Far from the light of day, and somewhere near Hampstead

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.

Cabinet war room junction box at Paddock [CC-BY-SA-3.0 Steve Cook]

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.

Twice a year – once in May for local residents, and again to the general public during Open House Weekend – the Housing Association kindly allow members of Subterranea Britannica to take members of the public into the bunker to see the place that Churchill allegedly described as:

far from the light of day […and…] somewhere near Hampstead

Churchill’s grasp of North London geography was apparently even worse than mine: the bunker is considerably nearer Neasden (or Neeeeeeeeasden, as the Jubilee Line announcements would have it)  than Hampstead. I’ve served as wrong-door-blocker and trip-hazard-pointer for open days twice now, and if you missed out on a trip to Paddock during Open House Weekend this year, I’d heartily recommend it for next.

We shall not explore the underlying reasons for my darling husband’s interest in dungeon-like holes in the ground:

Alex at Drakelow [CC-BY-SA-3.0 Steve Cook]

Alex calls in a tactical nuclear strike on Croydon from the Drakelow nuclear bunker

but like abandoned bunkers for their dankness, and for their decay, and for their reminder to us all of the essential futility of existence in the face of the Second Law.

I also like the fungi.

Paddock door with fungus [CC-BY-SA-3.0 Steve Cook]

Ph’nglui mglw’nafh Cthulhu R’lyeh wgah’nagl fhtagn

If you keep the wood in a building above about 25% moisture, it will slowly but surely be destroyed by fungi whose ecological niche is turning the presumptuous handiwork of humans into carbon dioxide. The most well-known of these is the dry rot fungus, Serpula lacrymans. Dry rot and other wood-destroying fungi make their living by breaking down wood to release sugars that they can use as food. Wood is a very complex material; a fibre-composite of many hollow tubes cemented together:

Scanning electron micrograph of hardwood [© Ian Morris, used with permission]

Scanning electron micrograph of a small block of hardwood. The wood is made of assorted hollow tubes, each of which is the remains of a dead cell’s multilayered cell wall.

Wood is made principally of cellulose, which is the same stuff from which cotton clothes and paper are constructed. Cellulose is difficult to break down, as the individual molecular strands are tightly packed together by hydrogen bonding, making a near-crystalline material that is very impermeable to water, and even more impermeable to digestive enzymes. Most herbivorous animals subcontract out the work of breaking-down cellulose to the bacteria and fungi that live in their guts.

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

Cellulose consists of thousands of glucose molecules chained together.

Although cellulose is difficult to break down, the other main component of wood, lignin, makes cellulose look positively fragile. Plants make lignin by secreting phenolic alcohols into their cell walls, and then semi-randomly polymerising these alcohols together using free-radicals. The mechanisms of lignin synthesis and its global structure are still areas of active research (or furious argument, depending on your point of view). From the plant’s perspective, lignin is a marvellous glue: it creates a substance that cannot be broken down by conventional enzymes, as you’d need hundreds of them, one for each of the many kinds of linkage found in the lignin. It also provides the concrete to the cellulose’s reinforcing bars. For would-be wood-eaters though, it poses a significant problem.

Lignin structure [CC-BY-SA-3.0 Steve Cook, based on User:Chino's structure on Wikipedia]

Small part of possible lignin structure.

Brown rot fungi like the dry rot, wet rot (a.k.a. cellar fungus, Coniophora puteana), mine fungus (Fibroporia vaillantii) and many of the others that infest the Paddock bunker (and who knows, maybe your basement too?) break down wood by more-or-less the reverse of the process by which lignin is made. Brown rot fungi release free-radicals into the wood. These tiny free-radicals can penetrate where no bulky enzyme every could, and they oxidise and smash the cellulose into fragments.

This is not the most elegant way of breaking down wood, and it leaves a lot of brown lignin muck behind (hence the name ‘brown rot’), much of which I trudged over my kitchen floor when I got home on Saturday.

White rot fungi, such as the honey fungus (Armillaria mellea), have a more delicate way of dealing with wood. They also generate free-radicals, but they are able to fully break down the lignin to carbon dioxide. As they break down the lignin, the remaining wood becomes a bleached and friable cellulose fluff. White rots use an enzyme called lignin peroxidase to make these free-radicals. Because free-radicals are not very fussy about quite what they oxidise, white-rot fungi can break down a lot more than just lignin. Some, like Phanerochaete chrysosporium, have been used in the bioremediation of soil that has become contaminated with explosive or creosote residues.

Lignin peroxidase [CC-BY-SA-3.0 Steve Cook; based on Blodig, Smith, Doyle & Piontek; PDB 1B82]

Lignin peroxidase. The flat thing in the middle is a haem group, similar to the one you find in haemoglobin in human blood. However, rather than binding oxygen, it binds hydrogen peroxide. The smaller highlighted bit below the haem is a tryptophan residue. The hydrogen peroxide oxidises the enzyme’s haem group, which in turn oxidises the tryptophan residue, which in turn oxidises lignin.

Contrary to what you may have guessed, the delicate white-rot approach actually seems to be the more evolutionary ancient mechanism, with the heavy-handed brown rot approach being a later innovation.

Wood destroying fungus phylogeny [CC-BY-SA-3.0 Steve Cook, with images from James Lindsey at Ecology of Commanster, Wikipedia's User:jensbn, User:ecornerdropshop, USer:Audriusa, and Flickr's Doug Bowman]

Highly abbreviated phylogeny of wood destroying fungi. White rots shown in grey; brown rots in brown. Note the way that the brown rot lifestyle has evolved at least twice (actually more!) from within separate groups of white rots. Schizophyllum is the closest relative of the cultivated mushroom (Agaricus bisporus) shown in the diagram above. Dry rot (Serpula) is not too distantly related to the penny bun bolete (cep, porcini, Boletus edulis). Based on Floudas, D. et al. (2012) The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336 1715-1719.

If it weren’t for lignin, we might have had a harder time bringing on the climatic Armageddon that we’re all working so hard towards. Coal is the buried and compressed remains of lignin-rich trees that died around 360 to 300 million years ago, during the Carboniferous period. In modern ecosystems, dead trees are generally recycled by brown and white rot fungi, but for 60 million years, trees apparently had enough of an upper hand over their undertakers that huge deposits of coal were laid down. The oxygen concentration of the air was boosted to 35% by the imbalance between oxygen-producing photosynthesis by plants and oxygen-consuming respiration by wood decaying organisms, allowing enormous insects with half-metre wingspans to fly. It is possible that it was the evolution of lignin that brought on the Carboniferous, and the evolution of lignin peroxidase that ended it, but attributing cause and effect in Deep Time usually results in data-egg on speculator-face, so perhaps you should forget I even mentioned it.

Wood destroying fungi are not only biochemical marvels, they are also splendid architects. Unlike plants and animals, fungi are not composed of cells containing a single nucleus, but rather of hyphae, which are fibrous tubes containing many nuclei. Like cells, hyphae can be packed together in various ways to make specialised tissues and organs, the most familiar of which is probably the mushroom, which are the tasty genitals of the fungus Agaricus bisporus. Wood destroying fungi produce genitals of highly variable tastiness, including jelly ears:

Auricularia auricula-judae on wood at Silwood Park [CC-BY-SA-3.0 Steve Cook]

Ear fungus (Auricularia auricula-judae); tasty despite the look of the thing

Brackets:

Hoof fungus (Fomes fomentarius) on tree at Silwood Park [CC-BY-SA-3.0 Steve Cook]

Hoof fungus (Fomes fomentarius); not tasty

And wobbly yellow things:

Fungal fruiting bodies from Paddock [CC-BY-SA-3.0 Steve Cook]

Something eating the remains of a desk in Paddock’s BBC radio broadcast suite; indeterminate tastiness.

One of the more wonderful structures created by wood-destroying fungi, and one that is much evident at Paddock and at Drakelow (another bunker I have known and loved) is the rhizomorph:

Rhizomorphs growing out of a door-frame at Drakelow [CC-BY-SA-3.0 Alex Lomas]

Rhizomorphs growing out of a door-frame at Drakelow

Rhizomorphs are thick, cord-like structures resembling plant roots. They allow some wood destroying fungi to grow over inedible surfaces and locate new planks and door-frames and skirting-boards to colonise and destroy. Some fungi, like the honey mushroom mentioned above, use them to hop from living tree to living tree, destroying whole orchards of wood in their wake. The rhizomorphs of dry rot are particularly hardy and capable of penetrating masonry in their search for food.

Since my last visit to Paddock two years ago, the brown rots have released just a little more of the organic fixtures and fittings back into the carbon cycle. All flesh is grass; and all wood is ash. Quietly the fungi triumph.

Fungus at Paddock [CC-BY-SA-3.0 Steve Cook]

My name is Ozymandias, king of kings: Look on my works, ye mighty, and despair!

A brief history of rubbish

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.

Setting aside the unjustifiable jibe against “lowly” non-human animals, this observation is as true today as it was in 1972, but you certainly wouldn’t know that from the way the results of the ENCODE project were reported last week. The ENCODE project has claimed that 80% of the human genome has a “specific biological activity”, and journalists have widely reported this as a scientific earthquake that has destroyed the “myth” of junk DNA.

I think this is a headline-baiting and flawed analysis (and I’m certainly … not … alone), but the argument is much more interesting than what one trumped-up Teaching Fellow thinks.

Ohno’s 1972 observation is an aspect of a bigger picture in genomics called the C-value paradox. The C-value of a cell is the amount of DNA contained in its nucleus. In the case of a human egg cell, this is about 3 billion base-pairs, but for comparable cells in different organisms, the C-value varies enormously:

C-value paradox [CC-BY-SA-3.0 Steve Cook]

Note the logarithmic scale (powers of 10) on the y-axis. Blue boxes represent ranges for groups of organisms, with examples of those groups shown as black bars to the right. I’m sticking with tradition, and presenting these data as a Scala Naturae, with the pointless scum on the left and the important organisms on the right. As we all know, evolution produces a Great Chain of Being, not a messy tree*.
* May be complete bollocks.

Bacteria such as Escherichia coli have typical genome sizes of one to ten million base-pairs. The genome size of single-celled organisms that pack their DNA into a nucleus (“protists” in the graph above) varies a great deal more, from about ten million to a trillion base-pairs. Multicellular organisms such as insects and vertebrates have a slightly higher lower limit (about one hundred million base-pairs), but a similar upper limit to the “protists”.

Although the lower limit of genome size in a group fits in with our (arrogant and ill-justified) presumptions about the “complexity” of an organism, the upper limit varies enormously, with the genome size of quite closely related organisms sometimes differing by as much as 100-fold.

Pufferfish (Fugu in the graph above) have a genome size about one tenth the size of a human’s, and salamanders (Amphiuma) have a genome size at least ten times larger. This is the C-value paradox: why would a salamander need ten times as many genes as a human, and – however much it deflates our egos– it’s very difficult to see why bald apes with delusions of grandeur would need ten times as many genes (or even regulatory DNA sequences) as a pufferfish.

Fugu sp. [CC-BY-SA-3.0 Alex Lomas]

Fugu! Poison, poison, poison, tasty fish

Ohno used the term “junk” to describe the apparently superfluous DNA that makes up the difference between an observed genome size for a particular organism, and the lower limit for the group to which it belongs. Pufferfish – for reasons unknown – contain very little of this “junk”, whereas salamanders are apparently even less in control of the proliferation of their “junk” than we humans are. This superfluous “junk” is the DNA sequence equivalent of a commensal organism, i.e.a largely harmless hanger-on that you might be fractionally better off without, but which generally isn’t worth the effort of getting rid of.

Tillandsia usneoides [CC-BY-SA-3.0 Alex Lomas]

Tillandsia usnoides (Spanish moss), a spindly upside-down pineapple which grows epiphitically on trees in the Americas, usually without ill-effect on the host tree

In 2001, a rough draft of most of the human genome was published by the Human Genome Consortium. A break-down of the data supports the suggestion that much of the genome of humans (and by implication, even more of the genome of salamanders) is “junk”:

Contents of the human genome

Only one or two percent of the human genome codes for the proteins that construct your body. This DNA is transcribed to messenger RNA, which is then translated to protein, a process whose details have been used to torture undergraduate students for many decades.

Another two or three percent of your DNA codes for functional RNA molecules, which are vital components of the machinery that translates messenger RNA into protein. A few more percent are structural, forming the ends of your chromosomes, or providing the anchor points needed to pull chromosomes around when your cells divide. One percent or so is of obvious regulatory function, helping to bind proteins that turn your genes on and off as required.

So, all in all, about 10% of your genome (the reddish segments of the pie chart above) is of well-known, long-established, and unambiguous function. The other 90% seems to be superfluous “junk”. Despite all the furore generated by the ENCODE project, nothing written above is news. Only about 1% of your genome directly encodes proteins, but it’s been well-known for a long time that at least 10% of your genome is “functional” by a slightly broader but uncontroversial definition.

So what changed last week?

If you read the press releases, it seems to be “everything”. If you read many of the blogs about this, it seems to be “nothing at all”. You have stumbled upon a genuine scientific argument, one with real mudslinging about real data, rather than the invented controversy of creationists and climate change ‘sceptics’.

ENCODE claims to have found “specific biological activity” for 80% of the human genome, because 80% of the genome appears to have a reproducible interaction with one of the very many proteins that bind, modify or transcribe DNA. An important implication is that much more of your genome is involved in switching your genes on or off than was previously thought.

The reason for the skepticism over the 80% claim, which I share, is that if you look at the pie chart above, you’ll notice a big chunk of blue and purple segments labelled “transposons”, “viruses”, “LINEs” and “SINEs”. About 50% of your genome is made of the corpses of various kinds of virus, indeed, a full 8% is made of broken copies of retroviruses similar to HIV.

In the evolutionary past of the human species, very occasionally, retroviruses similar to (but – I stress – not actually) HIV have inserted their genetic information into the DNA in the nucleus of a germ-line cell, i.e.a cell that is fated to make eggs or sperm. These integrated viruses can then be passed directly from parent to offspring, alongside the cell’s “own” DNA, without going through the rigmarole of escaping from the cell and being coughed, vomited or ejaculated into their next victim.

Integrated viral sequences, and the similar “long interspersed nuclear element” sequences (LINEs) – another 20% of your genome – can continue to replicate indefinitely by copying-and-pasting themselves into new sites in your genome. However, over evolutionary time, most of these inserted viral sequences (and their copies, and copies of copies, and copies of copies of copies…) accumulate mutations and lose the ability to replicate independently. They become fossilised ghosts of misery past. There is no terribly strong pressure from natural selection to remove the broken sequences from the genome, as they’re not terribly harmful. So these corpses tend to accumulate over time, like moribund copies of old Word documents on a hard-drive. Some organisms (salamanders) have come to have more of this decomposing genetic muck than others (pufferfish).

Parasitic sequences in the human genome [CC-BY-SA-3.0 Steve Cook]

LINEs replicate using the same enzymes as retroviruses: reverse transcriptase and integrase. The DNA sequence (green) of the LINE is transcribed by the host cell into messenger RNA (pink), which is then translated by the host cell to make reverse transcriptase (RT) and integrase. The reverse transcriptase makes a DNA copy of the messenger RNA, which is then pasted into a new site in the genome by the integrase. LINEs are parasites on the host genome. SINEs are a second class of parasitic element that don’t even encode their own enzymes: they are transcribed by the host cell, but then use the LINE’s enzymes to copy and paste themselves. They are parasites upon the backs of other parasites, yet they comprise another 13% of your genome!

50% of your genome is broken viruses. These make up a substantial fraction of the 80% figure that is causing the fuss, and this is where the controversy lies.

Having “specific biological activity” doesn’t mean the same as having “important biological activity”. Although there is precedent for viral sequences being co-opted for interesting new roles in the cell, these poachers-turned-gamekeepers appear to be a vanishingly small fraction of your genome. But the raison d’être of a viral sequence is to get transcribed, and old habits die hard, or at least, tail off slowly as the viral sequence rots away. Many rotting viral sequences are likely to retain some residual function, up to and including being transcribed to messenger RNA. Whether occasional transcription of broken viruses has any biological importance is a completely different question from whether they bind the relevant proteins to be transcribed at all. The messenger RNA could simply be degraded without interesting consequences, neither for good nor for ill.

Similar counterarguments can be made for DNA sequences in the rotting viral sequences that bind regulatory proteins. DNA binding proteins are not terribly specific, and even completely random DNA would be expected to have many binding sites for these proteins. Many of these binding sites may be completely irrelevant to gene regulation, in the same way that very few mentions of the phrase “the end” in a book will actually result in you closing the book because you have reached “The End” of it.

If I were feeling cynical (and you should note this is my ground state, so I barely know what the alternative is) I’d suggest the press-releases and headline figures of the ENCODE publications were deliberately chosen to court controversy of the sort I have now spent three hours adding to by writing this blog-post. When the dust settles, molecular biologists will have a very nice map of places to go looking for genuine co-option of “junk” to novel functions, but most of the “junk” DNA will still be just as much “junk” as it was a week ago.

Having said all of that, there is one way in which I hope that the end for “junk DNA” is nigh. The fossil viral sequences are indeed “junk” as far as the rest of the genome is concerned, but equally well, the 10% (maybe 20% by the time the ENCODE data has been properly considered) of the genome that is of “known function” could be equivalently described as “stupid” for replicating the parasites and commensals hitch-hiking on its back. Your genome is 90% “junk” DNA and 10% “stupid” DNA.

However, I wouldn’t describe the epiphytic orchids or white-rot fungi on a Brazil nut tree as being “junk” organisms, nor would I describe the tree as being “of known function” compared to them. Ecologists have a number of words like “parasite”, “commensal”, “mutualist” and “hyperparasite” for usefully describing the relationships between organisms in an ecosystem, and I wonder if using these might be a more illuminating way of describing the contents of your genome than dividing it into “important stuff” (important to whom?) and “junk”.

Beautiful butterworts

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:

Pinguicula sp. [cc-by-sa-3.0 Steve Cook]: unknown butterwort from German Alps, probably P. vulgaris or P. alpina. Tongue-shaped lime-green leaves form tight rosette, surfaces are covered with sticky mucilage secreted by tiny mucilaginous glands

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?

Pinguicula alpina [cc-by-sa-3.0 Steve Cook]: bank of alpine butterworts in flower in Slovenia

Pinguicula alpina in Slovenian Alps

I’ve seen wild butterworts once before (in the Slovenian Alps), where they were obligingly in flower, as you can see above. The two commonest species in the Alps are the white-flowered Pinguicula alpina (alpine butterwort) and the purple-flowered Pinguicula vulgaris (common butterwort): the latter is also found in the UK, but is by no means ‘common’ here. The photo at the top could be either of them, but without the giveaway flowers it’s difficult to tell which.

Pinguicula alpina flower [cc-by-sa-3.0 Steve Cook]: detail of butterwort flower. Flower is white and zygomorphic with five petals, lowermost petal is distinctly hairy and throat of flower leading to nectar tube is yellow

Pinguicula alpina, detail of butterwort flower

Like many carnivorous plants using the’ flypaper’ trapping mechanism, butterworts hold their flowers at some distance from their leaves: the usual explanation for this is that it helps the plant to avoid accidentally capturing its pollinators, but I can find no proper data that support this. The butterworts’ pollinators are evidently fairly large: probably butterflies with long tongues, judging by the very long nectar tube, which you can see in the image of one of the other native UK species (Pinguicula grandiflora) below:

Pinguicula grandiflora flowers [cc-by-sa-3.0 Alex Lomas]: flowers are purple, each has a nectar tube about 15 mm long projecting from the back of the flower

Each Pinguicula grandiflora flower has a nectar tube about 15 mm long projecting from the back of the flower

Butterflies don’t strike me as likely to end up as accidental prey, considering the usual prey is extremely small (about 1 mm) flies:

Pinguicula moranesis drowning a gnat [cc-by-sa-3.0 Steve Cook]: fungus gnat trapped in mucilage secreted by stalked glands covering the leaf surface

Death by butterwort

It’d be pretty easy to design an experiment to investigate this properly, perhaps with the cape sundew Drosera capensis or Alice sundew  Drosera aliciae which are not closely related, but which use a similar trapping mechanism. If you’d be interested, let me know!

Pinguicula moranesis glands [cc-by-sa-3.0 Steve Cook]: microscopic stalked glands covering the leaf surface secrete mucilage

Mucilage glands of Pinguicula moranesis (Mexican butterwort)

Farewell Gore Vidal

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.

Gore Vidal’s novels The City and the PillarMyra BreckinridgeJulianMessiah and Burr are amongst the most wonderful I have ever read. That there will be no more makes me very sad indeed.

An unheard farewell will have to do.

Gore Vidal by Carl van Vechten 1948

Gore Vidal, 1925 – 2012 (photo by Carl van Vechten, 1948)

The magnolia misunderstanding

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.”

The casual acceptance of this fallacy causes otherwise clever people to made the most asinine statements. I remember – as an undergraduate in the last millennium – being told by a now long retired entomologist that:

“Mosquitoes are lower Diptera [flies], so it’s surprising they are so successful, given how primitive they are”

I distinctly remember the dismissive lip-curl that accompanied the “lower”, as if mosquitoes had passed the port to the right at some point in their evolutionary history.

Describing groups as “basal” is merely the latest step on the euphemism treadmill that started with “lower”, and which has only recently started to view “primitive” with suspicion. All three words are (mis)used in exactly the same way: to describe a group of organisms that “branched off early” from the rest of a group, with the implication that such “basal” organisms are primitive, relictual, lower forms of life that deserve pity rather than study.

“With suspicion” is exactly how these words ought to be viewed. When they are applied to groups of organisms rather than to character states of those organisms, these words are wholly inappropriate. In the botanical world, it is the magnolias and their relatives which have long been on the receiving end of the “primitive” slur. Magnolias retain a number of features thought to be possessed by the common ancestor of all flowering plants, such as having pollen grains with one hole rather than three, and having spirally arranged petals in their flowers:

Angiosperm phylogeny stressing nonmagnoliids [cc-by-sa-3.0 Steve Cook]: magnolia appears as an outgroup to the ((thistle,rose),(onion,maize)) clade

Magnolia is basal to thistles and roses and onions and maize, oh my…

The magnolias do indeed appear to branch off early from the “main trunk” of the flowering plants, but this entirely depends on what you define as the main trunk. Here is another phylogeny based on the same data, but including a different but no less arbitrary subset of the flowering plants:

Angiosperm phylogeny stressing magnoliids [cc-by-sa-3.0 Steve Cook]: thistle appears as an outgroup to the ((magnolia,bay),(pepper,birthwort)) clade

But the thistle is just as “basal” to the magnolia (and bay trees and black pepper and birthworts) as the magnolia is to the thistle (and rose, etc).

With a little change of perspective, the allegedly “advanced, derived”  thistles appear as the basal group, branching off before the splendid diversification of the magnolia and its close relatives. The thistles presumably suffer from various evolutionary deficiencies such as having non-ephemeral antipodal cells. This is no less ridiculous a thing to choose as an overall marker of the “primitiveness” of an entire group than is the number of holes in a plant’s pollen grains.

There’s simply no objective way to define a “main trunk” in a phylogeny because there isn’t any such thing. There are branches, and every branch-point is a rotatable, symmetrical fork. Some of these branches, like those leading to the platypus (and echidna), or to the lungfishes, or to the magnolias, may not lead to a great plethora of still-living organisms compared to their sister groups (the other mammals, the land vertebrates, and most of the other flowering plants respectively), but this is nothing to do with their being “primitive” or “basal” as a whole.

There are perfectly good alternative ways to describe the relationship between magnolias and other plants:

  • The magnolia is an out-group with respect to (most of) the rest of the flowering plants. But, absoutely equivalently, any random member of the rest of the flowering plants is an out-group with respect to the magnolias and their relatives.
  • Magnolias and their relatives are the sister-group of (most of) the rest of the flowering plants, which stresses the symmetrical nature of the relationship.
  • The pollen of the magnolias retains the primitive character state of having a single pore through which the pollen tube germinates. But, this does not mean that magnolias as a whole are primitive: like the platypus and the cycads, the magnolias and their relatives have experienced genetic drift, natural selection, diversification and extinction like all other living, evolving things.

Isn’t it about time we started using these terms rather than value-laden arbitrary terms like “basal”? Isn’t it about time I got around to fixing the appalling article on Wikipedia rather than writing a rant to an audience of zero here? Ah…

Why living fossils need to die

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.

Cycas thouarsii, Christmas 2011 [CC-BY-SA-3.0 Steve Cook]

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.

Encephalartos ferox [cc-by-sa-3.0 Steve Cook]

Fierce cycad, with cones

Cycads are a beautiful and enigmatic group, and it is a great pity that if you’ve ever been introduced to these lovely plants at all, it will probably be in the clichéd context of the title of this post: “cycads are living fossils that were eaten by dinosaurs.”

The latter is quite true: cycad seeds, like those of many plants, are eaten and distributed by dinosaurs.

Blue-tit feeding at bird-feeder, London 2012 [cc-by-sa-3.0 Steve Cook]

I’m quite aware this is neither a good photo, nor is the blue-tit feeding on cycad seeds, but my patience has its limits

It is also quite true that the common ancestor of all cycads lived an exceedingly long time ago (maybe 260 million years ago), pre-dating the common ancestor of the blurry feathered dinosaur above and the dinosaur poster-boy Tyrannosaurus rex by as much as 70 million years.

But that doesn’t mean that cycads are living fossils.

A paper published in Science last year attempted to shed light on this, but really just threw more shade. Researchers at Kew Gardens took DNA from a representative sample of those 300 living species of cycads, many of which they have growing in the Palm House (botany nerds amongst you may wish to play “palm or cycad?” if you visit). DNA tends to accumulate changes over time at a predictable rate in particular genes in particular groups of living things. This allows you to use the number of differences in the DNA sequences from two different species to estimate how long ago those two species diverged from their common ancestor.

The two species shown above (Encephalartos ferox and Cycas thouarsii), are about as distantly related as two cycads can be. They appear to have diverged from a common ancestor that lived around 180 million years ago: about the same time that the common ancestor of blue-tits and Tyrannosaurus was strutting the Jurassic plains.

Interestingly, the six largest genera of cycads (Cycas, Encephalartos, Zamia, Macrozamia, Ceratozamia and Dioon) all seem to have rapidly diversified in the last 12 million years or so. The authors consider that “living fossil” is therefore an inappropriate term for these plants, because of this recent spurt of speciation. As ever, the science was variously misreported: spot the obvious mistake in this report compared to the simplified summary of the paper’s findings below.

Cycad evolution [cc-by-sa-3.0 Steve Cook, based on Nagalingum et al. 2011, DOI: 10.1126/science.1209926]

The six larger genera of cycads have all diversified rapidly in the past 12 million years, but share a much more ancient common ancestor, around 180 million years ago.

I don’t think the paper goes nearly far enough.

Cycads are not “living fossils”, but the reason is more fundamental than their recent diversification. “Living fossil” is – at best – an almost meaningless term, and – at worst – a thoroughly misleading one.

What exactly do people mean when they call something a “living fossil”?

“Living fossil” seems to be used to mean “a living species that appears to be the same as a species known only from fossils, and is the sole surviving representative of an archaic lineage“.

Biologists almost universally agree that all living things are descended from a population of organisms (or something along those lines) that existed some 3500 million years ago. Every bacterium is descended from this Last Universal Common Ancestor (LUCA); every human is descended from that same LUCA; the great-great-great-ur-grandmother of every cycad, dinosaur, toadstool and eyelash-mite was that same LUCA too.

When cycads, or coelacanths, or horseshoe crabs are called “living fossils”, there is an implication that these are very “ancient” organisms. But this is obvious bunkum: all living organisms are the descendants of LUCA; all living organisms have been evolving for at least 3500 million years; and all living organisms are therefore the venerable relics of an archaic lineage that stretches back to a time when the Earth was young and buxom and care-free. Being a “surviving representative of an archaic lineage” is something that all living things have in common; it’s not  something specific to “living fossils”.

It’s also very difficult to judge whether a living organism is genuinely similar to a fossil form. Many of the ‘cycads’ found in the fossil record have actually turned out to belong to a rather different group of plants called the Bennettitaleans. Bennettitalean leaves look very similar to those of cycads, but their cones were embedded amongst their leaf-bases rather than borne in the whorl of leaves at the top. There are fossils that are thought to be more closely related to cycads than to any other living plants, but even these true cycad fossils (e.g. Baenia/Nilssonia) often have dangly open cones quite different from the tight upright cones of living cycads. It’s almost as if someone deliberately chose to ignore the differences in those features that didn’t fit the nice story about cycads being decrepit relics of a bygone age.

Compare this with the damp blue-tit above. The bone structure of blue-tits (and other birds) is very similar to some theropod dinosaurs, so why don’t we refer to birds as “living fossils”? The similarity of fossil cycad and living cycad leaves is enough to get cycads branded as “living fossils” despite significant differences in their cones. So why shouldn’t similarity in the bones of fossil dinosaurs and living dinosaurs get birds branded in the same way, despite significant differences in the structure of their feathers? The choice of which features to fixate on is essentially arbitrary.

Even if a fossil cycad’s morphology were absolutely identical in every conceivable way to a living cycad’s, there is much that does not fossilise easily (or at all): soft tissues, behaviour, favourite TV show. Even if these invisible features were somehow recorded, it would be inconceivable that their DNA sequences would have remained wholly unchanged for millions of years. In fact, this is very easily disproved in most cases, including the case of the cycads, as we’ve seen. Larry Moran makes the argument much more eloquently than I: evolution is not just about obvious changes in the conveniently fossilisable bits of living things, and the term “living fossil” gives an unhelpful impression of how evolution works.

So, if a “living fossil” is just “a living species that appears to be the same similar in some rather arbitrary ways (but not in others) to a species known only from fossils, and is the sole surviving representative of an archaic lineage“, then the only thing that seems to distinguishes a “living fossil” from any organism we’ve arbitrarily decided looks like a fossil from a certain angle is that a “living fossil” is somewhat alone in the world, with no close living relatives.

The 300 species of cycad (which frankly stretches “sole” to breaking point) may not share a common ancestor with any other group of plants younger than 250 million years or more. But “having no close living relatives” does not mean that cycads (or coelacanths, or horseshoe crabs…) are evolution-shy “living fossils”. If it did mean that, there are only two things we’d need to do to make human beings a “living fossil”. Firstly, we’d need to wipe out every other species of ape on Earth (a goal that we appear to be making substantial progress towards. Go team Homo! Make Chicxulub proud!); and secondly we’d need ignore the fact that humans hold their cones upright – sorry – hold themselves upright rather than brachiate like gibbons or knuckle-walk like chimps. Without anything else living with which to compare ourselves, the difference in locomotion of these – now extinct – fossil apes would seem trivial. Humans will look like fossils by definition, if the only closely related things you have to compare them to are fossils.

“Living fossil” just means a species with no close living relatives. In which case, just say that, and stop using this silly value-laden term.

Of the 300 living species of cycads, about a third are endangered; some critically so. Calling cycads “living fossils” subtly suggests that these plants have been doddering around for millions of years, simply waiting for the curtain to fall. This is hogwash. Cycads are going extinct because of unscrupulous collecting and habitat destruction, not because of some grinding evolutionary inevitability. Using terms like “living fossil” gives us an unwarranted excuse to ignore our complicity in their loss.

“Living fossil” is an arbitrary and belittling term, and it needs to die.

Community payback for undergrads

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.

Unfortunately, a straw-poll of sixty students I was teaching recently turned up only one person who had contributed an edit of any kind. In 2011, Wikimedia estimated that only 6% of readers ever edit articles, and even this low figure is probably an overestimate, given that those who responded to the poll were the sort of helpful (but highly unrepresentative) people who respond to polls with something other than “send to trash”. The main reason cited for not editing was “happy to just read the articles”, but the other popular reasons were related to lack of confidence in how to edit, and lack of confidence in the ability to incorporate accurate information (“how to write”).

So, aside from the obvious barrier of actually caring enough to correct or write an article at all, there is a barrier to entry for that “Anyone” who wants to edit Wikipedia. Some potential editors find the wiki mark-up difficult: the days of students being on speaking terms with HTML entities are passing as surely as have the days of grues and 5¼ inch floppies. There is the worry that you’ll be treading on somebody’s toes if you edit that somebody’s favourite article. And, of course, there is the fear of releasing your fragile words upon the world, when that world is full of spiteful and joyless critics.

Brocchinia reducta, Hampton Court flower show 2003 [cc-by-sa-3.0 Steve Cook]

The first substantial thing I contributed to Wikipedia was a blurry image of a carnivorous bromeliad. It’s still there.

Having made a tiny contribution to the carnivorous plant Wikiproject many years ago, I thought I could design a decent workshop on Wikipedia-editing as part of an undergraduate course I was involved with this year. Students are well-practised at navigating and summarising primary literature in essays, and must have come across unhelpful articles frequently, so I focussed the workshop principally on “how to edit” rather than “how to write”, although we did cover the importance of pitching the explanation at a suitable level for a general science audience.

Mind-set

It’s important that potential contributors know the basics of what Wikipedia is, and its core principles: No Original Research, Neutral Point of View, Verifiability, Free Content, etc. In retrospect, I needed to make it clearer what NOR meant, as some misinterpreted this as “you can’t use primary literature” rather than “you shouldn’t include concepts/data not published elsewhere”.

Licensing of text, and particularly of images, is rather fiddly. GFDL, and CC-BY-SA-3.0, and Fair Use, and Lions and Tigers and Bears Oh My, tend to obscure the basic premise: “that which you upload should be your own work, and once you upload it, people can do whatever they like with it as long as they credit you”. The sourcing of free images to illustrate articles can be difficult, but it’s generally not difficult to create simple vector diagrams with e.g. Inkscape. I think it is worth spending more time on this than I did, as a good image is worth a substantial amount of text, even if that text should still end up as an alt tag for screen-reader accessibility.

Mark-up

The “Edit” tab does come with WYSIWYG-ish buttons, but using the mark-up directly is important for all but very simple edits. To help the students with this, I asked them to reproduce a simple page on an ex-wood-preservative, using a crib-sheet of the syntax for headings, italics, lists, images, etc.

Referencing syntax became much less vile at about the time I was involved in the carnivorous plant pages:

  Oceania has always been at war with Eastasia<ref name="Goldstein1984">
  {{Cite journal | author=Goldstein E | title=The theory and practice of oligarchical
  collectivism | journal=[[Journal of the Brotherhood]] | volume=1 | year=1984 |
  pages=1-666 |  doi=mini.luv/eablair.1949 }}</ref>

This makes “Verifiability” a (relative) breeze. Crossref is useful to find DOIs for papers that lack them. The only common question about the syntax I received was how to use the same reference twice. Several students worked out how to include tables, cladograms, protein infoboxes, embedded video, etc., by modifying the mark-up from pages that had them already, which is the sort of copy-and-paste from Wikipedia I can actually approve of!

Out-put

The articles edited by the students were:

Some articles started out as stubs, others were more complete before the editing took place. For a workshop done for course-credit, stubs are a simpler thing to assess, as the contribution is obvious. However, some stubs are stubs for the obvious reason that there’s precious little that you can say (let alone verify) about the topic, so allowing participants to edit more complete articles is sensible. It’s easy enough to use the diff to see what has been added and removed, providing the majority of the edit is committed as one big chunk (having been prepared in the participant’s sandbox).

If you think any of the improved articles are in need of further improvement, then you know what you can do.

On-wards

There are plenty of dodgy, incomplete and missing articles on Wikipedia, and it would be great to get students involved in editing articles much earlier in their careers. I’m going to offer a similar workshop to some first-year students in the summer term, and I provide my slides for your CC-BY-SA-3.0 delight.

Version 2

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.

To those who offered to adopt content from the old site, I should apologise up front. I never seemed to find the time to organise a hand-over, and by the time I did find time, the moment had well and truly passed. The Perl 5 tutorial was the thing requested more often than not, but that had become pretty moribund too, and I thought it better not to inflict blessed hashref horrors on baby hackers when they should be using Moose anyway.

Since then, I have been largely teaching, occasionally tweeting, and rarely finding a moment to do anything sufficiently creative to be worth sharing. Hopefully this will now change, or – at least – I shall be able to moan in slightly greater detail than 140 characters affords.

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