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Author Topic:   Flies and birds share flight-specific gene use
Tranquility Base
Inactive Member


Message 1 of 14 (13119)
07-08-2002 10:52 PM


With all the changes between the LCA of flies and chicks the same genes are specifically used, in the same way, to set up wing anatomy. God or unbelievably convegent evotution. It is the detailed genetics of wings that is the same, not just 'limbness'. I thought we might start seeing this from genomes and evo-devo work.

The point is that the LCA of flies and chicks did not fly! Chicks supposedly evolved from reptiles and amphibians well after the LCA of flies and vertebrates.

From Shubin NH (2002) Journal of Morphology 252, 15-28

Abstract: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list _uids=11921033&dopt=Abstract
PDF (need subscription?): http://www3.interscience.wiley.com/cgi-bin/fulltext?ID=90011061&PLACEBO=IE.pdf

quote:
Major groups are not assembled in a simple linear or
progressive manner — new features are often “cut
and pasted” on different groups at different times
. . .

The assembly of limbs over developmental and
evolutionary time offers examples of the major processes
at work in the origin of novelties.

Homologous genes, either orthologs or paralogs, are involved
with patterning the three ordinate axes of the wings
of Drosophila and chicks
(Shubin et al., 1997; Tabin
et al., 1999). These genetic similarities extend to
more than gene sequence, structure or expression:
there appears to be functional conservation in the
specification of the anteroposterior, proximodistal,
and dorsoventral axes as well.
Anteroposterior signaling
in both systems depends on a hedgehog/Shh,
dpp/BMP-2 signaling system (Lee et al., 1992; Ta-bata
et al., 1992; Basler and Struhl, 1994; Krauss et
al., 1993; Riddle et al., 1993).


[This message has been edited by Tranquility Base, 07-08-2002]


Replies to this message:
 Message 2 by wehappyfew, posted 07-09-2002 2:17 AM Tranquility Base has responded
 Message 10 by peter borger, posted 07-11-2002 2:25 AM Tranquility Base has not yet responded

  
wehappyfew
Inactive Member


Message 2 of 14 (13134)
07-09-2002 2:17 AM
Reply to: Message 1 by Tranquility Base
07-08-2002 10:52 PM


quote:
Originally posted by Tranquility Base:
The point is that the LCA of flies and chicks did not fly!

But the LCA and the intermediate forms all had LIMBS, and contrary to your peculiar interpretation of this article, these genes are, indeed, useful in the expression of ALL limbs (and antennae, too). Not surprisingly, such useful genes are highly conserved. Therefore, their continued function as limb expression, orientation, and position regulators is equally unsurprising.

Read some more from Shubin to clear up you confusion...

"Hox genes play a critical role in the development of the vertebrate axis and limbs, and previous studies have implicated them in the specification of positional identity, the control of growth, and the timing of differentiation.

These Hox genes [including sonic hedgehog] were initially involved in specifiying region identity along the primary body axis, particularly in caudal segments. This function is similar to the role of Hox genes in Drosophila development. "

to whit...

"In summary, hedgehog is a necessary element in the establishment of polarity during segmentation of the fly, and during the development of appendages"

In other words, the same gene that regulates the anteroposterior polarity of Drosophilia parasegments that later develop into head, thorax and abdomen (and thus prevents feet sticking out the fruitflies' back) is also used to establish polarity in the digits of the autopod compartment of all tetrapods (so you don't get thumbs where your pinkie should be).

In tetrapods, sonic hedgehog performs this polarity control function during growth of the zeugopod and autopod compartments. Note that this occurs in ALL tetrapods, not just flying ones, and in both feet and wings (or arms).

In Drosophila, hedgehog performs a similar task to control the polarity of the parasegments that will produce legs, wings, and antennae. Since arthropods lack any semblance of zeugopods and autopods, claiming that "the same genes are specifically used, in the same way, to set up wing anatomy. " as you put it, is wildly wrong.

The only common function in these homologous genes is that they are both used to control polarity. The fact that they do it using the same biochemical pathway and the same expression pattern is evidence of their common ancestry, not design, since establishing polarity in body segments has been essential since the LCA of chicks and flies. Not surprising at all. What is surprising is that you, trained in genetics and biology, would miss this obvious fact.

http://sdb.bio.purdue.edu/fly/segment/abdmlb2c.htm

http://sdb.bio.purdue.edu/fly/segment/hedghog1.htm

If you weren't so desperately eager to shoehorn any likely sounding data into your anti-evolutionary bias, you might have learned something about how useful genes like these are co-opted into new functions in different lineages long after their LCA.

The article you cited even told you this up front - "new features are often “cut and pasted” on different groups at different times." ... in other words, polarity regulating genes were borrowed from their pre-existing function in body segment polarity specification to perform a new polarity specification in the last two compartments of the tetrapod limb.

If you step back a bit and look at the larger picture, you might be interested in learning about how the Hox gene duplication events in evolutionary history are reflected in the present homeotic gene sets for arthopods (one), jawless fishes (3), and jawed fished and tetrapods (4 or 5). Thus the duplicated Hox genes became available to regulate the new structures at each major stage of evolutionary development. You might even argue that the duplication event caused the evolution of the new structures (head, jaw, tetrapod limbs).


This message is a reply to:
 Message 1 by Tranquility Base, posted 07-08-2002 10:52 PM Tranquility Base has responded

Replies to this message:
 Message 3 by Tranquility Base, posted 07-09-2002 2:30 AM wehappyfew has responded

  
Tranquility Base
Inactive Member


Message 3 of 14 (13136)
07-09-2002 2:30 AM
Reply to: Message 2 by wehappyfew
07-09-2002 2:17 AM


Wehappy

What you've said sounds right but isn't actually completely true.

Of course Hox/Hedghog etc are reused for non-wing limbs but it is the way they are used for wings that is the surprise. They are used in the same way for both very different wings. You'll notice I was careful in my above post and the title of the thread to take this subtlety into account.

Take a look here.

http://www.press.uchicago.edu/books/gee/shubin6.html

It is clear that the bird and fly wings are not homologous and yet have the similarities pointed out in my first post:

quote:
The limbs of these taxa are not homologous as appendages because phylogenetically intermediate groups do not possess comparable structures. This suggests at least two phylogenetic possibilities: either similar genetic circuits were convergently recruited to make the limbs of different taxa, or these signalling and regulatory systems are ancient and patterned a different structure (presumably another type of outgrowth) in the common ancestor of protostomes and deuterostomes.

For some reason the fly and the bird used these genes in exactly the same way even though nothing in between had wings.

PS - your also wrong about my lack of interest in evo-devo.

[This message has been edited by Tranquility Base, 07-09-2002]


This message is a reply to:
 Message 2 by wehappyfew, posted 07-09-2002 2:17 AM wehappyfew has responded

Replies to this message:
 Message 4 by Peter, posted 07-09-2002 4:12 AM Tranquility Base has responded
 Message 8 by wehappyfew, posted 07-11-2002 1:21 AM Tranquility Base has responded

  
Peter
Member (Idle past 2060 days)
Posts: 2160
From: Cambridgeshire, UK.
Joined: 02-05-2002


Message 4 of 14 (13139)
07-09-2002 4:12 AM
Reply to: Message 3 by Tranquility Base
07-09-2002 2:30 AM


This basically falls back to the 'it could be
common descent or common design' statement depending
solely on how you choose to interpret this
data.

It advances neither side of the debate to continue.


This message is a reply to:
 Message 3 by Tranquility Base, posted 07-09-2002 2:30 AM Tranquility Base has responded

Replies to this message:
 Message 5 by Tranquility Base, posted 07-09-2002 8:10 AM Peter has responded

    
Tranquility Base
Inactive Member


Message 5 of 14 (13147)
07-09-2002 8:10 AM
Reply to: Message 4 by Peter
07-09-2002 4:12 AM


Peter

If I have got it right, the use of these genes in such a specific manner would be highly unlikely for the evolutionary model.

The key point is whether these genes are also used this way for non-wing limbs but my reading indicates this is not the point made in the ref cited. Convergent evolution of the shape of a bone or tissue is one thing, but, at some point, the convergent use of genes in a very specific manner becomes evidence of design.

[This message has been edited by Tranquility Base, 07-09-2002]


This message is a reply to:
 Message 4 by Peter, posted 07-09-2002 4:12 AM Peter has responded

Replies to this message:
 Message 6 by Peter, posted 07-09-2002 9:49 AM Tranquility Base has responded

  
Peter
Member (Idle past 2060 days)
Posts: 2160
From: Cambridgeshire, UK.
Joined: 02-05-2002


Message 6 of 14 (13157)
07-09-2002 9:49 AM
Reply to: Message 5 by Tranquility Base
07-09-2002 8:10 AM


The abstract linked in your first post has ::

'Recent comparative developmental analyses demonstrate that
many of the mechanisms used to pattern limbs are ancient. One of the major consequences of this phenomenon is parallelism in the
evolution of anatomical structures.'

Which suggests that the full paper is using this evidence as
support for parallelism in evolution, or as having a positive
impact on the possibility of such parallelism.

The premise seems to be that since these genetic mechanism are
very ancient, they have been retained and re-used.

Do you have the full paper ?


This message is a reply to:
 Message 5 by Tranquility Base, posted 07-09-2002 8:10 AM Tranquility Base has responded

Replies to this message:
 Message 7 by Tranquility Base, posted 07-09-2002 8:36 PM Peter has responded

    
Tranquility Base
Inactive Member


Message 7 of 14 (13185)
07-09-2002 8:36 PM
Reply to: Message 6 by Peter
07-09-2002 9:49 AM


^
My quotes came from the body of the article. I had access to the pdf but now Wiley wont let me be get back to it! My instituion has access to it so I will have to report this as a bug. I'm convinced the aspects are peculiar to wings (although I agree the genes aren't necessarily all unique to wings as pointed out by Wehappy) but we'll see.

In any case the LCA of birds and insects did not have homologous limbs as stated in my second post web link to a mainstream collection of essays. Since that LCA the genes have been recruited in a parallel manner independently in the same way. I think the article strongly implies that this is even the case for flight specific use of these genes but I'll try and regain access to that pdf.

[This message has been edited by Tranquility Base, 07-09-2002]


This message is a reply to:
 Message 6 by Peter, posted 07-09-2002 9:49 AM Peter has responded

Replies to this message:
 Message 14 by Peter, posted 07-17-2002 9:06 AM Tranquility Base has not yet responded

  
wehappyfew
Inactive Member


Message 8 of 14 (13319)
07-11-2002 1:21 AM
Reply to: Message 3 by Tranquility Base
07-09-2002 2:30 AM


Sorry for the delay... work, and life, you know...

I was sort of halfway hoping you would use the time to reread the material, and my post, since I see major misunderstandings of the subject still evident.

start limb contruction 
get type from variable LIMBTYPE

This subroutine can be used to start any kind of limbs, so it is not surprising at all that this genetic circuit has been used in all descendents of the first creature with limbs. That's the kind of evidence expected to support common descent. It takes a very, ummm... peculiar interpretation to twist this into evidence of design - and you have provided exactly that. More context helps to untwist it back into Shubin's original intent.

To further complicate matters, it turns out that the Distal-less circuit does not actually code specifically for limb development, as might be inferred from only reading Shubin's figure caption. In a broader sense, it instructs the cells in which it is expressed to just stick out from the body axis...

http://zygote.swarthmore.edu/evo8.html

This site provides further evidence that Shubin's second choice (which you have tellingly omitted in your analysis)...

"these signalling and regulatory systems are ancient and patterned a different structure (presumably another type of outgrowth) in the common ancestor of protostomes and deuterostomes"

...is the more likely. Perhaps Shubin goes on to support this thesis in the actual essay. Have you read it? Does it support your conclusion? Or is your position tenable only when bits and pieces from the figure captions for Shubin's work are cited?

"The finding that a Distal-less homolog may exist in the nematode C. elegans suggests that the mechanism for developing appendages evolved before the actual production of appendages."

Because it really just codes for "sticking out"-ness.

See how far we have strayed from "flight-specific gene use" ???


This message is a reply to:
 Message 3 by Tranquility Base, posted 07-09-2002 2:30 AM Tranquility Base has responded

Replies to this message:
 Message 9 by Tranquility Base, posted 07-11-2002 2:01 AM wehappyfew has not yet responded

  
Tranquility Base
Inactive Member


Message 9 of 14 (13321)
07-11-2002 2:01 AM
Reply to: Message 8 by wehappyfew
07-11-2002 1:21 AM


Wehappy, thankyou for going over all this in detail. I will get more int othis too as time permits.

Let me just say this:

The LCA of birds and flies did not have homologous limbs - is that correct? The web site does say this in plain English. What sort of creature (in plain English) was this LCA (asks TB who never did high school biology)?

It is amazing then that birds and flies are using these genes in the same way in limbs.

I still read Shubin that the use of these genes is flight specific but I agree it is hard to ascertain this 100% becasue he doesn't say it in plain English. His writing implies it strongly! If it was not flight specific surely he would cite similar results in mouse legs or something.

[This message has been edited by Tranquility Base, 07-11-2002]


This message is a reply to:
 Message 8 by wehappyfew, posted 07-11-2002 1:21 AM wehappyfew has not yet responded

  
peter borger
Member (Idle past 5802 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 10 of 14 (13326)
07-11-2002 2:25 AM
Reply to: Message 1 by Tranquility Base
07-08-2002 10:52 PM


Dear Tranquility Base
With this example you provided just another falsification of evolution theory.
Fact is that the theory has fallen. However, evolutionists claim that there is no alternative (although this is not true), so they have to stick to this -- over and over falsified -- hypothesis.
Fact is that if you write an article that is not in accord with their theory they will reject it, so it will not be published in their peer reviewed journals and so they keep the wall up. (See: the discussion of Dr. Max with Dr. Spetner on the true-origin homepage).
In the meantime they brainwash the rest of the world with their simplistic vision of life.
But, what did you expect from a religion? All they do is the dispersion of another "meme" (word invented by Dawkins himself). Did you notice that they have a "Darwin Day" to worhip him (see: UTK website), and Dawkins proposed to chair the ceromony? Pathetic!
I've sent the organising commity an email with all the scientific facts that summarise the fall of Darwin's theory, but, of course, they didn't like to respond to it. (See my posting for the 4 arguments that summarise the fall of the theory.) Your example further falsifies common descent. And no evolutionist is able to reconcile this gene with the species tree.
I invite them to give a scientific explanation. Convergence is nothing but a word.
Best wishes
Peter
This message is a reply to:
 Message 1 by Tranquility Base, posted 07-08-2002 10:52 PM Tranquility Base has not yet responded

Replies to this message:
 Message 11 by Andya Primanda, posted 07-11-2002 3:01 AM peter borger has responded
 Message 12 by Peter, posted 07-11-2002 3:19 AM peter borger has not yet responded

    
Andya Primanda
Inactive Member


Message 11 of 14 (13328)
07-11-2002 3:01 AM
Reply to: Message 10 by peter borger
07-11-2002 2:25 AM


Mr. Borger, it seems that you have overthrown the theory of evolution, now let us see a positive point. State your alternative theory, because evolutionists cannot. There are many scientists here and they will be glad to do a peer-review of your theory. Can you do that? If not, please try and do that. People keep on saying that they have overturned evolution & such but nobody cares to put a decent alternative to it. I'll support you if you can do what they cannot. Show this forum what you are thinking.

PS: I'd love to see an alternative to evolution which does not appeal to Christianity (I am not a Christian). So your theory should not be like those ridiculous YECs' theories. You posted earlier that you are an agnostic scientist; I am sure you can do better than YEC Christians.


This message is a reply to:
 Message 10 by peter borger, posted 07-11-2002 2:25 AM peter borger has responded

Replies to this message:
 Message 13 by peter borger, posted 07-16-2002 10:02 PM Andya Primanda has not yet responded

  
Peter
Member (Idle past 2060 days)
Posts: 2160
From: Cambridgeshire, UK.
Joined: 02-05-2002


Message 12 of 14 (13330)
07-11-2002 3:19 AM
Reply to: Message 10 by peter borger
07-11-2002 2:25 AM


... but you have not even responded to my arguments
against your 4 points, purley on the basis that you
consider them story telling.

If you haven't thought your ideas through enough to
rebutt me, why do you expect a panel of 'experts' to
take your claims seriously ?


This message is a reply to:
 Message 10 by peter borger, posted 07-11-2002 2:25 AM peter borger has not yet responded

    
peter borger
Member (Idle past 5802 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 13 of 14 (13679)
07-16-2002 10:02 PM
Reply to: Message 11 by Andya Primanda
07-11-2002 3:01 AM


Dear Andya,
Thanks for your response. I am working and thinking a lot on a scientific alternative and I think I am able to present an alternative. Of course it has to be peer reviewed. All I am doing now is figuring out whether my examples can be rebutted. Next, it has to be validated by scientific approach. Await the theory (any contributions are welcome), which of course will not inlude the origin of life, since that matter cannot be addressed by science (due to genetic uncertainty). I hope that a lot of ideas will be spawned.
Peter
This message is a reply to:
 Message 11 by Andya Primanda, posted 07-11-2002 3:01 AM Andya Primanda has not yet responded

    
Peter
Member (Idle past 2060 days)
Posts: 2160
From: Cambridgeshire, UK.
Joined: 02-05-2002


Message 14 of 14 (13704)
07-17-2002 9:06 AM
Reply to: Message 7 by Tranquility Base
07-09-2002 8:36 PM


If you have the same start point and broadly similar
selective pressures in respect of this one gene, would
that effect the likelihood of current ToE thinking to
account for the similarity ?
This message is a reply to:
 Message 7 by Tranquility Base, posted 07-09-2002 8:36 PM Tranquility Base has not yet responded

    
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