Why would any evolutionary biologist expect there to be such abnormal nonfunctional appendages? That runs contrary to the very basic ideas of evolutionary biology. What we would expect of 'transitional appendages' are appendages that have two or more functions, neither of which it is solely optimal for, the previous dominant function being gradually or partially replaced by the new or novel function. For example, the bat's wing is still used as an appendage of land (well arboreal or cavern) locomotion. Watch fruit bats crawl along branches and use their wing claws to grab and dissect out fruit and nectar if you don't believe me. It is not ideally suited to that function. That arboreal-motility function, which is still selected for, of an appendage that also functions in motorized flight represents a 'compromise' or 'minimax' solution. In that sense, the bat's wing is a transitional appendage. It is not fully dedicated to the functionality of flight and still retains aspects of its former function as an arboreal-motility appendage. Of course, wings can also play other currently secondary functions unrelated to flight, such as in trapping food or sexual display or balancing while running bipedally. We know of organisms in which powered flight is more fully the primary function of wings (birds), but even there there are wings that do not, any longer, serve that function, but serve a different function and there are intermediate or transitional wings that serve two functions: Examples include penguins, in which wings serve flight in a different medium and cannot be used for flight any more, and many other birds that have wings that can still function for flight, but also are used, for short periods of time, for 'flight' in the same medium for which penguin wings are fully adapted.

Similarly, the fins of seals and walruses represent an intermediate compromise in functionality between appendages fully functional only in aqueous environments and variations of those appendages only fully functional on land. These also can be considered 'transitional' appendages.

Similarly, there is a fossil series backed up by an ontological series of changes in particular bones from being jawbones with a secondary function of transmitting vibrations to the inner ear to being bones solely involved in hearing and no longer involved in the function of the jaw.

All the above would qualify as 'transitional' in evolution precisely because there is no magical gap or magical state of abnormal non-functional appendages. There is only the orderly quantitative transition from an appendage that serves one primary function (with several secondary functions) to an appendage that serves a different primary function derived from one of those secondary function. Transitionals in such a process (the process we evil evolutionary biologists think of as evolution as opposed to your odd strawman ideas about evolution) will show intermediacy in functionality during the transition from one state (with its primary functionality) to a different state (with a different functionality). That is, the intermediates or transitionals will serve two functions, but neither one optimally. Such states can have long persistence precisely in conditions where the lack of specialization is selectively favored. It can also lead to specialization in either direction, if the conditions favor it and other aspects of organism allow it.

> >Would a flying squirrel
> >qualify as transitional between an arborial and a fully flying mammal?
>
> no, because there is nothing transitionally nonfunctional in the
> flying squirrel. You might as well look at a fully functional
> Volkswagen and a fully functional Porsche, and claim that the Porsche
> is a transitional from a Volkswagen to a Cadillac.
>
> >Why or why not? Would a fossil insect showing six stubby wings
> >qualify as transitional between wingless insects and insects with four
> >fully developed wings?
>
> no.
>
> >Why or why not?
>
> there must be developing morphology that is not yet fully functional,
> and this nonfunctioning appendage must be reproduced in offspring.

Would an insect whose mouthparts (jaws) are clearly only slightly modified legs qualify as a transitional?

I will answer that. By your definition requiring that the appendage pass through a stage of no functional utility at all, no. By my understanding of what evolutionary transitional stages ought to look like, both the fossil insect with short stubby wings incapable of flight, but capable of other functions (wings are modified 'second' rami and they also can serve as paddles in swimming insects and heat absorbers in land insects) on more than the current two segments (one in Diptera), and 'jaws' that are clearly merely only slightly modified legs near the mouth, represent 'transitional' stages. The wing changed its primary function. The legs that form the jaws changed their function and became more specialized to chewing food.

A common evolutionary pattern is that early fossils show simple repeated features like simple repeated similar teeth and evolution leads to a reduction in the number and specialization and differentiation within the organism. Thus the number of wings in insects, initially present on multiple segments, reduces to two and, in God's favorite group, the beetles, the front wings become specialized as armour, and in mankind's least favorite group, Diptera, the rear wing becomes reduced to halteres. Similarly, the repetitive simple teeth of reptiles become the reduced number of specialized teeth in mammals, with the front teeth often showing specialization for carnivory (but independently in marsupials and eutherians). You are the one who has to come up with a mechanism that merely poofs things into existence. Evolution is not 'creationism without God'. Its mechanism is entirely different (and is compatible with standard, rather than cultish, Christian ideas about the role of God in His nature). Evolution does not predict transitionals of the sort you imply it does. In fact, it implies that such transitionals will be vanishingly rare if they ever occur. Rather evolution predicts descent with modification and that appendages that change primary function will have intermediate states in which both original and new function co-exist as a minimax solution. This represents a quantitative analysis with gradual transition from one primary function to a different one, with varying degrees of remaining original function as possible secondary functions.

> >What would qualify as new beginnings?
>
> abnormal growths that contribute nothing to the life form's present
> function (abnormal indicating that the rest of its species do not
> carry these growths) and this abnormality must be genetically passed
> on in successful reproduction over several generations, becoming more
> and more functional with each generation.

What makes you think that this is what evolution requires?

> >How about a single bacterium
> >which grows into a colony, and that colony diversifies into three
> >populations that are specialized for different parts of the
> >environment where the bacteria live, and the specializations are shown
> >to have a genetic basis?
>
> no, they're still bacteria.

Bacteria differ from one another at least as much as one eucaryote varies from the next (and yes, that includes the variation between yeast and human). Perhaps even more so, since you probably lump Archae and Eubacteria together as "bacteria".

Apparently you have the creationist's view of life which is similar to the proverbial New Yorker's view of American geography (everything west of the Hudson is a very tiny sliver of land labelled 'the wasteland' until you get to Los Angeles): the creationist definition of "kind" becomes larger the further one gets away from H. sapiens. When she looks at humans, only H.sapiens (and sometimes not even all of these fossils) are a clear and distinct 'kind', yet when she looks at bacteria, the rock-eating photosynthesizers, the parasitic Rickettsias and Chlamydias, the giant Epulopiscium fishelsoni, the spirochetes, and the myxobacteria that form many-celled fruiting bodies (and I haven't even touched on the extremophile archae) all become lumped together as the single kind called "bacteria". This represents magical use of words. 'Kinds' defined this way is a meaningless word used as an amulet or talisman to hide from what creationists consider an ugly reality. It means whatever the speaker wants it to mean and thus comforts and blinds the user without fooling anyone else.

> I want something that reflects those
> outlandish claims of dinosaur to bird or primate to human. If you say
> that the common ancestor for the chimp and human no longer exists,
> then you are saying you have NO evidence for this common ancestry
> except some similarities between the two -- similar to similarities
> between a truck and an SUV.

Interestingly enough, most SUVs are directly built on truck structures. But saying that we are uncertain of which fossil represents "the" human ancestor (although it is pretty clear that the direct immediate ancestor of H. sapiens was probably H. erectus -- there are fossils that are hard to classify at this boundary) is different from saying that we have no fossil or DNA or morphological evidence of human ancestors or that this evidence unfailingly points to a common ancestry between humans and the other African great apes.

[snip]

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Subject:    Re: Signatures of Natural Selection in the Human Genome
Newsgroups: talk.origins
Date:       5 February 2003
Message-ID: 75200cbc.0302050406.70c27e3b@posting.google.com

Charlie Wagner wrote in message news:<3E4039D7.5030705@charliewagner.com>...
> Seems a bit myopic to me. I prefer to use my imagination to push
> the envelope. Sticking to known effects produces stagnation. The
> "central dogma" has always informed us that the role of RNA is as a
> "messenger" whereby the information in the DNA is simply copied and
> transferred to the protein synthetic apparatus. Turns out, there is so
> much more to know about RNA and its functioning, a lot of it still not
> well understood.

I know this is off topic, but I get back to it below. Charlie, scientists have known for years that RNA function is not well understood. The "central dogma" of DNA->mRNA->protein only holds for that chain of events! Nobody said RNA didn't have any other roles. We know RNA plays a central role in the machinery of the cell already...look at SNRPs, look at catalytic RNA, look at ribosomal RNA, and the list could go on...all well-studied phenomena, and it's known that there's plenty of surprises still waiting.

We KNOW a lot of RNA function and evolutionary history is not well understood. For instance, there's an entire RNA society out there, and has been for years. There are active conferences on RNA structure and function. There are entire journals devoted to RNA. That certainly does not indicate that RNA study is some kind of dogmatic "book shut" topic for all these years.

Be honest. That portrayal of some sudden release from a narrow-minded view of RNA function is purely media based. You know, when the media says, "This view of RNA completely upsets current dogma and tradition"...that kind of catch-phrase is usually a load of baloney. It might enlighten someone not trained in biology, someone who's only had an introductory biology textbook education, but for those who work with biological systems, it doesn't upset any dogma at all. It merely adds to information we already know.

And guess what...the stuff that's discovered isn't usually discovered by some outrageously-thinking guy in some little underfunded unrecognized laboratory. It's people with experience in all this "dogma" that know how to distinguish what we know from what we don't know.

That's a clue, Charlie. You can't discover something new unless you know what's already known.

>How do you discover new things unless you think
> outrageous thoughts?

Because you can think outrageous thoughts all you want, but biological systems are highly complicated. Thinking something outrageous outside of the context of what we already know about biological systems means you'll be wasting your money and your time. You should think creative thoughts with the "dogmatic" information already well understood, and study phenomena you don't understand yet, and try to piece it together. If it doesn't fit into the current paradigm, that's when you've made a cool discovery.

Get it? You have to understand with, and work with the knowledge gathered by generations of, thousands of, scientists and millions of laboratory-hours, study a system of interest, and if the phenomenon is unknown within the current knowledge set, you can start thinking creative thoughts to generate new experiments to get new results to try to fit your result in the larger picture. That's science. Not starting from square one, throwing away years of hard labor that used that very kind of method.

If we all acted like scientific cowboys, threw our education to the wind, and tried to invent a whole new reality around ourselves, we've essentially thrown away millions of human hours of labor to help build up an empirical scaffold, an observed reality check, and we'd end up with a fairy tale with some science struggling inside of it to hold it up, and failing miserably. That's insane.

> Most of science may be as you have described: "the...forces we
> know about are the ones that matter..." which may be the reason why most
> scientists go through their entire careers never having discovered
> anything new.

Once again you're insulting plenty of creative, daring people who go through their lives trying to push the envelope and discover something new, different, and unseen. That's the dream of the scientist. That's why people go into science. It sure as heck isn't to get rich, you know. The reason that people go into science IS to discover something new, and they do.

Got stats to prove that most scientists are not discovering anything new? Most scientists I know are discovering something new all the time. You have to, to publish, or to get on in a company. Else, you're not a scientist. You're a technician.

>The real scientists, IMHO, are the true iconoclasts who
> challenge everything and are never satisfied with the current thinking.

In other words, a "real scientist" is anybody who's willing to tear down all those human hours of scientific observation, ignore a century of human endeavor, all of which does not agree with your world view? :)

Be honest. You only like the idea of a "scientific cowboy" because the current evidence for evolution is supported by all the data you'd like to see thrown down and re-synthesized. Do you hope that if you could just get all the reality check (empirical evidence) out of the way, that suddenly a new paradigm of creationism/ID would emerge like a phoenix from the ashes?

If you re-synthesized all the information we have to date, all one hundred thousand (probably more) of biology papers, papers on the genome, papers on genetics, etc etc. you would get the same squishy and increasingly complex and lovely paradigm that we've been operating from, all these years.

One last thing: You seem to labor under the delusion that scientists are slaves to some kind of robotic nature that repeats (as a mantra) "central dogma, central dogma". That's scientific Hollywood-ism...purely born out of those movies where the white-bearded old scientist slaps his forehead and exclaims, "My goodness! Little Jimmy was right all along! The Martians DO exist! I was such a fool!"

That's not how reality works. The article I cited above has plenty of discussion about how to test current thought or where to go for new research ideas. If the "paradigm" as we can call it, is wrong, then these research endeavors should uncover it. If new research endeavors uncover something wrong in the core ideas of biology, they get revised. That is how science works.

I despair, Charlie, that you'll ever have an understanding of the vast undertaking that is science included in which are the uneasy truces, the arguments, the bickering, the measuring and re-measuring, the criticism, the one-upmanship, the competition between laboratories....there is not one big scientific conspiracy keeping theories like ID down. The "conspiracy" is in ID itself. It conspires not to work.

Thanks,
Deanne

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