Darwins Birthday

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

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

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.

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

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!!

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?

Evolutionary Novelties: Two Animal Nervous Systems?