Saturday, 31 August 2013

Southampton/Sydney differences - local wildlife

When I went to unlock the shed last weekend, I found this guy had set up residence in and around the padlock. Being in the south of England, I just admired the beautiful little critter. If the same thing happens to me once we've moved to Sydney, I think I might respond a little differently!

Monday, 26 August 2013

Portsmouth Kite Festival

This weekend is the Portsmouth Kite Festival, which featured some crazy kites and even crazier kite flying. We made it down for the afternoon and, as well as The Flying Fish, saw quite a few teams flying routines, including a couple of nine kite displays. (The photo below features French team, Cerfs-Volants Folies.)

Highlight of the day had to be the last set, however, which consisted of various quad line kite displays. “Revolution” four-line kites can do ridiculous things in practiced hands, including flying in basically any direction and spinning on the spot. The Japanese pair, Team Karasu, did a couple of very entertaining displays (one to a Captain Scarlet/Thunderbirds medley). The Decorators were also really impressive, with their “Come Together” routine.

Craziest of all, however, was the final 24 kite Mega Fly (below). I’m still not really sure how they managed to keep so many kites up in the air at the same time. Having said that, Carl Wright (I think) from Team Spectrum flying three kites in formation by himself might have been even more impressive!

(There are a few more photos on Google Plus if you want to see some more. You can also read Flying Fish's take on the festival.)

Friday, 23 August 2013

Beyond herbicides for weed control

Reported in last week’s Science News article, The War Against Weeds Down Under, Australian farmers have been getting creative with non-chemical warfare against the weeds that blight their island continent.

Increasingly, weeds are becoming resistant to herbicides and switching to a new herbicide often just results in new resistance after a few years. On top of this, there is generally a progression into nastier chemicals - and more of them - as favoured herbicides lose effectiveness, which is clearly not good for sustainability or the environment.

Australia has particular problems of pest plants with multiple herbicide resistance - one of the worst is a species introduced for sheep feed, Ryegrass - and have been pioneering new versions of more old-school solutions: physical warfare. One of the simplest is just burning the weeds after harvest to destroy their seeds. This is pretty effective - for Ryegrass, at least - but has some disadvantages including loss of nutrients from burning.

An alternative with particular promise is going sheerly physical and grinding weed seeds out of existence. As published in Soil Science last year, Australian farmers and scientists have converted mining equipment called a “cage mill” or “impact crusher” into the “Harrington Seed Destructor”, which is able to destroy a reported 95% of Ryegrass weed seeds. As well as being more effective than burning, all the nutrients from the destroyed chaff is put back into the soil, presumably reducing the need for fertiliser into the bargain.

“Nothing will survive in there…”

Picture from: Walsh MJ, Harrington RB & Powles SB (2012). Harrington Seed Destructor: A New Nonchemical Weed Control Tool for Global Grain Crops. Crop Science 52(3): 1343-1347.

Another advantage of physical destruction over chemical attack is that it seems more difficult for the weeds to fight back. Thanks to the awesome power of Natural Selection, it is probably only a matter of time before resistance evolves to any given herbicide. Whether they could evolve to have seeds small/tough enough to survive the Harrington Seed Destructor is less clear, especially without compromising their competitive advantage. Either way, it’s useful to have another weapon in the arsenal, even if it is a bit pricey at the moment at $A250k. It’s also good to see that future weed management could potentially be effective and environmentally friendly. Hopefully, other countries will follow suit.

Thursday, 22 August 2013

Little Changes: teaching evolution, one rhyme at a time

Today, I was catching up with some old podcasts. One was the Naked Genetics podcast from last January, which featured a book that I had never heard of but sounded rather cute. It’s called Little Changes and was written by Dr Tiffany Taylor from the University of Reading as a way to introduce evolution (by Natural Selection) to under 11s - and their teachers. I’ve not got it - I don’t have any under 11s - but the preview on Amazon looks fun and the illustrations look sweet too.

I won’t reproduce any sample text here as it is all copyrighted but you can “look inside” on Amazon if you are interested. Apart from someone who (ambitiously) got it for their three year old, the customer reviews are good too.

Wednesday, 21 August 2013

Darwin and Wallace at Burlington House

For more on Darwin and Wallace, have a read of today’s guest post on Why Evolution is True by Greg Mayer, Darwin and Wallace at Burlington House. With extensive references and direct quotes from Wallace himself, it makes an interesting read.

The accusations against Darwin are that he ‘stole’ one or more ideas from Wallace, and that the circumstances of the reading and publication of the Linnean Society papers were somehow unethical. Although ostensibly arguing on Wallace’s behalf, these authors must dismiss Wallace’s own accounts (e.g. 1870, 1889, 1905, 1908) of the contributions made by Darwin and himself, and paint Wallace as a victim. But, as his biographer Raby (2001:291) says, “Wallace was not a victim, and he did not see himself as a victim”; to do so “diminishes both Darwin and Wallace.”

Hopefully the conspiracy theorists will now stop diminishing both of these great Victorian scientists and celebrate them both.

Wednesday, 14 August 2013

Wallace was not forgotten and Darwin did not cheat him

A while ago, I watched - and really enjoyed - Bill Bailey’s Jungle Hero about Alfred Russell Wallace, the “co-discover of Natural Selection”. (I’m not sure why, like assassins of American Presidents, Wallace always has his middle name used.) It was an excellent two-part documentary in which Bailey retraces some of the steps of Wallace in his epic and life-changing - in fact, world-changing - expeditions through Borneo and Idonesia that resulted in the publication of his joint paper with Dariwn in 1858, On the Tendency of Species to form Varieties; and on the Perpetuation of Varieties and Species by Natural Means of Selection.

What annoyed me a little, however, was the degree to which the show seemed to buy into two legends about Wallace and his relationship with Darwin: (1) Wallace was forgotten whilst Darwin took all the credit, and (2) Darwin somehow cheated Wallace out his due recognition. As far as I can tell, neither is really the case.

Perhaps I have a twisted view of things as an evolutionary biologist but, even before this year’s activities in honour of the hundred years since his death, Wallace has not been forgotten. He is still lauded as a scientific hero among evolutionary biologists, with several key insights attributed to him. As well as a bunch of species, he has had geographical features named after him, including the Wallace Line and adjoining Wallacea, and is known as “the father of Biogeography”. There is a reason that Darwin is given more credit when it comes to evolution - he did come up with Natural Selection first and as it was the theory was largely ignored until On the Origin of Species was published. (It’s worth reading an interesting and informative post at Why Evolution is True by Greg Mayer, Why is Darwin more famous than Wallace?) But more credit to one does not equate to no credit to the other.

I’ve also never really understood the big deal about the chain of events that resulted in the 1858 joint publication. If, the story goes, if Wallace had only sent his idea direct to publication when he first had it rather than sending it to Darwin then it would have been just the Wallace theory of Natural Selection. (Except that Wallace did not use that term, so it probably would have been called something else.) Perhaps. But, equally, if Darwin had sent his theory for publication when he first had it, Wallace would never have thought of it because it would have already been a solved problem before he even went to Asia. It seems that Wallace is more lucky than unlucky to be heralded the "co-discoverer".

Then there is the even stronger claim that Wallace was not just unlucky, but that Darwin actively did the dirty and cheated him. Apart from the fact that this does not seem to fit with all the evidence that Darwin was an honorable and kind gentleman (included the friendship between Wallace and Darwin), I always thought that if he really wanted to do the dirty on Wallace then some “accident” could easily have befallen the letter.

Having said all that, I’ve not looked into it deeply and have often wondered whether it really was just anti-establishment conspiracy theories or whether there was more to it. I was therefore very interested to read John van Wyhe’s Guardian piece last Friday, Darwin did not cheat Wallace out of his rightful place in history. The title says it all really and you can (and should!) read the article if you are interested to know more - it’s not very long.

The reason why John van Wyhe’s viewpoint is so notable is that he is the founder and chief editor of the both the Darwin Online and Wallace Online websites and has studied the source material in depth. He has also just written a new book about Wallace, “Dispelling the Darkness:Voyage in the Malay Archipelago and the Discovery of Evolution by Wallace and Darwin” - you can read a review in another WEIT post. It looks interesting.

Monday, 12 August 2013

New(ish) Zooniverse Project: Worm Watch Lab

This post is actually about a month out of date but I was reminded of it after some “citizen science” on Dara O’Briain’s Science Club this week. Back in January, I posted about mapping Mars with Planet Four (also following a Dara O’Briain show!) and the Zooniverse team behind it brought out a new project last month, classifying videos of tiny nematode worms in Worm Watch Lab.

I have a bit of a soft spot for the little nematode species, Caenorhabditis elegans, which is used in labs around the world as a model organism. Not only is it cool in its own right - it was the first animal to have its genome sequenced and has had the entirety of its developmental cell lineages mapped - it was the basis of one of my first collaborative projects in Southampton as well as my only joint publication with my wife. As a well characterised model organism with (perhaps) surprising genetic and biochemical similarities to humans, C. elegans worms are a big part of the 3R’s effort in animal research (replacement, refinement and reduction) across British life science.

Worm Watch Lab constitutes one such project in association with the Medical Research Project:

We need the public’s help in observing the behaviour of tiny nematode worms. When you classify on you’re shown a video of a worm wriggling around. The aim of the game is to watch and wait for the worm to lay eggs, and to hit the ‘z’ key when they do. It’s very simple and strangely addictive. By watching these worms lay eggs, you’re helping to collect valuable data about genetics that will assist medical research.

With your classifications we can understand how the brain works and how genes affect behaviour. The idea is that if a gene is involved in a visible behaviour, then mutations that break that gene might lead to detectable behavioural changes. The type of change gives us a hint about what the affected gene might be doing. Although it is small and has far fewer cells than we do, the worm used in these studies (called C. elegans) has almost as many genes as we do! We share a common ancestor with these worms, so many of their genes are closely related to human genes. This presents us with the opportunity to study the function of genes that are important for human brain function in an animal that is easier to handle, great for microscopy and genetics, and has a generation time of only a few days. It’s all quite amazing!

To get started visit and follow the tutorial.

I’ve had a little play and it is quite fun. Not an awful lot of egg-laying but its interesting watching them move as there are clearly behavioural differences between the videos. (I wonder if they will start recording reversals etc. in future.)

Friday, 9 August 2013

Expanding Macbook Air disk space with SD cards

I’ve had my Macbook Air for over a year now (crazy how time flies) and I still love it. The only drawback really is the limited disk space - the price you pay for speedy flash storage. This would not be a problem were it not for the fact that I have accumulated a lot of photos and music over the years - far too much for the 128GB disk space.

Initially, I tried to get around this by having all my music on my MacBook but keeping photos on external media. This had two problems: (1) by the time that Apps etc. are included, iTunes was still cramping my space, and (2) it was inconvenient to keep plugging in external media every time I wanted to play with my photos, which, given their state of disorganisation at the time, was quite a lot! The problem was compounded further by iPhoto, which is an horrendous space-waster but useful with Photostream.

Plan 2 was to move my iTunes library to an external hard drive that I could plug in when syncing my iOS devices but otherwise not really worry about. This freed up lots of space for sorting out photos (though not all of them), which in turn allowed me to clean up and delete most of my iPhoto library in favour of using Picasa, which is altogether much more sensible in the way that it organises (and shares) pictures.

The problem with Plan 2, however, was that it made it really incovenient to listen to music/podcasts etc. and even to manipulate playlists and things if I was not entirely stably situated - not to mention the use of a USB port keeping the drive attached.

The obvious solution, which I had considered for a while but delayed due to cost, was to get an SD card big enough for my iTunes library and use this instead. As the picture above shows, SD cards do still stick out a little and so they do not provide the perfect permanent disk expansion that I first envisaged when I got my MacBook - I tried out a 32GB for a while - but they are considerably more securely attached than a portable hard drive, much easier to carry around and free up the USB ports for other things. I got myself a SanDisk Ultra 64GB SDXC card for about £40 and moved my iTunes library onto it. This is clearly more per GB than an external hard drive but pretty reasonable for the convenience - and it is convenient. Access times are pretty speedy and you can go for the Extreme SDXC card if such things worry you.

So far, it’s working out really well and I can heartily recommend it if you have similar Macbook Air storage issues. My only real fear is misplacing the SD card because it is so much smaller than a portable hard drive! As an added bonus, the Mac mini that I have just ordered for work has an SD slot too, so I’ll be able to take my whole library to work if I want to without having to use up valuable HD space on such frivolities! (In fact, it's worked so well that I’ve also ordered a 128GB card for working on both computers, which seems much more convenient (and faster) than using USB devices for the same purpose.)

Happy World Cat Day!

Apparently, today is World Cat Day. So here are some gratuitous cat photos to celebrate!

And, of course, the ubiquitous cats in boxes…

h/t WEIT.

Tuesday, 6 August 2013

Starbucks versus Costa iced latte - the key is not to blend it

This summer has been a scorcher and my coffee habits have been appropriately adjusted to increase the number of cold coffee drinks. I had dabbled in the odd frappuccino in the past but this year I really discovered the joys of the iced latte. The problem with blended drinks is that they get very watery at the end, whereas a lovely latte on ice retains all its coffee goodness. For that reason, a Starbucks iced latte is (for me) cold coffee perfection!

Costa, on the other hand, do something very weird. It all starts out like it’s going to be a regular iced latte, albeit with a artistic flourish of letting the coffee seep down into the milk rather than mixing it. (Why?) But then they do something really weird, and blend some of it up somehow. I’m not exactly sure what they do but you end up with a load of foamy stuff floating on top of your latte that (a) somehow seems to contain a lot of the coffee, and (b) is really hard to suck up the straw. (It just seems to float on top.)

I recommend sticking to Starbucks!