May 19

Organism of the week #31 – Tardigrades

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.

One of my first-year undergrads spotted this one in a sample of moss I pulled out of the down-pipe from my bathroom. The fact that my skin flakes and spittle contributed in some small way to this microteddy’s food-chain makes me feel about as paternal as it is possible for me to feel.

Tardigrades [CC-BY-SA-3.0 Steve Cook]

May 19

Organism of the week #30 – Sticky situation

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.

Nature has a sense of irony, but its comic timing needs work.

There’s nothing wrong with stamp-collecting. Science very often begins with stamp-collecting, because it’s only once you have enough stamps that you can start reliably identifying patterns in the stamps, and – from there – finding the interesting exceptions and edge-cases:

Baryon supermultiplet [CC-BY-SA-3.0 Studzinski.daniel]

Subatomic particle stamp-album [CC-BY-SA-3.0 Studzinski.daniel]

I have been an on-off collector of carnivorous plants since I was very little. Most of them attract insects, kill them, digest them to tasty soup, and then absorb that soup. The soup contains useful nutrients that are missing from the soil in which they are rooted, so this helps them grow and set more seed. But there are many plants that tick some of these carnivorous boxes, but not all of them. Roridula is one I’ve blogged about before: it subcontracts out the digestion part of the process to an assassin bug. Another plant that walks the line is a kind of passionflower:

Passiflora foetida bud [CC-BY-3.0 Alex Lomas]

Passiflora foetida bud

The charmingly-named stinking passionflower bears sticky hairs on tentacle-like growths around its flower buds. There is some evidence to suggest that these help protect the flower bud from hungry insects while it develops. Similar sticky hairs are also thought to protect the flower buds of a number of other plants.

The stinking passionflower kills insects, and even appears to digest them, but it doesn’t benefit from the nutrients this releases. However, it does benefit from not having its flowers damaged by herbivorous insects. This presumably means it sets more seed, so the ultimate effect – more baby plants – is the same as for ‘true’ carnivory.

Passiflora foetida flower [CC-BY-3.0 Alex Lomas]

Passiflora foetida flower. The reason these plants are called passionflowers is because the various parts of the flower are supposed to look like hammers, nails and a crown of thorns – items associated with the Passion (crucifixion) of Jesus – rather than the earthly passions you might have been considering

Is this plant carnivorous or not? Well, whether you ultimately choose to paste this stamp into the carnivorous plant album or not is very much less interesting than the reasons you have for making that decision. I’m just glad that someone discovered this particular stamp and took the care to stick it somewhere for us to study. Here’s to collectors and taxonomists, the unsung heroes of biology.

May 05

Adaptations evolve in populations

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.

There are two subtle problems with what is written above.

Firstly, adaptations do not evolve in individual organisms, because evolution isn’t something that happens to individual organisms. Evolution is something that happens to populations over time. A mutation that predisposes pea plants to making flowers that are purple will initially arise in a single, particular plant cell. But only if this plant’s offspring prosper (at the expense of peas with differently coloured flowers) will the population as a whole change over time.

Adaptations like flowers that attract pollinators – and the mutations that underlie them – arise in particular individuals, but they can only become more (or less) common in populations considered as a whole. Individuals mutate, but only populations evolve.

Biologists usually think of evolution as the change in frequency of an allele in a population over time. An allele is one of the various forms a particular gene can take. In the peas studied by Gregor Mendel, flower colour was determined by a single gene, which came in two variants: one variant – one allele – resulted in purple flowers, the other allele resulted in white flowers.

If – perhaps – the purple flowers were more attractive to pollinators like bees than the white, then the purple-flowered peas would tend to be fertilised more often, and would leave more offspring. The next generation of pea plants would then inherit a larger proportion of alleles causing purple flowers, and a reduced proportion of alleles causing white flowers. The purple allele would therefore increase in frequency at the expense of the white, and the population as a whole would become more purple over time.

Pisum sativum (white) [CC-BY-SA-3.0 Rasbak]

White-flowered peas (Pisum sativum) [CC-BY-SA-3.0 Rasbak]

Pisum sativum (purple) [CC-BY-SA-3.0 Rasbak]

Purple-flowered peas (Pisum sativum)  [CC-BY-SA-3.0 Rasbak]

For similar reasons, fitness is not a property of individual pea plants either; it is an average property of purple-flowered peas versus white-flowered peas. Any particular purple-flowered pea plant might get trampled by a cow and produce hardly any pea-pods; any particular white-flowered pea plant might get lucky and find itself in a cosy, well-fertilised spot near a beehive. But on average, the purple-flowered plants will do better and they will bequeath their purple-flower alleles disproportionately to the next generation: that is what we mean by the purple-flowered plants being ‘fitter’.

The second problem with the original statement is actually the smallest word: it’s that seemingly insignificant ‘to’. That ‘to’ is short for ‘in order to’, and there’s the rub. ‘In order to’ implies teleological agency and long-term purpose, which are not properties that you can reasonably attribute to natural selection.

Natural selection is a mindless algorithm, not a purposeful process. In essence natural selection is just this:

  • Organisms vary, and some of that variation is inheritable. Some peas have purple flowers, some have white, and this is (partly) due to purple- and white-flowered peas having different alleles of a particular flower-colour gene.
  • More offspring are produced than can survive and reproduce, so they will compete, and some variants will – on average – have greater success at making offspring than others. Pea plants produce more offspring peas than are ever likely to germinate, grow and get fertilised themselves. Some variants in the offspring may be better at competing for light, nutrients or pollinators: e.g. some flower colours may be more attractive to pollinators than others.
  • Those variants will contribute disproportionately to the next generation, and the frequency of their alleles will increase over time. If the purple-flowered peas are more attractive to pollinators, they will get fertilised more often, and contribute a larger number of seeds into the next generation. These seeds – and the plants that germinate from them – will inherit their parent’s purple-flower alleles, so we will see an increasing proportion of purple flowers as the generations tick over.
  • Rinse, repeat.

The match between the purple flowers and the purple preference of pollinators strikes us as clever and sensible and non-random, and it is all those things. But the process of natural selection that created this apparent design is just the mindless consequence of variation, heredity and differential reproductive success: it has no goals, no aims, no purpose.

Equally, this is a passive process for the pea population: they are subject to evolution by natural selection, but they are not active participants in the process.The peas do not strive supernaturally to make more purple flowers. The peas do not get magically instructed by the bees to make purple flowers. The peas certainly do not know what DNA sequences they would need to invent in order to make their flowers purple: new flower-colour alleles arise by mutation, which is just as mindless as natural selection, and even more heedless of what might be useful.

Populations do not evolve in order to do anything. Populations evolve, period. Purple flowers arise and become more common in pea populations because purple flowers happen to be attractive to bees; peas do not choose to evolve purple flowers in order to attract more pollinators. Mutation just throws up new alleles, and natural selection (and other important processes) make them more or less common over time.

It can become tedious describing this process passively and long-windedly every time: “purple flowers have become more common in the pea population because flower colour is highly heritable, and purple flowers are fertilised more frequently by bees”. If you want to write this more succinctly, you could say “purple flowers have evolved in peas because purple flowers are more attractive to bees” without loosing too much meaning.

Unfortunately, you might well see someone reword this as “peas have evolved purple flowers because bees prefer them”. This isn’t exactly wrong, but the ‘have evolved’ makes it sound very much like the peas are doing something actively, rather than having something done to them passively, and it’s all too easy to interpret this phrasing incorrectly. This puts us on the slippery slope to misconception.

If this is then reworded further to “peas evolved purple flowers to attract bees”, it sounds very much like like peas are active players in the process, and that they have a long term plan of improving their attractiveness to bees. This is almost guaranteed to mislead, unless you have your evolutionary biology filter turned up to maximum.

Do not write:

Some species evolved an adaptation to do some task

Write this instead:

An adaptation that does some task evolved in [a population of] some species

Given human nature (particularly on this subject), some people will still misinterpret your meaning, but at least you’re not implicitly misleading them with your language.

Jan 08


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

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

Jan 07


Bark [CC-BY-SA-3.0 Steve Cook]

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.

Jan 06

Wisley in Winter

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 [CC-BY-SA-3.0 Steve Cook]

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.

Botanerd highlights included the biggest pine-cone I have yet added to my collection (yes, it is a collection, not a sickness)…

Pinus × holfordiana cone [CC-BY-SA-3.0 Steve Cook]

Holford pine (Pinus × holfordiana) cone – nothing satisfies like a 12 inch Pinus

…and the – apparently legal – purchase of class A drugs from the attached garden centre:

Lophophora williamsii [CC-BY-SA-3.0 Steve Cook]

Peyote cactus (Lophophora williamsii)

From what I gather, owning a peyote cactus is legal in the UK unless you ‘prepare it for consumption’, which magically transforms it into a 7 year jail term. This presumably includes accidentally letting it die and dry out into a button whilst on holiday. I may be having a teesy bit of buyers’ regret.

Jan 06


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:

Euchlanis rotifer [CC-BY-SA-3.0]

Euchlanis rotifer

This is a rotifer (‘wheel animal’), which are famous for two things: being ridiculously small, and – in one infamous subgroup – being ridiculously averse to having sex. They’re also really cute when they turn on their feeding wheels. Happy New Year.

Dec 22

Bagging botanical Brussels

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.

That elsewhere was the Plantentuin Meise / Jardin Botanique Meise, which is to the north of Brussels, conveniently situated – for the purposes of this second attempt to visit them – between Brussels airport and Antwerp.

Brussels botanic gardens [CC-BY-SA-3.0 Steve Cook]

Botanic Gardens, Meise

We were visiting in autumn, and they were in the middle of renovating part of their main glasshouse – the Plant Palace – but there was still plenty to see, including a good arboretum, an orchid exhibition, and some lovely Japanese beautyberries:

Callicarpa japonica [CC-BY-SA-3.0 Steve Cook]

Japanese beautyberry (Callicarpa japonica)

The entry fee (€ 7) is very reasonable, and the restaurant helpfully ensures all sandwiches come with a colonic depth-charge of salad; just the ticket to cure the faecal impaction resulting from the ‘food’ served to us on the flight out with <insert awful British airline here>. When we were there, there was also an art installation by Roos Van de Velde in praise of the best plant in the world – the maidenhair tree Ginkgo biloba  but you’ve only got until mid-January to catch it:

Gingko biloba Meise [CC-BY-SA-3.0 Steve Cook]

Roos Van de Velde’s Gingko biloba installation

Botanerd highlights:

  1. Whereas Kew’s evolution house (currently being renovated as part of the Temperate House restoration) always felt like a holding pen for a few cycads and ferns that didn’t physically fit into the Palm House, the Meise version was much more complete, with a good selection of horsetails, ferns, and high-quality fakes of fossil plants like Cooksonia, Lepidodendron, etc. That said, I would very much like to see these ‘evolution house’ efforts re-branded as ‘biodiversity houses’ or similar, as the usual Scala Naturae bullshit of using modern mosses, lycopods, ferns, and conifers as stand-ins for prehistoric forms gets right up my arse.
  2. The pinetum is small, but has a good selection of species, including quite a few weird cultivars of Japanese cedar (Cryptomeria japonica) that I’ve not seen before.

Cryptomeria japonica cv. Cristata [CC-BY-SA-3.0 Steve Cook]

Cryptomeria japonica cv. Cristata

Previous baggings…

Oct 06

Organism of the week #29 – Galling

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…

Insects and flowering plants have been co-evolving for 200 million years or so, so it’s unsurprising that many of their interactions have become very intimate. The relationships between gall-forming insects and their host plants are particularly interesting. Gall-forming insects lay their eggs on plants, but when the larvae hatch, instead of munching through the plant in the usual fashion, the larvae make the plant build bizarre little houses for them. These are the galls. Galls provide protection from weather, some protection from things that might like to eat the gall-former itself, and food for the developing larva.

In the UK, there are many gall-forming insects that target oak trees. These are mostly very small wasps. One of the most obvious is the knopper gall, which are the sticky crater-shaped things you often see attached to acorns around August.

Rather like the fluke we met a few weeks ago, knopper gall wasps have a complicated life-cycle involving several different hosts, in this case two different species of oak: the English (Quercus robur) and the Turkey (Quercus cerris). Female wasps emerge in spring from the galls that fell from English oaks the previous autumn. These females then lay asexual eggs on the catkins of the Turkey oak, which hatch out, and form rather inconspicuous galls. The males and females that hatch from these galls in April then mate, and the females lay their eggs on the developing acorns of English oaks, where they develop into the knopper galls in late summer.

Andricus quercuscalicis on Quercus robur [CC-BY-SA-3.0 Steve Cook]

Knopper galls caused by the larvae of the wasp Andricus quercuscalicis, on oak (Quercus robur)

Like so many pests and diseases – the knopper gall is actually a fairly recent introduction: the first galls in the UK were recorded only in the 1950s.

Smaller but creepier, the silk-button spangle gall is a trypophobes’ delight. Like the knopper gall, they’re caused by small wasps, but are much less obvious until you flip a leaf over:

Neuroterus numismalis and Neuroterus quercusbaccarum on Quercus robur [CC-BY-SA-3.0 Steve Cook]

Mostly silk-button spangle galls caused by the larvae of the wasp Neuroterus numismalis, also on oak

The less creepy common spangle gall isn’t as likely to make you feel like you have maggots crawling under your skin, but like the silk-button spangles, that’s exactly what the plant has got.

Neuroterus quercusbaccarum on Quercus robur [CC-BY-SA-3.0 Steve Cook]

Common spangle-galls (Neuroterus quercusbaccarum) on – you’ll never guess what. There are a few older reddish spangles in the silk-button image above too.

The most famous and most useful gall found on oak is the oak apple. A mixture of mashed up oak apple galls and iron salts was – for a millennium and a half – what you dunked a quill pen into, if you were lucky enough to know how to write.

Oak apple [CC-BY-SA-2.0 Bob Embleton]

Oak apple gall: these are caused by the larvae several different species of by cynipid wasps [CC-BY-SA-2.0 Bob Embleton]

Like the knopper and spangle galls, oak apples are caused by the larvae of a tiny wasp, but it’s not just wasps that can cause galls, or indeed just insects. Roundworms (nematodes) can also form galls, usually on the roots of plants; as can some fungiMites, which are more closely related to related to spiders than to insects, are responsible for many galls of sycamores and other maples:

Vasates quadripedes on Acer saccharinum [CC-BY-SA-3.0 Steve Cook]

Bladder galls caused by the mite Vasates quadripedes on – gasp, not oak! – sugar maple (Acer saccharinum)

Aceria macrorhynchus on Acer pseudoplatanus [CC-BY-SA-2.0 Lairich Rig]

Mite galls caused by Aceria macrorhynchus on sycamore (Acer pseudoplatanus) [CC-BY-SA-2.0 Lairich Rig]

Why would a plant build a house for a parasitic insect or mite? The long answer is very long, but the short answer is that the parasite secretes plant hormones called cytokinins to manipulate the plant into forming the gall. In plants, cytokinins cause cell division and growth. They also act as “feed me” markers: sugars and other nutrients are preferentially directed towards tissues that have cytokinin in them. Cytokinins also cause plant cells to make red pigments. By secreting cytokinins (and other plant hormones) gall-forming insects, mites, fungi and nematodes manipulate the plant into building small – often red! – houses for them, and to supply those houses with sugar.

Zeatin [Public domain]

cytokinin hormone: the structure is a modified form of the DNA base adenine

The galls formed by insects and mites are amazing structures, but at a molecular level, the most extraordinary galls of all are formed not by insects or mites, but by bacteria:

Crown gall [CC-BY-SA-3.0 Bhai]

Crown gall on Kalanchoe, caused by the bacterium Rhizobium radiobacter (Agrobacterium tumefaciens) [CC-BY-SA-3.0 Bhai]

Crown galls may not look so impressive, but the way in which their inhabitants cause the gall to be formed most certainly is. The galls are formed by the bacterium Rhizobium radiobacter[For any biologists doing a double-take at this point: until recently Rhizobium radiobacter was known as Agrobacterium tumefaciens , but it’s been reclassified. This is Brontosaurus all over again…]

Rhizobium radiobacter is the world’s smallest genetic engineer. Rather than simply secreting plant hormones to make the plant direct food at it, like the gall-forming insects do, this bacterium actually injects a piece of DNA into the plant’s cells to bend them to its will. The DNA encodes enzymes for plant hormone synthesis, which causes the plant cells to grow into a cancerous mass: the crown gall.

But even that’s not enough for this bacterium. The nutrients directed into the gall by the plant are not quite to the bacterium’s taste, so the DNA it injects also encodes genes that turn plant cells into factories for bacteria-friendly food. This food even leaks out of the plant’s roots, feeding the bacterium’s sisters in the soil.

It took until 1982 for humans to develop the technology to genetically manipulate a crop plant to make better food. A mindless single-celled organism has been pulling off the same trick for millions of years. There’s nothing new under the sun.

Sep 17

Organism of the week #28 – Fractal art

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?

Athyrium niponicum cv. Pictum [CC-BY-SA-3.0 Steve Cook]

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:

Humata tyermannii [CC-BY-SA-3.0 Steve Cook]

Humata tyermannii

Self-similar shapes like this are called fractals. This fern’s leaf is not a true mathematical fractal, because its self-similarity goes only four levels deep, rather than infinitely so. Also, from a developmental point of view, the leaves of ferns are produced by interactions between signalling molecules that have very little in common with the maths of fractals. However, it is remarkable how easy it is to produce a fractal that looks very much like a fern – especially when someone else has done all the hard work of discovering one for you. This one is called the Barnsley fern fractal, after Michael Barnsley:

Barnsley fern [Public domain]

Barnsley fern

This rather cute simulator allows you to play about with the Barnsley fern without going to the hassle of coding up any R yourself, but for those who enjoy such things, here’s my version of the code written in R, based on the coefficients from its Wikipedia article. An entirely imaginary prize is available for anyone who can produce a good simulation of either of the two ferns above.

fm <- vector( "list", 4 )
fc <- vector( "list", 4 )
fp <- vector( "list", 4 )

# Stem
fm[[1]] <- matrix( c( 0.00, 0.00, 0.00, 0.16 ), nrow=2, byrow=TRUE )
fc[[1]] <- matrix( c( 0.00, 0.00 ), nrow=2 )
fp[[1]] <- 0.01

# Leaflets
fm[[2]] <- matrix( c( 0.85, 0.04, -0.04, 0.85 ), nrow=2, byrow=TRUE )
fc[[2]] <- matrix( c( 0.00, 1.60 ), nrow=2 )
fp[[2]] <- 0.85

# Left largest leaflet
fm[[3]] <- matrix( c( 0.20, -0.26, 0.23, 0.22 ), nrow=2, byrow=TRUE )
fc[[3]] <- matrix( c( 0.00, 1.60 ), nrow=2 )
fp[[3]] <- 0.07

# Right largest leaflet
fm[[4]] <- matrix( c( -0.15, 0.28, 0.26, 0.24 ), nrow=2, byrow=TRUE )
fc[[4]] <- matrix( c( 0.00, 0.44 ), nrow=2 )
fp[[4]] <- 0.07

n<-250000 # you might want to make this smaller if it takes forever to render
x <- numeric( n )
y <- numeric( n )
x[1] <- 0
y[1] <- 0

for( i in 1:(n-1) ) {
  choice  <- sample( 1:4, prob=fp, size=1 ) <- fm[[ choice ]] %*% c( x[i], y[i] ) + fc[[ choice ]]
  x[i+1]  <-[1]
  y[i+1]  <-[2]

plot( x, y, cex=0.05, col="dark green" )

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