The Fuzzy Biologist

Distraction from Blogging

2009-03-15T14:56:00.002Z

Hey Kids,
Sorry i haven't been active the last couple of weeks. I've been at the bench pushing back the boundaries of science in my own small way. Hopefuly next week i'll finish all the posts i've started writing and pop them on here for the masses to read (cough, hmm).
James

Google Search Meme

2009-03-01T12:07:00.002Z

Christie over at observations of a nerd meme tagged me with this little bit of Google silliness, far more fun than Google whacking, you have to try and find your blog with the funniest search terms you can think of. Here is what I came up with.

Fuzzy pubic lice
Biologist fever
James Hale is too friendly with fruit bats
James Hale is a diseased atheist

And my personal favorite, but I dispute its claim

James got pubic lice from gorillas and gave them to Darwin

I’m going to try and be a bit ambitious and tag Ben Goldacre over at Bad Science, My friend Ricardo and John Logsdon at sex, genes and evolution.

The use of twitter as a research tool/aid

2009-02-25T14:33:00.004Z

Ever since I’ve started using twitter, I've become increasing reliant and amazed at its use as a research tool. There seems to be a number of fellow scientists and research institutes/websites/publishers all using twitter. This not only makes keeping up with the latest stories, research and job information possible, but it’s become pleasurable and far from the monumental task of repeatedly checking numerous websites each day to keep up with the latest news.

Obviously it can be used to keep your friends updated with what you’ve just eaten for lunch but the research community has made something a bit more pure out of twitter.It seems we’ve built up quite a community on twitter and I’m looking forward to seeing how this type of media develops over the next few months

Here are some Twitters I recommend following

rdmpage / Roderic Page
Irradiatus / Daniel Brown
NerdyChristie / Christie
sciam / Scientific American
bengoldacre / ben goldacre
carlzimmer /carl zimmer
kejames / Karen James
evoldir / EvolDir
PLoS / PLoS
ResearchBlogs / ResearchBlogging.org

Yersinia pestis

2009-02-25T13:16:00.005Z

Yersinia pestis (formerly Pasteurella pestis) is a Gram-negative rod-shaped bacterium belonging to the family Enterobacteriaceae. It is a facultative anaerobe that can infect humans and other animals.

Also known as the plague, Y. pestis ravaged the European population through the dark ages (Justinian’s plague 541-767 AD) arriving from East and central Africa, spreading to most of the Mediterranean (1), and most of the Middle Ages radiating out from the Caspian Sea. Between the years 1347-1353 plague caused the death of one third of the European population, making it one of the most deadly of all human diseases. First characterized by Yersin in 1894 during the final plague pandemic, which spread out from the Yunnan region of China (ref 2 3).

Primarily a disease of rodents or other wild mammals that usually transmitted by fleas and often is fatal. Human disease is now rare but is usually contracted through contact with rodents and their fleas.
Y. pestis is split into three biovars; Antiqua, Medievalis, and Orentalis, based on small phenotypic differences. Each biovar has been attributed to a particular pandemic event; Antiqua to Justinian’s plague, Medievalis to, resident in central Asia to the pandemics of the middle ages and finally Orentalis to the final Yunnan pandemic of 1894 (4).

Recent DNA-DNA hybridization studies have revealed that Y. pestis is highly related to Y. pseudotuberculosis with the 16s rRNAs being an exact match.
Y. pestis and Y. pseudotuberculosis differ in the diseases that they cause, Y. pestis causes fatal bubonic plague and is transmitted by flea bites or person to person (pneumonic plague), whilst Y. pseudotuberculosis is transmitted person to person through fecal-oral route and rarely results in death.

Symptoms differ depending on the type of Y. pestis infection bubonic, septicemic and pneumonic (5).

Bubonic plague
There is an incubation period of 2-6 days, whilst the bacteria replicate in the lymph nodes. This s followed by lethargy, fever, headache and chills occur suddenly at the end of the incubation period. From this point the infection is resolved or lethal. There will also be the characteristic swelling of lymph nodes resulting in buboes; this is the classic sign of bubonic plague

Septicemic plague
Following the initial incubation period symptoms that may arise include, hypotension, hepatosplenomegaly, delirium, seizures in children, shock, fever. The other symptoms of Bubonic or Pneumonic Plague, not always present

Pneumonic plague
Characterised by Fever, Chills, Cough, Chest pain, dyspnea, hemoptysis, lethargy, hypotension and shock.

Y. pestis can now be treated with standard antibiotic therapies but there is evidence of resistant strains emerging

Brossollet J, & Mollaret H (1994) Pourquoi la peste? Le rat, la puce et le bubon (Gallimard, Paris, France).
Yersin A (1894) Ann Inst Pasteur 2:428–430.
Perry R D &Fetherston J D (
Perry, R.D.,, Fetherston, J.D. (1997). Yersinia pestis--etiologic agent of plague Clinical Microbiology Reviews DOI: 8993858
Devignat, R. (1951). Varieties of Pasteurella pestis; new hypothesis. Bulletin of the World Health Organization 4:247–263, pmid:14859080.
http://en.wikipedia.org/wiki/Yersinia_pestis

Marburg Hemorrhagic Fever

2009-02-16T11:47:00.008Z

Given that there have been a recent reports of a case of Marburg hemorrhagic fever arriving in the USA, I thought I would make it the next pathogen top trump.

Marburg hemorrhagic fever is rare hemorraghic fever that affects both humans and non-human primates. Caused by a genetically unique zoonotic (that is, animal-borne) RNA virus of the filovirus family, after its identification in 1967 it led to the creation of this virus family. The More recent additions to the filovirus family include the four species of Ebola virus, which are the only other known members of the filovirus family.

Marburg was identified when outbreaks of hemorrhagic fever occurred simultaneously in laboratories in Marburg and Frankfurt, Germany and in Belgrade, Yugoslavia (now Serbia). A total of 37 people became ill; they included laboratory workers as well as several medical personnel and family members who had cared for them. The first people infected had been exposed to African green monkeys or their tissues. In Marburg, the monkeys had been imported for research and to prepare polio vaccine. The more recent outbreak Within the USA was due to the infected individual being infected from contaminated fruit bat droppings after visiting python cave in Maramagambo Forest, Queen Elizabeth Park, Uganda. Fruit bats are also believed to a vector for Ebola virus but a true animal reservoir has still to be identified. Marburg virus is indigenous to Africa. While the geographic area to which it is native is unknown, this area appears to include at least parts of Uganda and Western Kenya, and perhaps Zimbabwe.

There is a prolonged incubation period of 5-10 days, yet after incubation the onset of the disease is sudden and is marked by fever, chills, headache, and myalgia. After 5 days of being sypmtomatic, a maculopapular rash, most prominent on the trunk (chest, back, stomach), may occur. There may be one or all of the following symptoms; Nausea, vomiting, chest pain, a sore throat, abdominal pain, and diarrhea. Symptoms will then become increasingly severe and may include jaundice, inflammation of the pancreas, severe weight loss, delirium, shock, liver failure, massive hemorrhaging, and multi-organ dysfunction. Marburg hemorrhagic fever is fatal in 23-25% of cases and there is no known cure or treatment other than the usual supportive hospital therapies.
After the infection has passed recovery is slow and prolonged and may be accompanied by the onset of orchititis, recurrent hepatitis, transverse myelitis or uvetis. Other possible complications include inflammation of the testis, spinal cord, eye, parotid gland, or by prolonged hepatitis.

Bausch DG, Borchert M, Grein T, Roth C, Swanepoel R, Libande ML, Talarmin A, Bertherat E, Muyembe-Tamfum JJ, Tugume B, Colebunders R, Kondé KM, Pirad P, Olinda LL, Rodier GR, Campbell P, Tomori O, Ksiazek TG, Rollin PE. (2003). Risk factors for Marburg hemorrhagic fever, Democratic Republic of the Congo. Emerging infectious diseases DOI: 14720391

Problems with Python Programming, second edition by Michael Dawson.

2009-02-12T12:55:00.005Z

I would like to say that learning python has gotten easier, but the book i'm learning from is so full of errors its taking me hours to get through each section. I find myself constantly trying to work out if its mine or the authors typos causing the programs not to work. Bad times. Does anyone know of any good books?

Darwins Birthday

2009-02-12T09:21:00.002Z

It's 200 years since the founder of our science was born, what better way to celebrate than to read some of the many blogs about his life and works at http://citizenship.typepad.com/blogfordarwin . Happy Darwin day one and all!

Pubic lice and Gorillas

2009-02-11T12:45:00.003Z

It appears that early man got more than meat from hunting gorillas. In an article from the Journal of Biology, Robin Weiss discusses the origin of the human pubic louse Pthirus pubis, actually came from Gorillas. Sequence comparisons between Pthirus pubis and the gorilla louse Pthirus gorillae, reveal that the two species split from each other 3.3 million years ago, at least 4 million years after the human-gorilla split from their most recent common ancestor. Obviously this could make for an awkward conversation with the respective humans other half, but not to worry as Weiss hypothesis’ that early man would of picked up the louse whilst butchering gorilla meat in a similar fashion to how the whale louse will crawl onto your hand when you touch a colonized whale.

Weiss, R.A., Journal of Biology 2009, 8:20

Pathogen top-trumps: Helicobacter pylori

2009-02-09T15:31:00.005Z

Updating the childhood game for the biologist. Each week I will publish a new card on a new pathogen, the following categories will be included

Annual Death Rate- Based on WHO statistics or equivalent.
Disease Severity- severity of symptoms and manifest disease; 0= mild discomfort, 10= death
Treatability- Disease treatability; 0=no treatment 10=fully treatable
Published Papers- Based on pubmed hits.
Lab Category – Containment category of the lab needed to work on the pathogen.

I will also include a brief introduction and summary of the organism.
This week I thought it would be best to start with the disease I know best, the subject of my thesis.
Helicobacter pylori is a gram negative, micro-aerobic, spiral rod bacterium that colonises the stomach First identified in 1983 by Marshal and Warren (1), and subsequently classified as a type one carcinogen by WHO. H. pylori is the cause of 80% of peptic ulcer disease and an important determining factor in the development of gastric adenocarcinoma (which leads to up to one million deaths globally each year (2,3) and mucosal-associated lymphoid tissue (MALT) lymphoma. About 50% of the global population is infected, however, only around 15% of these will develop gastric ulceration in their lifetime and only 0.5-2% develop gastric adenocarcinoma (4). H. pylori is passed between individuals by the oral-oral route and due to the intimacy required for disease passage, infection is familial in nature spreading from parent to child (5) (though in less developed countries horizontal transmission is also common). Once infection is identified it can be quickly cleared using triple therapy of 2 antibiotics and a proton pump inhibitor. However, if infection leads to gastric cancer only about one patient in five survives longer than five years after diagnosis.

1. Marshall BJ, & Warren JR. 1984. Lancet 1: 1311-5
2. Covacci A et al., 1999. Science 284: 1328-33
3. Figura N et al., 1998. Gut 42: 772-8
4. Solnick JV, & Schauer DB. 2001. Clin Microbiol Rev 14: 59-97
5. Delport W et al., 2006. Genetics 174: 2107-18

Blog for Darwin: What Darwin didn’t know but suspected.

2009-02-08T22:19:00.004Z

As the Bicentenary of Darwin’s birth approaches, I have revisited 'On the Origins of Species'. Like many people, I first picked it up at the start of my undergrad and found it to be truly inspirational. However, reading it several years later, with the benefit of my research career and now much more extensive knowledge of evolutionary processes, it amazed me the level of insight Darwin had without the molecular approaches and techniques that wouldn’t start becoming available for some 100 years. Darwin, with the same observational approaches that seemingly were available to mankind since we started to observe our environment, came up with the revolutionary idea of evolution, not only explaining how all organisms arrived at their current state but also allowing us to be intellectually empowered atheists, explaining in some degree where all organisms came from.

Here are a few examples

“… I presume, say that, after a certain unknown number of generations, some bird had given birth to a woodpecker, and some plant to mistletoe, and that these had been produced perfect as now we see them; but this assumption seems to me to be no explanation, for it leaves the case of conditions of organic beings to each other and to their physical conditions of life, untouched and unexplained.”

Here Darwin dismiss’ creationism and even to some extent and saltationism; offering up gradual changes as the method for for generating new species, rather than a complete change within a single generation.

“I am capable, that the view which most naturalist entertain, and which I formally entertained-namely, that each species has been independently created-is erroneous. I am fully convinced that species are not immutable; but that those belonging to what are called the same genera are lineal descendants of some other and generally extinct species, in the same manner as the acknowledged varieties of any one species are descendants of that species.”

This is probably on of the most important statements; here for the first time we are seeing the theory of natural selection laid bare.

Darwin also comments on the importance of sexual selection and how it confers somewhat inhibitory appendages, but the level of hindrance correlates with the fitness of the organism, the role of two organisms in the mating of hermaphroditic species. And talks about the importance of inheritance without the concept of the gene and Mendelian inheritance.

“it has been disputed at what period of life the causes of variability, whatever they may be, generally act; whether during the early or late period of development of the embryo, or at least the instant of conception. ….But I am strongly inclined to suspect that the most frequent cause of variability may be attributed to the male and female reproductive elements having been affected prior to the act of conception.”

Anyone can point out mistakes within the Darwin’s writings, after all it's like trying to put a jigsaw together without knowing what it looks like or even having all the pieces. For example, Darwin could not comment or conceive the intricate processes that were to be discovered in the following 150 years; such as the importance of neutral selection, endosymbiosis, hybridization to the creation of new species. But Darwin does give a general nod to all the clear methods of speciation that we understand today allopatric, peripatric, parapatric and sympatric. Without his important works we would not have the many schools of evolutionary thought that exist today: Punctuationalists, Saltationists, and Neo-Darwinists and in the early days Lemarkists to name but a few. As with the Modern synthesis, the coming together of evolutionary theories today will revolutionize our understanding, and admittedly allow for a number of 'Darwin was wrong' articles to be published, but on the whole, will leave us better placed to answer the question; where did life come from? We have much to be thankful for, the initial works of Darwin, Wallace and their predecessors have given us a starting point to explore the origin of life with a scientific method, something that may not have happened for sometime had their abstracts not been read at Linnean Society of London on that first day of July 1858. And so we must also remember as well that 'The origin of the species' was written not as fact or as an immutable idea but as simply an idea to be built upon by the succesive generations; as it has been. And it makes me glad that within many of our research careers we will all add to it in someway or another, getting closer to the truth that is evolution.

My first computer program: Humans versus Computers

2009-02-01T13:28:00.005Z

An essential part of modern evolution and population biology is knowing how to program. By being able to write scripts one is able to analyze data in a way of ones choosing as opposed to having to rely on someone else's program. This can also be used to quickly manipulate sequence files without having to go in and change them manually. Next week I'm going to learn how to use a powerful database program called BIONUMERICS, for this I need to understand the programming language Python. I have been teaching myself it over the last few weeks and i wanted to publish the first real program i wrote myself. This program is just a bit of fun really, basically you are asked to pick a number between 1 and 100 and then the computer will try and guess, in the fewest attempts what that number is. once the computer has guessed then you will have to guess the computers number. Whomever guessed it in the least attempts wins.
Python is a really powerful language and can be obtained from (http://www.python.org), I would advise learning how to use python as not only is it useful but quite fun too. There is lots of support for biologist and some specific verions of python with useful modules in like scipy (http:// www. scipy.org) and biopython (http:// www. biopython.org).

print "\t\t\tWelcome to \"Guess My Number\"!"
print "\nThink of a number between 1 and 100."
print "I will try to guess it in as few attempts as possible.\n"

import random

the_number = input ("Enter the number: ")

#the computer guesses the number using the random function

guess = random.randrange(100)+1
tries = 1

while (guess != the_number):
if (guess > the_number):
print "I chose", guess, "Wrong!!! The number is Lower ..."
guess = random.randint(1, guess-1)
else:
print "I chose", guess, "Wrong!!! The number is Higher ..."
#setting limits to guesses
guess = random.randint(guess+1, 100)
tries += 1

print "I guessed it! The number was",the_number
print "I got it in ", tries, "tries!\n"

#set intial values
computer_number = random.randrange(100)+1
human_guess=int(raw_input("take a guess"))
human_tries=1

#human_guess = loop

while (human_guess != computer_number):
if (human_guess>computer_number):
print "lower..."
else:
print"higher..."
human_guess = int(raw_input("take a guess:"))
human_tries += 1
print "you guessed it! The number was",computer_number
print "you got it in ", human_tries, "tries!\n"

if (human_tries>tries):
print "computers win"
else:
print"humans win"

raw_input ("To end press .")

Will Research For Food!!

2009-01-30T12:54:00.005Z

I've just signed on, I've admitted defeat and begun sponging off the state. I spent 6 years; 3 as an undergrad and 3 as a PhD student to get my PhD. I'm told I've obtained the highest qualification I could hope for, I’m a specialist in my field, its a fact that no-one else in the world knows what I know about my research, yet here I sit, drinking tea (that cost 2% of my weekly income), in despair about how hard it is to get a good job in science.
We have all these websites, Science, Nature, Evoldir and to a lesser extent jobs.ac.uk, yet it seems impossible to find a job that I'm truly qualified for or that I believe hasn't already had a candidate picked for it. Its not like I'm even concerned where I would go, I'm up for working anywhere in the world as long as the group is good.
I suppose it's my own fault, I have convinced myself that I would hold out for a fellowship, get my career of to a good start, yet there are simply none about at the moment. I've applied for the IRCSET Empower fellowship but that’s 20 weeks away from finding out if I’ve got it. So what now? Carry on signing on?
Well I have one thing keeping me sane, I have returned to my old lab and begun researching for free, it seems that it’s easier to get money for consumables than it is staff. I must admit it's liberating, not technically working for anyone but yourself, no time limits etc. exploring every facet of what could be done with your data as I simply don't have the concern that what happens when my funding runs out, as I simply don't have any.
Well I think I’m going to finish my tea and head out into the cold, stroll into the lab and get back to work. After all it could be worse I could be stuck at home watching Trisha.

Evolutionary Novelties: Two Animal Nervous Systems?

2009-01-29T00:41:00.000Z

Evolutionary Novelties: Two Animal Nervous Systems?

Observations of a Nerd: This Week's Sci-Fi Worthy Parasite

2009-01-28T16:35:00.000Z

Observations of a Nerd: This Week's Sci-Fi Worthy Parasite

Evolutionary Discussion Group Meetings Schedule

2009-01-27T14:33:00.003Z

Please find below the presentation schedule for the University of Nottingham Evolution Discussion Group.

Relevant School Seminar:
Professor John Endler (University of Exeter) 4.15pm, 29th January 2009 B3 Biology
“Testing hypotheses about elaboration, innovation and speciation with Australian Bowerbirds using visual physiology principles”

Dr. Penny Haddrill, University of Edinburgh 4.00pm, 30th January 2009 B3 Biology
'The evolution of noncoding DNA in Drosophila'

Relevant School Seminar:
Dr. Sarah Reece (University of Edinburgh) 4.15pm, 5th February 2009 B3 Biology
“The private lives of malaria parasites: sophisticated strategies for survival and reproduction?”

Relevant Friday Afternoon Seminar:
Francis Gilbert 4.30pm, 6th February 2009 B129, QMC
“The waters of the Nile”

Darwin’s 200th Birthday!
Relevant School Seminar:
Dr. Richard Durbin FRS (Sanger Institute) 4.15pm, 12th February 2009 LT4, QMC
“Studying human genetic variation by whole genome sequencing”

Dr. Tom Price (University of Exeter) 4.00pm, 27th February 2009 B3 Biology
“Selfish genes and polyandry: fertility and extinction”

Relevant Friday Afternoon Seminar
Tom Reader 4.30pm, 5th March 2009 D96 QMC
Title tbc

Liz Bailes 4.00pm, 13th March 2009 LT3 QMC
“Estimating the age of the primate lentivirus radiation”

Relevant first year PhD symposium for Behaviour, Ecology and Evolution groups in the School of Biology 9.30-12.00am, 26th March B3, Biology

No meeting on 27th March 2009, due to first year presentations

John Brookfield 4.00pm, 24th April 2009 LT3, QMC
“Hidden Markov Models, Monte Carlo Markov Chains, and their roles in evolutionary biology”

Speaker tbc 4.00pm, 8th May 2009 B3 Biology

James Hale 4.00pm, 22nd May 2009 D96, QMC
The familial transmission of Helicobacter pylori; a study of intrastrain diversity
Speaker tbc 4.00pm, 5th June 2009 Location tbc

The Pains of Printing

2009-01-27T14:29:00.002Z

I would have to say the most painful part of my whole PhD was not the viva or even the experiments that didn’t bare fruit. It would have to be the printing of my thesis. This is the last time I will have to print it, the third time overall. Each time of printing I have tried to second guess all the possible problems that may arise and every time Microsoft Word has found a new ways to effectively screw me out of several hours of my life not to mention the waste or trees associated with subsequent reprints. Oh well, I’m sure all this agro will be worth it in the end when I finally get a nice black, hardbound copy.

Hello World

2008-12-26T15:03:00.002Z

Tuesday

Nothing, existed.

The search to understand our existence has always consumed us, It certainly has consumed me. The words above are taken from a diary extract of the character Antoine Roquentin in Jean-Paul Sartre’s Nausea. To put the quote into context, Antoine has been struggling with what he calls the nausea, unable to decide whether he exists or not, on this particular day he believes he does. Antoine, like many of us, searches to find meaning in his life. He finally comes to a revelation into the nature of his being, such that, he accepts the indifference of the physical world to man's aspirations. This, it could be said, is the central tenet of evolution. As an evolutionary biologist i understand that evolution is directionless, there is no great plan, no puppeteer manipulating the strings, there is only the passing on of genes to the next generation. Everything we are or were is for this purpose and this is true down to the simplest form of mobile DNA/RNA. This is not to say that i have a rather jaded, even cynical view on the meaning of life, but quite the opposite in fact. I appreciate even more what it means to be alive. The fact that we have been monumentally lucky and can do far more that simply pass on our genes fills me with joy.

I study evolution because I enjoy the thrill of the hunt. The main questions that drive me are Why does evolution occur?
What drives evolution?
Is the process different between groups of organisms; if it is, then why?

I suppose I’m writing this blog to chart my journey into answering these questions. However, this won't be the only topic discussed on this blog. I hope to use this blog to talk about the great pieces of art and design I'll see on my travels, also anything else that happens to take my fancy. This, i suppose, helps explain the title of the blog 'The Fuzzy Biologist'. The title is adapted from The Fuzzy species concept described in Hanage et al., (2005), because the usual boundaries that seperate species aren't really observed in bacteria. I like to think that the usual criteria that classifies biologists dosen't discribe me, hence the name.

Thanks for reading,

James