Eukaryote Origins – reblogged

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Graur v Birney: A Haldane v Mayr for our times?

In case you have been living in a scientific vacuum for the past week, you cannot have missed the GBE article led by Dan Graur that criticised the ENCODE project and used some language that is not typical for a scientific paper.

I thought I would put my thoughts down about this.

First of all, it is a small world, I know Dan Graur and have met Ewan Birney once.

My first meeting with Dan was in 1995 at an EMBO course in Lyon, France. He was a teacher and I was a student. His first words to me were “Where are you from?”. I replied that I was from Ireland. He said “Trinity?” (referring to Trinity College Dublin) and I replied “No, Galway”. He then said to me “Well, you are nothing, then”.

What a bastard, I thought.

Though he said it smiling.

During the week, I learned that this is his style and in fact his comment was a parody of Trinity and the idea that, at times, some Trinity people are under the impression that there is only one university in Ireland. It turns out that Graur is a bit of a laugh, though I have never gotten on the wrong side of him….yet.

So, he criticised ENCODE in pretty trenchant terms….over to you Ewan Birney.

Birney got on to twitter and (it seemed to me) didn’t bat an eyelid, but said that the best thing for he and Graur to do is have some tea or beer.

That, ladies and gentlemen, is class.

Right there.

Bravo Birney.

Other folk took to twitter and their blogs to express their horror at what had happened.

Others tried to say it was merely a semantic issue.

Meh. It’s definitely not a semantic issue.

I happen to agree with Dan. The ENCODE definition of function is not one that I like very much. Large projects have to make compromises, take big decisions and go with them. This I understand.

However, let us do a small bit of thinking. If this estimate of 80% “function” is true and we are not creationists who think that humans are “special” and completely different to the rest of the natural world, then this value might/must be fairly standard for “Functional” “junk” DNA everywhere.

Let’s just go with that thought for a second.

So, if we do this analysis on the Trumpet Lilly, whose genome is 90,000,000,000 bp in length, are we to say that this genome has 30 times as much functional DNA as humans? The salamander Necturus maculosus has a genome that is 12 times a big as ours. Is it likely that it has 12 times as many functional genetic elements? While having maybe the same or fewer actual genes…

Or is a lot of non-coding DNA (the majority of it, I would contend) still really non-functional in any meaningful way, but perhaps just necessary or permissable for reasons other than effecting function?

So, I am worried that some/much of the ENCODE results won’t end up meaning much and indeed might specifically mislead.

If a bit of DNA is not conserved in evolution, then its “function” is not selected. It might be necessary to “just be there”, but is this of any relevance to healthcare or genomics etc. Do we know much more now than we did when we just aligned the sequences and saw a lack of conservation?

I’ll stay watching for updates, I am not working in this area so it is not directly relevant to me. What IS relevant to me is that I like big data projects, I use them all the time and if ENCODE is further criticised and these criticisms are borne out, then it is not good for our science.

Don’t shoot the messenger or the person asking the question. This is not a six-million-dollar question, it is a two-hundred-million-dollar question.

Have a listen to Ewan Birney and Chris Ponting debate the issue on the BBC: http://www.bbc.co.uk/programmes/b01qwhtp

Oh and the reference to Haldane and Mayr? This is a great read: http://ije.oxfordjournals.org/content/37/3/435.full

Introgressive descent

For some time, it has become apparent that many evolving entities (genes, cells, viruses, plasmids, genomes, etc.) are mosaic.  That is to say, we cannot describe their evolutionary history without telling more than one story about it. Genes can be chimaeric and indeed, it is arguable that it is almost impossible for them not to be chimaeric, if you go far enough back in time.  This means that we need to describe the evolutionary history of evolving units by using diagrams or ideas that can accept and incorporate mosaic history.

The whole area of phylogenetic network analysis has been in existence for at least three decades (depending on how you wish to define this field, you might feel it has existed for hundreds of years).  In fact, there is a superb review of the whole area in GBE from less than two years ago [1] that details all the different kinds of networks, how to construct them and what they mean.

However, this kind of analysis will only allow us to see network-likeness in a restricted kind of datum.  We can construct these kinds of networks either when we have recombination within an alignment of homologous sequences or when we have a collection of trees that manifest topological differences because they have different histories.  Using these approaches, we can identify hybrid organisms or recombined homologous entities.

What about the broader scope of evolving entities? What about when a gene X fuses with a different gene Y? How do we analyse the three related entities in this case? You have the unfused family X, the unfused family Y and the fused family XY.  Can we make a single alignment? Do we have a structure that we can use in order to understand their evolution? What do we do when it gets more complicated than this simple toy scenario?

What about microbial consortia? Or the dependence of a phage on a bacterium and vice versa? These organisms depend on one another for/during their evolutionary history.

Nobody would dream of writing an evolutionary biology textbook these days without including in that textbook some chapter on kin selection – we feel that our picture of evolution is incomplete without such a chapter.  So, why do we have a picture of life on this planet that rarely, if ever, mentions mosaic structures.  If they are mentioned, then they are usually mentioned in the narrow light of simply dealing with homologous recombination or perhaps hybridization between things of the same level – chromosomes or genomes or species.

Today PNAS published a manuscript [2] where, along with some distinguished co-authors, we set out the case for including mosaic entities more centrally in our discussions of things like the Tree of Life Hypothesis. The paper describes mosaic entities: some familiar and some not-so-familiar.  We ask the reader to think about what we might know if we focussed on trying to understand these entities in an evolutionary framework.

I think there is a lot of biology, computer science and mathematics to be done in our efforts to understand these entities and I think there is a proper programme of research in this area.  I also feel that in 10 years time we might look back on many of our evolutionary analyses and feel that they were somewhat naiive because they left out the analysis of mosaic entities.

 

[1] Huson, D. H., & Scornavacca, C. (2011). A survey of combinatorial methods for phylogenetic networks. Genome Biology and Evolution, 3, 23–35. doi:10.1093/gbe/evq077

[2]  Bapteste, E., Lopez, P., Bouchard, F., Baquero, F., McInerney, J. O., & Burian, R. M. (n.d.). Evolutionary analyses of non-genealogical bonds produced by introgressive descent.

The five biggest evolutionary transitions?

Have been thinking recently about what the five biggest evolutionary transitions might be.  Naturally, there are several transitions and indeed it is arguable that at every speciation event, there has been a transition – indeed at every mutational event, even.

But which ones are the biggest?  Also, in this vein – what evolves and what is selected?

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New Research visitor – Dr. Marco Fondi

We are pleased to welcome a new visitor to our research group – Dr. Marco Fondi.

Dr. Fondi is joining us as part of a Science Foundation Ireland funded project on understanding networks in biology.

Marco has been working at the Dipartmento di Biologia Evoluzionistica in the Laboratorio di Evoluzione Microbica e Molecolare.

In the last four or five years, Dr. Fondi has made some significant findings in the whole area of analysing gene fusions, recombination and the evolution of plasmids.

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

 

Research returns to Ireland far exceed investment

by Dick Ahlstrom

Financial returns from Ireland’s expenditure in research have easily outstripped the original investment, according to a study released on 19 September.
It claims that while the Exchequer put in almost €1.2 billion over the period 2000-2006 the returns amounted to about €1.8bn.
The study by PA Consulting said that the figure for returns was probably a gross underestimate. This was because it decided against including financial returns—for example, from the construction phase—and measured only the direct commercial impact of expenditure, according to the report’s authors.

It did not attempt to factor in the enhanced ability to attract direct foreign investment from an improved science infrastructure or the indirect returns from downstream contracts and the value of the skills base arising from investment in research.

“As such, the study presents a minimum valuation of impact at this stage,” the authors concluded, so the results were “very encouraging”.
The minister of state for science, Sean Sherlock, welcomed the report, saying it underlined the positive impact of Exchequer investment in R&D.
It also showed that the benefits measured by commercial returns for companies were weighted towards the later years of the study period. Given the type of investment involved, “it is to be expected that the full effect will only be realised over an extended period of time”, Sherlock said.

PA Consulting was asked by the Higher Education Authority to assess the financial impact of Exchequer investment in research. The authority is the body through which money flows into the higher education sector but it also manages a key research funding scheme, the Programme for Research in Third Level Institutions (PRTLI).
The study looked at 45 investments in research centres and other initiatives funded via the PRTLI in 2000-2006. The consultants assessed the impact of the spend on the current and anticipated income derived as a direct result of the investment.

The report identified 50 companies which together valued returns so far at €753 million. The companies estimated that accumulated returns over the coming five years would add a further €1.11bn to reach a total of €1.86bn.