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Author Topic:   An ID hypothesis: Front-loaded Evolution
Trixie
Member (Idle past 2978 days)
Posts: 1011
From: Edinburgh
Joined: 01-03-2004


(1)
Message 70 of 216 (653475)
02-21-2012 3:25 PM
Reply to: Message 64 by Genomicus
02-20-2012 10:24 PM


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.

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.(Lifted straight from the description of HTH_ARSR)

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.


This message is a reply to:
 Message 64 by Genomicus, posted 02-20-2012 10:24 PM Genomicus has replied

Replies to this message:
 Message 71 by jar, posted 02-21-2012 3:42 PM Trixie has seen this message
 Message 74 by Genomicus, posted 02-21-2012 5:33 PM Trixie has replied

  
Trixie
Member (Idle past 2978 days)
Posts: 1011
From: Edinburgh
Joined: 01-03-2004


(1)
Message 80 of 216 (653500)
02-21-2012 6:36 PM
Reply to: Message 74 by Genomicus
02-21-2012 5:33 PM


I understand that you feel snowed under, but you didn't really address my post. You said

Actually, the capacity for eye development is encoded at the root of the phylogenetic tree of life. Pax6 is a gene involved in eye development, for example. When you BLAST (blastp; default search parameters) the protein encoded by Pax6 (accession number: P63015) against the domain Prokaryota, you get significant hits (E-values < 1e-05). A PSI-BLAST search would almost certainly uncover hits with even greater significance. This suggests that eyes (and other major organs in Metazoa) were anticipated by the first genomes.

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 http://en.wikipedia.org/wiki/Transcription_factors where there's plenty of information.


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Trixie
Member (Idle past 2978 days)
Posts: 1011
From: Edinburgh
Joined: 01-03-2004


Message 121 of 216 (653748)
02-24-2012 3:58 AM
Reply to: Message 115 by Genomicus
02-24-2012 12:30 AM


You need to deal with this
You stated in Message 64

Actually, the capacity for eye development is encoded at the root of the phylogenetic tree of life. Pax6 is a gene involved in eye development, for example. When you BLAST (blastp; default search parameters) the protein encoded by Pax6 (accession number: P63015) against the domain Prokaryota, you get significant hits (E-values < 1e-05). A PSI-BLAST search would almost certainly uncover hits with even greater significance. This suggests that eyes (and other major organs in Metazoa) were anticipated by the first genomes.

In 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

In fact, I'm more than willing that the matches don't indicate front-loading.

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.


This message is a reply to:
 Message 115 by Genomicus, posted 02-24-2012 12:30 AM Genomicus has replied

Replies to this message:
 Message 122 by Genomicus, posted 02-24-2012 4:02 AM Trixie has seen this message
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Trixie
Member (Idle past 2978 days)
Posts: 1011
From: Edinburgh
Joined: 01-03-2004


Message 128 of 216 (653756)
02-24-2012 4:44 AM
Reply to: Message 119 by Genomicus
02-24-2012 3:46 AM


Re: General Response to Objections
It's about "stacking the deck," and anticipating the rise of plants and animals, for example.

Alternatively, the front-loading designers could have designed such a population from the start: where some cells have genes for plants, and others have genes for animals.

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?


This message is a reply to:
 Message 119 by Genomicus, posted 02-24-2012 3:46 AM Genomicus has replied

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Trixie
Member (Idle past 2978 days)
Posts: 1011
From: Edinburgh
Joined: 01-03-2004


Message 129 of 216 (653757)
02-24-2012 4:48 AM
Reply to: Message 125 by Dr Jack
02-24-2012 4:27 AM


Re: You need to deal with this
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

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Trixie
Member (Idle past 2978 days)
Posts: 1011
From: Edinburgh
Joined: 01-03-2004


(1)
Message 183 of 216 (654185)
02-27-2012 4:23 PM
Reply to: Message 174 by Genomicus
02-26-2012 10:39 PM


Re: General Response to Objections
Genomicus writes:

Perhaps, but I think you'd be willing to agree that loading the first genomes with rhodopsins, globins, actins, kinesins, - or their sequence/structural homologs - that this would increase the chances of Metazoan-like life forms appearing on the scene.

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.


This message is a reply to:
 Message 174 by Genomicus, posted 02-26-2012 10:39 PM Genomicus has replied

Replies to this message:
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 Message 191 by Genomicus, posted 02-28-2012 5:31 PM Trixie has taken no action
 Message 199 by Genomicus, posted 02-29-2012 5:54 PM Trixie has taken no action

  
Trixie
Member (Idle past 2978 days)
Posts: 1011
From: Edinburgh
Joined: 01-03-2004


Message 185 of 216 (654188)
02-27-2012 4:50 PM
Reply to: Message 184 by Blue Jay
02-27-2012 4:33 PM


Re: General Response to Objections
It's a bit of a stretch, but we're talking about similar 3 dimensional structure coupled with similarity of function.

This message is a reply to:
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Trixie
Member (Idle past 2978 days)
Posts: 1011
From: Edinburgh
Joined: 01-03-2004


Message 195 of 216 (654305)
02-29-2012 3:48 AM
Reply to: Message 194 by Genomicus
02-28-2012 11:08 PM


Re: General Response to Objections
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.

This message is a reply to:
 Message 194 by Genomicus, posted 02-28-2012 11:08 PM Genomicus has taken no action

  
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