here and I am wrong in this statement.

David Hicks; good question. i was unsure what MacMillan's statement meant ("a loss of usable, relevant genetic information") when i first read it, and i am still not sure what it means now, although it definitely implies an incorrect understanding of what microevolution actually is, so instead of arguing over MacMillan's choice of words, i think it is more useful and relevant to use a more precise and scientific definition of microevolution to clear up this confusion;

basically, microevolution is the change in gene frequency within a group of individuals that breed with each other. this group of interbreeding individuals is typically known as a "population".

microevolutionary change occurs in four different ways, any combination, or usually all, of which might be operating simultaneously; mutation (a change in the DNA sequences encoding a particular allele), gene flow (movement into or out of a population by individuals that possess a particular "version" of a particular allele), genetic drift (randomly occurring change in the frequency of a particular version of a particular allele), and natural selection (individuals carrying a particular version of a particular allele are more, or less, likely to survive long enough to reproduce).

hope this helps.

It's really hard to interpret what creationists are saying when they talk about a "loss of information". DSMIII has inserted a few extra ambiguous qualifiers ("usable" and "relevant") that make it easier to slide goalposts. The terms "usable" and "relevant" are not part of the language of molecular biology.

The information canard has been address at www.talkorigins.org in a number of places, you'll just have to search there.

The long and the short of it is that creationists are puffing a lot of smoke. It's based on a large number of misconceptions and outright falsehoods. The best example that tears them down is gene duplication, which is one way of getting a new gene.

In the genomes of, say, animals, there are hardly any unique genes when we compare across phyla. For instance, axial patterning of a developing embryo is controlled by Hox genes, whether you're a jellyfish or a swordfish or a human being. The difference is the number of these you have. All the Hox family genes share conserved structures and motifs and are all more or less different variations on the same sequence or sequences. Clearly, duplication and sub-modification of these genes is a perfectly good explanation for their emergence. There's nothing 'esoteric' about a duplication, this has been observed in the lab and we can cite a number of mechanisms for it (unequal crossing over during meiosis, for instance -- these are things you'll have to look up).

What mutations always do is change pre-exiting information, delete it, or add it. It's demonstrably false that they decrease information. Their effects may be antagonistic, yes. For instance, sometimes pathogen resistance compromises the native function of some particular protein in the body. However, there are ways to compensate for it, either by further changes to that protein or the modification of other proteins in the related pathway. Nevertheless, it is well-known that there are 'costs' to evolution. To take the subject of this thread, for instance, the origin of terrestriality obviously came at the cost of aquatic performance. However, a tetrapod can out-do a fish on dry land anyday. Thus, the tetrapods can exploit that niche and diversity. Similarly, mult-resistant bacteria have a whole new host of places they can exploit now that they no longer have to worry about those pesky antibiotics.

One topic I'd like to see replied to at more length is David S. MacMillan III's assertion that microevolution only results in "a loss of usable, relevant genetic information." But doesn't microevolution through natural selection also select for favorable traits so that it can result in a GAIN of "usable, relevant information?" Please correct me if I have misunderstood something here and I am wrong in this statement.

Natural selection removes genes unfavorable to survival. If a mutation produces a gene which gives its owner an "edge" over other creatures, the other creature's genes are made "unfavorable", and they are slowly weeded out.

If we want to find examples of evolution, first we need to find a beneficial mutation that gives its owner an edge. This could take a while.

Examples, anyone?

Sorry; typo in my last comment.

"If a mutation produces a gene which gives its owner an 'edge' over other creatures, then those creatures without the mutated gene are slowly weeded out because their genes are now 'unfavorable'. What is 'unfavorable' is relative to the perfect set of genes ... which varies according to the environment that the creature is in."

Sorry!

In Him,

David S. MacMillan III

you are correct, most mutations are detrimental to the organisms that carry them since genes have been shaped by natural selection to fit the demands of their environment. this means that a deviation away from the functional form of each gene will probably harm the organism that carries that gene.

however, that said, when organisms are placed into environments where the environmental demands are radically changed, some of the randomly occurring changes that their genes normally experience anyway will be beneficial to that organism, giving it a competitive edge over other organisms within that same population. further, a 2001 research study found that beneficial mutations are not as rare as thought. the researchers of this study found that at least three mutations (12%) that occurred in a population of E. coli had significantly improved their fitness to live on a diet restricted to maltose, a novel energy source for this bacterial species. so the data suggest that beneficial mutations are not as "rare" as one might like to believe.

anyway, that said, there are hundreds examples of beneficial mutations documented in the literature, but here are a few;

Observed Instances of speciation (a collection of references along with a long and interesting essay that cites lots of data)

Beneficial mutation in the fruit fly, Drosophila melanogaster.

Beneficial mutations in humans

Natural selection removes genes unfavorable to survival.

But David M. III, if favorable genes (mutations et al) occur, why can't natural selection select for them, i.d. favor their survival over unfavorable genes? Unfavorable genes would be removed, favorable ones would be preserved or added.
Even if only 0.001 % of the population carried the favorable gene, if it gives enough of a competitive, reproductive edge over the other 99.999 % of the population, what's to keep it from spreading throughout the population if the favorable gene is preserved in enough progeny?
I thank everyone for their thorough and learned responses. Some of the language is quite technical and it has been a couple of decades since my basic biology courses but I'll dust off my old textbooks and enhance it with some Internet research, especially on the talkorigins archives and the online biology textbook. I really appreciate all your hard work and attention to answering my questions.
David Hicks

Tiktaalik also has bearing on another controversy...this pre-amphibian was discovered about 600 miles from the North Pole. Not too many cold-blooded land-dwelling animals found in those parts these days...seems the world must have been a lot warmer then. So who was driving all the SUVs back then?

"who was driving all the SUVs back then?"

Trilobites maybe? Offroading on the benthic ooze. They went extinct only 175 million years after Tiky Iky.

There are many roads to global warming besides those wheeled and heeled by SUVs, trucks, high-performance sports cars and cows.

".this pre-amphibian was discovered about 600 miles from the North Pole."

Currently ~600 miles from the North Pole, you mean. Things have changed a bit since the Devonian.

Questions for ID proponents:

Is the Intelligent Designer also the Intelligent Manufacturer?
Why does the ID-er design creatures that look transitional if they are not transitional?
What processes does the ID-er use; what tools, what sources of power, etc.?
What are the intentions of the ID-er in each case of an organism's design and manufacture; for example, in the cases of Plasmodium falciparum and Yersinia pestis?
Why were plants designed that are addictive to humans, such as tobacco, coffee, alcohol-containing ones (fermented grapes, wheat, rice, etc.), marijuana, opium, etc.?
Why was the human brain designed to be potentially addictive to the abovementioned substances?
Did the ID-er also design (and manufacture), the Earth, the Sun, the stars and all other heavenly bodies, the galaxy, the universe? Are these also irreducibly complex?
If life is irreducibly complex and so could not exist without being the work of an ID-er, does that mean non-living things do not need to owe their existence to an ID-er? If so, if non-living things need an ID-er to exist, then why bother with proving living things have need of an ID-er?
Why did the ID-er design organisms to experience pain? Could they not have been endowed with a painless system, e.g., lights, bells, digital readouts, to alert them to harm without having to experience pain? (I am glad we organisms are endowed with the ability to experience pleasure rather than a sensationless instrumental system!).
Why are many organisms designed with rudimentary organs? Why not just leave them out?
Why did the ID-er see fit to design the predator-prey relationship?
Why wasn't the world designed so that we could get meat and other food, including vegetable nutrition, from something non-living, for example rocks, so that this consumption does not conflict with the other uses of organisms, (e.g. photosynthesis)?
Why wasn't the ID-er intelligent enough to foresee that designing and manufacturing the ecosystem complex of organisms would lead to conflicts between its design and fabric and that of the needs of humanity? For example, that forests would be depleted because of man's need for wood. Why design trees and other flora to be essential in manufacturing oxygen and transporting water to the atmosphere and yet design them so that their component material, wood, would cause these other essential abilities to be eliminated by their use by man for building and fuel and food? Uses by man eliminate their usefulness in the other life-supporting abilities demanded by ecosystems.
Wouldn't the Earth have been better designed if blank, nonfertile areas of land (no life existing) been set aside for human developers to build houses, roads, parking lots and other structures on? Then there would be no conflict between ecosystems and man's developments.
Why were so many organisms designed to have no defenses against man's power and are thus in danger of extinction by him? Presumably the ID-er should have known this when it designed them. Wasn't the ID-er foresighted enough to anticipate this?

I could go on and on but I am sure many readers, including ID proponents themselves, could think of countless examples of where the ID-er's wisdom falls a bit short, to say the least.

I just thought of one more question that has bugged me ever since ID became a hot topic:
If ID does not necessarily have anything to do with religion, why are so many religious people enthused about it? Don't they realize that ID proponents themselves say the ID-er is not necessariy supernatural? They don't even say the ID-er is necessariy a single entity. Maybe it's a committee of agencies--like the human manufacturing process: it generally takes several to thousands of people to design and manufacture anything that humans make.
Yet one more question:
If human design and manufacture is the inspirational model for ID, why aren't the obviously evolutionary qualities of the human process of artifice cited in speculations about the process of the ID-er? For example, the wheel has a long history of evolutionary design; car, airplanes, nearly everything that man makes, but the ID proponents never seem to mention evolution in the design of organisms, except for conceding microevolution. Yet you can see macroevolution in human inventions too. I would cite the bullet and thegun as macroevolutionary descendants of the bow and arrow.
Why fight evolution so hard if ID shows evolution too?
I kind of know the answer to that last question but I'd be interested in seeing how well ID endorser's answers correspond with what answer I am thinking.