Tuesday 20 November 2007
Monday 1 October 2007
Misconceptions in microbiology #1
In a vain attempt to inject some science into this blog, I thought I might consider some popular "facts" about bacteria which appear in some science textbooks and are thus perpetuated as urban myths within the scientific community. The most popular one, which I'll start with is:
Bacteria have a singular, circular chromosome
Many bacteria, including the "model" bacterium Escherichia coli, that do have only one chromosome. However, there are numerically more bacteria in the world that have not one, or two, but many chromosomes. For example, Rhodobacter sphaeroides has two circular chromosomes, and Paracoccus pantotrophus has at least 4, one of which is linear. The possession of a linear chromosome isn't unusual. One of the most important organisms in biotechnology, Streptomyces coelicolor, has a single linear chromosome too.
Bacteria have a singular, circular chromosome
Many bacteria, including the "model" bacterium Escherichia coli, that do have only one chromosome. However, there are numerically more bacteria in the world that have not one, or two, but many chromosomes. For example, Rhodobacter sphaeroides has two circular chromosomes, and Paracoccus pantotrophus has at least 4, one of which is linear. The possession of a linear chromosome isn't unusual. One of the most important organisms in biotechnology, Streptomyces coelicolor, has a single linear chromosome too.
Term has well and truly started
The term at Oxford Brookes has started, and I have a flock of M.Sc. Biotechnology students to tend to. I thought the type of student might be different from the M.Sc. Microbiology course I helped run at Birkbeck, University of London. However, we have the same sort of mix of students.
The beginning of the university term also means that for me, its the end of the time trialling season, which has been quite successful on the whole. I was pleased that I managed to get my name in the local paper most weeks, with consistent top-ten placings throughout the year meaning that I can look forward to receiving one or two prizes at the club dinner. However, my highlight of the year was going "under the hour" during an open time trial two weekends ago. The quest to cycle at 25 miles an hour for one hour is delightfully pointless, and if you are going to do it, why not cycle 25 miles in 58 minutes and 14 seconds? Thanks to Hounslow & District Wheelers for organising the event, but could they please send out the results sheets soon?
More ground-breaking news is that the book I co-authored last year (Instant Notes in Microbiology) is now number 99,357 in the amazon.co.uk bestseller list, and 1,652,746th in the equivalent amazon.com list. Surely I can expect the offers of interviews on daytime TV to start flooding in? The pleasing thing is that on the whole the book has been well-received, with quite a few positive reviews in journals as well as on Amazon. The one fly in the ointment is that one reader felt that this was more of a GCSE book than a university-level one. This disturbs me a little as my part of the book was based on a series of lectures I gave to postgraduate students. Which sort of brings me around, circularly, to the subject of the first paragraph of this post...
The beginning of the university term also means that for me, its the end of the time trialling season, which has been quite successful on the whole. I was pleased that I managed to get my name in the local paper most weeks, with consistent top-ten placings throughout the year meaning that I can look forward to receiving one or two prizes at the club dinner. However, my highlight of the year was going "under the hour" during an open time trial two weekends ago. The quest to cycle at 25 miles an hour for one hour is delightfully pointless, and if you are going to do it, why not cycle 25 miles in 58 minutes and 14 seconds? Thanks to Hounslow & District Wheelers for organising the event, but could they please send out the results sheets soon?
More ground-breaking news is that the book I co-authored last year (Instant Notes in Microbiology) is now number 99,357 in the amazon.co.uk bestseller list, and 1,652,746th in the equivalent amazon.com list. Surely I can expect the offers of interviews on daytime TV to start flooding in? The pleasing thing is that on the whole the book has been well-received, with quite a few positive reviews in journals as well as on Amazon. The one fly in the ointment is that one reader felt that this was more of a GCSE book than a university-level one. This disturbs me a little as my part of the book was based on a series of lectures I gave to postgraduate students. Which sort of brings me around, circularly, to the subject of the first paragraph of this post...
Tuesday 31 July 2007
Playing catch up
I've not had much time to keep up with this blog of late, what with acting as promoter for a large cycle race (the Bicester Millennium 4up team time trial), trying to write lectures, organise my growing research group (working on surfactin production and biosurfactants) and... and... and...
To catch up a bit on things I've posted about before, the Tour de France has come and gone. Probably gone for good, what with the reputations Vinokourov, Moreni, Rasmussen and now Mayo tarnished by missed drugs tests or positive ones. It's not really a surprise that such things happen (a quick reread of Paul Kimmage's book is enough to put anyone off the "glory" of Pro cycling) which says quite a lot about my attitude to the whole thing. I hope that the witch hunt that is going through cycling at the moment is extended to other sports. I can't believe that the footballers, tennis players, track athletes and swimmers of this world are somehow whiter than white, particularly given their larger disposable incomes compared to most cyclists.
In the end what bothers me most about the drugs in sport issue is that it reflects on me. I might only be a club cyclist who races five times a year in time trials, but on the odd occasion I win, do the others in the field suspect that I have doped to do it? Would I be that shallow that I would?
To catch up a bit on things I've posted about before, the Tour de France has come and gone. Probably gone for good, what with the reputations Vinokourov, Moreni, Rasmussen and now Mayo tarnished by missed drugs tests or positive ones. It's not really a surprise that such things happen (a quick reread of Paul Kimmage's book is enough to put anyone off the "glory" of Pro cycling) which says quite a lot about my attitude to the whole thing. I hope that the witch hunt that is going through cycling at the moment is extended to other sports. I can't believe that the footballers, tennis players, track athletes and swimmers of this world are somehow whiter than white, particularly given their larger disposable incomes compared to most cyclists.
In the end what bothers me most about the drugs in sport issue is that it reflects on me. I might only be a club cyclist who races five times a year in time trials, but on the odd occasion I win, do the others in the field suspect that I have doped to do it? Would I be that shallow that I would?
Friday 29 June 2007
PCR primer design
Must remember about this site "PCR Primer Design" at the University of Capetown in Zuid Africa. Its a little outdated, but gives some of the basics of PCR primer design in a compact and manageable form. It would be nice to do a similar thing somewhere somehow sometime...
New cork, old bottle
Craig Ventner is back in the news again, after the on-line publication of his experiments involving "Changing One Species to Another". I haven't read the full article (and look forward to doing so) but the experiment seems straight forward enough: isolate genomic DNA from Mycoplasma mycoides (which has a very small genome but possesses a tet resistance gene); transform Mycoplasma capricolum with this DNA and select for tet resistance. The abstract suggests rigorous testing to ensure that all the genetic properties of M mycoides are present in the new species, and none of M capricolum. A very neat experiment, but does this really show one species being changed to another?
In the rather fluid species definition of Bacteria, the genome is the most important thing. It alone defines the characteristics of the bacterium. Isn't this procedure a bit like (by very very dodgy analogy) implanting a sheep foetus into a goat and calling the whole thing a new hybrid?
Nothwithstanding the semantics of the use of the word species in the title, it does signal a small jump forward in the quest to design bacteria with particular properties.
There are a few more details here though this is a dynamic link that may not repsond for very long.
In the rather fluid species definition of Bacteria, the genome is the most important thing. It alone defines the characteristics of the bacterium. Isn't this procedure a bit like (by very very dodgy analogy) implanting a sheep foetus into a goat and calling the whole thing a new hybrid?
Nothwithstanding the semantics of the use of the word species in the title, it does signal a small jump forward in the quest to design bacteria with particular properties.
There are a few more details here though this is a dynamic link that may not repsond for very long.
New Specialized Transition
VeloNews have some pictures of the new Transition:
It includes a hidden rear brake for reasons I can only guess at - why wasn't the front one hidden too?
I've always liked these, but I wonder what the seat angles are like?
Friday 15 June 2007
Firefox extensions again
My experience with Firefox is on the whole good. The capability of using extensions is particularly useful, though not always a good experience. I found the Google Reader extension caused the browser to occasionally mis-load, though I have used Zotero (as an alternative to EndNote, click here) and NoScript (a script and Flash media blocker, click here with great success.
NoScript does an excellent job at blocking scripts, but I do wonder about the difference between malicious and trusted scripts. Why does CyclingNews run scripts from its website? Should I care? Having said that, I've just put some script in this blog, an excellent test for anyone reading this to see if NoScript is working.
NoScript does an excellent job at blocking scripts, but I do wonder about the difference between malicious and trusted scripts. Why does CyclingNews run scripts from its website? Should I care? Having said that, I've just put some script in this blog, an excellent test for anyone reading this to see if NoScript is working.
Today I have mostly been...
..concerned with random words and images for some reason.
This site seems to fit the bill!
This site seems to fit the bill!
Wednesday 6 June 2007
Obsessive behaviour
Its quite possible that I am obsessed with cycling. Unfortunately the Tour de France starts in London this year. Why is this so unfortunate? Mainly because the prologue falls on the 7th July, a day on which I am not overly keen to go to London.
The next day the Tour winds its way from London through Kent. The map suggests that it might be possible to see it in more than one place (for a pdf of the route click here).
There is only one, you know...
The next day the Tour winds its way from London through Kent. The map suggests that it might be possible to see it in more than one place (for a pdf of the route click here).
There is only one, you know...
Thursday 24 May 2007
More black news from cycling
Well, it seems Eric Zabel, as well as the current DS of T-Mobile, has admitted using EPO. Another body blow for professional cycling.
See news item here, and no doubt all through the cycling press from later today...
I'm not sure what to make of it, it all seems a bit inevitable. How long until a famous Texan also makes some sort of confession?
Fluidigm (commercial website here) seem to have some interesting new technology for QPCR. To quote their marketing they are "doing for biology and chemistry what integrated circuits have done for computing". Reading through the investor-attracting hyperbole, there does seem to be some cause for optimism though..
Firefox
I sometimes wish I had the competence, or is it time, to be able to use Linux and other esoteric non-Windows programmes, a little like Neil has made a career of (see his blog here, its worth a read). However, in a sort of half-cocked way I end up using Firefox. There are a few problems with it, but it does have some plus points. One of them is the add ons, such as Foxmarks, a small program plus server access that allows book marks made on one computer to be transferred to another.
In the world before Firefox, I used to do this with my iPAQ< creating a mobile favourite. However, the sync for this took ages. This may have been cured now, but in the meantime I'll see if the web-based approach works any better...
In the world before Firefox, I used to do this with my iPAQ< creating a mobile favourite. However, the sync for this took ages. This may have been cured now, but in the meantime I'll see if the web-based approach works any better...
Thursday 10 May 2007
Rhythm & Bounce
Some interesting news from the world of the Chemical Brothers... a "free" gig in Trafalgar Square in early September. Register on their site and look through the forum for more information...
First steps
Thought I might enter the wonderful world of blogging, even if it is only to remind myself of stuff I have come across.
Today chatted to geneservice (website here) in an effort to get my group's molecular biology effort under way again.
Today chatted to geneservice (website here) in an effort to get my group's molecular biology effort under way again.
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