Older blog entries for danstowell (starting at number 60)

A great question about birdsong

There are many mysteries about birdsong, some obvious and some not. This one hadn't occurred to me, but it's a great question:

"Why does a sedge wren with 300-400 different songs take days to reveal them, as if he didn't care whether anybody knew how many songs he was capable of singing?"

(From Nature's Music: The Science of Birdsong, chapter 4.)

Syndicated 2013-08-07 05:52:32 (Updated 2013-08-07 05:52:58) from Dan Stowell

Open access: green does NOT mean CC-BY-NC

There's been a fair amount of confusion around the new UK guidelines that mean we have to publish our research articles as open access. One of the urban myths that has sprung up is rather curious, and it's the idea that if you choose to publish under the green route, you're supposed to publish under a Creative Commons NonCommercial licence. This is not true. (It's just one of the many licences that would work.) But I have heard it from heads of research groups, I've heard it from library staff. We need to be clear!

(BACKGROUND: "Green" and "gold" are terms often used to describe two different sorts of open access, and they're also the two terms used by Research Councils UK [RCUK] to tell us what to do. "Gold" means that the publisher has to provide the article freely to everyone, rather than charging people for access; in lieu of that, most publishers will charge us researchers in order to publish under gold. "Green" means the publisher doesn't have to do anything, except to agree that the author can put a copy of the paper on their website or in an online repository. So, both enable free access to research, but in different ways, and with different costs and benefits.)

Now, in RCUK official guidance we have the option of green or gold publication. If we go the gold route, RCUK requires a specific licence: Creative Commons Attribution, aka CC-BY. If we go the green route, the RCUK policy doesn't exactly specify the licence, but it does say that it has to be published "without restriction on non‐commercial re‐use". Pause for a second to unpick the triple-negative in that turn of phrase...

The reason for that wording is that RCUK didn't want the publishers to "lock down" green OA by saying things like "you can self-archive the paper, but only under these strict terms and conditions which don't actually let people get the benefits of OA". For whatever reasons, they decided that it was OK for publishers to forbid commercial reuse (perhaps to prevent other publishers profiting from simply re-publishing?), but they would draw the line and say they weren't allowed to forbid non-commercial reuse. However, the policy doesn't require any particular licence.

But we might be tempted to ask, well, fine, but what is an example of a licence that would satisfy these RCUK rules? Well, Mark Thorley of RCUK gave an example of this: the Creative Commons Attribution-NonCommercial or CC-BY-NC would be fine. It's an appropriate example because it forbids commercial reuse but allows non-commercial reuse. OK so far?

Unfortunately, when you look at Mark Thorley's slides on the RCUK website, that's not exactly what is conveyed. If you go to slide 10 it says:

"Green (at least post print) with a maximum embargo period of 6(12) months, and CC-BY-NC"

OK that's pretty clear isn't it? It doesn't say that CC-BY-NC is just an example, it basically says CC-BY-NC is required. This is not what Thorley meant. I raised this issue on a mailing list, and he clarified the position:

"The policy does not define a specific licence for green deposit, provided non-commercial re-use such as text and data mining is supported. In presentations I say that this 'equates to CC-BY-NC', however, we do not specifically require CC-BY-NC. This is because some publishers, such as Nature, offer specific deposit licences which meet the requirements of the policy. However [...] this is the minimum requirement. So if authors are able and willing to use more open licences, such as CC-BY, we would encourage this. The more open the licence, the less ambiguities and barriers there are to re-use of repository content."

This clarification is welcome. But unfortunately it was provided in a reply on a mailing list discussion, and the RCUK website itself doesn't provide this clarification, so the misunderstanding is bound to run and run. This week I heard it repeated in an Open Access forum, and I hope that if you've read this far you'll help stop this misconception getting out of hand!

Syndicated 2013-07-17 10:43:33 (Updated 2013-07-17 11:02:52) from Dan Stowell

Birds of Manhattan

It doesn't surprose me that the trees still grow in Manhattan. After all they're captives. They still grow, because life always tries to grow.

What amazes me is the birds cheeping away. You can fly! You must have visited quieter, calmer places? Here in the city no-one can hear you sing. The machinations of the city drown everything out beyond a couple of metres - the cars, the subway, the helicopters. Not a place for easy singing.

Do you like it here? Do you have a good territory? All this human noise, is it a curse or an irrelevance? Or maybe, is it all worth it for the central park?

Syndicated 2013-06-01 11:43:05 from Dan Stowell

An app for a conference - with a surprising set of features

I'm going to a conference next week, and the conference invites me to "Download the app!" Well, OK, you think, maybe a bit of overkill, but it would be useful to have an app with schedules etc. Here is the app listed on google play.

Oh and here's a list (abbreviated) of permissions that the app requires:

"""This application has access to the following:

  • Your precise location (GPS and network-based)
  • Full network access
  • Connect and disconnect from Wi-Fi - Allows the app to connect to and disconnect from Wi-Fi access points and to make changes to device configuration for Wi-Fi networks.
  • Read calendar events plus confidential information
  • Add or modify calendar events and send email to guests without owners' knowledge
  • Read phone status and identity
  • Camera - take pictures and videos. This permission allows the app to use the camera at any time without your confirmation.
  • Modify your contacts - Allows the app to modify the data about your contacts stored on your device, including the frequency with which you've called, emailed, or communicated in other ways with specific contacts. This permission allows apps to delete contact data.
  • Read your contacts - Allows the app to read data about your contacts stored on your device, including the frequency with which you've called, emailed, or communicated in other ways with specific individuals. This permission allows apps to save your contact data, and malicious apps may share contact data without your knowledge.
  • Read call log - Allows the app to read your device's call log, including data about incoming and outgoing calls. This permission allows apps to save your call log data, and malicious apps may share call log data without your knowledge.
  • Write call log - Allows the app to modify your device's call log, including data about incoming and outgoing calls. Malicious apps may use this to erase or modify your call log.
  • Run at start-up.


Now tell me, what fraction of those permissions should a conference-information app legitimately use? (I've edited out some of the mundane ones.) Should ANYONE install this on their phone/tablet?

Syndicated 2013-05-20 00:06:07 (Updated 2013-05-20 00:06:25) from Dan Stowell

20 May 2013 (updated 4 Jun 2013 at 15:23 UTC) »

Boulder Colorado IPAs

Not only is Boulder Colorado the Hebden Bridge of the USA (I'm told it's "where all the hippies went"), but it also has a really impressive amount of craft beer. Following a tip-off (thanks Bob), tonight I went to sample a few IPAs in the Mountain Sun pub. For the education of no-one except myself, here are my tasting notes - first in visual form:

then in words:

  • Illusion Dweller IPA: described as "biscuity" and "english-style" but still with a hoppy sour tang at the back of the mouth, very clear and nice. Tastes like a modern American IPA to me, doesn't remind me of England - but a great balance of tang and biscuit, super drinkable.
  • Vagabond IPA: almost a pure grapefruit hit, reminds me of that Metal Man which I loved in Ireland.
  • FYIPA: "piney" is the main impression. However it's not got the sharp piney poke of Becherovka which I really like. Maybe it's unfair to compare a beer against a spirit, but Becherovka integrates its alcohol flavour in with the pine, whereas FYIPA has a kinda noticeable alcohol taste separate from the pine, which is a bit of a shame IMHO.
  • Hop Vivant: yes it's a hoppy IPA, but more balanced, multivalent, colourful than the others I'm tasting tonight. Not a session beer, a bit too rich for that.
  • Cat Burglar: black IPAs are really confusing. Erm. I like it less than the Thornbridge Raven, but I don't know why.

Not to look a gift-horse in the mouth, these are all lovely beers, very well served, but when they're sitting next to each other I have to compare them. Hence the ups and downs in the notes. The winner for me is definitely the Illusion Dweller. The ratings over at ratebeer tell almost the opposite story for some reason, with Illusion Dweller the only one not scoring ninety-something. Who knows what to make of that.

Updates - more beer I've tried from Mountain Sun:

  • Java Porter - a lovely perky porter, coffee flavours as the name suggests but not too exaggerated.

More beer from other breweries:

  • 90 Shilling by Odell - I was not into this at all. Too caramely I think?
  • Old Elk Brown Ale by Walnut Brewery - really really straightforward brown ale. Not too sweet which is good.
  • 1123 IPA by Walnut Brewery - really very nice IPA, perky and floral, assertive yet balanced.
  • Hoppy Knight by Twisted Pine - this black IPA is much nicer than the Cat Burglar, IMHO. It does remind me of Thornbridge Raven, both of them having a kind of clarity to the taste that other dark things like Guinness have (though they don't taste like Guinness! much hoppier etc etc etc). This has a very refreshing taste up-front, with a clearly-separated coffee flavour at the end - neat! And not weird either.

My faves, I think, are 1123, Hoppy Knight, Illusion Dweller.

Syndicated 2013-05-19 23:13:49 (Updated 2013-06-04 11:04:46) from Dan Stowell

Haggis and orange salad

Haggis and orange - why of course! This salad serves 2. The red wine vinegar really helps the flavours marry, and the beansprouts add a nice bit of crunch - if you're being posh you could also/instead add some pomegranate seeds.

  • 1 portion of cooked haggis
  • 1 medium orange
  • 1 generous handful rocket
  • 1 very small handful beansprouts (probably no more than 10 sprouts)
  • 3 tsp olive oil, approx
  • 2.5 tsp red wine vinegar

In a large bowl, break the haggis into small pieces with a spoon. The haggis we had was a little dry so I also added a dab of oil at this point.

Now prepare the orange. First, with a zester, scrape off about 1/4 of the orange's zest, into the haggis. Then, with a knife slice the top and bottom off the orange, then stand the orange on a chopping board and slice off the rest of the peel. Then cut the orange into segments, and cut each segment in two, so you have little bite-sized bits. Pick out any pips. Add the orange pieces to the haggis, and also tip in the small amount of juice from the chopping board.

Add the rocket and the beansprouts, and mix. Add the olive oil and red wine vinegar and mix it to dress evenly. You won't need to season much, since the haggis brings a lot of seasoning.

Serve with toast.

Syndicated 2013-05-12 14:29:31 (Updated 2013-05-12 14:33:42) from Dan Stowell

python: combining interpolation with heatmaps

I saw Brandon Mechtley's splmap which is for plotting sound-pressure measurements on a map. He mentioned a problem: the default "heatmap" rendering you get in google maps is really a density estimate which combines the density of the points with their values. "I need to find a way to average rather than add" he says.

Just playing with this, here's my take on the situation. You don't average the values, you create some kind of interpolated overall map, but separately you also use the density of datapoints to decide how confident you are in your estimate at various points on the map. Python code is here and here's an example plot:

Dataviz folks might already have a name for this...

Syndicated 2013-04-16 10:33:02 (Updated 2013-04-16 10:42:43) from Dan Stowell

16 Apr 2013 (updated 17 Apr 2013 at 17:13 UTC) »

Sandwich of the week

The Little Woodford Cafe does a nice line in sandwiches. They often have a Sandwich Of The Week which adds variety. Here I'm just noting down some good ones they've done, for the purposes of sandwich-filling-inspiration:

  • Salmon, freshly-poached, with cucumber and a homemade tartare sauce
  • Tuna fiorentina (with boiled egg and spinach)
  • Christmas special (turkey, sausage, cranberry sauce, stuffing - oh my)

Syndicated 2013-04-16 09:14:36 (Updated 2013-04-17 12:59:53) from Dan Stowell

9 Apr 2013 (updated 10 Apr 2013 at 07:14 UTC) »

How many persons under trains on the tube, so far in 2013?

There seem to have been two separate person under a train incidents on the London underground today. I know nothing about either of them, but there was also one last Friday - and the cluster of events, well, first it made me feel awful, but then I wondered if there were any stats to help understand how common these events are.

Well yes there are. For example you can see some old-ish data for 1998-2005 here. I couldn't find any more recent data - you could file an FOI request if you like. BUT - TfL's twitter feeds tell the public whenever travel is disrupted. And since they use the standard form of words, it's quite simple to go through and find all occurrences, for example, for 2013 so far. So here they are:


Fifteen in total, so far for 2013. Roughly one per week. This is not the same type of data as the old data I linked above (it includes fatalities and nonfatalities, I expect, whereas the old data is just for the former).

You can do some basic statistical modelling on this: if you assume these are independent events and model them with a Poisson distribution, then you find the probability of seeing two-or-more incidents on one day is 1.04% - which essentially means there's nothing particularly weird about seeing it happen at some point over the past three-and-a-bit months.

Syndicated 2013-04-09 17:36:27 (Updated 2013-04-10 02:19:44) from Dan Stowell

29 Mar 2013 (updated 3 Apr 2013 at 13:11 UTC) »

Clementine cake

This clementine cake is lovely and juicy, with a nice sweet chewiness to the crust. And look at that crumb:

When I took the next photo I accidentally left the flash on - but it does show off some of the bright orange colouring in the cake:

It's an easy cake to make. Cos of the juiciness it doesn't keep for that long... but that's no problem. If you have a pressure-cooker it really speeds up the bit where you cook the clementines (or tangerines, or whatever).


  • 4-5 clementines (350--375g)
  • 6 eggs
  • 225 g sugar
  • 225 g ground almonds
  • 25 g flaked almonds
  • 3 or 4 cloves
  • 1 heaped tsp baking powder

Put the clementines (WHOLE AND UNPEELED, but without any stalky bits) into the pressure cooker, or a big pan with a lid. Add cold water to cover. If it's a pressure cooker, put the lid on, bring it up to pressure, and cook for 15-20 mins. If it's a normal pan, simmer gently (covered) for 2 hours.

Then turn off the heat, release the pressure, and let the clems and the water cool down. You have to let them cool before the next step, so the clementines don't scramble the eggs! Here's a picture of our clems cooling on the back step.

Put the clems into a food processor and blend them up. (It's handy to keep some of their cooking water in case the mixture needs a bit more liquid, but in my experience it's generally not needed.)

Crush the cloves in a pestle and mortar. Add the flaked almonds and crush them too. No need to crush the almonds too fine - the point of the flaked almonds is to give an occasional bit of crunch to the cake.

In a mixing bowl, whisk the eggs, then mix in the clementines. Then add everything else, and mix it up.

Pour into a 21cm springform tin (greased, and with baking paper in the bottom) and bake at 180 degrees (gas mark 4 or 5) for about an hour. Cover the cake loosely with greaseproof paper or a tray, for the last 20 minutes or so.

Take out of the oven and let it sit in the tin for 10--20 minutes or so, before turning it out onto a wire rack to cool properly.

Syndicated 2013-03-29 16:18:11 (Updated 2013-04-03 09:07:24) from Dan Stowell

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