Thursday, 26 July 2012

Advanced Alpinism

“It’s not for Pleasure but for the Challenge” said Matt, This one sentence alone sums up alpine rock but I feel it needs some context.
It’s the second day of the Advanced Alpinism course and we’ve just outrun the more than timely afternoon storm back to the Sciora hut. That day I felt like we’d all been challenged. We’d set off at 0800 that morning and after the hour long walk we’re at the bottom of the Torre Innominata.  Two of us sitting atop a bergschrund and two standing in it looking up at a 8 pitch route. This route goes at 6b with obligatory 6a climbing so we know it's going to be interesting. Especially as he frequent storms have inevitably left some of the pitches wet but from our rather poor vantage point its relatively impossible to tell which and besides if we were to wait for perfect conditions we’d be back at the hut looking wistfully out of the window.The plan is to climb as two pairs, Owen my guide and I first, then Harry and his guide Matt second.  

The climb starts with a 5c pitch up a slab requiring one point of aid. Owen quickly sets off confidently leading the pitch and before I know it I’m wiping the snow off my rock shoes and starting up behind him. I arrive at blank section of rock with a quickdraw and 3m of traverse before the route continues; with some bemused thoughts of how the hell did Owen do this. I flag my right leg behind me and drop left hip into the wall and do possibly the biggest rock over on the tiniest granite nodule you could imagine and make it across. Owen shouts down at me ‘How’d you do that?’ I explain and he promptly points out it was an aid section and I was suppose to ‘French Free’ it (pull on gear to get across). I give myself a silent ‘go James’ (little victories are what you need here) and continue climbing. Matt has already started leading up behind and making ground all the time. This is what they mean by being alpine fast.

The next few pitches go well until we arrive at the second hardest pitch on the climb (going at 6a+) it's sopping wet, and it’s a slab. This is not a dream combination by any means. Owen asks me to watch him closely as he leads up. His skill as climber and a guide really shine here. Every move is confident and solid. More Importantly, he isn’t only thinking of protecting himself for the climb but making sure that myself, Matt and Harry have an easier and safer time of it. Owen leaves slings out for us to pull on where the route might be too wet and slippery for our unpractised client hands and feet. I'm glad of this after all, for me anyway, I’m a trad climber who goes out of his way avoid the merest suggestion of damp rock routes. This is also where the fun begins! Owen arrives at the belay and then begins to rain down profanity. The anchor is atop a ‘cornflake’ This is a term I could of gone the rest of my life without hearing. It means the flake is basically held to the face in a similar way that a damp cornflake might be held to a breakfast bowl. He warns me of the flake and instead of setting up a belay here he links into the next pitch and continues climbing quickly going out of sight. The next thing I know I’m climbing, gunning to get past the large detached flake for both my own safety and those behind me, lest I be the one to fall and kick it free. We’re all get past this point safely and suddenly arrive in the sun. The rock is dry and the climbing eases off. We finish the route in good style, the 6b pitch goes easily it’s a lay back to fist crack with good feet and I’m not leading it anyway.  So I relax and with a few grunts and murmurs before I ease into the fist crack. (I hate lay backing. this is the complete reverse for Harry. He shames me with his lay backing prowess but hates jamming). I have grown to love jamming which certainly gives me an easier time on alpine rock and to quote Stevie Haston, you could hang a bus off me when I’m jamming.

So great, we’re on top of the route now, this is where you relax right? Wrong?! To get back down we have to traverse across the ridge, abseil down to a bit of high consequence grade II scrambling then along another ridge to a snow field, this is all before we get to the meat of the descent. The aforementioned meat is known as the Cacciabella pass. I think it’s Italian for (F**k that if you think I’m going to down here pass?!?!). This pass consists of a few hundred metres of bolted chains and ladders, let go of said chains and ladders and you’ll get down all the quicker if you get my drift. Owen seems delighted to point out all the sections of chains that have fused together because of lightning strike, and the bent rungs where snow and rocks have taken their toll. This is so far out of my comfort zone my discomfort has lapped itself. 

We get down and the heavens open, well at least it waited until we're safely at the valley floor. From here we move with haste back to the hut. I’m fried, not physically mind, but mentally. All I learned on this route is running around my head. I now have an enhanced respect for the mountains, I’m sharper as a climber, safer as hiker. Amazingly these enhancements were all just passively absorbed. There wasn’t time for lengthy explanations or the need. I watched, listened and experienced. When I had questions they were asked on the way to and from the huts. As a result, I know the basis of a perfect pack and it’s contents. The importance of getting the chalet host on side. How every gram counts, and most importantly knowing what the weather is going to do even if it doesn’t know itself. I experienced so much on this course and I felt challenged every minute of it. This is what advanced alpinism is, extreme type II fun and as you see you don't do it for the pleasure but for the challenge!

Sunday, 15 March 2009

Distraction from Blogging

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).

Sunday, 1 March 2009

Google Search Meme

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.

Wednesday, 25 February 2009

The use of twitter as a research tool/aid

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
ResearchBlogs /

Yersinia pestis

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

  1. Brossollet J, & Mollaret H (1994) Pourquoi la peste? Le rat, la puce et le bubon (Gallimard, Paris, France).
  2. Yersin A (1894) Ann Inst Pasteur 2:428430.
  3. Perry R D &Fetherston J D (
    Perry, R.D.,, Fetherston, J.D. (1997). Yersinia pestis--etiologic agent of plague Clinical Microbiology Reviews DOI: 8993858
  4. Devignat, R. (1951). Varieties of Pasteurella pestis; new hypothesis. Bulletin of the World Health Organization 4:247263, pmid:14859080.

Monday, 16 February 2009

Marburg Hemorrhagic Fever

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

Thursday, 12 February 2009

Problems with Python Programming, second edition by Michael Dawson.

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?