Post-doctoral applicants sought for IRCSET grants.

post-doc applicants wanted

We are looking for post-doctoral applicants for the upcoming IRCSET grant deadline. The name of the programme is EMPOWER and it is aimed at relatively early-stage postodoctoral applicants. Here is some of the information form the website:

EMPOWER: Government of Ireland Postdoctoral Fellowships in Science, Engineering and Technology
IRCSET will continue to offer their sought-after fellowships based at an Irish host laboratory.   The candidates must have been employed for no more than 36 months as a postdoctoral researcher before the closing date of the Call, and propose pursuing their work for 24 months at an Irish research laboratory.  They must be able to provide evidence of at least one significant research output, such as a published peer-reviewed article or equivalent intellectual property output.  For more detailed information on the eligibility criteria, please download the ‘EMPOWER Terms & Conditions’ document from the EMPOWER page.  Applications for EMPOWER will be accepted via one call for Postdoctoral Fellowships in autumn each year.

We are looking for applicants for the Pisani, Fitzpatrick and McInerney laboratories.

If you have been working in the areas of bioinformatics and/or molecular evolution, please feel free to contact us through our contact page.  The deadline for completed applications is December 7th, 2011.

Survival of the sexiest

 

 

This is to announce that on Tuesday next (the 15th of November), there will be a talk given by Dr. James McInerney in JH2 in the John Hume Building at NUI Maynooth at 7:30pm, entitled:

 

Survival of the sexiest: Why females want a mate with a good sense of humour, a brightly coloured tail and nice antlers.

 

 

The event is open to the public and is part of Science week and there is no admission charge.

 

Please share this notice using the social network links below.

Where are you all coming from?

The new website has had about 1,500 visitors, so welcome to all of you.  If you want to know where you all have come from, here you go….

 

SMBE2012 in Dublin

The annual meeting of the Society for Molecular Biology and Evolution will be held in Dublin next June from the 23rd to the 26th. In the coming week we will make the decisions on which symposia will be included in the final programme. This will be a great thing on one hand, because we get to see who is likely to speak at the meeting, what they are proposing to speak about and we get to see for the first time what the science is going to look like. But because we will have to turn some people down, I guess that is the downside. In any case, by Friday of this week the conference will begin to take shape for the first time and that is quite exciting. Below is a promotional video for people travelling to Ireland

 

Planctomycetes and Eukaryotes are both interesting, but not specifically related

We have finally published our analysis of the relationships between Planctomycetes, Verrucomicrobia and Chlamydia (the so-called PVC group) and Eukaryotes.  In other words, we have shown that these two groups of organisms share superficial similarities, but have no close relationship.  The manuscript has been published in BioEssays and you can access it here [1].

If you take a look at two papers in particular [2,3] – though there are many more on the subject – you can see that thousands of eukaryotic genes can trace their origins to prokaryotic taxa, but there has been no systematic large-scale study to date that has been able to show that any appreciable number of genes group eukaryotes and PVC bacteria together to the exclusion of all other taxa.

This is the gold-standard test.  Can we use careful reconstruction of the evolutionary histories of large numbers of genes to infer the prokaryotic ancestry of eukaryotes?  To a certain extent, we can.  However, it is fraught with difficulties, both in modeling evolutionary history and also incorporating horizontal gene transfer, which tends to obscure the histories somewhat.

Nonetheless, when we actually carried out these analyses, we can see clear patterns emerge.  We can see that there is a large component of the eukaryotic cell that is specifically linked to organisms that are in the alpha-proteobacterial group.  We can see a large component that is specifically associated with the archaebacteria and we can see a large component associated with the cyanobacteria.

The fine-grained placement of these eukaryotic genes is very difficult and I feel that more work needs to be done in this area, but nonetheless, one other thing emerges: There is no strong association between PVC bacteria and eukaryotes.

Right now, as far as the data is concerned (and remember, the data wins, not our pre-conceived notions or our preferences – we have to do science, after all) there is no specific link between PVC bacteria and eukaryotes.

Which is why it is annoying when people ignore the evidence and put forward claims that only look at part of the data [4].

A number of papers have tried to claim that PVC bacteria are in some way intermediate between bacteria and eukaryotes.  This is nonsense. Emboldened with this kind of success, the authors have gone off on a tangent claiming that this in some way validates ideas about autogenous evolution of the eukaryote cell (that the eukaryote cell arose first without any fusion event) and so on.

The problem for these other scientists and their claims is that the real evidence is out there, it has been published and it is very difficult to get around.  Several labs from several countries have looked at these data and there is no real problem with interpreting the data – the phylogenetic signals linking eukaryotes to prokaryotes are easy to find and they link eukaryotes to three main lineages – cyanobacteria, alpha-proteobacteria and archaebacteria.  All other linkages can be explained by small amounts of horizontal gene transfer of some kind.

Finding endocytosis-like processes in Planctomycetes is great [5].  This is indeed an interesting feature of a bacterium.  Does it automatically follow that by studying this bacterium, we will know more about eukaryotes?  Not necessarily.  It might, but it is not a logical conclusion that it will.  Consider, for instance, a birds wing and the wing of a jumbo jet.  Nothing about a birds wing will tell you how a jumbo jet’s wing works.  Engineers gave up at a very early stage when they tried to make aeroplanes with flapping wings.  The two entities both are used for flight, but it is not logical to say that studying one might provide an insight into the other.  The only insights we might get will be dull and uninformative for the most part.

So, if you want to study eukaryote endocytosis, then study it in eukaryotes – there are plenty eukaryotes.

I say it again: PVC bacteria are not specifically related to eukaryotes.  You can find more detail in the paper.

References

1. McInerney JO, Martin WF, Koonin EV, Allen JF, Galperin MY, Lane N, et al. Planctomycetes and eukaryotes: A case of analogy not homology. Bioessays 2011; 33:810-7.

2. Pisani D, Cotton JA, McInerney JO. Supertrees disentangle the chimerical origin of eukaryotic genomes. Mol Biol Evol 2007; 24:1752-60.

3. Esser C, Ahmadinejad N, Wiegand C, Rotte C, Sebastiani F, Gelius-Dietrich G, et al. A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol 2004; 21:1643-60.

4. Devos DP, Reynaud EG. Evolution. Intermediate steps. Science 2010; 330:1187-8.

5. Fuerst JA, Sagulenko E. Protein uptake by bacteria: An endocytosis-like process in the planctomycete Gemmata obscuriglobus. Commun Integr Biol 2010; 3:572-5.