on being a scientist

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This is absolutely my favourite quote from The Guide:

"I'm a scientist and I know what constitutes proof. But the reason I call myself by my childhood name is to remind myself that a scientist must also be absolutely like a child. If he sees a thing, he must say that he sees it, whether it was what he though he was going to see or not. See first, think later, then test. But always see first. Otherwise you will only see what you were expecting. Most scientists forget that. ... So the other reason I call myself Wonko The Sane is so that people will think I'm a fool. That allows me to say what I see when I see it. You can't possibly be a scientist if you mind people thinking you're a fool."

-- Wonko The Sane

how the hell did this guy get a PhD AND run for parliament?!?!?!

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

A good article from The Indy. I love the idea of requiring MPs to engage with science ( David Tredinnick, you poisonous little sociopath) but I don't imagine for one second that it will change the way parliament works. It makes me wonder why Julian Huppert would want to be an MP anyway. Surely he doesn't think that a single semi-rational voice will make a difference in parliament?

state of the planet

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Here is a powerful article from Nature to kick-start a decade of science-led world-saving. The diagram reproduced below shows nine planetary systems: climate change; rate of biodiversity loss (terrestrial and marine); interference with the nitrogen and phosphorus cycles; stratospheric ozone depletion; ocean acidification; global freshwater use; change in land use; chemical pollution; and atmospheric aerosol loading. Safe thresholds for each system are indicated by the green ring and the current state of each system is illustrated by the size of the red wedge. As you can see, we have already exceeded the safe thresholds for biodiversity loss, the nitrogen cycle and climate change.


So there you have it: A concise and heavily evidenced review of the state of the planet in one of the most prestigious journals. Everyone should have to read this. Ignorance is a crime.

surreal science moment

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

I just happened upon a friend of mine carrying a tray of my sperm across campus. We found it rather amusing.

Here they are, BTW:


The sex chromosome in each nucleus has been FISH stained. Red means its a girl and greens are boys.

excellent blog

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Its called Information Is Beautiful.

Check it out.

it always amuses me how "thesis" sounds so similar to "faeces"

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Here it is, kids. The whole chibang:

punkscience: helping to understand swine flu

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

I read this article on swine flu and was surprised to come across the demographic parameter R0. This is something that I have regularly encountered in my work on demographics and I revel in the opportunity to explain a little straightforward maths to the pubelic: R0 is the net reproductive rate of an individual or a population.

From my thesis' scrap file:

R0 can be calculated from the equation:

R0 = V(α) . b . E(α)

Where: V(α) = Survival rate to the age of first reproduction.
b = is the product of the lifetime average rate of offspring production.
E = is the average adult life span of an individual at the age of first reproduction.

For semelparous organisms this equation can be further simplified to:

R0 = V(α) . S(α)

after Charnov (1997)

Where: V(α) = the reproductive value of an individual at the age of reproduction (b multiplied by E)

It is possible to determine several factors which influence either V(α) or S(α) and these factors have often been quantified as surrogates for fitness (eg. McDowell et al. 1999; Kashian 2004). Bearing in mind that fitness is a product of both genes and the environment in which they operate any assessment of fitness will be specific to the environment in which it is assessed (Stearns 1992).

The only problem, of course, is that a flu virus is not semelparous. In which case all of the above isn't relevant. So that's a lot clearer then. Yes.

Good Science: Why fertilisers reduce biodiversity

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

'Nuff said.

NMR results

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

WARNING: This post contains ecotoxicology: Non-biologists may be incredibly bored!

This is the result of Principle Component Analysis on the non-polar spectra from my methanol-chloroform extracts. The different symbols represent three different populations of animals. As you can see they are completely separated by PCs 2, 3 & 4. This is quite a weak differentiation as these three PCs account for 15.29, 9.74 and 7.95% of the variability in the data, respectively. However, differentiated they are, demonstrating that significant differences in fundamental metabolism exist between the three populations. Now I've just got to work out what those differences are. Which is a lot harder.

stupid observation of the month

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Holy, fuck! This is sooooooooooooooo STUPID! New Scientist should be ashamed:

"The virus's severity will depend on how many people who catch it die."

No. Shit Sherlock.

how to extract RNA from biological samples

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This is a protocol I'm currently using which was developed by two PhD student friends and a postdoc. Its really detailed so I thought I'd share it with the world because a lot of this stuff isn't intuitive and is only understood after much trial & error.

By the way, this protocol doesn't work for plant material. Planty RNA is protected by thick cell walls and is not easily isolated from the rest of the planty rubbish you find in there.

RNA Extraction with TRI reagent

1. Homogenize tissue in 0.5ml of TRI (or put on ice to defrost if this has been done)
- Stand for 5 min
- Centrifuge for 5 min @ >10,000 @ 4degC
- Remove supernatant if messy sample and place in a new tube. Dispose of pellet
- Don’t use polytron homogenizer if extracting DNA – shear forces can break strands

2. Add 0.1ml Chloroform
- Shake for 15 sec (vigorously).
- Stand for 15 min (room temperature)

3. Centrifuge 15 min @ 12,000 @ 4degC
- Extract RNA phase (top/clear) into fresh tube straight away!
- Avoid white cloud above white layer as this is genomic DNA.
- If has been standing to long, or there are still bits in supernatant, then
- spin down again.

4. Add 0.25 ml Isopropanol + 1 ul LPA (linear polyacrylamide – coprecipitant for very small amounts)
- Stand for 10 min @ room temp OR over night @ -20degC
- Centrifuge 30 min @ 13,000 @ 4degC
- Mark where pellet is with marker
- Pour Isopropanol gently out into a beaker, keep an eye on pellet. Don’t lose it!

5. Spin 30 min @ >13000 @ 4degC
- Decant supernatant

6. Wash “Back down” with 1 ml 70% Ethanol
- Vortex
- Centrifuge 10 min @ 13,000 @ 4degC
- Decant Ethanol – pour off gently onto blue roll, watch pellet.
- Make sure pellet re-attaches

7. Repeat Ethanol wash
- Allow pellet to dry - upside-down on blueroll (not in sun)
- Try to take as much of EtOH as possible so doesn’t take too long to dry
- Dry completely – approx. 1 hour. But not too long.

8. Resuspend RNA with H2O (in minimum amount of water)
- 8-40 ul dependant on pellet size
- If pellet is hard to dissolve, heat solution for 10 min at 55-60 degC, then aliquot
- immediately and freeze at -80.

9. Transfer to clean 0.5ml tube and freeze at -80
- Don’t transfer if low amounts.
- Aliquot solution immediately and freeze at -80 – RNA is very unstable at room temperature.

After this step you have to remove DNAases and then create cDNA from the RNA.

crazy fish that can see through its own head!

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The green spherical things are its eyes! Mental!

real punkscience from Science Punk

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This site rules.

this is what I call "art"

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Word.

Pure Energy Systems Wiki

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

If you're as fascinated by renewable generation as I am then you should love this Wiki. I found my way there through their algal biofuels page, which is awesome!

science puts an end to racism

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Nice work.

Demonstrating once and for all that racism is purely a product of prejudice, arrogance, bigotry and selfishness.

religion is a byproduct of the evolution of imagination

Word.

New Scientist rules.