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Author
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Topic: Opening Darwin's black box
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Nel
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posted 10. September 2003 00:49
Pim writes:
quote:
So winged insects lost their wings and in some lineages it re-appeared most likely through the same regulatory complexes.
You're not responding to what I wrote concerning "same regulartory complexes".
Pim writes:
quote:
What do you think these data show?
![[Confused]](confused.gif) I already explained this.
Pim writes:
quote:
And which six lineages?
The first 6 major lineages of these insects were wingless, and wings evolved in the derived lineages.
[ 10. September 2003, 00:49: Message edited by: Nelson-Alonso ]
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Pim van Meurs
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posted 10. September 2003 01:05
quote:
I find the concept of front loading a somewhat vague concept to describe what we do not know and thus treat as initial or boundary conditions.
Nelson: I don't see it as vague at all.
I am surely interested in some of the details then. What is exactly front loaded? Is this front loading internal or external? Is front loading a concept which looking back in time may be confused with teleology? How does front loading work in a chaotic world? What is the concept of front loading?
I see some useful concepts that may relate to front loading. The historical pathway for instance limits to a large extent the path evolution can take. Other limitations, and Ruse describes many more, would include laws of nature, which would direct or limit certain options to evolution. For instance the Hox gene as a concept of front loading: What does Nelson suggest front loading means in this context? I see front loading as something similar to initial condition. Somehow hox genes arose and with these hox genes, it is not surprising that we see evolution take certain pathways in which hox genes are conserved, in which duplication of genes can lead to novelties and in which the eye, once thought to have arosen "independently" more than a few dozen times may find its common denominator in the Pax gene.
Is the pax gene front loading or would it be more helpful to refer to it as a historical constraint? Front loading may suggest both purpose and teleology and can easily lead to confusion.
But perhaps Nelson holds a different view and I am certainly open to see such a view developed in a scientifically fruitful manner.
So far front loading is a vague concept that describes something looking back in the past.
Nelson responds to my quote: quote:
So winged insects lost their wings and in some lineages it re-appeared most likely through the same regulatory complexes.
Nelson: You're not responding to what I wrote concerning "same regulartory complexes".
What did you write?
Me: What do you think these data show?
Nelson: I already explained this
You used some vague language which does not really help me understand where you are going with this example. Do you for instance think that this is a problem for evolution? Do you think this is helpful in infering ID? I am interested in the details.
I ask: And which six lineages?
Nelson: The first 6 major lineages of these insects were wingless, and wings evolved in the derived lineages.
Perhaps if you could mention the names of these major lineages? The ancestor of all lineages had wings, and wings were lost in many lineages. In a few of the lineages, 4 of them exactly, wings re-evolved after being lost.
It would be helpful to have some clear identification of the lineages.
The confusion all started when Nelson suggested that
quote:
Ancient insects don't even have wings. Timema, for example, is the most primitive living stick insect lineage and it is wingless.
Ancient insects don't even have wings.... Perhaps Nelson meant the most ancestral stick insect did not have wings which is correct but their ancestors surely did. So the ancestral walking stick lost its wings, and in a few the wings re-evolved, using similar genetic regulatory mechanisms that were conserved since they are also used in limb development.
Whiting identifies 4 events in which wings re-evolved. So I am not clear to what 6 lineages Nelson is refering. Perhaps some names may be helpful in understanding Nelson's argument here.
So far the picture that emerges is simple
insects with wings have descendants that lose their wings, one of such descendants is the walking stick. However over time wings re-evolve in some lineages, and are lost in some once again. Using the same basic genetic instructions that were conserved since they played a role in limb development as well.
Does Nelson agree with this interpretation which is based on Whiting's paper? If not could Nelson take the same data and show us his best hypothesis?
The only reference to 6 in the paper that I have found is
quote:
These results support the hypothesis that the ancestral condition in Phasmatodea is wingless, that the first six basal phasmid lineages are entirely wingless, and that fully developed wings were derived later in phasmid evolution, on as many as four occasions.
[ 10. September 2003, 01:44: Message edited by: Pim van Meurs ]
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Nel
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posted 10. September 2003 13:09
A lot of the frontloading questions that Pim asked was already partly answered in this thread, and in others . However, his other questions (regarding Pax-6) would require a seperate thread to answer, since I would have to go in depth concerning hox genes, co-option etc. I may change my mind later tonight though. So for now let me just keep this focused on the Whiting paper.
Pim asked:
quote:
And which six lineages?
I answered:
quote:
The first 6 major lineages of these insects were wingless, and wings evolved in the derived lineages.
Pim then writes:
quote:
Perhaps if you could mention the names of these major lineages? The ancestor of all lineages had wings, and wings were lost in many lineages. In a few of the lineages, 4 of them exactly, wings re-evolved after being lost.
But you yourself quote the paper which states precisely what I state above:
quote:
These results support the hypothesis that the ancestral condition in Phasmatodea is wingless, that the first six basal phasmid lineages are entirely wingless, and that fully developed wings were derived later in phasmid evolution, on as many as four occasions.
compare this to what I said:
quote:
The first 6 major lineages of these insects were wingless, and wings evolved in the derived lineages.
Hope this helps.
[ 10. September 2003, 13:12: Message edited by: Nelson-Alonso ]
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Pim van Meurs
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posted 11. September 2003 00:09
I am still confused about Nelson's claim that "Data from Whiting suggests to me that wings appeared in 6 lineages convergently. ", in fact the data do not seem to show this at all.
I still wonder why Nelson raised this issue, does Nelson disagree with Whiting? On what basis? I find it fascinating that regulatory genes etc for wings may have been largely conserved since they were used for other purposes as well. It provides us with a fascinating insight into evolutionary theory.
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Nel
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posted 11. September 2003 00:22
Pim writes:
quote:
I am still confused about Nelson's claim that "Data from Whiting suggests to me that wings appeared in 6 lineages convergently. ", in fact the data do not seem to show this at all.
The confusion should have been resolved in my posts.
Earlier I stated:
quote:
The first 6 major lineages of these insects were wingless, and wings evolved in the derived lineages.
This is supported by the paper:
quote:
These results support the hypothesis that the ancestral condition in Phasmatodea is wingless, that the first six basal phasmid lineages are entirely wingless, and that fully developed wings were derived later in phasmid evolution, on as many as four occasions.
Pim writes:
quote:
I find it fascinating that regulatory genes etc for wings may have been largely conserved since they were used for other purposes as well. It provides us with a fascinating insight into evolutionary theory.
How can genes be both conserved and have had a different function?
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Pim van Meurs
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posted 11. September 2003 01:06
Nelson, you still seem to confuse a few issues here, the first 6 lineages were wingless and in 4 other lineages wings arose.
I even provide the figure 3 that helps one determine this.
Notice that from the first top triangle there are six lineages which remain without wings, two follow one which developed wings only to have them lost in two sub lineages and retained.
the other lineage has three lineages in which wings re-evolved. Nelson himself quotes the '4 occasions'.
Nelson: How can genes be both conserved and have had a different function?
Fascinating isn't it. I hope that Nelson realizes that function and genotype are not necessarily equivalent?
From the paper
quote:
For instance, in Drosophila and other insects, leg and wing imaginal discs have a common origin
from a single group of cells and the developmental pathway for wing determination has been largely co-opted (recruited) from the
pathway required for limb formation15,16. Therefore it is not surprising that the basic genetic instructions for wing formation are conserved in wingless insects, because similar instructions are required to form legs, and probably other critical structures16.
I assume you have the actual paper now?
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Nel
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posted 11. September 2003 17:19
Pim wriets:
quote:
Nelson, you still seem to confuse a few issues here, the first 6 lineages were wingless and in 4 other lineages wings arose.
I am not confused on this issue, since for quite a few posts now, I have been pointing this out.
I'm a little confused why you would keep repeating this point though.
When I asked:
quote:
Nelson: How can genes be both conserved and have had a different function?
Pim oddly answered:
quote:
Fascinating isn't it. I hope that Nelson realizes that function and genotype are not necessarily equivalent?
This is false. When you say that genes are evolutionary conserved, it refers to function:
quote:
Many developmental pathways found in Drosophila have been conserved, in the evolutionary sense. This means that across a wide variety of animal species, pathways sharing a common function, also share a common origin in the biological past.
http://sdb.bio.purdue.edu/fly/aimain/aadevinx.htm
Earlier Pim wrote:
quote:
Somehow hox genes arose and with these hox genes, it is not surprising that we see evolution take certain pathways in which hox genes are conserved, in which duplication of genes can lead to novelties and in which the eye, once thought to have arosen "independently" more than a few dozen times may find its common denominator in the Pax gene.
However, Pax6 is not a gene that encodes the information for eye formation, it's location, etc. It seems to encode neural fates in ectoderm.
Now, because of Pax-6, as you suggest, many have stated that perhaps eyes have not convergently arisen after all. However, what is interesting is that the cephalopod eye, although it is built very similarly to the vertebrate eye (Pax-6 orthologues are involved), they are not homologous to eachother, they don't share a common ancestor (cf Gred B. Muller).
Going back to insects, it seems that they have indepenendtly reogranized the regulatory systems controlling various pattern formation.
I've had the Whiting paper all along.
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Pim van Meurs
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posted 11. September 2003 22:47
Nelson originally wrote
quote:
Ancient insects don't even have wings. Timema, for example, is the most primitive living stick insect lineage and it is wingless. Data from Whiting suggests to me that wings appeared in 6 lineages convergently.
Now he writes
quote:
The first 6 major lineages of these insects were wingless, and wings evolved in the derived lineages.
And as the paper shows these wings arose in different lineages, in fact Whiting identified four occasions of re-evolution.
I am not sure sure on what Nelson based his original comments.
Nelson then seems to make the fascinating commnet that "This is false. When you say that genes are evolutionary conserved, it refers to function:"
This seems to be a revision of historically usage of the term, perhaps Nelson can suggest why he prefers a different usage from the more common usage?
Now often conservation of genotype results in conservation of phenotype but that is not necessarily true. Nevertheless the argument is irrelevant, the genes were conserved genotypically only to be later re-expressed.
Nelson then comments on the Pax-6 gene and refers to Muller and the cephalopod eye. Without however any references this is not very helpful and in fact while this may have been an older view, recent views seem to have changed.
for instance
quote:
The evolution of eyes, as complex organs, could still be polyphyletic. Consider one of the most compelling cases of convergent evolution: the image-forming eyes of the cephalopod mollusks and those of the vertebrates (6). Though these eyes look extraordinarily similar in design, these similarities are not homologies.
...
Thus, phylogenetic and embryological considerations strongly suggest that the two
eyes must have evolved independently. Moreover, it seems highly unlikely that the structural similarities in the adult are due to a conserved developmental program. However, the expression of Pax-6 in the development of the squid eye challenges this conclusion, as reported in this issue (9) from a collaboration between the laboratories of Gehring and Piatigorsky.
Pax-6: Where to be conserved is not conservative
William A. Harris
Proc. Natl. Acad. Sci. USA
Vol. 94, pp. 2098–2100, March 1997
and
Squid Pax-6 and eye development
STANISLAV I. TOMAREV*†, PATRICK CALLAERTS‡, LIDIA KOS§, RINA ZINOVIEVA¶, GEORG HALDER‡, WALTER GEHRING‡, AND JORAM PIATIGORSKY*
Proc. Natl. Acad. Sci. USA
Vol. 94, pp. 2421–2426, March 1997
quote:
Until now Pax 6 homologs (true orthologs) have been identified in vertebrates, Amphioxus, ascidians, sea urchins cephalopods, nemerteans, nematodes and platyhelminths, and for Amphioxus, Phallusia, Loligo and Caenorhabditis Plaza, Dozier & Seimiya unpubl.) we have shown that their
Pax 6 genes are capable of inducing ectopic eyes in Drosophila. The only exception is the Dugesia tigrina gene that has diverged to the extent that it is no longer capable of inducing ectopic eyes in Drosophila (the second Dugesia gene has not
been tested yet). In all cases the Pax 6 genes are expressed in the eyes, in the brain and in several cases in chemosensory organs.
The genetic control of eye development and its implications for the evolution of the various eye-types b y WALTER J. GEHRING in Int. J. Dev. Biol. 46: 65-73 (2002)
or
Pax 6 mastering eye morphogenesis and eye evolution TIG September 1999, volume 15, No. 9
Perhaps Nelson can provide us with Gerd B. Mueller's reference?
[ 11. September 2003, 22:52: Message edited by: Pim van Meurs ]
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Nel
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posted 12. September 2003 22:40
Pim writes:
quote:
I am not sure sure on what Nelson based his original comments.
I simply mixed up the 6 original lineages with the 4 derived lineages. However, I cleared this up in subsequent postings. Either way, my point remains the same. So I'm still not sure why you keep bringing it up.
Pim writes:
quote:
This seems to be a revision of historically usage of the term, perhaps Nelson can suggest why he prefers a different usage from the more common usage?
No this is the original use of the term conservation and I referenced an article that discusses this.
Pim writes:
quote:
Now often conservation of genotype results in conservation of phenotype but that is not necessarily true. Nevertheless the argument is irrelevant, the genes were conserved genotypically only to be later re-expressed.
Yes, this is one interpretation of the data, that I also mentioned and discussed.
with regard to Pax-6, Pim references material that supports what I said considering it's independant evolution:
quote:
The evolution of eyes, as complex organs, could still be polyphyletic. Consider one of the most compelling cases of convergent evolution: the image-forming eyes of the cephalopod mollusks and those of the vertebrates (6). Though these eyes look extraordinarily similar in design, these similarities are not homologies.
... Thus, phylogenetic and embryological considerations strongly suggest that the two
eyes must have evolved independently.
Pax-6: Where to be conserved is not conservative
William A. Harris
Proc. Natl. Acad. Sci. USA
Vol. 94, pp. 2098–2100, March 1997
Thanks Pim
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Pim van Meurs
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posted 12. September 2003 22:59
Nelson: I simply mixed up the 6 original lineages with the 4 derived lineages. However, I cleared this up in subsequent postings. Either way, my point remains the same. So I'm still not sure why you keep bringing it up.
Because I was confused. Your argument changed in the middle and I had not noticed causing some confusion.
Nelson: No this is the original use of the term conservation and I referenced an article that discusses this.
I am still not sure, conserved genes are identified through similarity in genotype. Only recently are phenotype issues considered.
Nelson quotes from Harris but forgets to read to the conclusion namely that new data seems to suggest that this interpretation may be erroneous.
quote:
However, the expression of Pax-6 in the development of the squid eye challenges this conclusion, as reported in this issue (9) from a collaboration between the laboratories of Gehring and Piatigorsky.
Seems that the introduction was more of a rethorical device...
Could you also provide me with the Gerd B Muller quote reference?
More goodies
quote:
Pax 6: mastering eye morphogenesis and eye evolution.
Gehring WJ, Ikeo K.
Department of Cell Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland. gehring@ubaclu.unibas.ch
Pax 6 genes from various animal phyla are capable of inducing ectopic eye development, indicating that Pax 6 is a master control gene for eye morphogenesis. It is proposed that the various eye-types found in metazoa are derived from a common prototype, monophyletically, by a mechanism called intercalary evolution.
Trends Genet. 1999 Sep;15(9):371-7.
Unraveling the multiple functions of Pax6 in eye development by conditional mutagenesis
[ 12. September 2003, 23:07: Message edited by: Pim van Meurs ]
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Nel
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posted 17. September 2003 20:12
Pim writes:
quote:
Because I was confused. Your argument changed in the middle and I had not noticed causing some confusion.
My argument never changed, simply the number of derived lineages. My point remaines the same.
Pim writes:
quote:
I am still not sure, conserved genes are identified through similarity in genotype. Only recently are phenotype issues considered.
This makes no sense. What conservation usually refers to is common function:
quote:
Many developmental pathways found in Drosophila have been conserved, in the evolutionary sense. This means that across a wide variety of animal species, pathways sharing a common function, also share a common origin in the biological past.
http://sdb.bio.purdue.edu/fly/aimain/aadevinx.htm
Pim writes:
quote:
Nelson quotes from Harris but forgets to read to the conclusion namely that new data seems to suggest that this interpretation may be erroneous.
How so?
Pim writes:
quote:
Seems that the introduction was more of a rethorical device...
Huh? Why would you reference a paper that supports what I said about Pax-6? Are you indirectly agreeing with me?
Pim writes:
quote:
Could you also provide me with the Gerd B Muller quote reference?
Origination of Organismal Form.
Pim writes:
quote:
More goodies
Trends Genet. 1999 Sep;15(9):371-7.
Unraveling the multiple functions of Pax6 in eye development by conditional mutagenesis
From your own reference:
quote:
The evolution of eyes, as complex organs, could still be polyphyletic. Consider one of the most compelling cases of convergent evolution: the image-forming eyes of the cephalopod mollusks and those of the vertebrates (6). Though these eyes look extraordinarily similar in design, these similarities are not homologies.
... Thus, phylogenetic and embryological considerations strongly suggest that the two
eyes must have evolved independently.
[ 17. September 2003, 20:13: Message edited by: Nelson-Alonso ]
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Pim van Meurs
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posted 18. September 2003 23:34
Nelson quotes from the paper I referenced but fails to provide the full context leading one to a conclusion not necessarily argued by the paper
Nelson's quote
quote:
... Thus, phylogenetic and embryological considerations strongly suggest that the two eyes must have evolved independently.
versus
quote:
Thus, phylogenetic and embryological considerations strongly suggest that the two eyes must have evolved independently. Moreover, it seems highly unlikely that the structural similarities in the adult are due to a conserved developmental program. However, the expression of Pax-6 in the development of the squid eye challenges this conclusion, as reported in this issue (9) from a collaboration between the laboratories of Gehring and Piatigorsky.
Gerd B Muller's quote seems to also remain somewhat elusive..
Getting references from Nelson sometimes feels like pulling teeth :-)
Now Nelson adds the still cryptic reference quote:
Origination of Organismal Form.
Seems to be a book. Could Nelson provide the full context that supports his claim about Mueller?
Page numbers would be helpful as well.
More goodies
quote:
A possible strategy used to evolve complex image-forming eyes from the primitive eyes present in the last common ancestor is the use of similar developmental mechanisms with the same or closely related transcription factors. If this assumption is correct, one would expect that in cephalopod molluscs a Pax-6 homolog is involved in visual system development as it is in Drosophila and vertebrates. In this report, we present evidence corroborating this prediction by way of the structural and functional characterization of a Pax-6 homolog of the squid, Loligo opalescens.
and
quote:
Our data support the idea that morphologically distinct eyes of different species have arisen through elaboration of a common conserved Pax-6-dependent mechanism (11, 14, 15) that is operative at early stages of eye development and that the anatomical differences among eyes arose later in evolution. Consequently, we believe that eyes in cephalopods and vertebrates have a common evolutionary origin and are products of parallel rather than convergent evolution (56).
Source
Fascinating
[ 18. September 2003, 23:49: Message edited by: Pim van Meurs ]
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Nel
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posted 19. September 2003 01:13
Pim quotes two paragraphs from the paper that agrees with eachother. So why he put "versus" in the middle is a complete mystery.
Pim writes:
quote:
Gerd B Muller's quote seems to also remain somewhat elusive..
Getting references from Nelson sometimes feels like pulling teeth :-)
I gave the title of the book, should be easy to find as it came out very recently. But then again, since you provided the reference for me which supported what I said, why are you still questioning it?
Pim writes:
quote:
Could Nelson provide the full context that supports his claim about Mueller?
Sure I can, but since the full context was given by your very own reference, (and my discussion of it) and yet you are still asking what I mean, shows that you may be having trouble understanding these issues. You should ask questions rather then shooting from the hip and disagreeing with everything an ID proponent says.
More evidence that Pim is having trouble understanding these issues is by his latest statement:
quote:
More goodies
Pim quotes:
quote:
Our data support the idea that morphologically distinct eyes of different species have arisen through elaboration of a common conserved Pax-6-dependent mechanism (11, 14, 15) that is operative at early stages of eye development and that the anatomical differences among eyes arose later in evolution. Consequently, we believe that eyes in cephalopods and vertebrates have a common evolutionary origin and are products of parallel rather than convergent evolution (56).
This conclusion is simply based on the fact that Pax-6 is found to be involved in both systems. However, Pax-6 in these organisms are orthologues. They are not homolgoous eyes. Another example of this with Pax-6 is that it also controls vertebrate nasal placode formation which is completely unrelated, I doubt that the eyes were the result of parallel evolution rather then convergent evolution. I'll get into this more when I participate in the convergent evolution thread.
[ 19. September 2003, 01:15: Message edited by: Nelson-Alonso ]
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Pim van Meurs
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posted 19. September 2003 12:01
Nelson may have missed the relevant part when he wonders about me using 'versus'
quote:
However, the expression of Pax-6 in the development of the squid eye challenges this conclusion, as reported in this issue (9) from a collaboration between the laboratories of Gehring and Piatigorsky.
That is the paper discusses data which puts to doubt earlier ideas about the origins of the eye.
Same here:
quote:
Metazoan eye is a fascinating organ to be used for evolutionary studies. Early morphological studies have suggested that eye has evolved multiple times during the course of evolution. In contrast, more recent genetic data indicate a central role of Pax6 in eye development in most of the animals. In addition, other genes acting dowstream of Pax6 in the regulatory cascade (e.g. Six, Eya or Dach genes) are also highly evolutionarily conserved. However, most of our current knowledge is based on experimental work done in vertebrates and Drosophila melanogaster.
Originally the idea was independent origins but recent data seem to indicate that this may not be completely accurate.
Gehring
quote:
Our work on Pax6 as a master control gene for eyemorphogenesis and the implications for eye evolution have been summarized for Trends in Genetics (Gehring & Ikeo, 1999). Pax genes from various animal phyla are capable of inducing ectopic eye morphogenesis, indicating that Pax6 is a master control gene for eye development. It is proposed that contrary to the dogma, the various eye-types found in metazoa, are derived monophyletically, from a common prototype. In order to explain the evolution of the different types of eyes, we have advanced the hypothesis that different genes are intercalated into the prototypic eye developmental pathway in the various animal phyla.
Nelson's suggestion that thus this paper suppors his claims should be rejected.
When asked about Mueller Nelson tries to distract from the issues using some ad hominem distractions but still fails to provide for Mueller's comment and the context.
My sources show clearly that recent findings support the common origin of the eyes through parallel evolution.
I find it somewhat confusing that Nelson uses evidence for common descent of the eyes as supportive of his case. Surely the quote in full context seems to paint a somewhat different picture.
Fascinating how science is discovering more and more evidence of common ancestry of the eyes.
Nelson may doubt that eyes arose through parallel rather than convergent evolution however the (recent) data seem to point to a different story so far.
Nelson may also want to check the paper again when he states 'This conclusion is simply based on the fact that Pax-6 is found to be involved in both systems.'
For instance sequence similarity
quote:
We have isolated cDNAs corresponding to the squid Pax-6 gene. Squid Pax-6 shows the highest overall amino acid identity (78%) with Pax-6 from nemertines, consistent with nemertines being coelomate animals and molluscs and nemertines having a close evolutionary relationship (27, 39).
and
quote:
Despite the fact that only the paired- and homeodomain regions of Pax-6/eyeless are well conserved between squid and Drosophila, squid Pax-6 can induce the formation of ectopic eyes in Drosophila as was previously demonstrated for Drosophila eyeless and mouse Pax-6 (14).
It's all in the discussion section of said paper.
More goodies
quote:
Pax genes and eye organogenesis.
Pichaud F, Desplan C.
Curr Opin Genet Dev. 2002 Aug;12(4):430-4.
Pax6 is a highly conserved gene that controls eye development in all species where it has been tested. In spite of this common 'master control regulator', the eyes of different animals are morphologically very different and it is believed that they have evolved independently multiple times through evolution. Recent works looking at eye development in 'primitive' species offer some explanation as to the surprising amount of conservation in genetic and morphogenetic pathways involved in eye development. These studies not only implicate the Pax genes but also the So/Six gene family in playing a crucial ancestral role in visual system development.
Nelson states: However, Pax-6 in these organisms are orthologues. They are not homolgoous eyes.
I am unclear about which definitions of homology, orthology etc Nelson is using but let me provide for its common definitions
quote:
homolog: A gene (or protein) sequence that is related to the gene (or protein) sequence under consideration due to descent from a common ancestral sequence. It is an important concept because structure and function tend to be conserved among homologues. The terms "homology" and "similarity" are often, incorrectly, used interchangeably. Homology is either true or false (with respect to a given time in the past), while there are gradations of similarity depending on what is being measured. There are two kinds of homologs, orthologs and paralogs.
ortholog: A homologue that first diverged through speciation. (alpha-hemoglobin in mouse and alpha-hemoglobin in human are orthologs).
paralog: A homologue that first arose through gene duplication. (Example: alpha and beta-globin in human are paralogs). As this example demonstrates, paralogs are less likely than orthologs to have the same structure and function as the gene or protein sequence under consideration.
[ 19. September 2003, 12:43: Message edited by: Pim van Meurs ]
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Nel
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posted 19. September 2003 19:56
Pim writes:
quote:
Nelson's suggestion that thus this paper suppors his claims should be rejected.
Why would you say this? Lets read the paper you referenced again:
quote:
Thus, phylogenetic and embryological considerations strongly suggest that the two
eyes must have evolved independently.
You still havn't answered my question as to why you referenced this paper and behaved as if the paper contradicted what I said. I think you should address this very serious concern. You do the same thing in a most recent post.
As to the two new papers you reference, the only basis they have for saying that the two eyes are homologous is the presence of pax-6. The only problem is, that begs the question. As I wrote,they are not homolgous eyes. Pax-6 seem to be orthologs. Another example of this with Pax-6 is that it also controls vertebrate nasal placode formation which is completely unrelated, I doubt that the eyes were the result of parallel evolution rather then convergent evolution.
Pim writes:
quote:
When asked about Mueller Nelson tries to distract from the issues using some ad hominem distractions but still fails to provide for Mueller's comment and the context.
What ad hominem? I referenced the quote already.
Pim writes:
quote:
I find it somewhat confusing that Nelson uses evidence for common descent of the eyes as supportive of his case. Surely the quote in full context seems to paint a somewhat different picture.
But I don't use evidence for common descent of eyes. I show how eyes seem to have arisen independantly. If you are having trouble understanding these issues, you should ask questions rather then attempting to disagree with everything I say.
Pim writes:
quote:
Nelson may also want to check the paper again when he states 'This conclusion is simply based on the fact that Pax-6 is found to be involved in both systems.'
Pim I don't think you undestood this reference either. The sequence similarity in your first quote is between coelomate animals. What I am saying is that cephalopods and vertebrates eyes are not homologous. Your second quote shows very little sequence similarity. From your own reference:
quote:
Although squid Pax-6 and Drosophila eyeless C-terminal domains show appreciable differences in sequence and have different lengths (168 and 368 amino acids, respectively), both are proline-, serine- and threonine-rich (33% and 37%, respectively). It seems reasonable to propose that structural features such as secondary or tertiary folding, rather than direct similarity in amino acid sequences, are responsible for the common functional properties of squid Pax-6 and Drosophila eyeless, as was proposed for the C-terminal domains of vertebrate Pax-3 and Drosophila Gooseberry and Paired proteins
Pim writes:
quote:
I am unclear about which definitions of homology, orthology etc Nelson is using but let me provide for its common definitions
Ok whats your point? Again if you are having trouble understanding you should ask questions. Don't read to contradict.
[ 19. September 2003, 20:22: Message edited by: Nelson-Alonso ]
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