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Text of the page (random words):
to content home about older posts an update posted on february 10 2014 1 comment today is monday 10th february it s 19 weeks until i start my new job not academia surprise surprise it s under 4 months until i get married yeah so that happened and it s about 7 weeks until i have to submit my thesis my staggeringly not finished thesis progress has been slow but steady since christmas but today i have got in and felt completely unable to write so i ve tidied my desk a bit and drunk some tea a lot and wondered just how long it had been since i d written anything on here answer more than 6 months how did that even happen so no promises but i ll see if i can keep some sort of log of the last few weeks of phd dom on here if not for anybody else then for myself just keep swimming 1 comment posted in uncategorized tagged grad school thesis writing crowd sourcing genetics ash die back on facebook posted on august 13 2013 leave a comment sometimes i am astounded by the sheer volume of data that we create in science nowadays where a few years ago we were sequencing individual genes made up of a few thousand letters now with a single illumina run we can generate terabytes of data but what to do with that data a lot of genomics at the moment is concerned with targeted resequencing and bulk segregant analysis producing genome 1 is a lot of hard work and doesn t tell us all that much producing genomes 2 to 10 for the same species tells us a lot more why does wheat cultivar 1 have a higher yield than wheat cultivar 2 why is apple variety 1 susceptible to a disease when apple variety 2 is not continue reading leave a comment posted in biology genetics science tagged ash ash dieback chalara crowd sourcing disease epidemiology facebook fraxinus fungus games genetics jic john innes centre microbiology plant pathology sainsbury laboratory science communication round up 6 posted on august 6 2013 leave a comment unlike its predecessors this round up doesn t feature on a friday it features on a day when i ve struggled to concentrate ever since i got in to work i don t want to launch into a full length blog when i m not achieving anything else what can i say my mum never let me go to brownies if i hadn t been at school either but equally having all of these tabs open is probably preventing me from achieving anything else so without further ado and in no particular order tamsin edwards writes a thoughtful piece in the guardian about whether scientists should air their political viewpoints scientists at bristol university discover that the four kinds of virus causing dengue fever may be quite different to one another six turkish academics have been charged with terrorism after what appears to amount to nothing more than secularism scientists from the united arab emirates have identified a mutation that gives plants reduced susceptibility to two fungal pathogens botrytis cinerea and alternaria brassicicola in case you missed it scientists produced the world s first synthetically grown beef burger this week new scientist unpacks the story groups in australia and new zealand have identified a potential new insectide produced by bacteria along the way they showed that the bacteria keep this toxin in a special vesicle allowing it to build up to high levels without damaging the micro organism leave a comment posted in biology genetics round up science tagged artifical meat biology dengue fever epidemiology fungi genetics lab grown burger mutant plant pathology policy science virology viruses a juicy candidate gm oranges take on citrus greening posted on july 30 2013 leave a comment the story of gm oranges begins in pretty much the same way that every other gm story begins nowadays an unstoppable disease the fastest developments all start with a fungus or virus or bacteria that is wiping out a major crop this time it s huanglongbing or citrus greening as caused by candidatus liberibacter a bacterium carried by psyllids like aphids but not in 2005 this long dreaded disease reached the citrus orchards of florida sparking a state wide campaign of insecticide spraying and preventative chopping down of trees the problem is that being spread by a parasite keeping infected trees away from each other isn t enough just like how people can t be protected from malaria just by keeping them away from malarial patients as long as psyllids can make it from infected trees to uninfected trees the disease continues to spread whenever a devestating disease appears the first port of call is to find a source of immunity ug99 is a name known and feared by people in my line of business a variety of wheat stem rust originating in uganda in 1999 go figure that wiped out huge parts of the african wheat harvest when it began rampaging across africa and europe in 2006 the first port of call was to find a naturally resistant variety of wheat that could be used to breed with other elite cultivars a variety of einkorn wheat a diploid wheat from turkey was found to contain a gene sr35 that conferred resistance well sort of technically they found a qtl and then the gene earlier this year i ll talk about that another time only there was no resistant variety of citrus tree to be found anywhere the only option it seemed was to search further afield early contenders included one from a bacteriophage i e a virus that kills bacteria but concerns that people would react more strongly to an organism modified with genes from a virus put that one to bed similar fears about a well performing tree with a gene from pig put that one on the back burner too an alternative was a gene from spinach and in 2010 this was finally trialled sunday s new york times carried this lovely piece about the fight to win both regulatory approval and consumer acceptance of the new gm orange trees which will hopefully be available for juice production in the next 5 years ______________________________________________________ c saintenac w zhang a salcedo et al 2013 science identification of wheat gene sr35that confers resistance to ug99 stem rust race group science doi 10 1126 science 1239022 leave a comment posted in biology genetics science tagged biology food science genetics gm gmos oranges science ug99 wheat stem rust gmo company launches gmo answers posted on july 30 2013 leave a comment today could well be a day for gm blogging i feel as a start gm giant monsanto has launched a new website called gmo answers gmo answers is an initiative committed to responding to your questions about how food is grown its goal is to make information about gmos in food and agriculture easier to access and understand i m skeptical about how far they ll get with this i imagine it s going to take a lot of moderation and they ll be fielding a lot of angry comments from the anti gm brigade but i really hope there ll be the chance for some sensible dialogue on there as well leave a comment posted in biology genetics science tagged biology genetics gm gmos monsanto science monsanto pulls out of europe posted on july 25 2013 leave a comment in a move surprising to nobody monsanto the agri super giant responsible for roundup ready maize and soy has pulled its gm research out of europe for the time being citing the legislation that makes it next to impossible to get anything approved on this side of the pond this comes not long after basf plant science the german agri business responsible for one of two gm crops grown in the eu amflora high starch potato moved its base to the us due to anti gm feeling in the eu the path from developing a new crop to getting it approved in europe involves regulation by the european food safety authority efsa followed by a proposal by the european commission and subsequent voting by all of the eu member states although the efsa has approved eight crops in the past decade the european commission hasn t allowed them to be commerically grown due to anti gm feeling in some of the member states among the crops still waiting to be approved are three maize cultivars and a soy bean which are all produced by monsanto three of these are to be abandoned monsanto will only continue to pursue one variety of gm maize mon810 which is already grown in the eu but is up for re approval soon the other companies waiting for approval dupont pioneer and syngenta are still waiting leave a comment posted in biology science tagged biology genetics gm in the news monsanto science finding the misery molecule more like imaging a candidate posted on july 24 2013 2 comments depression like just about every other mental disease is a strange and mysterious beast we ve reached the stage where most people finally understand that it s really an illness really a physical problem not something can be controlled we know that there are myriad drugs that can help citalopram sertraline paroxetine fluoxetine but we still can t reach out and touch it we still can t predict it there s still not a physical test that you can do an assay that proves that no this person isn t just lazy or melancholy or antisocial they are depressed the headlines over the weekend the news outlets got a bit excited at the prospect that scientists had finally discovered the molecule responsible for causing feelings of depression independent the brain s most miserable molecule the sunday times the little bastard molecule that causes depression msn the thing responsible for depression jezebel and the science i wish i could say i m as excited as they are but of course the science is never as simple as this the actual paper released is a slog to say the least and more physics than biology but i ll give it a go continue reading 2 comments posted in biology science tagged biology depression diamond in the news physics protein science science journalism synchotron giant viruses shake up the status quo posted on july 19 2013 leave a comment a quick microbiology primer before we begin for the uninitiated or those who don t have a 14 year old in their lives to ask microbe is a catch all terms that we use to describe microscopic organisms these may or may not be pathogenic disease causing they include but are not limited to bacteria like e coli and s aureus which cause food poisoning fungi like athlete s foot and brewer s yeast protists like plasmodium which causes malaria and naegleria which you might have seen in an episode of house we probably shouldn t include viruses like the common cold or prions like variant cjd in there because they re not really classified as organisms they re not alive simply inert particles that harness other living things to replicate themselves as my year 8s would tell you they don t do mrs nerg movement reproduction sensitivity nutrition excretion respiration or growth continue reading leave a comment posted in biology genetics science tagged biology in the news microbes pandora science viruses i smell a rat and it isn t in the pig sty posted on july 15 2013 leave a comment one of the things that i find most disappointing in any debate is the realisation that somewhere along the line somebody knows that what they are saying is not true it s the reason that i get angry at comments from the catholic church about the ineffectiveness of using condoms against hiv and it s the reason that i get pretty frustrated by large parts of the anti gm lobby too we ve all heard claims that gm foods aren t safe because they aren t properly tested yet or they haven t been independently validated by scientists with nothing to be gained from their success in 2013 there are around 600 peer reviewed journal articles documenting the safety of genetically modified groups of these around a third were funded by independent organisations around 3 billion gm meals have been eaten since the vast majority of american soy and maize is now gm without a single human health law suit this is not to say that the case is closed and there s nothing left to be learned just that the public perception about these things is remarkably skewed continue reading leave a comment posted in biology genetics science tagged bad science biology gm in the news pigs science the ramen diaries part 9 the thesis plan appears posted on june 14 2013 leave a comment with 9 months left on the clock before i have to submit it s time for the bakingbiologist to start writing given i haven t exactly finished lab work this is a slightly terrifying prospect but two weeks ago i took to it with gusto on the instruction of my supervisor it turns out that you should start writing is actually supervisor speak for we should have a meeting about how one writes a thesis and what i expect from you and cheerfully producing a first draft of chapter 1 is liable to lead to cross words rather than exclamations of joy but more on that another time this week s most valuable lesson is before you start writing a thesis write a thesis plan for one thing it allows you to defend your structural choices and talk about figures before you ve put in two weeks of solid work and when you re not feeling protective about the work because you haven t already done it continue reading leave a comment posted in biology grad school science writing up tagged grad school phd ramen supervisor thesis thesis plan writing up older posts search for recent posts an update crowd sourcing genetics ash die back on facebook round up 6 a juicy candidate gm oranges take on citrus greening gmo company launches gmo answers categories baking biology book review ecology environmentalism evolution feminism genetics grad school in the lab just me molecular biology 101 opinion protein religion round up science singing teaching things that make me laugh uncategorized women in science writing up blogroll double x science dreams and hopes of a former post doc faraday s cage gmo pundit happy science minor revisions on becoming a domestic and laboratory goddess phd talk philosophically disturbed plant cell biology prof like substance scientopia guest blogs the thesis whisperer blog stats 15 563 hits summergoals activists advice agriculture alternative medicine asperger syndrome autism baking biology bread breeding cake careers chemicals christianity conference conferences crops depression disease dna education epidemiology everyday lab fail feminism food security friends general synod genetics genomics gm government grad school human genome project in the lab in the news just for fun mental health misogyny mutant next gen open access ordination of women other blogs pastry pcr poster protein proteomics public outreach qpcr ramen religion rna running scepticism science science communication science journalism scientists sequencing sex singing snps support networks teaching the church ttfb twitter viruses weekly round up wheat women in science writing up archives february 2014 august 2013 july 2013 june 2013 may 2013 april 2013 march 2013 february 2013 january 2013 december 2012 november 2012 october 2012 september 2012 august 2012 july 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