Re: [asa] TE/EC Response - ideology according to Terry

> 1.  I'm not downplaying the importance of the primary cause.  I am saying
> that it is not a "local" cause in the sense that static electricity is.

God, being omnipresent, is as local as you can get.

> Alternately, if are thinking of God as "powering" the laws of
> nature at every moment, a sort of continuous creation, so that God "powers"
> the lightning bolt locally, I could go for that, too.  God is, as it were,
> within the lightning bolt, within the laws of nature, manifesting his power
> at all times through particular natural events.  This is no problem for me.

"Continuous creation" as a phrase might suggest that God is
essentially remaking everything every second. I hold that creation is
firmly distinct from God (i.e., not pantheism, panentheism,
panninitheism, whatever) and that it is in continuity with what was
existing before.

> But it sounds very much to me as if you and Terry are saying that in
> addition to all such ways that God can be construed as acting "locally", he
> performs some *extra* action of some kind to make *that particular lightning
> bolt* fall, an action that he does not perform in the case of any other
> lightning bolt.

No, God is acting locally in every actual lightning bolt, whether it
obeys the regular laws of nature or it doesn't.

> And I don't see how you can say that without stepping outside of the rigorous naturalism that you and Terry seem to be endorsing.<

My naturalism isn't all that rigorous. What I assert relating to
methodological naturalism is that a) it works pretty well for the vast
majority of situations; b) it's about all that science is capable of;
c) as far as we can tell, it's working with regard to describing
evolution.

> Neo-Darwinism says that God doesn't have to do anything extra, because
> nature already has the capacity for macroevolutionary change.

As a biological concept, Neo-Darwinism says that populations change
over time in certain ways due to certain factors. It doesn't say
anything about God.

God doesn't have to do anything extra because He's doing everything
already anyway. (Not to deny our responsibility, etc.) God is
capable, as far as we can tell, of creating the observed diversity of
organisms by following the patterns that we recognize as natural laws.

> 2.  I've known about lungfish since I was five years old, when I read my
> first book on dinosaurs (my favourite subject as a child).<

Then why do you repeat the error of claiming that lungs and gills are
mutually exclusive? Going from gills to lungs is not that hard,
either-millions of tadpoles make the transition from gills to lungs
every year.

> You line up a bunch of existing features of animals -- animals with different levels of complexity in their eyes, or animals with gills, gills plus lungs, then just lungs, etc. -- and then you infer from this functional sequence an actual historical process of development.  You ask me to imagine a historical process by which the forms shade into each other.<

No. I am a paleontologist doing DNA work in vain hope it will get me
a job. For the fish-amphibian transition (not to mention many other
transitions in taxa with good fossil records), we have a series of
fossils providing detailed evidence on the transition. Many types of
relatively primitive bony fish have air-breathing, and the swim
bladder seems to likely derive from such a predecessor. This suggests
that a lung was present in the common ancestor of regular ray-finned
fish and lobe-finned fish. The lungfish had lungs and leg bones
(burrows provide fossil evidence of relying on lungs; most modern
lungfish have reduced fins); leg bones are evident for the extinct
fish most closely related to the amphibians and lungs presumably were
not lost and then re-evolved despite the limited direct fossil
evidence about lungs. We also have the molecular data indicating that
lungfish are indeed more similar to tetrapods genetically than to any
other fish; coelacanths are next most similar genetically. The oldest
fossil amphibians have traces of continued aquatic life (e.g., lateral
line, relatively weak limbs), showing that full replacement of side
fins with legs and feet preceeded significant terrestriality. (Even
lungfish could probably wiggle across wet ground; tail fins probably
had not changed much).

Certainly there are organisms with different levels of complexity,
though it is also true that living organisms all have diverged in some
ways from their ancestors. "Living fossils" retain certain components
that were also present in relatively distant ancestors, but not all.
Ironically, the incorrectness of merely lining up modern things
underlies a problem of "irreducible complexity"-type arguments-they
tend to assume that everything has to appear at once in the final
form. Nevertheless, the fact that organisms do fall readily into such
evolutionary lineups is good evidence for evolution.

> Of course, I can *imagine* such a process.  I can imagine such a process by
> which a centaur and horse, or centaur and man, are related as well.  I could
> even dream up a "natural selection" explanation of how centaurs could, in
> certain environments, have a survival advantage over horses (or men, take
> your pick).  But I have absolutely no evidence that the genome of any
> horselike or anthropoid creature is capable of such a transformation.

You have no evidence that the genome of any horselike or anthropoid is
incapable of such a transition. The chief difference is the fact that
we don't have any evidence of centaurs and so have no evidence that
such a process has taken place, whereas we do have plenty of evidence
that fish did transition into amphibians.

> Nonetheless, what evidence do I have that the genome is capable of such transformations?  Transitional forms such as Tiktaalik give me no clue about the mechanism.<

Actually, they can provide some clues-the paleoenvironment tells us
something about the selective pressures, as do associated fossils.
The details of fossil anatomy can be combined with studies on genetic
controls on the relevant bits of modern organisms to get an idea of
the exact genetic changes.

Study on the genetic details of development in modern relatives will
probably be the most productive for tellign you just what genes were
involved in a particular transition.

>  Am I to imagine that chance mutations, without any co-ordination, happened to produce viable intermediate forms?<

This is painting the target around the arrow after it hits. Mutations
that are as "chance" as anything else produce viable variation. Any
variation is intermediate. If you are shorter than about 186 cm, I am
transitional between you and taller people.

The fish-amphibian transition is not a perch suddenly sprouting feet.
Sarcopterygians developed stalked fins, aka lobe fins, with bones in
the stalk. Still a fin on the end. Some then develop toes along with
the fin. Other rearrangements are going on in other parts of the body
as well.

However, suppose the arthropods had developed lungs rather than
tracheae and consequently grew big enough on land to keep the basal
amphibians from getting onto land and being successful there. The
arthropods might then be researching how one obscure group of fish
developed some features that helped them do well in shallow, variable
water settings, but never amounted to more than that. If you look at
the series from sarcopterygians to amphibians (or reptiles to mammals,
or any number of other well-documented transitions), no one step is
all that big. It's only in hindsight that we get excited about the
changes (and most people only get excited about the changes that lead
to us).

>  Then I need a proposed genetic pathway, or I can't test the assertion.<

The paleontological evidence, as well as the genetic and anatomical
similarities, etc. point towards the assertion that the change
occurred. A genetic pathway related to how it occurred. There's all
sorts of ongoing work in evo/devo, gene function, etc. that help us
tell what the genes are that affect things such as limb development,
growing lungs or gills, etc. We don't know their full activity in
model organisms like fruit flies, nematodes, mice, zebrafish, humans,
etc., so it's premature to expect full details to be worked out for
lungfish or coelacanths. However, we do have a good idea of what are
some of the genes that ought to be looked at to get a better handle on
this. I don't know if anyone has had success in raising lungfish in
the lab.

> The difficulty with macroevolutionary theory at this point is that it is
> still premature.  Until we know the workings of the genome and of
> developmental processes the way a mechanic knows the workings of a car, all
> proposed genetic pathways are largely guesswork.

No, it depends on for what. We have very good genetic pathways for
various molecules, because the genetic question then is relatively
straightforward. For the evolution of a particular feature such as a
limb, there are many more genes involved and we need to know about
more of them. However, we do not have to know exactly what all the
genes invovled are to know something about the most critical issues.
For example, looking at genes involved in triggering and localizing
bone growth would provide the most critical information related to
limb evolution. Other genes are involved in various ways, but that's
the key question-how do you get leg bones or toes or a shoulder girdle
or whatever part you are looking at, not the precise determinant for
the number of toes or configuration of the ankle bones.

> If evolutionary biologists want to play a guessing game -- may have, coulda, mighta (note that the
> conclusion of the article Preston Garrison cited is filled with subjunctives) -- that's their own in-house academic business, but they shouldn't leave the public with the impression that they know how evolution works, when they are almost completely in the dark about how it works when it comes to the hard-nosed details.<

We do know much about the evolutionary sequences for any group with a
good fossil record that is well-studied evolutionarily. (Many
microfossils have only been studied to name them and assign them to
ages to help tell if your well is at the right depth for oil or other
drilling question.) Molecular data give us a fairly good picture of
general relationships of organisms, though there are a lot of details
to fill in.

We also know a lot about the mechanisms. We know about how DNA works,
how natural selection works, other factors than influence evolution,
etc.

What we don't have is the full details of exactly how everything
happened. In part, that would require a time machine. However, we
are gradually getting an increasingly better picture of how it
happened. We are not running into any walls that would point to a
need for miracles in the process.

> By the way, since you've said the mutations aren't simultaneous, what is the
> current Darwinian narrative explaining how being able to walk on crude
> foot-fins would give a selective advantage, if the fish couldn't breathe out
> of water yet?

Once again, you forgot the lungfish. They could breathe out of water
before they had feet, and probably before they even had any equivalent
of legs.

The first amphibians with reasonably good legs seem to have still been
essentially aquatic, though presumably they could cross a mudflat.
Presumably the legs functioned mostly for walking on the bottom of the
water or crawling through debris (logs, roots, etc.). Fast swimming
is not the only way to go in the water.

> (Let me guess: tidal pools on the ocean shore, where fish
> with gills and legs could perhaps survive for a few seconds out of the
> water, snatch some snails and worms from the mud, and quickly waddle back to
> a deeper stretch of water to plunge under for some air?)

Have you ever been fishing? Fish do not die in a few seconds of
coming out of the water (not counting a predator). If it's humid,
they can survive quite a while. Several fish with no lungs tend to
cross land on wet nights (e.g., eels, walking catfish; grunions are
somewhat in this category). I don't recall just what mudskippers do
to breathe air, but they spend much of their time out of the water.
(It was rather odd in Fiji seeing something skim across the surface of
the water and climb out on a rock and then realize it was a fish.)

> Or perhaps you are insisting that the fish already had lungs, in addition to their gills,
> before they developed the feet?  In that case, remind me how, in the absence
> of surviving soft tissues, palaeontologists can be certain that fish with
> both lungs and gills existed, before feet (or lobe-fins) were developed?

Yes, I am insisting that. Lungfish again are a big part of the
answer. The lung plus gill condition is evidently the state for the
common ancestor of lungfish and amphibians. Many primitive ray-finned
fishes essentially have lungs of some sort, so lungs probably were a
significant supplemental source of oxygen long before anything got
close to becoming an amphibian. Even now, tarpons will drown unless
they can get air, and they're a reasonably standard ocean fish.

Gills are associated with particular bones, though fairly standard in
any fully aquatic amphibian.

Additionally, amphibians can breather through their skin and mouth
lining. A large chunk of amphibian species have neither lungs nor
gills as adults.

> And even if fish did have both lungs and gills before developing lobe-fins,
> what *Darwinian* reason can be given for the simultaneous existence of lungs
> and gills -- two different and redundant oxygenation systems?  That uses a
> lot of bodily resources for a something that isn't needed -- fish don't need
> lungs.

Many do-as noted above, some modern fish can drown if they don;t
breathe air. Lungs let you get air, very rich in oxygen. Gills let
you breathe underwater, but it's a lot poorer in oxygen. Lungs also
provide buoyancy.

> The simultaneous existence of lungs and gills makes much more sense
> on Dentonian than Darwinian lines.  If Denton is right, the lungs may have
> evolved before they were put to use because the genome, as it were, "thinks
> ahead".  So once again, design comes out on top and neo-Darwinism comes out
> on the bottom.

But why did it think ahead in assorted fish, only one of which
actually went to amphibians? The pattern is not that of thinking
ahead, it's a pattern of making use of what's handy, as far as the
biological aspects go.

-- 
Dr. David Campbell
425 Scientific Collections
University of Alabama
"I think of my happy condition, surrounded by acres of clams"
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