Posts on Polypompholyx

Pythogenies

Mon, 23 Mar 2020 11:01:25 +0000

I had to teach myself a bit of Python recently, so decided to do it by implementing this parse_phylogeny.py thing (it’s uploaded here as a text file). It takes a nice intuitive mark-down for phylogenetic trees (below) and spits out a Newick file (-f nwk), or a Wikipedia clade format (-f wp). It’s not amazing (hey, it was my first attempt at Python in anger) and I know there’s a bunch of repetitious stuff in the functions that could be lifted out, but whatever. Maybe you’ll find a use for it.

Concrete jungle

Wed, 02 Jan 2019 13:14:25 +0000

The Barbican is a sprawling concrete brutality as apt to divide opinion as Marmite or skinny jeans. Built in the 60s and 70s as a housing estate and cultural centre on a vast bomb-site in the City of London, it does not sound like a promising place to go botanising, but after the fire-weed was concreted over, other plants moved in…

Fleabane (Erigeron karvinskianus) growing on a bastion that formed part of the original London Wall

Aside from the fleabane gussying up the scheduled monuments, and the friendly rivalry of the residents’ window-boxes, the Barbican also houses a large conservatory containing more than 2000 species of plant. It is open to the public most Sundays.

Moosgartenrückreisefreude

Mon, 22 Jan 2018 12:33:14 +0000

When we went to the Berlin Botanischer Garten in 2005, we saw some pretty cool stuff, including a flowering Welwitschia and some fantastic tree ferns. However, like every other botanical garden I’ve ever visited, mosses , hornworts and liverworts were effectively ignored, or - worse - treated as dreary also-rans at the start of one of those ’evolution houses’ so beloved of curators without the wit to find something accurate to do with their cycads.

Here be dragons

Sun, 14 Jan 2018 16:49:23 +0000

Previously on Bagging Botanic Gardens: Maspalomas et al., Wisley, Brussels, Down House, Much Else Besides.

The minute I found out there was a botanic garden in the north of Gran Canaria as well, a return visit became inevitable.

The Jardín Botánico Canario “Viera y Clavijo” is in the outskirts of Las Palmas, and is much larger than its Maspaloman sibling. As well as showcasing a Canary Island pine woodland, it also has a impressive path carved into the side of the cliff that overlooks the site. This affords splendid views across the gardens - assuming you can stomach them.

Hairy kneecap

Fri, 22 Dec 2017 11:17:25 +0000

Our microscopy practical always turns up something new, which is the main reason I enjoy it. This year it was a ciliate called Euplotes patella. This kneecap-shaped critter is a single-celled organism masquerading as a tiny animal. The appendages that look like long hairs or legs are bundles of extra-long cilia called cirri, which it uses to scuttle about like a microscopic woodlouse. The cirri around the front of the cell (top of the image below) are also used to sweep food into a region of its cell membrane that acts like a mouth. Euplotes will eat bacteria, yeast, algae, pretty much anything it can fit into its mouth really: much like me at Christmas.

Stems all the way down

Fri, 07 Jul 2017 15:14:03 +0000

In the days when potted plants were more than just disposable land-filler, my Nan would try to force her wizened poinsettia to flower by sticking it into a bin-liner with some apples every night from October until December. Sum total of flowers she ever saw: zero. Ho hum. But how many poinsettia flowers can you see in the picture below?

Poinsettia (Euphorbia pulcherrima)

If you’re wondering whether you can include the ones that are partly off-screen, you are asking the wrong question. There are many hundreds of flowers here, not six or ten. The red leafy-looking things you might have been cruelly mislead into thinking were petals are actually brightly coloured leaves. The flowers themselves are found in the tiny yellow-green blobs in the middle…

More botanical baggings

Thu, 13 Apr 2017 14:02:08 +0000

Previously on Bagging Botanic Gardens: Wisley, Brussels, Down House, Much Else Besides.

Eden Project

An old clay pit in Cornwall doesn’t sound like the most promising place to find a tropical forest, but the alleged proximity of the entrance to Magrathea might go some way to explaining it. The Eden Project’s bubble-wrap domes are now such a familiar part of the Cornish tourist board’s marketing that you’re not really expecting them to be as impressive as they actually are in the flesh:

Modular origami

Wed, 04 Jan 2017 16:58:25 +0000

A few months ago, I went to a creative origami lunchtime session organised by some lovely people at $WORK. I’d done origami a bit when I was younger, but mostly just frogs and cranes, which have since helped me while away the hours when invigilating exams. However, at this lunchtime session I was shown how to make modular origami. This involves making lots of (generally quite simple) origami parts, and then slotting them together to make larger structures.

Organism of the week #31 – Tardigrades

Thu, 19 May 2016 15:25:28 +0000

Tardigrades make me squee. These little relatives of the arthropods and velvet-worms are found in the water around mosses, and they are quite easy to find if you have a cheap microscope and a little patience. Like spiders, they have eight legs, but unlike the legs of a spider, they’re plump and stumpy, and end in the little ‘fingers’ you can just about make out in the photos below. Ignoring the excess of legs, it’s easy to see why they’re sometimes called water-bears.

Organism of the week #30 – Sticky situation

Thu, 19 May 2016 15:11:17 +0000

All science is either physics or stamp-collecting.

This rather mean-spirited dismissal of chemistry and biology as “stamp-collecting” is attributed to Ernest Rutherford, the physicist usually (not wholly fairly) credited with discovering the atomic nucleus and the proton.

Shortly after Rutherford’s death in 1937, particle physicists discovered the muon, pi mesons, kaons, the electron neutrino, the anti-proton, the lambda baryon, xi cascades, and sigma baryons. It took physicists the thirty years following Rutherford’s death to make sense of this veritable album of subatomic stamps.

Adaptations evolve in populations

Thu, 05 May 2016 18:35:46 +0000

Organisms evolve adaptations to increase their fitness

There are few ideas in science that explain as much of the natural world as does natural selection, but there are few ideas in science that are more frequently misunderstood.

Often the misunderstandings are deliberate or disingenuous, but I’ve seen quotes like the one above even in undergraduate essays and popular science books.

Recursion

Fri, 08 Jan 2016 12:28:07 +0000

Recursion [CC-BY-SA-3.0 Steve Cook, Andreas Thomson, Frank Vinzent]

Bark

Thu, 07 Jan 2016 11:53:00 +0000

Top left to bottom right: Betula utilis var. jacquemontii, Pinus sylvestris, Prunus serrula, Pinus pinaster, Quercus suber, Araucaria araucana, Metasequoia glyptostroboides, Pinus bungeana, Betula ermanii × pubescens, Pinus nigra ssp. laricio, Betula albosinensis cv. Red Panda, Platanus × acerifolia.

Wisley in Winter

Wed, 06 Jan 2016 16:43:57 +0000

It’s not really a botanic garden, but the Royal Horticultural Society’s gardens at Wisley is near enough as makes no difference. We visited in what should have been the dead of winter, but which in reality was this weird sprautumn mash-up that is now December in the UK. The heather garden was particularly pretty, despite the wind:

RHS Wisley heather garden

At £12, the entry price is a bit steep: even Kew does reduced rates when most of the plants are underground, sleeping off the summer’s excesses.

Imposter

Wed, 06 Jan 2016 16:02:48 +0000

Most years the pond-water microscopy practical throws up an exciting ciliate (or two, or three), but this year, the only ones we saw were duplicates, or too bloody fast to photograph. Ho hum.

So this year you’ll have to make do with an imposter. It’s still got cilia, but it is not a ciliate, and although it’s no bigger than a single-celled organism, it is in fact a full-blown multicellular animal:

Bagging botanical Brussels

Tue, 22 Dec 2015 14:38:08 +0000

The last time we went to Brussels, I got terribly excited that the hotel we were staying in was right next door to the Botanical Garden of Brussels. Unfortunately - as we discovered in short order - at some point in the 1930s the plants had mostly been shipped off elsewhere, leaving the garden not very botanical, and Dr Cook not very impressed.

Organism of the week #29 – Galling

Tue, 06 Oct 2015 10:33:53 +0000

Today is the first day of the new (academic) year at $WORK, but - aside from a couple of intro lectures - this is the calm before the real storm, which arrives in the form of a deluge of biological chemistry in November. If you’re lucky, you’ll get a few mugshots of some weird ciliate or other around then, otherwise, expect tumbleweed until the new (calendar) year…

Organism of the week #28 - Fractal art

Thu, 17 Sep 2015 12:49:05 +0000

Flowers are essentially tarts. Prostitutes for the bees. (Uncle Monty, Withnail and I)

Our tiny garden has only passing acquaintance with sunshine, so about the only plants that really thrive in its dingy clutches are shade-loving ferns. This Japanese painted fern is my current favourite: who needs flowers anyway, when leaves look like this?

Japanese painted fern (Athyrium niponicum cv. Pictum)

The colour is spectacular, but I also love the shape of the leaves. I have a rabbit’s-foot fern on my windowsill at $WORK, which branches not once, not twice, not thrice, but fwice, with each leaflet at each level looking very much like a miniaturised version of the whole leaf:

Living dangerously

Sun, 06 Sep 2015 12:19:58 +0000

Towards the end of the last millennium, I spent a lot of time befriending arsenic. The last two years of my PhD involved measuring how much iodine had fallen off a chemical used as a wood preservative day-in, day-out, and arsenic trioxide was the most exciting component of an otherwise excruciatingly dull test for iodide ions.

My little bottles of arsenic warned me to beware of pirates…

Organism of the week #27 - Alien haemorrhoids

Sun, 06 Sep 2015 11:31:41 +0000

A quickie this week: magnolia fruit look like something from another planet.

Magnolia ×soulangeana fruit

Statistical power

Wed, 26 Aug 2015 15:35:13 +0000

In a recent(ish) post, we saw that if a fair coin is flipped 30 times, the probability it will give us 10 or fewer heads is less than 5% (4.937% to be pointlessly precise). Fisher quantified this using the p value of a data set: the probability of obtaining data (or a test statistic based on those data) at least as extreme as that actually observed, assuming that the null hypothesis is true.

Organism of the week #26 - Oxymoron

Sun, 23 Aug 2015 15:01:38 +0000

Plants can have some very odd names. Bears are not renowned for their trousers, and this spiky sod is the last thing anyone would want to make a pair of trousers from, but “bear’s breeches” it is. Even its Latin name is odd: acanthus means spiny, and mollis means smooth; a literal oxymoron.

Acanthus mollis

It might not look very familiar, but it may be the most quietly famous plant in the world, having been immortalised in stone through much of the world for over 2000 years.

Organism of the week #25 - Bull headed

Mon, 17 Aug 2015 09:18:47 +0000

This is another of the things we have found down a microscope in one of our undergraduate practicals, but for once it’s not a ciliate.

Bucephalus minimus

This is the larva of a parasitic fluke called Bucephalus, which is the Greek for ‘bull headed’. It’s appropriate for this fluke not because it looks like Alexander the Great’s horse, but because its two “tails” (furcae) look like horns when they are fully extended.

A graph to show

Mon, 10 Aug 2015 15:13:19 +0000

I’ve never been sure where “a graph to show…” comes from. As far as I can tell, A-level specifications don’t use or specify this wording, and you wouldn’t typically see it in a figure legend in a scientific paper. But if you ask first-year students to put a title on a graph without any further guidance, almost every one of them will default to this mindless boilerplate.

Organism of the week #24 - Danse Macabre

Mon, 10 Aug 2015 10:34:01 +0000

For three centuries, the Black Death was routinely epidemic in London. The first outbreak - in 1348 - probably killed half the population of England; the last outbreak - from 1665 to 1666 - probably killed a quarter of the population of London.

In 1665, Isleworth was a small village several hours’ walk (or row) from London proper, but the Great Plague found its way there anyway. As in many places, so many died that digging individual graves became impractical, so instead, the bodies were interred in communal plague pits.

Organism of the week #23 – Rattled

Mon, 03 Aug 2015 10:32:14 +0000

My annual summer ritual to stave off death for one more year involves running round Kensington Gardens and Hyde Park, which are situated conveniently close to $WORK.

I lumbered merry as a shroud.

That aches and sweats o’er trails and heights,

When all at once I saw a crowd,

A host, of golden parasites:

Yellow rattle growing in the north of Kensington Gardens (Rhinanthus minor)

Yellow rattle is a member of the broomrape family, which are almost all parasites of other plants. Broomrape itself is completely parasitic, and obtains all the sugars and other nutrients it needs to grow from other plants.

Phage vs. host

Fri, 10 Jul 2015 10:21:09 +0000

For a recent schools’ outreach day, I put together a card-game based around the arms-races that develop between bacterial hosts and their viruses (bacteriophages). It’s mostly just a bit of fun, but if anyone finds it useful or can suggest improvements (or just make them! I release this under a CC-BY-SA-4.0 license) I’d be happy to hear them.

Stentorian

Tue, 16 Dec 2014 10:13:47 +0000

We had the annual “looking at muck down a microscope” practical last week. As usual, the best thing we saw was a ciliate in some pond water, in this case a little trumpet animalcule:

Stentor sp. The green bits are either symbiotic algae, or dinner, possibly a bit of both.

Previous winners: Vorticella and Lacrymaria. The Ciliata really are the phylum that keeps on giving.

A queen's Christmas message

Mon, 15 Dec 2014 16:40:50 +0000

Well, at least 2:8 is plausible.

2:1 And it came to pass 10 years after the death of Herod the Great, that there went out a decree from Caesar Augustus that all the world - except those irrelevant bits that the Romans hadn’t conquered - should be taxed.

2:2 (And this taxing was first made when Quirinius was governor of Syria during what - by a large stretch of the imagination - may have been his second term, his first (entirely undocumented) term having been in 4 BCE, during which an (entirely undocumented) census almost certainly didn’t take place either.)

Organism of the week #22 - Faking it and making it

Wed, 02 Jul 2014 11:39:50 +0000

Nettles have a rather unhappy reputation as bringer of painful welts, and - at this time of year - dribbling noses too. The welts are probably caused by histamine, and the pain by oxalic and tartaric acids, which the nettle injects into your skin through the tiny brittle hairs that cover its stems and leaves. If you’re stung badly, the pain can last for several hours.

Half a life

Fri, 20 Jun 2014 09:36:16 +0000

As of today, I will have spent precisely half of my life at $PLACE_OF_WORK.

I first arrived at what would become my workplace as a badly coiffured youth in 1995 to do a biology degree. South Kensington seemed a great improvement over Croydon, where I had endured my previous 18 years: there was a refreshing absence of casual street violence, and a greatly improved proximity to the grubby delights of Soho. At that time, my Hall of Residence was directly above the first-year lecture theatre, and in the same building as the Students’ Union. Despite this tempting proximity to cheap vodka - and even cheaper dates - I somehow managed to attend almost every lecture of my first year, aside from a week (a week!) of lectures on algae, which I traded for bossing Munchkins about in the Questor’s Theatre in Ealing. I met my personal tutor at least twice, survived two under-catered field-trips to somewhere, somewhere in a field in ~~Hampshire~~Berkshire, and made friends whom I treasure to this day.

Organism of the week #21 – Flying machines

Wed, 04 Jun 2014 10:41:33 +0000

It is frequently, and largely accurately, said that an area of Amazon rainforest the size of Wales is deforested every year. Horrendous though this statistic is, it’s worth remembering that the UK deforested an area at least the size of Wales (including most of the area commonly known as “Wales”) before anyone started keeping notes.

Bagging botanic gardens

Wed, 23 Apr 2014 11:55:01 +0000

I’m not sure whether bagging botanical gardens is better or worse than bagging Munros, Michelin stars or the numbers off of rolling stock, but it keeps me off the streets…

This Gunnera at Edinburgh makes me look even more like a lawn-ornament

London (Kew)

Just ten stops down the District Line from $WORK lies the Royal Botanic Gardens Kew. The gardens have three enormous glasshouses, a number of smaller glasshouses, and 121 hectares of trees, beds and desperately awful architecture to explore. Unfortunately, it also has an entry fee (for non-concession adults) of £14.50, which is a little steep, and possibly one of the reasons that disappointingly few of my students seem to have visited it, despite its proximity.

Organism of the week #20 - Don't point that thing at me

Thu, 06 Mar 2014 08:56:50 +0000

It’s amazing how informative an anus can be.

Take this sea urchin. The orange pucker in the middle of the spines is its “around-the-bum”, although zoologists would insist on writing that in Greek as “periproct”. The bright orange ring-piece is characteristic of this species, and marks it out as Diadema setosum, rather than any of the less rectally blessed species of Diadema.

Nonlinear regression

Mon, 03 Mar 2014 09:00:42 +0000

Nonlinear regression is used to see whether one continuous variable is correlated with another continuous variable, but in a nonlinear way, i.e. when a set of x vs. y data you plan to collect do not form a straight line, but do fall on a curve that can be modelled in some sensible way by a known equation, e.g.

(v = \frac{ v_{max} \cdot [S] }{ K_M + [S] })

Analysis of variance: ANOVA (2 way)

Mon, 24 Feb 2014 09:00:37 +0000

The technique for a one-way ANOVA can be extended to situations where there is more than one factor, or - indeed - where there are several factors with several levels each, which may have synergistic or antagonistic effects on each other.

In the models we have seen so far (linear regression, one-way ANOVA) all we have really done is tested the difference between a null model ("y is a constant", “y=y̅”) and a single alternative model ("y varies by group" or “y=a+bx”) using an F test. However, in two-way ANOVA there are several possible models, and we will probably need to proceed through some model simplification from a complex model to a minimally adequate model.

Analysis of variance: ANOVA (1 way)

Mon, 24 Feb 2014 09:00:36 +0000

Analysis of variance is the technique to use when you might otherwise be considering a large number of pairwise F and t tests, i.e. where you want to know whether a factor with more than 2 levels is a useful predictor of a dependent variable.

For example, cuckoo_eggs.csv contains data on the length of cuckoo eggs laid into different host species, the (meadow) pipit, the (reed) warbler, and the wren.

Comparison of expected and observed count data: the χ² test

Mon, 17 Feb 2014 09:00:40 +0000

A χ² test is used to measure the discrepancy between the observed and expected values of count data.

The dependent data must - by definition - be count data.
If there are independent variables, they must be categorical.

The test statistic derived from the two data sets is called χ², and it is defined as the square of the discrepancy between the observed and expected value of a count variable divided by the expected value.

Correlation of data: linear regression

Mon, 10 Feb 2014 09:00:39 +0000

Linear regression is used to see whether one continuous variable is correlated with another continuous variable in a linear way, i.e. can the dependent variable y be modelled with a straight-line response to changes in the independent covariate x:

(y = a + bx + \epsilon)

Here b is the estimated slope of the best-fit line (a.k.a. gradient, often written m), a is its y-intercept (often written c), and ϵ is the residual error. If the x and y data are perfectly correlated, then ϵ=0 for each and every x,y pair in the in the data set; however, this is extremely unlikely to occur in real-world data.

Statistical testing

Mon, 03 Feb 2014 09:00:44 +0000

If you want a random yes/no answer to a question, like “who should kick-off this football match?” it’s very common to entrust the decision to the flip of a coin, on the assumption that the coin doesn’t care which side gets the advantage.

But what if that trust is misplaced? What if the coin gives the answer “tails - your opponent kicks-off” more often than “heads - you kick-off”, and so gives the advantage to your opponent more often than to you? And, most importantly, how could you tell if the coin is biased before you entrust your decision-making to it?

Comparison of means: the t test

Mon, 03 Feb 2014 09:00:37 +0000

A t test is used to compare the means of two data sets, and it relies on calculation of a test statistic called t. This statistic is derived from the two data sets and it is defined as the difference between the means of the two data sets, x̅₁ and x̅₂ (or the difference between a mean x̅ and a reference value, x_ref) divided by the pooled standard error of the mean(s).

Comparison of variances: the F test

Mon, 03 Feb 2014 09:00:13 +0000

An F test is used to compare the variances of two data sets:

As it is used to compare variances, the dependent data must - by definition - be numeric.
As it is used to compare two distinct sets of data, these sets represent the two levels of a factor.

The test statistic we use to compare the variances of the two data sets is called F, and it is defined very simply: F is the larger of the two variances divided by the smaller.

Organism of the week #19 – Bird-brained humans

Thu, 30 Jan 2014 14:01:36 +0000

Most people who want to attract birds to their gardens put out bird-seed, or - if they’re really adventurous - mealworms. However, on the East London dockside where I lived until recently, one of the residents strewed the quayside with livers in December last year. Was this was a deliberate ploy to attract carrion crows for bird-on-variety-meat action? I don’t know, but whether or not this was the intention, it was certainly the result.

Descriptive statistics

Mon, 27 Jan 2014 09:00:30 +0000

Statistics can be used to describe a data set, or they can be used to infer how well a model fits a data set. In this post, we’ll look the the former kind of statistics, and how to extract them from R. The remaining posts in this series will mostly deal with statistical tests and modelling.

Descriptive statistics should usually give a measure of the central tendency of a data set (the mean and/or median), and of the variability of the data set (the range, quartiles, variance and/or standard deviation).

Organism of the week #18 – Feeling rotten

Mon, 20 Jan 2014 12:29:24 +0000

It’s been ages since I did one of these, and today’s will not be terribly long or exciting, for the reason that is the very title of this post. Whilst bumbling around in the fridge looking for something bland and bowel-friendly, I chanced upon a lemon that had fallen into a oubliette in the bottom of the salad drawer. Perhaps it’s just the sickness talking, but I found it rather beautiful:

Plotting data

Mon, 20 Jan 2014 09:00:39 +0000

You can plot data using plot(). This can be used in several ways. The simplest is to plot some numeric x-values against some numeric y-values using:

plot( x.variable.vector, y.variable.vector )

For example:

x<-c( 1:10 )
y<-1 + 2*x
plot( x, y )

However, for data you have imported into a data frame, the x and y variables are now named columns in a data frame, rather than separate vectors. To plot data in data frames, there are two options. The first is to use the dollar $ syntax to access the vector of data within the data frame (here sycamore_seeds.csv) by its column name:

Formatting data

Mon, 13 Jan 2014 14:03:50 +0000

Although you will occasionally type data directly into R, more often than not, you will have a spread-sheet containing data which you want to import. R can easily import data from a comma-separated variable (CSV) file. If you open a CSV file using a text-editor, you will see that they look something like this inside (this is dose_response.csv):

C,mu
0.125,0.69
0.25,0.68
0.5,0.687
1,0.63
2,0.467
4,0.252
8,0.091
16,0.021

The first row contains labels for the columns, and the remaining rows contain the data. The pair of labels, and the pairs of data, are each separated by a comma.

Kinds of data

Mon, 13 Jan 2014 10:47:27 +0000

The sort of data you want to analyse in R may come in many forms. You will often be trying to model the interaction of some independent variables (a.k.a. input, predictor or explanatory variables, the things you’d plot on an x axis) to explain the values of some dependent variable (a.k.a. output, outcome or response variable, the thing you’d put on a y axis).

Running R code

Wed, 01 Jan 2014 20:42:33 +0000

The R interpreter is controlled by typing in plain-text commands at its command-line prompt >|. R commands are just text, so you can prepare a chunk of them in a text-editor, and then copy-and-paste them directly into R to run them immediately. Try copying and pasting the line below at the prompt:

print("Hello world")

Lo and behold, R will spit out what you knew it would:

Teardrops of the swan

Wed, 16 Oct 2013 09:24:35 +0000

Last year, the most marvellous thing we saw in the pond-water microscopy practical was a ciliate, and this year the prize goes to that same clade. Ciliates don’t disappoint.

This is Lacrymaria olor, the “teardrop of the swan”. It’s a predator, like the Vorticella from last year, but rather than sitting rooted to the spot, Lacrymaria is an actively swimming hunter, with an enormously extendable proboscis that it uses to capture prey:

The Wason card problem

Wed, 09 Oct 2013 19:09:26 +0000

The Wason card problem is a well-known psychological test that probes how people think about hypothesis testing. The version I use in one of my first-year lectures is shown below. I think the original version used letters and numbers, but I’m a biologist, so obviously I use pictures of dead pets instead of numbers.

We know that each of the four cards shown below has a letter on one side and an animal on the other.
We suspect that if there is a vowel on one side of a card, then there is a mammal on the other. Which card(s) do we need to turn over to determine whether this hypothesis is false?

It’s well worth doing this for real yourself before reading any further:

Organism of the week #17 – Daughter of Ungoliant

Sun, 22 Sep 2013 14:40:32 +0000

I’d never noticed that a garden spider’s third pair of legs is much shorter than the others before.

Araneus diadematus, common European garden spider

Youth of today

Mon, 02 Sep 2013 14:50:28 +0000

One consequence of being an evolutionary dead-end is that I do not get exposed to new cultural touchstones through watching crap children’s telly with offspring I haven’t produced. As an alternative, monitoring the dwindling intersection of history I share with my incoming undergraduates serves the same salutary purpose of reminding me how out-of-touch I am.

The Beloit Mindset is the definitive tool for rubbing the noses of American faculty into time’s unyielding ripsaw, but 2013 is particularly special. This time it’s personal. My incoming first-years were mostly born in 1995 or thereabouts, so - as well as post-dating one of the worst premises for a film by almost a decade - they have also been alive for almost exactly as long as I have been installed at $PLACE_OF_WORK.

Organism of the week #16 - From tiny acorns do mighty oaks grow

Fri, 09 Aug 2013 19:31:43 +0000

There’s something very satisfying about growing plants from seed, and none more so than growing a monster from next-to-nothing:

Sequoiadendron giganteum, eighteen months old

At the moment, this little redwood seedling is just 18 months old. Given 500 years or so, it’s going to get a wee bit bigger:

Somewhat more elderly Sequoia sempervirens in Muir Woods

The seeds of redwoods are absolutely titchy, as you can’t see in the picture, below because the idiot who took the photo forgot to put a scale bar on it. Each seed has a mass of about 5 milligrams.

Enzymes provide alternative routes to product with a lower activation energy

Fri, 09 Aug 2013 16:04:40 +0000

An enzyme lowers the activation energy for a reaction

Like a previous post, the problem here is not so much that this idea is flat-out wrong, but that it’s very prone to misinterpretation.

Text-books often state that an enzyme, or any other catalyst, lowers the activation energy of a reaction.

The activation energy for a reaction (written ∆G^‡ or E_a in most texts) is supposed to be a measure of how energetically two molecules need to collide with one another to react. If the the molecules collide too slowly, the collision won’t be energetic enough to break bonds, and the molecules will leave the collision unchanged. If they collide into one another fast enough, the collision will be energetic enough for a reaction to occur and for product to form.

The wisdom of crowds

Fri, 09 Aug 2013 09:50:31 +0000

I tried this about five years ago, with more or less the inverse of these results. The nerdy grammar fascist bit of me is pleasantly surprised by the improvement, but poor Karl Albert still has some way to go…

[Fischer projection](https://www.google.co.uk/search?q=%22fischer+projection%22&nfpr=1 “Google for “Fischer projection””): About 38,800 results
[Fisher projection](https://www.google.co.uk/search?q=%22fisher+projection%22&nfpr=1 “Google for “Fisher projection””): [sic] About 8,090 results
[Lineweaver Burk](https://www.google.co.uk/search?q=%22Lineweaver+Burk%22&nfpr=1 “Google for “Lineweaver Burk””): About 234,000 results
[Lineweaver Burke](https://www.google.co.uk/search?q=%22Lineweaver+Burke%22&nfpr=1 “Google for “Lineweaver Burke””): [sic] About 28,600 results
[Henderson Hasselbalch](https://www.google.co.uk/search?q=%22Henderson+Hasselbalch%22&nfpr=1 “Google for “Henderson Hasselbalch””): About 168,000 results
[Henderson Hasselbach](https://www.google.co.uk/search?q=%22Henderson+Hasselbach%22&nfpr=1 “Google for “Henderson Hasselbach””): [sic] About About 70,400 results

Organism of the week #15 – Try not to think about the poo

Sun, 28 Jul 2013 12:52:28 +0000

Apologies for the long gap between postings; it’s been exam season at work, and I’ve not had much time to blog.

The garden was buzzing with green-bottles yesterday, thanks to a combination of warm weather and overflowing brown bins. These flies tend to get a bit of a bad wrap, what with the spitting onto dog shit, sucking up the slurry, and then tramping it all over our food.

Organism of the week #14 - Turtles all the way down

Sun, 26 May 2013 16:00:02 +0000

Cassiopea, which looks rather like a spelling mistake (but isn’t), also looks a bit like an anemone (but isn’t):

Cassiopea 'upside-down jellyfish' in the aquarium beneath the Palm House at Kew Gardens

It’s actually a jellyfish, but one that spends most of its time living upside-down (relative to its relatives). Unlike its close relatives, it gets much of its energy from sunbathing rather than from fishing.

Organism of the week #13 - Unlucky for some

Fri, 03 May 2013 15:51:02 +0000

I’m a sucker for things that are both poisonous and pretty. Datura metel definitely meets both criteria.

Datura metel (flower)

These photos were taken in southern Spain, where this purple variety of the plant seemed to have naturalised itself out from someone’s garden .

Ominously looming over the Spanish countryside

Datura metel is closely related to Atropa belladonna, the deadly nightshade, and - like it - the plant contains high concentrations of atropine and scopolamine. If eaten, these chemicals clog up receptors in the nervous system, the normal job of which is to cause the body to “rest and digest”. By blocking these receptors, high doses of atropine or scopolamine cause a “flight or fight” response: increased heart rate, dry mouth, reduced gut movement, and dilated pupils. The last of these effects is the source of the belladonna (‘beautiful lady’) of Atropa belladonna: juice from deadly nightshade was used cosmetically during the middle ages to dilate the pupils alluringly - and, one suspects - alarmingly.

The Michaelis-Menten model is not applicable to most enzymes in a cell

Wed, 01 May 2013 15:32:48 +0000

Enzymes in cells can be modelled using the Michaelis-Menten model

Enzymes can be, and often are, modelled by the Michaelis-Menten (well, Briggs-Haldane) model:

v = v_max · [S] / (K_M + [S])

Where:

v is the velocity of the enzyme, which is the rate at which product accumulates
v_max is the maximum velocity of the enzyme (i.e. the velocity to which it tends as substrate concentration increases towards infinity)
[S] is the concentration of substrate
K_M is the Michaelis constant for the enzyme, which is the concentration of substrate needed to make the enzyme run at half its maximum velocity

This model works out very well when you mix together an enzyme and its substrate in a test-tube and measure the initial rate of product accumulation. Here are some data from a practical I run with my first-year biology students, showing a nice hyperbolic curve as predicted by the model:

Lacklustre butterworts

Thu, 25 Apr 2013 09:45:42 +0000

I’d like to be more excited about this than I am, but Pinguicula agnata is not the most crowd-pleasing of my butterworts, even whilst in flower (as it currently is). Ho hum. Strange specific epithet though. No idea why Casper (whoever s/he might have been) thought it appropriate. Could be worse though, I guess.

Metabolic pathways don't really have end products

Tue, 23 Apr 2013 13:50:51 +0000

The end product of glycolysis is pyruvate

This, and equivalent statements about other metabolic pathways:

The products of Krebs cycle are ATP/GTP, NADH and carbon dioxide

are not exactly wrong, but they are easily over-interpreted in a way that leads to misunderstanding. They are also easily swallowed as explanations without considering quite what ’end product’ is supposed to mean.

Glycolysis is the metabolic pathway in cells that converts glucose to pyruvate

Organism of the week #12 - Preying mantis

Wed, 17 Apr 2013 11:04:35 +0000

This is mostly just to see if I can get embedded video to work. Mantis religiosa…

Om nomnomnom.

Explain again why I need to install a plug-in to get WordPress to embed video from its own local media library?

Down amongst the butterworts

Sun, 14 Apr 2013 17:24:11 +0000

I lived within 30 minutes’ drive of Charles Darwin’s house for the whole of my childhood. It’s been open to the public since it was acquired by English Heritage in 1998. I’ve been a biologist of sorts for about 18 years.

It’s taken me until today to actually visit Down House, and to wander down the famous sandwalk behind the house, where Darwin used to do his thinking. I am a very bad, and very lazy boy. Also a very lucky one to have a husband prepared to schlepp to yet another greenhouse.

Moose objects and roles

Fri, 12 Apr 2013 15:48:41 +0000

Mr Moose’s Newfangled Object Framework

Creating objects from scratch by hand-rolling them is somewhat fragile, and you end up drowning in the writing of endless boilerplate accessor methods. I would strongly suggest that rather than doing objects the hard way, you use the Moose object framework unless there’s some particular constraint (speed, memory footprint) on your code that would make it inappropriate.

The kraken wakes

Wed, 10 Apr 2013 09:01:20 +0000

My butterworts have been waiting with unbated breath for the long, slow arrival of the spring. In winter, they cut their losses and produce small non-carnivorous leaves as there’s not enough prey around to justify investment in glue. In spring, they awaken and start making larger, insecticidal leaves again. Tina has already captured a fungus gnat with one of her freshly unfurled leaves.

Enzymes don't necessarily increase the rate at which products are formed

Tue, 09 Apr 2013 15:29:39 +0000

An enzyme increases the rate of product formation

What happens if you add the enzyme malate dehydrogenase to a mixture of of its substrates NAD and malate (both at 1 mM for the sake of argument)?

A brief look on BRENDA indicates that the reaction malate dehydrogenase catalyses is:

malate + NAD → oxaloacetate + NADH

So you might very well expect that the NAD would oxidise the malate, and the products oxaloacetate and NADH would rapidly accumulate.

The product of succinate dehydrogenase is ubiquinol not reduced flavin

Tue, 09 Apr 2013 11:20:05 +0000

Succinate dehydrogenase (SDH) produces reduced flavin (FADH₂) as a product

This misconception is so widespread, even the exam boards get it wrong. Page 41 of the Edexcel GCE specification for A-level biology (2008 onwards) states that students should be able to…

Describe the role of the Krebs cycle in the complete oxidation of glucose and formation of carbon dioxide (CO₂), ATP, reduced NAD and reduced FAD (names of other compounds are not required) and that respiration is a many-stepped process with each step controlled and catalysed by a specific intracellular enzyme. [my emphasis]

Misconceptions in life sciences

Tue, 09 Apr 2013 11:18:53 +0000

Last month, I was involved in teaching on a life science communication course, some of the results of which you can see on Wikipedia. One of our guest speakers was Alom Shaha, who demonstrated the misconceptions students have about e.g. the forces acting on a ball in flight:

The ball has recently been thrown from the left of the image, the ground is beneath it.

A typical response demonstrates some common misconceptions, particularly about Newton’s First Law of Motion:

Organism of the week #11 - Not even primitive

Mon, 08 Apr 2013 15:53:49 +0000

It’s not much to look at, but Psilotum nudum‘s naked fronds* *hold a cautionary tale for biologists:

Psilotum nudum, finally bagged at the Oxford Botanic Gardens

Psilotum looks a great deal like some of the earliest fossils of land plants. One of the earliest such fossils is Rhynia, the first specimens of which which were unearthed in Aberdeenshire around 1910, a mere 410 million years after they were originally buried.

Vegetable empire 2013

Fri, 29 Mar 2013 23:07:26 +0000

By popular demand, I have resurrected this phylogeny from my old website for Easter 2013. I have added a number of extra groups, updated the angiosperms according to APG-III, and repositioned the Gnetales according the apparently ascendent gnetifer hypothesis. The rotated titles in the table appear to work in IE9, Chrome and Safari, but YMMV.

Organism of the week #10 - The shapeless cock-of-the-gods

Thu, 21 Mar 2013 15:41:43 +0000

I missed last week, so this week’s is a biggun, to make up for my tardiness.

Bow down before The Shapeless Cock-of-the-Gods:

Amorphophallus titanum inflorescence

Apparently, when this plant was filmed for The Private Life of Plants in 1995, David Attenborough decided to invent the term “titan arum” to avoid using the plant’s Latin (well, Greek, really) name on prime-time BBC-1:

Educational RCTs

Wed, 20 Mar 2013 14:19:56 +0000

Around a decade ago I did a PGCE. Part of that PGCE involved a small-scale investigative study, from which I learnt a great deal about educational research, but not - I suspect - any of the intended learning outcomes.

I was teaching a year-7 class, whose graphing skills needed improvement. Students would often forget to give meaningful titles* to graphs. They would forget to label axes; they would join-the-dots rather than adding a line of best fit; and so on.

Organism of the week #9 - Not even what it doesn't seem to be

Thu, 07 Mar 2013 14:26:58 +0000

See Roridula’s* *glistening leaves. See the fly suffocating in her sticky embrace. Quake at her insecticidal prowess.

Roridula gorgonias at Kew Gardens

Or not. Things are not quite what they seem with Roridula. For sure, she can catch flies, but her carnivory is impotent. She cannot make the enzymes she needs to break down her prey, so they remain stuck to her leaves, and do not give up their fertilising innards to her.

Organism of the week #8 - Brought to you by the number 5 and the letters L, S and D

Thu, 28 Feb 2013 10:52:15 +0000

If sea cumbers are an example of intelligent design, then God - sorry, an unspecified supernatural intelligence that somehow doesn’t infringe on the First Amendment - needs to lay off the acid. Echinoderms are what you get when you give evolution the number 5 and half a billion years to piss around.

A sea apple (Pseudocolochirus violaceus) at the Monterey Bay Aquarium

You’ve simply got to love any animal that can ~~vomit up its own bowels~~ crap out its own gills to annoy predators.

Classes and objects

Wed, 20 Feb 2013 15:14:28 +0000

Mr Wall’s Olde Fashioned Objeckts

Caveat lector. Despite some cosmetic surgery, this post, like the previous one on writing modules, may show its age. It was originally written when Perl 5 wasn’t even 10 years old, and things have moved on substantially since then (and no, I don’t mean Perl 6). However, there’s a lot of code out there using blessed hashref objects, so before I post something about using the Moose object framework (quick-ref guide), this post will explain how to use objects, and how to hand-roll “traditional” Perl 5 hashref objects.

Organism of the week #7 - Bringing the kids up on junk

Wed, 20 Feb 2013 13:03:30 +0000

Another quick one this week. Life finds a way…

Coot brings up its kids on junk

The neighbourhood coots build these landfill nests annually, and I’m never quite sure whether to be impressed or appalled.

Packages and writing modules

Wed, 20 Feb 2013 12:34:56 +0000

Modularisation is a virtue

The previous post showed you how to install and use other people’s modules; this post will address how to write your own.

At some point, you will probably find yourself copying-and-pasting code from one script to another. When you find yourself doing that, you should consider what would happen if it later turns out there is a bug in that pasted code. Ten copy-and-pastes down the line, you’re going to wish like hell you’d put that bit of code into a module, so you only needed to fix the bug in one place rather than ten.

Exterminate

Thu, 14 Feb 2013 15:41:12 +0000

Love my new Dalek t-shirt:

This is also relevant to my interests.

Organism of the week # 6 - Enigmata of the Gnetales

Thu, 14 Feb 2013 13:47:30 +0000

Three for the price of one this week.

Most seed-bearing plants fall into one of two main groups: the flowering plants (grasses and magnolias and butterworts and so on), or the conifers (pines and yews and monkey-puzzles and so on). However, there are three smaller groups of seed-bearing plants that don’t fit into this neat division: the cycads, the ginkgo, and an enigmatic group of plants that are sufficiently obscure they haven’t attracted a nice englishified name, so we shall have to stick with calling them the “Gnetales”.

Obfuscated pancakes

Tue, 12 Feb 2013 07:21:10 +0000

Anything is better than an recipe that uses volume measurements for highly compressible powders. I’m looking at you America, and your ridiculous ‘cup’ nonsense.

####### Materials

0.110 kg powdered wheat endosperm (without added carbonates or tartrates)
4.28 mmol NaCl
2 unfertilised jungle-fowl eggs (between 63 and 73 g in mass)
275 mL of 75% (v/v) aqueous diluent of cow’s milk
45.0 cm³ cow’s milk butter
1 hesperidium from a lemon-tree, cut into ungulae with semidisc dihedrals of π/2
55.8 mmol granular α-D-glucopyranosyl-(1→2)-β-D-fructofuranoside (particle size c. 350 microns)

####### Method

Illuminating error

Sat, 09 Feb 2013 11:17:34 +0000

Yesterday’s first-year biology practical involved forcing the laboratory work-horse bacterium Escherichia coli to take up a circular piece of DNA called pGLO.

pGLO contains a few genes, but the most interesting of these DNA sequences encodes a protein from a jellyfish. This protein fluoresces green under UV light, and goes by the thoroughly unimaginative name of green fluorescent protein (GFP). The production of the GFP is regulated by a second DNA sequence, this time taken from a bacterium. The normal job of this regulatory DNA sequence is to switch on and off the production of enzymes that degrade an uncommon sugar called arabinose. Since bacteria don’t often encounter arabinose, the enzymes are not produced unless there is actually some arabinose around to eat. This save resources.

Organism of the week #5 - Something's wrong here

Thu, 07 Feb 2013 10:41:45 +0000

Busy teaching this week, so it’ll have to be a quick one…

Drosophyllum lusitanicum, Portuguese "sundew"

I particularly like this plant because of a very specific and unusual thing about its leaves. The more observant of you may spot what it is without having to resort to Wikipedia…

Organism of the week #4 - Toadstools

Thu, 31 Jan 2013 14:11:03 +0000

Imperial’s campus in Berkshire, Silwood Park, is a fabulous place to go fungus spotting. The fly agaric (Amanita muscaria) is very common there as there are a lot of birch trees around, and this fungus forms a symbiosis with the roots of those trees:

Fly agarics are rather poisonous (for some value of ‘rather’), by virtue of containing muscimol, and ibotenic acid; the former is a psychoactive dissociative that can cause visual and auditory hallucinations. There is an enormous amount of folklore (i.e. lies) associated with this mushroom that I shan’t bother repeating. There’s not even much evidence that it’s any use for killing flies.

Organism of the week #3 - Switch off all electrical items on the approach

Thu, 24 Jan 2013 08:35:23 +0000

There are many good reasons to visit San Francisco, some of them thoroughly unsafe for work, but one I didn’t consider was to see this amazing sight on the approach to the airport:

Salt ponds at the southern end of San Francisco Bay

The pink colour in the water is caused by a bloom of single-celled organisms I must refrain from calling bacteria, since they are not. Nor are they eukaryotes, the group to which you and I, and plants and fungi and protists belong. The things living in the water are halo’bacteria’, named before it was realised we needed a whole new classificatory scheme to accommodate their weirdness. Halobacterium is a member of the Archaea, which includes many extremophiles. Some are capable of living in near-boiling water, hot acid, or - as here - in very salty water indeed, but some are much more commonplace and allow some humans to set light to their farts.

More butterworts

Mon, 21 Jan 2013 14:30:35 +0000

After the trip to Königssee, I was inspired to retail therapy and bought myself as many butterworts as Hampshire Carnivorous Plants could supply:

OCPD butterwort collection (Pinguicula cv. Tina, P. cv. Wesser, P. agnata, P. cyclosecta, P. esseriana)

They did me proud over this summer, with two of them flowering despite the root disturbance (on which butterworts are not keen), the chunky cultivar ‘Tina’:

I gone done made me a satire

Mon, 21 Jan 2013 10:26:35 +0000

Tortured artists have tuberculosis, not iPhone apps.

Farewell Marlowe

Sat, 19 Jan 2013 12:49:45 +0000

Marlowe, the cellar spider who has been living behind my beside cabinet for the last 18 months, disappeared a few weeks ago, but I wasn’t too worried as they’d done that before and then turned up again a few weeks later, fatter and of greater span.

On Monday, however, Alex found Marlowe’s mortal remains beneath the bathroom radiator. Marlowe is no more.

Organism of the week #2 - Now wash your hands

Thu, 17 Jan 2013 09:42:12 +0000

I have delusions of being a competent recogniser of things that turn up in UK gardens, but when this started growing in what had previously been a pot of basil in the garden, I was clueless:

Mystery thing

It looked a little like moss from a distance, but the bibbly bobblies were most certainly not moss-like close-up, and the whole thing had a rather unpleasant squeaky texture. Touching it left brownish-green stains on my fingers. Definitely not a moss.

Organism of the week #1 - Chimaera

Thu, 10 Jan 2013 13:26:29 +0000

I’ve been neglecting the blog of late, for reasons too dreary to explain. So I am taking the astonishingly original step of racking up a load of pretty pictures of organisms to release on a semi-regular basis. I am creativity incarnate.

Today, +Laburnocytisus ‘Adamii’.

+Laburnocytisus 'Adamii'

Technically, this is a bit of a cheat for an organism of the week, as this organism is technically two organisms, one growing inside of the other.

Glockentierchen

Wed, 17 Oct 2012 09:20:36 +0000

It’s nice to find out that - old and jaded as I am - biology can still delight me.

Earlier this week, I covered a first-year practical teaching microscopy skills to first-years, through the medium of pond water. As well as the usual desmids, rotifers, Daphnia and nematodes, one lucky student found a little clump of *Vorticella *(or some near relative, I’m not a protistologist!)

Installing modules

Fri, 05 Oct 2012 19:35:08 +0000

CPAN

With bits and bobs, we’ve covered much of the core functionality of Perl, but perl also comes with dozens of useful modules in its standard distribution. CPAN expands this with an enormous wealth of other contributed modules that you can install. There are three ways of doing this:

The most direct method is to go directly to CPAN, download the module you want (as a zipped tarball), unzip it and untar it, change directory to the folder you’ve just unzipped, and build the module with dmake or whatever make program you have available. So, if we wanted to install the Parse::RecDescent module, you’d download the Parse-RecDescent-1.967009.tar.gz tarball from CPAN, and then:

Command line

Fri, 05 Oct 2012 09:24:25 +0000

Command line Perl

Despite being a suitable for large projects, Perl grew out of Unix shell scripting, so it allows you to run it from the command line directly:

perl -e "print 'Hello'; print 2 + 2;"

if you’re on Windows, or:

perl -e 'print q:Hello:; print 2 + 2;'

if you’re on Unix. The quotes matter. The -e is the execute switch, and there are several others:

Debugging

Thu, 04 Oct 2012 15:30:16 +0000

Debuggering

So now you know how Perl works, and how to use it both for scripts and one-liners. But what do you do when it doesn’t? And how do you use it for larger projects?

Perl has some bugs and misfeatures, but it’s extremely unlikely that you’ve found a new one that’s not in the docs, so if a program fails to run as you expect, the chances are it’s you that’s buggered up. How can you find out where you’ve inserted a problem?

Bits and bobs

Thu, 04 Oct 2012 14:20:56 +0000

This post is a bit of a rag-bag of useful stuff that doesn’t fit elsewhere.

Creating code at runtime

There’s another way of creating code on the fly, besides closures. This is eval. eval comes in two flavours: string and block. The block eval looks like:

$number = <STDIN>;
my $answer;
eval {
 $answer = 2 / $number;
};
print $@ ? "Divide by zero error or similar: $@" : $answer;

This is a useful (and indeed the only way) to catch exceptions, that is, divide-by-zero errors and their ilk. Note you need a ; at the end of the eval { BLOCK }; because eval is a statement. If something goes wrong in the block, the special variable $@ is set with what went wrong. So eval-ling a block allows you to test Perl code, and make fatal things non-fatal.

References and data structures

Thu, 04 Oct 2012 14:06:40 +0000

References

Arrays and hashes and lists and the manipulation thereof are very useful, but sometimes you want something a bit less flat; a little more multidimensional. Perl does indeed allow for multidimensional arrays (of a sort), but the syntax is a little odd. Let us enter the world of the reference.

References are like signposts to other data. To create a multidimensional array, what you actually need to do is create a normal 1-dimensional array whose elements are these signposts to other arrays. In this way, we can fake a multidimensional array. So, how do we create a reference? There are two ways. The first is to use the \ operator, which creates references to bits of data you have named and defined previously:

Substitutions, splitting and joining

Thu, 04 Oct 2012 12:31:11 +0000

Substitution and transliteration

Matching patterns is very useful, but often we want to do something more than just match things. What if you want to replace every occurrence of a certain thing with something else? This is the domain of the s/// and tr/// operators. s/// is the substitution operator, and tr/// is the transliteration operator. tr/// is useful for simple things:

Regexes

Thu, 04 Oct 2012 09:38:51 +0000

Regular expressions

Before we looked at file manipulation, we covered how to write comparisons with conditionals:

if ( $string eq "Something we're interested in" ) {
 print "Ha, ha!";
}
else {
 print "Boring";
}

What happens if there’s more than one thing you’re interested in though? Writing a gigantic if/elsif/else structure or even a given/when switch will make your head spin, and you’ll never be sure you’ve got every possible version of the thing you’d like to match. Take for example, matching something as simple as a letter, number or underscore character:

Files and directories

Wed, 03 Oct 2012 20:34:09 +0000

Reading and writing to files

The symbol table is a little esoteric, so let’s get back to practicalities. How do you mess about with files and directories in Perl? A simple example:

#!/usr/bin/perl
use strict;
use warnings;

open my $INPUT, "<", "C:/autoexec.bat"
 or die "Can't open C:/autoexec.bat for reading $!\n";

open my $OUTPUT, ">", "C:/copied.bat"
 or die "Can't open C:/copied.bat for writing $!\n";

while ( <$INPUT> ) {
 print "Writing line $_";
 print $OUTPUT "$_";
}

Here we open two files, one to read from, one to write to. The $INPUT and $OUTPUT are filehandles, just like STDIN was, only we have created these two ourselves with open. It’s a good idea to give filehandles uppercase names, as these are less likely to conflict with Perl keywords (we don’t want to try reading from a filehandle called print for example).

Symbol table

Wed, 03 Oct 2012 19:47:55 +0000

Symbols

That’s pretty much everything for hashes, except for one topic usually missed out from introductory tutorials (possibly rightly!) This post will tell you a little about the innards of what you’ve been doing when you create variables. It’s not really necessary to know this stuff to be able to use Perl for day-to-day stuff, so do feel free to skip to the next post if this one becomes too esoteric.

More hashes and sorting

Wed, 03 Oct 2012 19:21:03 +0000

Hash manipulation: `each`, `delete`, `exists`

Before we got side-tracked with subroutines and conditionals, we covered arrays in some detail, and saw the various functions, like push and pop that you can torture them with. The functions for torturing hashes are our next port of call. Perl stores the key => value pairs of a hash in essentially random order (well, unhelpful, if not actually random), so operations like pushing and popping don’t make any sense, as hash items are not ordered in a useful fashion. We’ve already seen how to extract single items and slices of hash:

Conditionals

Wed, 03 Oct 2012 15:33:33 +0000

Conditionals: `if` and `unless`

We’re on the home-straight in understanding the code from the last post now:

#!/usr/bin/perl

use strict;
use warnings;

my @peas = qw/chick mushy split/;
while ( my $type = pop @peas ) {
 print "$type peas are ", flavour( $type ), ".\n";
}

sub flavour {
 my $query = shift @_;
 my @peas = qw/chick garbanzo/;
 foreach ( @peas ) {
 if ( $query eq $_ ) {
 return "delicious";
 }
 }
 return "disgusting";
}

The very last bit is the conditional statement in the flavour() subroutine. This part compares the type of pea the subroutine was passed with all the peas in its own @peas, and if it matches any of them, the subroutine returns ‘delicious’. The if conditional has the general form:

Bondage, discipline and subroutines

Wed, 03 Oct 2012 14:46:29 +0000

Lexical `my` variables and `use strict;`

You may have noticed a little thing I slipped in the last script: the keyword my in the chomp. my is a very important keyword, although you’ll note that it doesn’t seem to make any difference if you delete it and run the program. What my does is pin a variable to a particular part of your program, so that it can’t be seen from elsewhere. This may not seem very useful at the moment, but is exceedingly important as your programs get bigger. Such as here:

Prettier loops and nicer code

Wed, 03 Oct 2012 14:12:43 +0000

Idiomatic Perl

The original code we were studying is very ugly, and Perl makes writing short, diabetogenic code easy. It also makes writing shoddy, abominable code easy too, but I wouldn’t recommend this as a course of action. A much more attractive way of writing the horrible code from the last page is:

#!/usr/bin/perl
print "What is your name?";
chomp( $name = <STDIN> );
@beans = qw( adzuki haricot mung );
print "\@beans contains ", scalar @beans, " members, @beans\n";
foreach ( @beans ) {
 print "$name likes $_ beans.\n";
}

This is much tidier, and probably more readable even without any further explanation. There are a few new things though. The assignment of <STDIN> ("Steve\n" or whatever) to $name actually returns the variable $name, which is exactly what chomp needs to work on. So those two lines can be combined:

Simple loops

Wed, 03 Oct 2012 13:55:29 +0000

Loops

Hopefully you’re now happy with the fundamental data types in Perl: scalars, arrays and hashes, so most of the script below shouldn’t be too mysterious:

#!/usr/bin/perl
print "What is your name?\n";
$name = <STDIN>;
chomp $name;
@beans = ( "adzuki", "haricot", "mung" );
print( "\@beans contains ", scalar @beans, " members: @beans\n" );
for ( $i = 0; $i < scalar @beans; $i++ ) {
 print "$name likes $beans[$i] beans.\n";
}

@beans contains 3 members: adzuki haricot mung
Steve likes adzuki beans.
Steve likes haricot beans.
Steve likes mung beans.

Don’t get scared by the line-noise (i.e. all the punctuation): if you do, regexes will probably be fatal. The very beginning should be quite obvious now:

Hashes

Wed, 03 Oct 2012 13:20:52 +0000

Hashes

Perl actually has two sorts of array. Simple arrays like those we’ve already discussed are simply called arrays. The second sort of array is called an associative array, or hash. They’re very similar to dictionaries, if you’re a Python programmer. Hashes are created with a % for %we_ran_out_of_sensible_symbols, and contain pairs of data (ah, maybe it was for the two blobs in a % sign) called keys and values. Here are some typical hash creations:

Arrays and slices

Wed, 03 Oct 2012 13:06:13 +0000

Types

You should now be able to create very simple scripts that can take input from the keyboard, assign it to scalar variables, and echo it back to the screen with print. Time for some technicalities.

Perl is often (and wrongly!) termed a weakly typed language. For those of you coming from bondage and discipline languages like C or Java, this means Perl does not require you to explicitly point out what kind of variable your variables are: floats, doubles, integers, characters, booleans, strings, etc.

Input and output

Wed, 03 Oct 2012 12:27:14 +0000

Input

The “not a hello world script” script is a little dull. Let’s try something a more useful:

#!/usr/bin/perl
print "What is your name?\n";
$name = <STDIN>;
chomp( $name );
print "$name likes beans.\n";

Don’t forget the semicolons at the end of each statement.

The first line of this program should be obvious now, but the others may need a little explaining. The second line contains the line-reading operator < > and the STDIN filehandle. STDIN (the “standard input filehandle”) is automatically opened whenever you run perl, and is where things inputted through pressing buttons on the keyboard live. If you surround a filehandle like STDIN with the < > line reading angle brackets, you will read a line from that filehandle. A line to perl is some text followed by a newline character, hence:

Not a hello world script

Wed, 03 Oct 2012 12:12:16 +0000

Rather than employing the usual tactic of showing you how to write the accursed ‘hello world’ program, so beloved of all computer programming introductions, let’s start with something entirely different:

print "This is most definitely not a hello world script.\n";

If you save this as the file thing.pl, or similar, then you can run it from the command line (i.e. DOS prompt, bash shell, terminal window) thusly:

Educated guesswork

Wed, 03 Oct 2012 11:15:46 +0000

Someone recently asked me, “How many cells are there in the human body?”

I have quite a lot of correspondence of this kind, just to be clear.

I have to confess my first thought was “Not a bloody clue”. My second thought was “I bet the Internet knows”; but my third was “The Internet is full of bloody lies”.

My fourth thought went on for so long, it became part of the introduction to cell biology and genetics lecture I gave this year, and is reproduced below for your pleasure.

Domestic science

Sun, 30 Sep 2012 13:43:19 +0000

Humans share their homes with a surprising number of other species, even discounting the ones they deliberately import to serve as allergen distribution machines. Autumn is a particularly good time to go spotting the spiders that cohabit with us, as many of them are grown fat and sleek on the flies of summer, and are therefore easy to spot.

The cellar spider (Pholcus phalangioides) is sometimes called the daddy long-legs, but unhelpfully, this refers to at least two other whole groups of animals, the harvestmen, and the crane-flies, neither of which are closely related. The confusion this causes is one reason why biologists insist on using Latin names instead.

Far from the light of day, and somewhere near Hampstead

Tue, 25 Sep 2012 19:33:09 +0000

Paddock is the codename of a bunker that was built in the late 1930s as a back-up for the better known Cabinet War Rooms located in Whitehall.

Junction box in the upper basement floor of the Paddock bunker; CWR-AWR almost certainly stands for 'Cabinet War Room - Air Raid Warning'

The bunker was abandoned at the end of the war, and was only used intermittently after that by the Post Office, whose Research Station sat atop it. In 1998, the surface site and the bunker were sold off, and a housing development was built on top. Unfortunately, during the development, the concrete slab that kept the bunker watertight was damaged, and since then, Paddock has been slowly decaying.

A brief history of rubbish

Mon, 10 Sep 2012 15:10:42 +0000

In 1972, the geneticist Susumu Ohno coined the term “junk DNA” to explain why the genomes of closely related organisms vary so much in size:

The mammalian genome […] contains roughly […] 3.0 × 10⁹ base pairs. This is at least 750 times the genome size of E. coli. If we take the simplistic assumption that the number of genes contained is proportional to to the genome size, we would have to conclude that 3 million genes or so are contained in our genome. The falseness of such an assumption becomes clear when we realize that the genome of the lowly lungfish and salamanders can be 36 times greater than our own.

Ohno, S. (1972) So much ‘junk’ DNA in our genome, In: Smith, H. H. (ed) Evolution of genetic systems, 23, 366-370.

Beautiful butterworts

Sun, 26 Aug 2012 10:14:45 +0000

A recent hike in Königssee to see Germany’s highest waterfall was a little underwhelming but the hydrological shortcomings were entirely forgotten when I spotted this beauty growing in a crevice above the lake:

Unknown butterwort (Pinguicula sp.) in German Alps, probably P. vulgaris or P. alpina.

Butterworts are amongst my favourite carnivorous plants: their murderous ways are so delicately concealed. Who would suspect such a pretty bank of flowers to be a veritable morgue of fungus gnats?

Farewell Gore Vidal

Wed, 01 Aug 2012 09:26:01 +0000

There is no human problem which could not be solved if people would simply do as I advise

Being an avowed atheist, a form of words appropriate to death has always eluded me: “rest in peace” has always seemed inappropriate, implying - as it does - that something is left after death that could be at rest or otherwise. In similar vein, it has always struck me as terribly unfortunate that the one person who will never be aware of an obituary is the deceased; Alfred Nobel being a notable and salutary exception.

The magnolia misunderstanding

Thu, 26 Jul 2012 12:30:50 +0000

T. Ryan Gregory has a great post at Genomicron on the ‘Platypus Fallacy’. He imagines a platypus professor explaining the wonders of the Human Genome Project to a group of student platypodes:

“The lineage of which humans are a part is a very ancient offshoot of our mammalian family tree, so it was 166 million years ago that we last shared a common ancestor with humans, and that puts them somewhere between mammals and reptiles, because they lack a lot of specialized characters that we have gained but the ancestral amniote also lacked; for instance, they have no electroreception, no bills, no webbed feet, and no venom. So we can use them to trace the changes that have occurred as we went from being a reptile, to having fur to making milk to having our specialized features.”

Why living fossils need to die

Fri, 27 Apr 2012 16:02:52 +0000

I’m the proud owner of a Madagascan cycad. He or she (I won’t know until s/he gets older) gets an annual decking with baubles at Christmas, but spends most of the rest of the year getting in the way of the television.

Deck the cycad with Pantone baubles, fa-la-la-la-lah la-la-la-lah

Cycads look a lot like palms, but rather than producing flowers and fruits, they make cones and bear fruitless naked seeds. This hints at their origins. They are much more closely related to pine trees and other gymnosperms, than to flowering plants like palms.

Community payback for undergrads

Thu, 19 Apr 2012 15:27:57 +0000

Two acquaintances of mine, both teachers of one kind or another, tell me that they no longer feel comfortable steering students away from Wikipedia, because they can no longer maintain the prim pretence that they themselves aren’t consulting it on a daily basis.

I’ve long appreciated Wikipedia for its convenience; and been amused by its unforgivable mis-prioritisation. On the other hand, I’ve been irritated by the scrappiness of articles on concepts I’ve taught and saddened by the thoughtless pasting of its content into some of the essays I mark.

Version 2

Mon, 16 Apr 2012 20:31:52 +0000

Several years ago, I pulled my old website, as it had become a compost-heap of reformatted lecture notes that I no longer had time to maintain, and which Wikipedia had rendered redundant in any case. The pleasures of writing HTML by hand had begun to pall, and the hand-rolled CGI guestbook made even a coding Luddite like me shudder with embarrassment.