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Author
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Topic: Opening Darwin's black box
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Pim van Meurs
Member
Member # 541
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posted 19. September 2003 20:35
Nelson, if you want to read the sentence outside its context then it may suggest that the paper supported your (outdated) view of Pax-6 and eye evolution.
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.
I fail to see how "challenges this conclusion" can be seen as supportive of the conclusion.
Despite all this Nelson seems to consider this paper which places quite some doubt on his position as supportive of his position.
Nelson seems to still confuse homology and orthology when he states "As I wrote,they are not homolgous eyes. Pax-6 seem to be orthologs"
But orthologs and paralogs form the 'family of' homologs. Did you see my definitions/figures which clarified this?
Nelson further muddles the issue by stating that the Pax6 genes are involved in other developmental pathways without explaining why this should be a problem.
Nelson about Mueller "What ad hominem? I referenced the quote already."
When I asked Nelson for a full quote in context he responded with some unnecessary 'ad hominem' comments rather than with the quote in context.
Nelson, without much evidence states that 'No, these are old sources are from the beginning of the "master gene" craze. ' when in fact Gehring's paper(s) are quite new overthrowing the original ideas about eye evolution. So far Nelson has not explained why these ideas should be rejected.
Nelson then claims "Your second quote shows very little sequence similarity." but what does the quote actually say?
"appreciable differences" which can be explained by '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'
Sequence similarity needs to take into account structural similarity as well before it should be rejected.
Nelson: Ok whats your point? Again if you are having trouble understanding you should ask questions. Don't read to contradict.
It seems obvious what the question is: How does Nelson use the terms homologs/orthologs. Perhaps a definition that would help understand Nelson's statement that "As I wrote,they are not homolgous eyes. Pax-6 seem to be orthologs." and "However, Pax-6 in these organisms are orthologues. They are not homolgoous eyes."
I am certainly interested in what Nelson considers 'more modern' results. So far Nelson has given no reasons to doubt these Pax-6 results.
More goodies
quote:
Some of these genes are expressed in the eye primordia during regeneration and in the differentiated adult eyes. RNA interference (RNAi) experiments provide functional evidence that Gtsix-1 is essential for maintenance of the differentiated state of photoreceptor cells, for opsin expression and for eye regeneration. Such results support the conservation of the early genetic pathway in the different eyes of metazoans.
Evolutionary conservation of the initial eye genetic pathway in planarians Belg. J. Zool., 131 77-82, 2001
And before Nelson considers the following to be supportive of his case I urge him to read to the end of the quote.
quote:
The comparative embryological and morphological
studies of metazoan eyes show different developing mechanisms and different morphologies suggesting an independent evolution of the different types of eyes (SALVINI-PLAWEN & MAYR 1961). However, molecular studies in the last decade have revealed the universality of rhodopsin as the visual pigment and the conservation in all studied Metazoa, including Platyhelminthes, of the early genetic cascade initiated by the gene Pax-6. Such molecular
results suggest that all different eye types observed in Metazoa derive from a common prototypic eye and as a consequence have a monophyletic origin. Such prototypic eye can be found in some Platyhelminthes. The current work suggests that the development of the prototypic eye is controlled by a similar early genetic cascade.
and
quote:
The similarities in eye design in molluscs compared with the other metazoan eyes can be interpreted as evidence for a phenomenon of parallelism in the mechanisms which the different Metazoa evolved their eyes from a common prototypic eye, using initially the same genetic
network. The recruitment of different genes by intercalary evolution (GEHRING & IKEO, 1999) in the eye gene networks of the various evolutionary lines can lead to eyes with dramatically similar designs as a consequence of comparable developmental constraints, or, of course, to
radically different final structures.
DNA Union posted this on ARN
code:
1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 #
-----------------------------------------------------------------
Homo sapiens L Q R N R T S F T Q E Q I E A L E K E F 0
Mus musculus L Q R N R T S F T Q E Q I E A L E K E F 0
Phallusia L Q R N R T S F S Q E Q V E A L E K E F 2
Paracentrotus L Q R N R T S F T A Q Q I E E L E K E F 3
Loligo L Q R N R T S F T A A Q I E A L E K G F 3
Drosophila L Q R N R T S F T N D Q I D S L E K E F 2
Lineus L Q R N R T S F T N A Q I E A L E K E F 2
Caenorhabditis L Q R N R T S F T Q V Q I E S L E K E F 2
-----------------------------------------------------------------
# of substitutions 0 0 0 0 0 0 0 0 1 4 5 0 1 1 3 0 0 0 1 0 16
-----------------------------------------------------------------
-----------------------------------------------------------------
2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 4
1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 #
-----------------------------------------------------------------
Homo sapiens E R T H Y P D V F A R E R L A A K I D L 0
Mus musculus E R T H Y P D V F A R E R L A A K I D L 0
Phallusia E R T H Y P D V F A R E R L A S K I D L 1
Paracentrotus E R T H Y P D V F A R E R L A Q K I D L 1
Loligo E R T H Y P D V F A R E R L A H Q I D L 2
Drosophila E R T H Y P D V F A R E R L A G K I G L 2
Lineus E R T H Y P D V F A R E R L A Q K I D L 1
Caenorhabditis E R T H Y P D V F A R E R L A Q K I Q L 2
-----------------------------------------------------------------
# of substitutions 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 1 0 2 0 9
-----------------------------------------------------------------
-----------------------------------------------------------------
4 4 4 4 4 4 4 4 4 5 5 5 5 5 5 5 5 5 5 6
1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 #
------------------------------------------------------------------------
Homo sapiens P E A R I Q V W F S N R R A K W R R E E 0 100%
Mus musculus P E A R I Q V W F S N R R A K W R R E E 0 100%
Phallusia P E A R I Q V W F S N R R A K W R R E E 0 95%
Paracentrotus P E A R I Q V W F S N R R A K W R R E E 0 93%
Loligo P E A R I Q V W F S N R R A K W R R E E 0 92%
Drosophila P E A R I Q V W F S N R R A K W R R E E 0 90%
Lineus P E A R I Q V W F S N R R A K W R R E E 0 93%
Caenorhabditis P E A R I Q V W F S N R R A K W R R E E 0 93%
------------------------------------------------------------------------
# of substitutions 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 94.5%
quote:
NOTES:
(1)Homo sapiens (human)
Mus musculus (mouse)
Phallusia = Phallusia mammillata (ascidian)
Paracentrotus = Paracentrotus lividus (sea urchin)
Loligo = Loligo opalescens (cephalopod)
Drosophila = Drosophila melanogaster (fruit fly)
Lineus = Lineus sanguineus (nemertean)
Caenorhabditis = Caenorhabdititis elegans (nematode)
(2) "For the vertebrate Pax-6 proteins only the identical sequence of human (homo) and mouse (mus) are shown because all other vertebrate sequences are very similar or identical."
(3) Sequences are for the 60-amino-acid homeodomain of Pax-6.
[ 19. September 2003, 21:09: Message edited by: Pim van Meurs ]
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Nel
Member
Member # 614
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posted 19. September 2003 20:51
Pim writes:
quote:
Nelson, if you want to read the sentence outside its context then it may suggest that the paper supported your (outdated) view of Pax-6 and eye evolution.
I didn't take it out of context. For example, you quote:
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.
However, he then says:
quote:
A photopigment, however, is not an eye. 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.
Did you miss this part or are you still indirectly agreeing with me?
Pim writes:
quote:
But orthologs and paralogs form the 'family of' homologs. Did you see my definitions/figures which clarified this?
Again, whats your point? I think that Pax-6 did diverge from a speciation event. But that the eyes in both vertebrates and cephalopods are not homologous. What is the problem exactly?
Pim writes:
quote:
Nelson further muddles the issue by stating that the Pax6 genes are involved in other developmental pathways without explaining why this should be a problem.
Because it's involved in a completely unrelated task.
Pim writes:
quote:
When I asked Nelson for a full quote in context he responded with some unnecessary 'ad hominem' comments rather than with the quote in context.
Which ad hominem comments? I'm not going to quote the entire book for you.
Pim writes:
quote:
Sequence similarity needs to take into account structural similarity as well before it should be rejected.
It is precisely the structural and functional similarity which I am pointing to.
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Pim van Meurs
Member
Member # 541
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posted 20. September 2003 16:37
I am not sure which paper Nelson is reading but when he suggests that
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 collaboretion between the laboratories of Gehring and Piatigorsky.
Nelson suggests "he then says" when in fact this part is before the statement of [b]however[\b]
The whole introduction is to set up ideas which now seem to be challenged by Gehring et al's paper. If that should be considered evidence in favor of the old position then let if be so.
Source
I am surely looking forward to the evidence supporting Nelson's claims.
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Nel
Member
Member # 614
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posted 20. September 2003 17:38
Pim,
I was referring to how he says this first:
quote:
Conserved sequences in the opsins of vertebrate and invertebrate photoreceptors (1), and homologous genes such as Pax-6 involved in eye development across phyla (2), challenge the hypothesis that the eyes of vertebrates and invertebrates had distinct evolutionary origins (3, 4).
and this second:
quote:
A photopigment, however, is not an eye. 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.
He points to the Gehring's work first, and then mentions that the two eyes are not homolgous. He discusses the two possibilities (common origin or convergence) and indicated that more work would settle the issue. However, the fact that the two eyes do not show any homologies is evidence that supports my claims. Notice this comment:
quote:
A simple explanation is that such develop-mental mechanisms might function like modules that canbe deployed at different times in different places to pro-duce particular types of structures, and that we cannot in-fer homology based simply on similar patterns of geneexpression. This conclusion has important implicationsfor comparative neurobiologists, and should be consid-ered when assessing ideas such as the popular claim thateyes in insects and vertebrates are homologous becausethe Pax-6 gene plays an important role in their develop-ment [Harris, 1997].
source
[ 20. September 2003, 17:41: Message edited by: Nelson-Alonso ]
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Pim van Meurs
Member
Member # 541
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posted 20. September 2003 17:48
I suggest that those interested in the paper read it here and decide for themselves.
Harris starts of pointing out that conserved sequences and the homologous nature of Pax-6 genes involved in eye development across phyla challenges the hypothesis that the eye had multiple origins.
Harris then continues to point out that a photopigment is not an eye and that the eye can be polypheletic. Harris then points out the cephalopod eye as an example of convergent evolution. Harris ends his argument however by pointing out that these ideas are all challenged by the recent work of Gehring et al.
Working through the work by Gehring Harris concludes that
quote:
It shows that there is a homolog of Pax-6 in squid that is expressed in the eye-forming
region and that squid Pax-6 misexpression can lead to ectopic eye formation in Drosophila. If the morphological similarities between the eyes of cephalopods and vertebrates evolved twice, why then do these eyes share a conserved transcription
factor that might regulate these processes? Is it a coincidence?
The fly story makes this unlikely. The hypothesis that there has been an evolutionary reason to conserve the role of Pax-6 in eye development must therefore be taken seriously.
Gehring's article concludes
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).
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Nel
Member
Member # 614
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posted 20. September 2003 17:53
Pim writes:
quote:
Harris ends his argument however by pointing out that these ideas are all challenged by the recent work of Gehring et al.
No he ends by noting that Pax-6 functions in organisms that don't even have eyes:
quote:
The function of Pax-6 homologs in these animals may shed light on the ancestral function of Pax-6. Mutants in these genes have defects in
peripheral sense organs of the tail (mab-18), or abnormalities in the head (vab-3) (28, 29). But—nematodes do not have eyes or any known photoreceptive cells, and neither do adult sea
urchins, which express a respectable Pax-6 gene in their tube feet (30)!
and then states:
quote:
There may be too many unresolved questions to allow skeptics to buy into the bold hypothesis at present, but neither can they rule it out. It will therefore be interesting to continue
the evolutionary survey of Pax-6 expression and function, especially in organisms that have either no eyes or very primitive eyes.
[ 16. February 2006, 20:36: Message edited by: Nel ]
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