twitter

Two weeks ago I visited collaborator Adam Eyre-Walker at the University of Sussex in Brighton. Adam and I have been working on a paper exploring what selective forces underly the rate with which bacteria take up new genes, using insights from theory developed to explain the rate at which point mutations occur. The manuscript is close to submission and I hope to post about it sometime soon. Adam also has a blog, where he writes both about population genetics (primarily the fitness effects of mutations) and the sociology of science (primarily scientific publishing): recommended reading! It was great to catch up and also to meet the people in his group. Our converation in the pub turned not to blogs but to twitter, as Adam mentioned his recent tweets describing his experience with PLoS ONE asking him for his personal bank statements to prove he really did qualify for a publication fee waiver, which garnered quite some attention. I have always been  suspicious about twitter, mainly associating it with every man and his dog spouting uninteresting opinions about everything and anything all the time.anabodiodicsThere seems to be an element of truth in this assessment. Idiocy, in-jokes and self-promotion aside, of course there are also plenty of interesting tweets. In Adam’s experience, twitter is a good tool to promote his research, as well as an effective way of finding out about interesting new papers and events in his field (something collaborator Britt Koskella told me before). I realize that twitter can be a very efficient medium to keep updated on specific interests. It might actually be a little bit too good at its job by offering an endless source of procrastination. For instance, scrolling for just a minute through Adam’s twitter feed I found a cool clip on false positives, an interesting discussion of Adam’s analysis of lab size and productivity and a witty comment on The Sun’s page 3. Considering that I have the attention-span of a prawn anyway, I have not yet signed up…

Michiel

P.S. A nice post by Beryl Lieff Benderly on the pro’s and cons of using twitter in science can be found here.

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Pitch: a Guide to the Bacteria and Archaea

Background: inspired by a post by Jonathan Eisen on his blog ‘the tree of life’, I wrote a little post on ‘a Field Guide to the Bacteria’ last year. Both our posts were about the rather megalomaniacal (in a good way) idea of sampling, sequencing and identifying bacteria from the environment in ‘real time’. So rather than walking through the field with binoculars identifying birds, walking (anywhere) with a small sequencing device+computer and identifying microbes. This is obviously quite futuristic, but I have been thinking about a guide book to bacteria (from now on read ‘bacteria’ to mean both bacteria and archaea) that would be perfectly feasible. I think it is a very cool idea, but it would be great to have some of your feedback to see if it is actually worth pursuing. I am starting with the premise that a) bacteria cannot be identified in the field and b) a guide on bacteria cannot be in any way, shape or from be representative of actual diversity (in contrast to say most regional bird guides). More positively, I also think that c) bacteria can be beautifully illustrated and d) that they have very diverse and interesting life-styles that would make for some good reading. Applying a ‘traditional’ natural history format focusing on species diversity could be a very good way of bringing the sophistication of bacteria to the attention of the general public.

The pitch: a guide book where 100 bacterial species are represented by a page of text and an opposing page with a Scanning Electron Microscopy (SEM) picture. The format will be like any other guide book, utilizing pictograms to signify key characteristics (e.g. genome size, metabolism and habitat) and a short text segment on general biology as well as a segment on how the species impacts on us humans. Using 100 species would allow covering a lot of bacterial variation: many different taxonomic groups, many different habitats and niches and many different types of metabolism. Examples would include oceanic species, soil species, gut species, phyllosphere species, pathogenic species, hotspring species, food fermenting species, endosymbiotic species, photosynthesizing species, lithotrophic species, multicellular species, tiny species, ‘giant’ species, magnetic species, halophilic species, Bacteroidetes, Actinobacteria, Chloroflexi, etc etc. Each species would serve to highlight one specific, interesting behaviour.

The illustrations: beautiful SEM colour illustrations will be essential. Hands down the most beautiful SEM pictures of bacteria I have seen so far are those of award-winning ‘micronaut‘ Martin Oeggerli. Martin uses highly sophisticated post-processing colouring for an ‘acrylic finish’. See below for a fantastic image of a consortium of gut bacteria (including a plant fibre and the eukaryotic parasite Giardia on the far right):06-intestinal-bacteria-670

The format: there is some precedent: MicrobeWiki features illustrated descriptions of selected bacterial species (example page here). Although this is a great resource, it is not comparable to the coffee table book I have in mind. There is a case to be made to not produce a book, but build an app instead. This might be cheaper to do and also allow reaching a wider audience. Also, it will be relatively easy to add many more species to the app when the project is succesful. And it will allow linking to relevant websites, such as those hosting genome sequences etc (the downside to this is that the app needs curating to prevent dead links and just having a multi-FASTA file with millions of A’s and T’s and C’s and G’s pop up by itself is not that helpful to the average reader and would need a lot of extra context).  Of course, the two formats are not mutually exclusive. I still think a book is nicer though.

An example page: because a picture is worth a 1000 words, my sister Leonie helped me to produce an example page using my favourite bacterium Myxococcus xanthus. The SEM is by Juergen Berger at the MPI and was used a cover for Current Biology for one of my papers with Gregory Velicer (although beautiful, I think the colours are a bit artificial, soil is not blue!). I am not sure about the pictograms yet. Most conventional guides have a little map with a distribution range coloured in. I do not think that will be very helpful for most bacterial species, as they are generally very widely distributed and they definitely do not migrate (my thoughts on bacterial biogeography are summarized in this paper and this other paper). A pictogram of the habitat would be very useful however. Likewise, a pictogram summarizing genome information (genome size, chromosome and plasmid number and shape (circular or lineair) and number of genes) would be essential. More tricky but absolutely necessary would be a clear pictogram summarizing metabolism (and whether the species is aerobic or anaerobic). There are many other small interesting pieces of information that could be summarized in such a standard way. BOOK

The contributors: this will have to be a team effort. Here’s who would be needed:

  • the scientific community. PI’s that work on an interesting model system would be asked to a) write two pages on what is cool about their model system (+ provide a list of basic information needed to produce the pictograms) and b) send a sample to an SEM facility. In return they will have an outlet to educate the public about their favourite organism by being featured in a book and they will have permission to use a beautiful picture of their bug in their future talks. I know (of) many labs that I could ask to contribute and I do not see any problems there.
  • an SEM wizard. The production of SEMs and, as importantly, the post-processing of images would need to be done by a single person/facility to guarantee continuity and consistency. The quality of the images would be vital to the project.
  • an editor. That would be me. As with the images, the text needs to have a consistent format and style. Editing text provided by other scientists would be much less work than writing copy on 100 species myself from  scratch. I like writing; this should be doable.
  • a graphic designer. The book needs to look slick. The pictograms need to be informative and beautiful at the same time.
  • a  couple of expert microbiologists. Guides usually have a background section at the start featuring more general information about habitats, morphology and life history. This will be a must for this guide, as most readers will know comparatively little about the featured organisms. For instance, having an expert on metabolism on board to briefly explain this complicated topic to the lay person would make the guide much more valuable. The same goes for genome sequencing. Hopefully Jonathan Eisen would want to write the foreword.

How to get there: I am not sure! I guess there are three ways of securing money to make this happen: approaching publishers, crowdfunding and outreach grants. I do not have a good idea about the costs involved and the sales needed to cover them. I would greatly appreciate your comments on the book idea itself and about financing!

Michiel

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Is every bacterium everywhere?

I posted some excerpts from a paper in progress a while back (How many species of bacteria are there? and Bacteria vs. Animals). Here another post on the question “Is every bacterium everywhere?” (then I will stop and just link to the published version!).

Through the narrow sea strait between the Indonesian islands Bali and Lombok, past Borneo and Sulawesi on towards the Philippines runs the Wallace line, named after the co-conceiver of the theory of evolution through natural selection Alfred Russell Wallace. The fauna west of this invisible line is Asiatic, and includes for example tigers and orang-utans, whereas the fauna east of this line shares Asiatic and Australian characteristics, missing most of the Asiatic megafauna species. To understand why such biogeographic boundaries exist, it is necessary to look into the geological past. During the last Ice Ages, seawater levels were dramatically lower and the islands on the Asiatic side of the line were connected to each other as well as to mainland Asia. However, deep waters separated this landmass from more easterly islands such as Lombok and Sulawesi. Without land bridges, these islands could only be colonized by animals capable of surviving journeys over sea or through the air. The debate on whether there exist equivalents of the Wallace line for bacteria is well over a century old (1) and has still not been resolved. One important reason for this lack of progress is that biogeographic patterns change depending on the taxonomic or genetic resolution used (2). For example: different monkey species occur on both sides of the Wallace line and so when only the broad classification ‘’primate’ would be used, no biogeographical patterns would be apparent. Only when looking at the level of species, patterns would emerge, for instance showing that the Crab-eating macaque is the only primate species occurring on either side of the Wallace line. Moreover, it is likely that high resolution sequencing data would reveal subtle genetic differences between populations of a species inhabiting different islands on one side of the Wallace line. As the methods used to differentiate bacteria are often relatively crude, biogeographic differences thus could be overlooked.

 
One other problem with the study of bacterial biogeography is that different researchers use different definitions of the term ‘biogeography’. In its broadest sense, biogeographic patterns could be said to exist when finding different species in different geographical locations. In a narrower sense, biogeographic patterns are recognized only in the subset of cases where geographically distinct, but environmentally very similar locations harbour different species. In this latter case, barriers to dispersal must have prevented a single species to colonize all suitable habitats (3). In its broad definition, bacterial biogeography is uncontroversial: different environments select for different bacteria. In its narrower definition, things are not so clear. The very small sizes of bacteria combined with their large population sizes are likely to make dispersal by water or wind highly effective, and presumably not much hindered by potential barriers such as seas, mountain ranges or just sheer distance. Indeed, there are no known cases of bacteria that are restricted to one geographical location, whereas there are many documented cases of bacterial species (be it in forest soils, hot springs or the open ocean) that occur globally. This is not to say that there is no geographic structuring within these species: isolates that are geographically more distant often are on average also genetically more distant. To some extent, the differences must be due to chance, with different populations experiencing different mutations with small effects on fitness that persist without spreading to other geographic populations. To a large extent, these genetic differences must be due to adaptation to local differences in habitat. It is hard to figure out which ecological differences between locations are relevant to bacteria as there are many and they can be subtle (some could even be related to the biogeographic differences in animals and plants). The effects of habitat on bacterial diversity are therefore likely to be underestimated (2).

 
1. O’Malley MA. 2007. The nineteenth century roots of ‘everything is everywhere. Nat Rev Microbiol 5:647-651.
2. Hanson CA, Fuhrman JA, Horner-Devine MC, Martiny JB. 2012. Beyond biogeographic patterns: processes shaping the microbial landscape. Nature Reviews Microbiology 10:497-506.
3. Martiny JB, Bohannan BJ, Brown JH, Colwell RK, Fuhrman JA, Green JL, Horner-Devine MC, Kane M, Krumins JA, Kuske CR, Morin PJ, Naeem S, Ovreas L, Reysenbach AL, Smith VH, Staley JT. 2006. Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4:102-112.

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Self-funded PhD positions available

Advertised on the site FindAPhD: an advert describing opportunities to work with Will Gaze or myself at the European Centre for Environment and Human Health. Just to make it abundantly clear: this is and advertisement for a SELF-FUNDED PhD position, so you have to apply for a grant yourself first. This blog gives you a bit of a taste of what we do, but we are relatively flexible in accomodating project ideas (after all, you have been awarded the money, not us!). So come join us in lovely Cornwall!

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Lab Visitor: PhD student Katia Djenadi

Will Gaze recently hosted PhD student Katia Djenadi from Algeria for a collaborative project; below she has written an account of her stay:

From Algeria to United Kingdom: Algeria is a country located in North Africa giving on the Mediterranean Sea; it’s considered as the tenth largest country in the world with a varied climates and natural habitats harbouring a wide range wildlife, from a large Mediterranean coastline in the north to the Sahara desert in the south with a large areas of hills, mountains, valleys and plateaus in the middle. Many scientists work in this natural environment and collaborate with the pharmaceutical industry and agriculture. In addition, researchers study multidrug resistance of bacteria in hospitals and many other areas.Picture Nu00B005  Mediterranean Coast and Flora  (Between  Jijel and Bejaia Town )Defined as a major problem in public health; antibiotic resistance has been investigated bacterial ecosystems. This resistance can be explained by bacterial acquisition of new resistance genes via mobile genetic elements. The presence of resistance genes and the development of multidrug resistance in the natural environment enthused us to carry out screening for the presence of Gram negatives multidrug bacteria resistant to carbapenem antibiotics in aquatic and soil environments. In order to perform the molecular investigation and define the resistance mechanisms of a collection of multidrug resistant bacteria, collaboration was built with the University of Exeter Medical School (United Kingdom) in the Coastal Pathogen laboratory under supervision of William Gaze and Lihong Zhang.

Seventy days stay within the Coastal Pathogen Team, was an enjoyable experiences. I had a good opportunity to enrich my knowledge in new molecular techniques and perform relevant parts of our investigations. In order to study the resistance mechanisms of bacteria from the Algerian natural environment, characterized by high resistance to carbapenem antibiotics, we carried out transformation and conjugation methods. Species identification was carried out by sequencing 16S rRNA genes after DNA extraction using a biology molecular kit and PCR amplification. Clones that initially showed carbapenem resistance will be sequenced and the genes identified by sequence analysis. At the end, I hope that the hard work undertaken within the Coastal Pathogen laboratory will crowned with success helping me to complete my PhD and result in a collaborative paper.

The Coastal Pathogen staff were very helpful, attentive and generous. I really appreciate working and being with them. Sightseeing Cornwall and London was a great opportunity for me to admire the wonderful region of Falmouth “Gylly beach” and the beautiful green space and rivers in the south of England and London such as the Royal Parks, Hyde Park and without forgetting places such as the Natural History Museum. This agreeable stay was an amazing experience and a great opportunity to discover British culture and building new friendships. It was an incredible experience.

katia

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a lottery system for grant proposals

I read a series of commentaries a couple of weeks ago in Dutch newspaper ‘de Volkskrant’ on the functioning of national research council NWO. As science funding generally works the same across different countries, most of the discussion could be of interest to people outside of the Netherlands too. Lamenting the lack or arbitrariness of grant allocation is of course a common theme and tends to be relatively boring, but thinking about how ‘the system’ could work in a better way is of course always an interesting and worthwhile endeavor. Professor in Public Policy and Governance Willem Trommel at the Free University in Amsterdam wrote a short opinion piece in which he outlines some suggestions for a better way of funding research grants which I found interesting (article in Dutch here).

Very briefly, funding money is down and only a small percentage of proposals get funded. As a result, scientists spend more time on writing more grants and less time on actual research, often playing it safe and proposing less exciting projects (that cannot be shot down by reviewers) and getting demotivated because even very good grants only have a relatively small chance of getting funded. A single grant can be crucial to a researcher’s career: it might allow a person to start a lab, get another job (or keep a job) or not having to let lab members go because there is no money for contract renewal. Also, there is a bit of a downward spiral effect, as not having had a grant will make it more difficult to get another grant. In short: it is all about grants. Having a process in place that rewards the best grant proposals is crucial to promoting good science and necessary for the fair treatment of scientists.

Stupidly, Unfortunately, I have lost the link, but there is evidence that grant reviewers are pretty good at sorting out the crappy proposals from the pretty good (top 20%) proposals. However, this is not so relevant, as there is only money for only a few of the very good grants in the pool anyway. What matters is: are reviewers good in ranking excellent research proposals? Differences in valuations of excellent grants will get increasingly small and increasingly prone to all types of biases. Whether a grant will get funded or not, could depend on the opinion of only one of three reviewers (it could be rated excellent, say an A+, A+, A rating, or just very good, say an A+, A+, B rating).

Grant writers might not write perfect grants, but grant reviewers might not write perfect grant reviews either. Reviewers sometimes misunderstand an experiment or interpretation. They might not be a fan of a particular research area. They might want to see research that is more safe. They might want to see research that is more daring. They might have a grant deadline themselves and not have taken enough time to properly read and assess a grant. More sinister, they might actively dislike the grant proposer or be worried about competition and slightly, but significantly, mark a grant down. Even if I am exaggerating, and grant reviewers are generally unbiased, knowledgeable, unrushed and fair, there is evidence that they still are not very good at their job. (Remember, grant writers and grant reviewers are generally the same pool of people and so I am not specifically dissing grant reviewers but scientists in general.) A study by clinical scientists, eloquently discussed in a post by Jalees Rehman at his SciLogs blog, measured whether there was a good positive correlation between the ranking of grant proposals that had been rewarded and the scientific impact of papers coming out of the same grants. The conclusion was that reviewer ranking was not a predictor of subsequent scientific success.

Trommel proposes to have an initial reviewing round to separate the top grants from the not-so top and outright bad grants, and then use a lottery to decide which ones of the top grants gets funded. I think this is a brilliant idea for several reasons. First, it saves money and time; researchers lose time by writing grants but also by assessing grants. Also, it will speed up the funding process. Second, I reckon that in general, researchers would be less disappointed with having written a top grant that did not get funded through random bad luck rather than through a *&%^%£ reviewer wrongfully shooting it down. You would be able to report back to the university that you were in the top bracket as a measure of scientific excellence (although note that this also could be done in the current system). Third, this system would promote more daring research proposals (a very good proposal could not be downweighted by risk averse reviewers). Fourth, there would be less other forms of personal reviewer biases. The one negative aspect I can think of, is that doing away with a more detailed reviewing process would minimize useful reviewer criticism, because, let’s be fair, there are plenty of constructive reviews too.

For a discussion on some other ways of potentially improving the grant allocation system see this post on the Dynamic Ecology blog by Brian McGill. Note that I have not researched other blogs on which earlier and better posts on this same subject have appeared; please let me know of any relevant posts and I will link to them. I am interested to hear what you think!

Michiel

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Introducing BSc student Abigail Colclough

Bachelors student Abigail (Abi) Colclough started her year long placement in the lab in July: high time for an introduction! She has written a first blog post here and will write more on her project on a blog she has just started (see below). MV

Mick is currently supervising me on an exciting project: ‘A wide-scale screen for antimicrobials in native seaweed’. The year-long project is sandwiched into my degree, giving me valuable experience before I graduate. Next year, I will go back to studying for my final year of BSc Medical Science at Exeter University. Medical Science tries to bridge the gap between the laboratory bench and the patient bedside by combining traditional bioscience subjects with modules provided by the medical school. During my year at the ECEHH, I will also be completing modules set by the university, which will involve writing a report about the project and reflecting on my professional development. The project itself is very exciting- seaweeds have been noted for their health benefits and are frequently eaten around the world (notably in Asia). Seaweed may have antimicrobial activities, by either killing, inhibiting growth or stopping bacterial communication. The plan is to extract these antimicrobial compounds and test them against pathogenic bacteria. We are discussing a number of research questions, such as whether resistance to antibiotics used in the clinic is correlated to resistance to seaweed antimicrobials. I will be collecting throughout the year, both with the Cornish Seaweed Company, as well as rock pooling at local beaches. Mick has also been diving and rock pooling for seaweed, further adding to the number of species collected so far. I am currently writing a light-hearted blog aptly named ‘A year on weed’ to keep track of my experiences throughout the year- but mostly just for fun! AC

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