Re: [asa] Nature: Peer Review Trial and Debate

On 6/13/06, Janice Matchett <janmatch@earthlink.net> wrote:
>
>
> Much that passes for "peer review" today is merely political payoff, so
> it's going to be fun to watch those who reject the "consensus" opinions
> being allowed to open the curtain, let the sunshine in, and start spraying
> the BSR into every nook and cranny. ~ Janice :).

I believe a more open process is a good thing in order to show that
Janice's perception is what is B.S. Let's take the following example
(http://www.biology-direct.com/content/1/1/8/abstract/) entitled
Origin and evolution of the peroxisomal proteome. This challenges the
conventional wisdom that origin peroxisome is endosymbiotic, that it
is evolved from a foreign organism. The authors said, no, it is
autogenous and came from the Endoplasmic Reticulum. So, the
"consensus" is challenged. Let's look at the peer review. I'll take
reviewer 2 as an example of how a well-written paper can sucessfully
challenge the conventional wisdom and how the interaction between
author and reviewer improve the paper and is not some political
payoff. Janice, where is the political payoff or BSR here? For the
non-Americans, BSR stands for Bull Sh** Repellent.

This paper makes a compelling argument for the autogenous evolutionary
origin of the peroxisome. Although this was not a surprise given
recent cell biological findings showing that peroxisomes grow from the
endoplasmic reticulum, the autogenous origin of the organelle is now
clearly backed by the systematic bioinformatic analysis of its
proteome. Most interestingly Gabaldón et al. found that some
components of the peroxisomal proteome (the Pex5 pathway) are
evolutionary derivatives of the endoplasmic reticulum assisted decay
(ERAD) pathway.

The paper is technically sound and well written, I only have a few comments.

1) I have a problem about how the authors define that a protein has
eukaryotic origin. For example the Cdc48/Sec18/Pex6 family seems to
have descended from archaebacterial AAA ATPases. What the tree shown
in Fig. 1A shows is rather that the multiplication of this ancestral
ATPase leading to several paralogs was an eukaryotic event. So the
protein family clearly has prokaryotic origin, it is the formation of
distinct paralogs that occurred during eukaryote evolution. This
should be explained better in the text and this group should be
referred to differently, like 'originated by eukaryote-specific
duplication'.

Response:

We specifically want to make a distinction between horizontally
transferred genes and "ancient genes" that were already present at the
evolutionary split between the lineage leading to the Archaea and the
one leading to the eukaryotes. Although in the case of CDC48 and Pex1
a case can indeed be made that CDC48 represents the ancestral
function, given its level of sequence identity with the Archaeal
sequences, and that PEX1 resulted from a gene duplication, such a
clear scenario is rarely present. We have put more emphasis on the
distinction between horizontally transferred genes and genes already
present in ancient eukaryotes in the text, and mention the CDC48
duplication explicitly now.

2) The reconstruction of the ancestral state of the peroxisomal
proteome hinges on the accepted topology of the eukaryotic tree. If
Kinetoplastids are not early branching but the root lies between
animals and plants, then one would probably get a different picture.
This alternative reconstruction should also be presented and/or the
effect of tree topology on the results should be discussed.

Response:

The consequences of using an alternative topology in the
reconstruction of the ancestral proteome are now mentioned in the
figure legend. They indeed lead to a larger set of ancestral
Peroxisomal proteins.

3) Several of the eukaryote-specific Pex proteins are not discussed in
the text. One is left wondering what could have been the evolutionary
origin of these proteins. If it is not clear for most of them, this
should be mentioned briefly.

Response:

We tried hard to ascertain the origin of all Pex proteins,
unfortunately for the Pex proteins not discussed in the text we could
not find homologies with other proteins of known function or these
were too weak to be considered reliable. We now explicitly mention
this fact.

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Received on Wed Jun 14 09:01:52 2006