An ID hypothesis: Front-loaded Evolution

You might want to do your PSI-BLAST before making claims about what it will find. The results are pretty much what you get with a BLASTP.Interestingly, the conserved domain is in the first 140-odd amino acid residues. It's a helix-turn-helix DNA binding domain required for regulation of gene expression. Even then it's only a part of the PAX6 which is similar.So it's hardly surprising that it's found from prokaryotes to humans - there's very strong selection pressure to conserve these areas which control gene expression.

I understand that you feel snowed under, but you didn't really address my post. You said It does not show this at all. It shows that the ability to regulate the expression of genes has remained crucial from prokayotes to humans, since it is the regulatory part of PAX6 which shows homology and in fact the whole family of PAX genes show homology with prokaryotic transcription facors, hardly surprising given that a common method of regulating gene expression is DNA sequence-specific binding by these proteins. Some bacterial TFs can bind to host cell DNA and alter genexpression of the host cel in order to increase their own pathogenic effects, for example Xanthomonas, as mentioned in the article below.Take all the time you want in addressing this.For a good overview of transcription factors, anyone interested can go to Transcription factor - Wikipedia where there's plenty of information.

You stated in Message 64In Message 70 I tackled your "front-loaded eye" statement by pointing out that the similarities found by BLASTP are found only in the regulatory part of the protein,he helix-turn-helix.In Message 80 I again requested you address the above.In Message 80 Wounded King requested that you address this.In Message 114 Mr Jack brings up the same thing.You responded to that by saying Doesn't that contradict your statement in Message 64? Are you now withdrawing your claim that the BLASTP results suggest that eyes were anticipated?All I see is that a method of control of gene expression is required in prokaryotes and this helix-turn-helix arrangement has remained a mechanism of control in higher organisms.

Obviously your argument in favour of front-loading requires an entity or entities to "anticipate", to be the "front-loading designers". It now seems that it may require constant intervention in the form of "tinkering".I'm not sure I understand why you propose this when we have an explanation which accounts for all the diversity without invoking a tinkerer? Is there specific evidence that you have which demonstrates that tinkering occurs and therefore natural mechanisms are insufficient?

There seems to be about two lines missing from my post! That'll teach me to rush things and not proof-read. My laptop keyboard is rbbish nd I kep losing letters, clauses and sentences because I'm not hitting them hard enough. I'e not bothered to check this post so you can se whtIm p against

The implications of sequence homologues is totally different from structural homologues. If homology is structural only, it suggests that the same solution has been hit on by different organisms independently of each other. If homology is seen in the DNA sequences it suggests relatedness and descent. Bacterial rhodopsins, according to Wikipedia "While all microbial rhodopsins have significant sequence homology to one another, they have no detectable sequence homology to the G-protein-coupled receptor (GPCR) family to which animal visual rhodopsins belong." Additionally, they serve a purpose in prokaryotes. Globins are found all over the place, but the important thing about those found in prokaryotes is that they serve a function in prokaryotes. Actin, according to Wikipedia "is one of the most highly conserved throughout evolution because it interacts with a large number of other proteins, with 80.2% sequence conservation at the gene level between Homo sapiens and Saccharomyces cerevisiae (a species of yeast), and 95% conservation of the primary structure of the protein product." In addition "All non-spherical prokaryotes appear to possess genes such as MreB, which encode homologues of actin; these genes are required for the cell's shape to be maintained." So, again, actins are serving a purpose in prokaryotes. Kinesins don't seem to have any representation in Prokaryota. Using the rat kinesin Kif18B mRNA sequence (Accession Number NM_001039019.1) I carried out a BLASTn search - that's a search looking for "somewhat" similar sequences - so that the search was as broad as possible and searched in "prokaryotes (taxid:2157)".Matches covered from 1% down to 0% of the sequence and E values were at lowest 3e-5 (Aeropyrum pernix K1 DNA, complete genome), the next E value was 0.68 (Halorubrum lacusprofundi ATCC 49239 chromosome 1, complete sequence, Metallosphaera sedula DSM 5348, complete genome, Pyrobaculum arsenaticum DSM 13514, complete genome) Coming in with an E value of 2.4 are Vulcanisaeta moutnovskia 768-28, complete genome, Acidilobus saccharovorans 345-15, complete genome and Methanocaldococcus vulcanius M7, complete genome.Finally the last 11 which I'm not going to bother identifying have E values of 8.3. When I carried out the same search in prokaryotes (taxid:2) I got a total of four hits, all as feeble as the above.I think this is sufficient to show that kinesins don't have a counterpart in prokaryotes so how on earth can you cite them as evidence for front loading?The prediction made by front-loading is that we would find something in prokaryotes which has absolutely NO function below the Metazoa, but has a distinct function above that point. So far you haven't been able to provide a single example of this.I'd like to add that what I did with the BLASTn search is something you should have done before making your claim, just as the sequence analysis I and others did which refuted your claims for PAX6.

It's a bit of a stretch, but we're talking about similar 3 dimensional structure coupled with similarity of function.

You've already proposed some predictions made by your FLE hypothesis and then provided evidence which you claim fulfills the predictions. So far none have stood up to scrutiny, in fact they seem to be evidence against your FLE.