Dear Mr. Pitman,

Hi, my name is Zach, and I find your website very interesting and helpful,
but I do have some problems with your article on dinosaur feathers. I do not
think that the feather impressions on the dinosaurs are collagen fibers for
several reasons.

First, when the Confuciusornis specimens were found in the Liaoning deposits
in China, and had beautifully preserved integument, nobody claimed that these
were collagen fibers. Nor did researchers claim when they found similar
mammal remains with fur around their bodies that it was collagen fibers. I
think that was inconvenient for some creationists that dinosaurs had
feathers, or feather-like integument. But I do not believe, that feathers or
"protofeathers" on dinosaurs provide evidence for evolution in the way that
many have thought. For example, fur on bats does not alone provide evidence
that they evolved from rats, or whatever group they are claimed to have
evolved from.

Second, I believe that all the reasonable skeletal evidence in "Dinosaurs of
the Air" (by Greg Paul) gives strong proof of the relationship between
dinosaurs and birds. This does NOT mean, however, that I think that birds
evolved from dinosaurs. It just proves that they are from the same basic
group of animals.

Third, I believe that this evidence supports a possibly new view that I have
of the creation account in Genesis. (I believe firmly the scripture at  2
Timothy 3:16,17, "All Scripture is inspired of God and beneficial for
teaching, for reproving, for setting things straight, for disciplining in
righteousness, that the man of God may be fully competent, completely
equipped for every good work.") The account where God puts Adam to sleep and
builds Eve from a rib at Genesis 2:21,22 may in fact give us a glimpse of how
God created all living organisms. He may have similarly taken "parts" of
other animals and built upon them to create new animals (such as birds from
theropod dinosaurs, etc.) Thus I do not think that the reasonably derived
conclusion from the physical evidence in fossils that dinosaurs may have been
feathered is a problem.

I have also attached an essay that I wrote about a month ago that deals with
evolution to a degree and another essay that deals with it more in full that
I wrote earlier (over a year ago).

If you would comment on these and the above comments in my email and reply,
it would be much appreciated.

Sincerely,

Zach Armstrong

---

Hey Zach,

Thanks again for your thoughts on this issue.  Most interesting.  I will have to look into a few of your points further. 

Until then, it seems like some of your arguments are quite debatable, even in the mainstream community.Take your argument that Caudipteryx is a clear example of a dinosaur with unambiguous feathers. While no one argues that this creature was indeed feathered, the idea that it was a clear dinosaur is debatable. 

  

Others, such as Stephen Czerkas and Larry Martin have concluded that Caudipteryx is not a theropod dinosaur at all. They believe that Caudipteryx, like all maniraptorans, is a flightless bird, and that birds evolved from non¨Cdinosaurian archosaurs.  Also, while there are those who disagree, Halszka Osmolska et al. (2004) ran a cladistic analysis that came to the conclusion that Caudipteryx was a bird, not a dinosaur. They found that the most birdlike features of oviraptorids actually place the whole clade within Aves itself, meaning that Caudipteryx is both an oviraptorid and a bird. In their analysis, birds evolved from more primitive theropods, and one lineage of birds became flightless, re-evolved some primitive features, and gave rise to the oviraptorids. This analyis was persuasive enough to be included in paleontological textbooks like Benton's Vertebrate Paleontology (2005). (Link) 

So, at the very least, it doesn't seem to me that Caudipteryx as an non-debatable example of the close relationship of birds and dinos - even from a mainstream perspective.

As far as dino air sacs, that's a very interesting argument.  It seems like some real dinosaurs did have very avial-like air sacs in similar locations.  However, establishing that dinosaurs had a bird-like air sac system leads to yet another question: did these pneumatized dinosaurs breathe like birds ¡ª did they use their air sacs to pump air through their lungs in a continuous flow? If saurischian dinosaurs did have this sort of "hot-rod" respiratory system, it could overturn current views of how active dinosaurs were. But answering that question will require more work, suggests Matt. (Link) In other words, this very important aspect of respiration isn't answered yet.  Interesting argument though.

As far as Sinosauropteryx goes:

I'm not so sure that these features are "far too long to be collagen fibers".  It seems at least plausible to me that the reason why these fibers were not preserved around the feet and hands is because they were likely structural to projections like dorsal frills and other supported skin assemblages. The same thing goes for the Dilong fossil "proto-feathers".

As far as the ¦Â-keratin argument goes, ¦Â-keratin is generally found in reptilian skin (in the stratum corneum to supply both rigidity and water-proofing) as well as the claws, beaks, and feathers of birds.  I really don't see how this is some sort of distinguishing feature - to distinguish between a collagen-based frill and feather-like structures. 

As far as the retroverted pelvis of dromaeosaurs, some researchers, like Larry Martin and Stephen Czerkas, believe that dromaeosaurs, along with all maniraptorans (as discussed above) are not dinosaurs at all. (Link) So, this argument really isn't what I would call conclusive either.

Interesting thoughts in any case - especially for a tangent issue.

Thanks again . . .

Sean

---

On 2/3/08, Zachary Armstrong <arms0095@metnet.edu> wrote:

Hey Sean,

I was not claiming that birds evolved from dinosaurs. What I was saying is
that they probably are from the same basic group of animals (i.e., birds
(Aves) are to the superoder Dinosauria what bats (Chiropterans) are to the
superoder Archonta or to the cohort Ferungulata). I do agree with you that
dinosaurs are dinosaurs, and birds are birds and there are enough
morphological differences to separate the two groups. However, their
morphological similarities outweigh the differences.

For instance, both the forearms of dinosaurs and birds have a lunate carpal.
Dromeosaurs such as Deinonychus and others have a very birdlike breastplate,
some even have a keeled sternum, just as birds. Also, many of the small
theropodian dinosaurs of the Maniraptora have a hyperextendable second toe,
like the cassowary and some other extinct birds. Also, the dromeosaurs have
retroverted pelves like birds. Some dinosaurs, such as Nomingia had a
pygostyle-like mass of vertebrae at the end of its tail. Also, all dinosaurs
had an extensive air-sac system that rivaled birds; even the long-necked
sauropods had air sacs to lighten their skeletons. Many of the small
maniraptorans also had honey-comb structured bones. So I think the air-sac
argument against dinosaurs is also rendered moot.

Not one of these animals mentioned above are particularly closely related to
basal birds, yet had many similar features as birds. Anti-dinosaur theorists
often use "parallel" evolution to sweep this evidence under the rug, claiming
it is convergence. Since both you and I do not believe macroevolution is
responsible for the diversity of life on earth, this point of "convergence"
is moot. It is interesting that many anti-dinosaur theorists use Alan
Feduccia, Storrs Olson, and L. Martin to refute the dino-bird connection.
However all of these are evolutionist who favor more basal archosauriforms as
evolutionary ancestors.

Obviously, anti-dinosaur theorists do not claim these origins, they simply
say that just as these scientists do not put much stock in the dino-bird
connection, as it were, that a similar non-evolutionary argument can be made.
I understand this, but I think a more likely explanation can still be
asserted, from a non evolutionary standpoint, that dinosaurs and bird are
related based on the morphological and integumentary evidence.

Furthermore, unambiguous evidence is found of feathers on dinosaurs on
Caudipteryx (where contour feathers are found) and on a juvenile
sinornithosaur skeleton where the feathers are so long that a
"collagen-fiber" argument is unreasonable. Caudipteryx is an oviraptor-type
dinosaur based on the unusual fusion of the upper palate in its skull and by
its pelvis (among other morphological evidence). The Sinornithosaur is
obviously a dinosaur based on its skull, rod-strengthened tail, and over-all
similarities to other maniraptorans.

What about in Sinosauropteryx, from which your argument (and other's) is
based? Well, first of all look at this image:
http://en.wikipedia.org/wiki/Image:Fossil_of_Sinosauropteryx.jpg

You can clearly see there are impressions, not just dorsally, but also under
the tail and the thorax region. This clearly is not from some dorsal frill or
what-have-you. They stick out much to far to be collagen fibers, etc. I will
admit however that the specimen's impressions however are too unclear to show
whether they are "true" feathers or more kiwi-like furry feathers. This will
be up to some debate for a long time, but even if we state that the evidence
is too ambiguous, Dilong paradoxus shows us conclusively that non-bird
theropdian dinosaurs had feathers. (Also, if it is collagen fibers, why are
they not preserved around the feet and legs in these specimens? That's
something to wonder about.)

Go here to see pics:
http://www.amnh.org/science/papers/feathered_tyrannosaur.php

If you scroll down the third picture clearly shows distal tail vertebrae that
have long filamentous fibers that are undoubtedly ratite-like feathers, too
long to be collagen fibers. Additionally, collagen has great tensile
strength, and is the main component of fascia, cartilage, ligaments, tendons,
bone and teeth (why is collagen strongly preserved around the dorsal
vertebrae and caudal vertebrae when it should be found most densely packed by
the strong tendons in the foot and arms (it would not be sticking out by the
way like feathers? It should lie more closely and flatly on the specimen's
bones)

Furthermore the the fossil feathers of Shuvuuia deserti, have even tested
positive for beta keratin, the main protein in bird feathers, in
immunological tests (from Wikipedia). I believe this is conclusive (to the
degree possible) that dinosaurs had feathers.

Finally, the icing of the cake is put on when I read this article, and
especially the comments ( the first and second comments especially)that imply
that both Feduccia and L. Martin have to some degree sided with the dino-bird
theorists:
http://ngm.typepad.com/stones_bones_things/2007/09/feathers-for-ve.html

Best regards (and thanks for listening to my tangential rants),

Zach A.

P.S.: It is interesting to note that the relationships of the Chiropterans
(bats) are unclear too.

---

Hey Zach,

Thanks again for your thoughts on this issue.

The beta-keratin (without alpha-keratin) was found in Shuvuuia deserti.  At least some are arguing that Shuvuuia deserti "belongs to a group of primitive, flightless birds." (Link)  As with Caudipteryx, Shuvia deserti is classified as a maniraptor.  As noted in my last reply and as you note in your most recent reply, maniraptorians are considered by some scientists to be birds, not reptiles or dinosaurs.  As you yourself have noted, Stephen Czerkas and Larry Martin have concluded that Caudipteryx (and Shuvuuia deserti as well as all maniraptors) is not a theropod dinosaur at all. They believe that Caudipteryx, like all maniraptorans, is a flightless bird, and that birds evolved from non–dinosaurian archosaurs.

So, it seems as though the beta-keratin argument is at best debatable - does it not?

Now, I understand that this entire discussion is tied up with the definitions of "birds", "reptiles", and "dinosaurs".  The same problems are present with the discussion of humans and apes and the like.  Certainly there are similarities.  There are also interesting differences.  Where is the dividing line?  The same problems come when one is talking about "species".  These terms are often very subjective.  That's really my main point here.  Scientists have a habit of making conclusive declarations based on morphology that may in fact be way off base when it comes to genetics and functional systems that are unique between two different "species" or "kinds".  Also, what sometimes seems to be unique isn't always unique.  Often different creatures have been given different species and even genus and higher level classifications until it was found later that they were simply morphological or sexual variations of the same breeding pool.

This is one of the big problems with the theory of evolution.  To much weight it put on fossils and morphological features in my view.  Such interpretations are often not significantly more reliable than fairy tales told to children.  I mean, you may be right with the feathered dinosaur idea.  It isn't an unreasonable notion.  It is just hard to really use as an evolutionary argument is all because of the problem of determining what is and is not a true evolutionary "intermediate" or "missing link".  Again, conclusions based on morphology and even on genetics are often very misleading . . . and, obviously, quite debatable.

_________

Toward the end of your last response, you ask about examples of non-beneficial gaps.  The size of the smallest non-beneficial gap between what exists and what might exist to some benefit grows in a linear manner with each increase in the minimum structural threshold requirements for potentially beneficial systems under consideration.  I call these various minimum requirements "levels of functional complexity".  Higher level systems are separated from each other in sequence/structure space by a larger average gap size that is linearly greater in size than lower-level systems.

Consider also that the minimum gap size is always smaller than the minimum structural threshold size requirement.

For example, consider functional level that requires a minimum of 100 fairly specified amino acid residues producing a ratio of potentially beneficial vs. non-beneficial of 1e-40.  This size and specificity requirement or "level" translates into an average gap size of around 30 residue differences between potential targets.  Depending on the size of the population that is searching for new targets via random walk/selection, the minimum gap size between what the population already has and the next closest potential target to at least one member of that population is always smaller than the average gap size - along a Poisson distribution.  A very large population of, say, 1e30, may have a likely minimum gap size of only one or two residues changes.  That is why evolution at such a low level is fairly commonly observed in real life.  However, when it comes to higher-level systems, evolution is much less common - exponentially so.  In fact, evolution has not been observed beyond the 1000aa threshold level (given the same degree of specificity). 

There isn't a single example in literature of evolution, in action, at or beyond this level - not one.  Yet, every living thing has many systems that go far beyond this level.  Such systems, in my view, clearly require an intelligent origin and deliberate creative power. 

I go into this concept in more detail in several essays on my website (Kenneth Miller, Steppingstone Problem, and Flagellar Evolution).

Hope this helps and thanks again for your thoughts.

Sean 

---

  On 2/4/08, Zachary Armstrong <arms0095@metnet.edu> wrote:

Hey Sean,

Thanks for your insights. However (uh-oh, here I go again), collagen fibers
do not have beta-keratin protein. If they were scales, yes they would have
beta-keratin protein. However, they were obviously not scales.

Interestingly, some of the Sinosauropteryx specimens have scales preserved
around their feet. This means two things, (1) the dorsal frill, had it been
scaled would have preserved the scales NOT the collagen fibers, (2) collagen
fibers are microscopic and are not fossilized in the way the integument is
seen.

The only pictures I have seen of fossilized collagen fibers are seen only
through electron microscopy, a far cry from the dark preservations on
Sinosauropteryx. Sinocalliopteryx and Dilong also have these preservations
although much lighter in color, yet still are to large and obvious to be
collagen fibers. Also, although I have not seen the actual material in
photos, Dilong is supposed to have a fairly large fan of  feather-like
integument at the tip of its tail. This indefatigably provides evidence of a
non-bird, theropodian dinosaur with feathers.

Your argument, from Czerkas et. al, that maniraptorans are birds I have heard
before, even from hardcore dino-bird scientists such as Greg Paul (I strongly
recommend reading his book "Dinosaurs of Air" at any rate, because in order
to refute an argument you, as I'm sure well aware with the evolution debate
in general, must understand it). I think it muddies the waters ("what is a
bird? what is a dinosaur?" and the like). I think since the Caudipteryx
wikipedia article shows that an even amount of cladistic analysis's have
either supported or refuted the "its a dinosaur/bird)" argument, its not an
"either or" situation. Generally, the case is in science when you
consistently get "contradictory" results, they are not contradictory but
rather complementary (see my article on Philosophy, God, and Truth that I
sent you previously for further details--about a priori v. a posteriori
arguments)or we're asking the wrong question (or sometimes both). As Greg
Paul so eloquently stated in "Dinosaurs of the Air", p. 272:

"We have previously discussed how, in this view, if some feathered dinosaurs
were in Aves, then they were birds, not dinosaurs. In other words, some or
all avepectoran "dinosaurs" are not really dinosaurs. Instead they form an
arboreal avian clade with birds that parallels the true, terrestrial theropod
dinosaur clade. This arrangement may appeal to those who have opposed the
dinosaur-bird connection but find it increasingly difficult to deny that the
most birdlike dinosaurs are very close to birds, especially as feathered
"dinosaurs" continue to appear. This kind of thought process is already
happening in a certain sense with Protarchaeoppteryx and Caudipteryx, which
are being called secondarily flightless birds despite the strongly
dinosaurian nature of their skeletons.

"This way lies phylogenetic madness. The problems and issues that surround
the naming of various groups and grades cannot be allowed to influence the
restoration of taxonomic categories. First, we must gather and analyze the
data contained within various groups considered WITHOUT BEING BIASED BY
PRECONCEPTIONS OF TRADITIONAL VIEWS OF WHAT IS WHAT. Only after the data
analysis is complete can the problem of what to call certain birdlike
dinosaurs be considered. If we agree that Archaeopteryx is a basal member of
Aves and that certain dinosaurs areeven closer to modern birds than
Archaeopteryx, then the dinosaurs are in Aves and then are birds in a broad
sense. But, because nothing in the skeletons of these dinosaurs separates
them from dinosaurs proper, and because their anatomical grade remains more
dinosaurian than avian, they are still dinosaurs as well as birds. We find
ourselves in the messy, murky gray zone between major groups; what we need is
a simple, informal term that combines the aspects of both types. That term is
"dino-bird"."

(The caps letters in the quote are not my emphasis, they are Paul's, although
he italicizes it, but I cannot use italics in my email system)

Thus, my main argument from this is that all birds are dinosaurs, but not all
dinosaurs are birds (i.e., all squares are rectangles, but not all rectangles
are squares). This is a similar situations as the Chiropterans (bats) and
mammals (which I will not go in to, the situation is far more complicated
than this (oy!), just know that David Peters has noted that there are at the
very least four different groups that bats may be related to, yet the
evidence is so far inconclusive, that does not mean, however, that we should
make the Chiroptera its own class). This really has nothing to do in itself
with evolution, just classification, but many people who defend creation
often feel that this issue must be attacked because it deals with evolution,
although I think there is a happy middle-ground which far to few people take,
namely birds are to dinosaurs what bats are to the Archontans or
Ferungulatans.

Also, I should remind you that the beta-keratin analysis were based, not on
Sinosauropteryx, but on Shuvuuvia, which does not have a "frill" and is in
fact much more birdlike skeletally than Sinosauropteryx, and has been
considered in some analysis's to be a basal bird, yet it has the filaments
that are almost a carbon-copy of Sinosauropteryx found on it. Interesting...I
don't think basal birds have scales or beta-keratin based "frills". Another
nail in the coffin for the non-dinosaur argument.

I think this example at any rate is a great metaphor for the
evolution-creation debate. The scientist say there must be an answer, yet the
answer must be evolutionary, materialistic, non-intelligent. This is an a
priori argument which scientist are supposed to reject, as you have so
correctly pointed out on your website, yet for some reason when it comes to
evolution, they sweep this point under the rug.

Also, interestingly, both the evolution-creation debate and the dinosaur-bird
debate have several things in common. One, there is a variety of competing
explanations that differ slightly (and all are reasonably on-the-level with
each other). Two, both usually take an "all or none" attitude. And three, the
closer we look the more the issue is muddied. A good rule of thumb when this
happens is that we either are not being open-minded enough, or we have
started out with a wrong assumption(s). This is partly why I find this so
fascinating.

But as one of the essays that I sent you shows, there must be an explanation.
So we drum our fingers as we wait for more evidence to come in (as one
blogger, Zach Miller, often states, "We need more fossils!"). although I'm
fairly confident that birds are dinosaurs.

------------------------------------------------------------------------

On another note, I have some questions on the "non-randomness" of evolution.
I know that Richard Dawkins's main argument in "The God Delusion" is that
evolution is nonrandom, it chooses between "bad and good" genes or memes
(that is oversimplifying it, I know, but bear with me). I also know that you
have stated that evolution cannot bridge the gap of neutral functions, and
that this is the major hole in his argument. What are some examples of
"neutral gaps?" Also, does Dawkins explain his comment on "purpose directed
physics", even though he claims purpose is illusory? That seems
contradictory.

On the nonrandomness issue I would like to note that even if there are
certain "good or bad" functions, they are not necessarily equal in number,
thus finding "good" functions might still be, in essence, random. (In fact
his whole argument about religion and morals being "good mutations gone bad"
seems to argue against evolution being nonrandom, or as elegantly simple as
Dawkins would hope or imply.)

Also, in the new issue of "Discover" magazine a very interesting theory about
the origin of life in ice and I was wondering if you have read it and if so
what are your thoughts on it?

"Over and out"

Best regards (and again, hats off to you if you made it this far through my
tangential rant(s) (without skimming, that is)),

Zach A.

---

Hey Zach,

I'm not convinced that Shuvuuia has filaments that are clearly the same as Sinosauropteryx. The filaments of Shuvuuia are described as "long" and, in particular, "tubular" in structure (Link).  It seems to me that the filaments of Sinosauropteryx are neither long nor obviously tubular in nature.  Now, the word "long" is admittedly subjective.  However, the term "tubular" is not.  A tubular filament is quite a bit more complex and "feather-like" than a simple non-tubular filament - especially given the additional immunologic evidence.  In short, establishing a clear morphologic connection between Shuvuuia and Sinosauropteryx on their filaments is a bit strained at this point - in my opinion.

So, again, we are back to the weakness of establishing relationships, evolutionary or otherwise, based on morphology alone.  

___________

As far as neutral gaps, the majority of mutations that occur in each generation are functionally neutral - or at least very close to it.  There is even a "Neutral Theory of Evolution" which was proposed a while back by Motoo Kimura (Link). For example, on average, every human being suffers between 200 to 300 mutations from one generation to the next.  Of these, less than 10 (some suggest as few as 2 or 3) are functionally detrimental and only a tiny fraction of these are "beneficial" (ratio of 1000 detrimental vs. 1 beneficial). (Link)

So, there you have your real life example of neutral mutations. 

Of course, the non-beneficial gaps are measured from what already exists as staring points within a gene pool to potentially beneficial targets that only exist within the potential of sequence space.  Non-beneficial gaps take in both potentially neutral as was a detrimental mutational changes.  

As far as the term "1000aa" it means 1000 amino acid residues.  Amino acids are the building blocks of proteins.  There are 20 different amino acids - similar to the 26 letters in the English alphabet.  These "characters" are used to build protein sequences similar to the building of English words, phrases, and sentences.  Most molecular machines, of course, are built of these amino acid characters and are therefore protein-based.  The more complex the minimum structural requirements of the molecular machine, the greater the gap that will exist between it and the next closest potentially beneficial machine at the same level or one level up or one level down.  

For example, what is the ratio of meaningful vs. meaningless 2-character sequences in the English language system?  About 1 in 7.  3-character sequences? About 1 in 18. 7-character sequences? About 1 in 250,000 . . . etc.

This same pattern is seen in protein-based systems.  Higher-level systems are exponentially more rare in sequence/structure space relative to all the junk that surrounds them and makes them like island oases in a vast desert.  Getting from one island to the next via any form of random walk or step of any kind gets exponentially more difficult with a linear increase in the distance between the starting point(s) and the next closest potentially beneficial island oasis.  

Make sense?

Anyway, hope this helps - - and thanks again for your thoughts.

Sean      

 

---

On 2/4/08, Zachary Armstrong <arms0095@metnet.edu> wrote:

Hey Sean,

I do understand what you are saying now. For instance Steve N.G. Howell said
(even though he was talking about two species of gulls),"We can't learn how
much they interbreed until we can distinguish them, but we can't distinguish
them because they appear to interbreed." Thus your problem is with the
reliability of taxonomy and genetic based separations. I wholeheartedly
agree.

I think you may have missed my point on Shuvuuia, though. My point was taht
since it had filaments like Sinosauropteryx (which is clearly a dinosaur) and
Shuvuuia is considered by many to be a flightless bird, how come they have
the same hairlike/feather-like integument ? Since the only integument that
covers birds (besides their feet and bills) is feathers, we must conclude
that since they have the same hairlike integument, it must be hairlike
feathers that adorn both birds and some theropodian dinosaurs, thus cementing
at least this part of the dino-bird link: some dinosaurs must have had
feathers of some sort (that is because Shuuvuia must be a bird if we take
Caudipteryx to be a bird because the pelvis of Shuuvuia is far more birdlike
than that of Caudipterx; so is its skull and other features.

---------------

I have question concerning the neutral gaps. I was actually asking for a real
life example of a gene mutation that is neither "good" nor "bad", that thus
cannot be dealt with by natural selection (not the theoretical gaps that
increase exponentially, although they must exist, I am inquring of a real
life example).

Also what does "1000aa" mean? Could you explain these "functional gaps of
complexity" more, that is, dumb it down a little (I have less experience with
molecular chemistry jargon and the like--confusion on my end can be avoided
by clear, concise, yet specific definitions if you could provide them)?

Thanks for the information and communication--it is much appreciated,

Zach A.