Alpha diversity and beta diversity

At today's journal club meeting, we discussed Alexander Pyron's opinion piece We don't need to save endangered species - extinction is part of evolution. I mentioned it in passing before and still think that his core argument, which is also reflected in the title, is logically equivalent to saying that murder is okay because all humans are going to die of natural causes one day anyway. But reading his piece more thoroughly than before, I now notice a few other, um, problems. The highlights:

Species constantly go extinct, and every species that is alive today will one day follow suit. There is no such thing as an "endangered species," except for all species.

What weirds me out here is the lack of a phylogenetic perspective in a piece written by a systematist - species are discussed as individuals that pop out of thin air and then disappear again. Of course, in the very long run every species will one day go extinct when the sun expands and boils off the oceans. But until then, in the time frame that Pyron discussed, no, not every species will go extinct, quite a few of them will diversify and survive as numerous descendant species, as did the ancestor of all land vertebrates or the ancestor of all insects in the past. They thus become effectively immortal (until, once more, the sun explodes anyway, etc.).

Yet we are obsessed with reviving the status quo ante. The Paris Accords aim to hold the temperature to under two degrees Celsius above preindustrial levels, even though the temperature has been at least eight degrees Celsius warmer within the past 65 million years. Twenty-one thousand years ago, Boston was under an ice sheet a kilometer thick. We are near all-time lows for temperature and sea level ; whatever effort we make to maintain the current climate will eventually be overrun by the inexorable forces of space and geology.

This is sadly a classic of climate change denialism. Yes, there was change in the past too, but there are some major differences. One is the rate of change - the impacts we are having are coming much faster than most natural changes (excepting e.g. meteorite strikes and similarly sudden events), so that animals and plants have less of a chance to migrate or to adapt than they had in past cycles of warm and ice ages. Second, they have even less of a chance to migrate because we have fragmented their available habitats by putting roads, towns, croplands and pastures into their way. Third, past changes did not affect a highly urbanised human population of more than seven billion people; the potential of global change producing catastrophic results even just for us is much greater now than when we were just a few million widely dispersed hunter-gatherers. So yes, it is true that we cannot freeze the status quo in place forever, but I think we would do well to slow the rate of change as far as possible.

Infectious diseases are most prevalent and virulent in the most diverse tropical areas. Nobody donates to campaigns to save HIV, Ebola, malaria, dengue and yellow fever, but these are key components of microbial biodiversity, as unique as pandas, elephants and orangutans, all of which are ostensibly endangered thanks to human interference.

I just don't even. What is the logic here? "Nobody cares about conserving diseases that horribly kill us humans, so we should not care about conserving harmless pandas either?" How does that follow?

And if biodiversity is the goal of extinction fearmongers, how do they regard South Florida, where about 140 new reptile species accidentally introduced by the wildlife trade are now breeding successfully? No extinctions of native species have been recorded, and, at least anecdotally, most natives are still thriving. The ones that are endangered, such as gopher tortoises and indigo snakes , are threatened mostly by habitat destruction. Even if all the native reptiles in the Everglades, about 50, went extinct, the region would still be gaining 90 new species -- a biodiversity bounty. If they can adapt and flourish there, then evolution is promoting their success. If they outcompete the natives, extinction is doing its job.

And this is perhaps what frustrates me most, because while this is not an uncommon argument against biosecurity measures one would expect a biologist to know about different types of biodiversity instead of confusing them. To explain more clearly what is going on, consider the following diagrams. First, we have three areas, roundland, squareland, and hexagonland, with two endemic species each.

Then humans recklessly move species between the areas, allowing them to invade each other's natural ranges. It turns out that three of the species are particularly competitive and prosper at the cost of the other three, driving them to extinction.

Now there are three types of diversity to consider. The first is alpha-diversity, which means simply the number of species in a given place. As we see it has gone up by 50% in all three areas, from two to three species. Yay, more diversity! This is what Pyron proudly points at in Florida.

What is lost, however, is beta-diversity or turnover, that is the heterogeneity you observe as you move between areas. It was very high originally, as every area had its unique species, but now it has been wiped out entirely. Beta-diversity in the second diagram is precisely zero. Under the first scenario a squarelander can go on a holiday trip to roundland and admire the unique flora of that part of the world; under the second scenario they will travel to roundland and merely see the same few weeds that they have growing in their own front yard back home. And the endemic plants of hexagonland have all gone extinct, a 100% loss of that area's irreplaceable evolutionary history.

(Note that beta-diversity would also be zero if all six species survived everywhere. But that is clearly not a realistic assumption, as it would require each area to have such a high carrying capacity that they should each have evolved more than two species to begin with. We would not expect that all the plant species of the world could survive next to each other in, say, Patagonia, even if they were all introduced there.)

Finally, in our example global diversity has of course also been reduced, by 50%. So yeah, great to have more alpha-diversity in Florida, but does that make up for a massive net loss in both beta-diversity and global diversity? The argument seems rather misguided.

No, the blockchain does not actually appear to be useful for anything much

Merry belated Christmas and a happy new year! For the following note that this is my personal opinion, which I present not as a professional statement and as not necessarily representative of the views of my employer, colleagues, friends and family. I am not a specialist in investment, nor in blockchain technology.

So it is fairly clear that the blockchain based crypto-"currency" Bitcoin is in a speculative bubble. Owning a Bitcoin is not like owning a useful commodity or the share of a company. The price of Bitcoin is entirely based on the assumption that others are willing to pay at least that price at some point in the future, which sounds like a good definition of speculative bubble thinking. (The same may well apply to some degree to the Australian housing market, but at least there you still have a house even if it is currently overvalued; with Bitcoin you will only have a bunch of electrons when the price is corrected to $0).

It is also fairly clear that the ICO (Initial Coin Offering) market is in a speculative bubble. I have been reading the finance section of Charles Mackay's Memoirs of Extraordinary Popular Delusions and the Madness of Crowds, and his descriptions of the various stock offerings during the English South Sea Bubble of 1720...

In the mean time, innumerable joint-stock companies started up every where. [...] Some of them lasted for a week or a fortnight, and were no more heard of, while others could not even live out that short span of existence. Every evening produced new schemes, and every morning new projects.
[...]
Some of these schemes were plausible enough, and, had they been undertaken at a time when the public mind was unexcited, might have been pursued with advantage to all concerned. But they were established merely with the view of raising the shares in the market. The projectors took the first opportunity of a rise to sell out, and next morning the scheme was at an end. Maitland, in his History of London, gravely informs us, that one of the projects which received great encouragement, was for the establishment of a company "to make deal boards out of saw-dust." This is no doubt intended as a joke; but there is abundance of evidence to shew that dozens of schemes, hardly a whit more reasonable, lived their little day, ruining hundreds ere they fell. One of them was for a wheel for perpetual motion--capital one million; another was "for encouraging the breed of horses in England, and improving of glebe and church lands, and repairing and rebuilding parsonage and vicarage houses." [...] But the most absurd and preposterous of all, and which shewed, more completely than any other, the utter madness of the people, was one started by an unknown adventurer, entitled "A company for carrying on an undertaking of great advantage, but nobody to know what it is." Were not the fact stated by scores of credible witnesses, it would be impossible to believe that any person could have been duped by such a project.

 ... read eerily similar to the current craze in ICOs. Check out this excerpt from David Gerard's book Attack of the 50 Foot Blockchain, which I can recommend, by the way. I am not an investment expert, but even I can tell that "whatever these people do, I'm going all in" is not so much a sophisticated investment strategy as mania.

Blockchain technology

It is amazing how often one will read from otherwise sensible people something to the effect of "clearly Bitcoin is worthless, and ICOs are a bubble, but the blockchain is an amazing technology". In fact I was shocked some weeks ago to be sitting in a meeting of taxonomists and hearing somebody say words to the effect of, "it would be great if we could somehow use blockchain in taxonomy", apparently just to be in on something newfangled.

Even without going into any details this seems kind of odd. Surely the rational way to go about one's business is to say, hey, here is a problem, does anybody know a solution?, as opposed to, hey, here is a supposed solution, can we all pretend that we have a problem that it solves?

But let's take a closer look nonetheless. What is a blockchain? And what could it be useful for, perhaps even in taxonomy?

I am going to simplify here, obviously, but to the best of my understanding a good mental model of a blockchain is as follows. Imagine you have a database or, even simpler, an Excel style table. In the realm of taxonomy, let's assume it is a big sheet showing, for each published species name in your country, what its type specimen is, where the name was published, and what the currently accepted name is. This latter piece of information may be a reference to a different line on your sheet if the name has been synonymised, and if the field is empty then the name is accepted. (Again, simplified assumptions.)

One way of managing this taxonomic database is to have one authoritative version of your sheet sitting on the computer of a trusted, central authority, where everybody can look it up and download it, for example like this one. When changes need to be made the central authority implements them on their master copy, done.

As I understand it, the blockchain way would be to have no central authority. Instead, the sheet is distributed in numerous identical copies across lots of different networked computers. The network needs some kind of process for deciding who gets to make a change to the sheet ever so often. Bitcoin uses a tremendously wasteful procedure, but it seems as if there are less wasteful ones that could be used instead. The point is still that instead of one central authority we have lots of copies that constantly need to be harmonised against each other.

Notice something? Of course you do. The whole affair can be made considerably more efficient by simply centralising it, by creating a central trusted authority that manages the one accepted copy, and by dispensing with all the equivalent copies that constantly have to be harmonised against each other. The blockchain approach is just a waste of storage space and computing power.

Really the only reason anybody ever seems to have thought that the decentralisation inherent in blockchain is a good idea is a pathologic distrust of central authority, and concerning crypto-currencies like Bitcoin specifically a pathological distrust of government.

(I am wondering a bit whether there is some kind of psychological projection at work. As an illustrative example take conservative, fundamentalist Christians. Why do they constantly fear that secularists are going to outlaw Christianity, including harmless things like saying "Merry Christmas"? Is it perhaps because outlawing every belief system except their own is what they would do the second they had the power to do so, and they cannot fathom that there are other people out there who are very different, people who genuinely believe that everybody else should be allowed to practice their religion as they see fit, even if they personally don't believe in it? Similarly here I wonder if the proprietarian-libertarian anarcho-capitalists who are constantly afraid that Evil Government Thugs will print so much money that inflation will be at 10,000% are so afraid because abusing government power to enrich themselves is what they would do the second they had such power. Maybe they simply cannot fathom that there are many other people out there who are very different; people who do not constantly obsess about Getting Rich Quick and gloating at the less fortunate but who are happy to live on a modest salary; craftspeople who are simply proud of making high-quality products; academics who simply enjoy figuring out how the world around us works; public servants who genuinely find satisfaction working for the common good; and central bankers who take serious their mandate of keeping inflation near 2%. Not a psychiatrist myself, but wondering.)

So again, nearly every system using a blockchain could immediately be improved by removing the blockchain. But there is another problem. One of the main selling points of the blockchain is that it is "tamper-proof" or in other words "immutable". Again this is an expression of pathological distrust, here the fear that others would tamper with a list of transactions or some other kind of valuable information. For Bitcoin, for example, one of the selling points is that all transactions are irreversible, the idea being that a merchant has the confidence that the customer cannot reverse a payment.

The problem should be immediately obvious: What if a mistake has happened? What if fraud has happened, and the result has already been written into the blockchain? In reality, there is simply close to no market for immutability and irreversibility. All human relationships and interactions have an element of trust, and trying to replace that with the blockchain is doomed to failure.

In financial transactions the merchant benefits more from customers having the confidence that they can reverse transactions with fraudsters than they would from customers becoming very hesitant to make any transactions at all. In other systems the same principle applies: If I were running a taxonomic database, for example, I would want the ability to reverse vandalism or mistakes. As far as I can tell blockchain technology is superfluous and wasteful, and most of its supposed selling points actually appear to be drawbacks.

For a more thorough examination of the issue I can recommend Kai Stinchcombe's essay Ten years in, nobody has come up with a use for blockchain, but of course he does not consider taxonomy :-).

Everything is about white male privilege, even writing advice it seems

I read a headline saying Why the writing advice 'show, don't tell' is inherently political and thought, well, this should be good. The links ultimately lead to an essay called Let me tell you by one Cecilia Tan.

The author discusses 'show, don't tell' (SdT) entirely in the context of world building, i.e. info dumps about the background of a story. She then argues that SdT relies on a shared cultural background, and thus this writing advice privileges writers who can rely on sharing such a background with their readers, i.e. white males.

Now, first, I would not see anything particularly wrong with this in principle, because why should it only apply to white males? If an Iranian woman wrote a novel for Iranian women, it would work the same.

But more importantly, at least to me, and while I appreciate that I am not an author of novels who has run into that criticism myself, her understanding of SdT totally misses the point. Every single time I have seen people complain about being told instead of being shown by a poor writer it was something like this (if necessary search that page for "show-don't" to find what I mean) or this.

So it is not about world building info dumps at all. It is entirely about being too poor a writer to communicate the abilities and emotions of one's characters. It is about merely stating that your protagonist is a good debater instead of introducing her by winning an argument. It is about thinking that your reader is too stupid to understand that the protagonist is sad when you simply write "Frodo cried" and instead writing something to the effect of "Frodo cried because he was sad, and he was sad because as you may not remember Gandalf had just fallen to his death, see previous page". It is quite simply about poor and lazy writing, in a way that is independent of cultural context except to the degree that some other cultures may not even have a tradition of fiction writing (e.g. if it is a culture without a written language).

But apparently everything has to be about Western privilege all the time; there is nothing in the universe that is not about Western privilege.

It's the same hubris that led the white Western establishment to assume its medicine, science, and values superior to all other cultures. We'll come back to that shortly.

Eh, no. A medicine is superior to other medicines if it heals more reliably, and a scientific methodology is superior to other scientific methodologies if it produces more reproducible and accurate descriptions of reality. There are things that demonstrably work (often including substances found in traditional healing herbs) and there are things that demonstrably don't (including the Western tradition of bloodletting). That is all there is to it, no Western or Eastern or whatever needed.

Also, apparently a story about a protagonist having an impact on the outside world is quite simply "colonialism". What? No, people interacting with each other, helping each other against a dark lord's attempt at world conquest, learning from each other isn't colonialism. Invading with an army and taking over other people's countries to exploit them, that is colonialism. Words have meanings. Or at least they should.

Phylogenetic trees in XML format

I recently had the extremely frustrating experience of having had to look into how phylogenetic trees are coded in XML format. To illustrate why this was frustrating, let us start by considering a small phylogenetic tree as an example. I got one sequence each for the genera Nassauvia, Erigeron, Xerochrysum, Matricaria, Lactuca, Senecio, Ursinia, Calycera, Kippistia, and Synedrella from Genbank, and produced a likelihood tree in PAUP. In graphical representation it looks as follows.

So how is it generally saved? The most concise way of scoring a phylogenetic tree in plain text files is the venerable and widely accepted Newick standard. It consists of OTU names separated by commas and grouped into clades by round brackets. There may be numbers after colons, which are branch lengths, and if there is a number directly after a closing bracket it indicates some kind of support value, such as bootstrap or Bayesian posterior probability. The Newick representation of my little example tree is as follows.

Again, very concise. If we want just a tiny bit more bells and whistles we can use the Nexus format. In the context of phylogenetic trees it is just the Newick format plus "#nexus [line break] begin trees;" at the beginning and "end;" after the trees, and then each Newick tree has "tree [name of tree] =" in front of it and another semicolon at the end. The main advantage is that multiple trees in the same file can now have informative names, whereas in a Newick file they cannot.

If we want to find out how this would look in XML format, we can head over to the nexml.org website, where we will find an online tool that can transform our boring old Newick or Nexus trees into shiny, exciting, newfangled NeXML trees (for Nexus-inspired XML I guess, although as we will soon see there isn't really any similarity at all). Of course for this post I have done that with the example tree.



So, what do we see? As the name XML implies, the format is similar to HTML in that it consists largely of nested sets of tags starting with is-smaller-than signs and ending with is-larger-than signs. But those are just the optics. What about functionality?

As a Newick file, my phylogenetic tree was 448 bytes in size. After transformation into NeXML, the new tree file is now 2645 bytes in size, an increase by 490%. This has several obvious benefits in particular for the results of Bayesian analyses where thousands of trees have to be saved and may take up megabytes even in Newick format, for example I can't think of any right now.

And I am not even going to go into how NeXML scores data matrices beyond observing that it appears to require a tag assigning character type for every individual character. In other words, instead of saying something like "characters 1-9000 are anonymous genome-wide SNPs with the possible states 0, 1, 2 and ?", as in Nexus files, you would have 9000 lines of code (!) each saying "character 4306 is a SNP character" and then "character 4307 is a SNP character", and so on, wasting enormous amounts of disk space and/or bandwidth. Efficiency!

More generally, the structure of the tree coded as NeXML is extremely convoluted compared to what it looks like in Newick format. Newick is, as mentioned above, a set of nested brackets indicating clades; consequently it can be examined and read relatively easily, and even allows the user to copy subtrees in or out in manual editing (it helps if you have a text editor like SciTE that shows which brackets belong together). In fact I have often produced hypothetical example trees to illustrate a point on this blog by typing them out in Newick format and then opening them in a tree viewer. NeXML, however, has a list of nodes and edges that are referring to each other via obscure identifiers, making it virtually impossible to read, type out and edit manually, especially for larger trees. But I am sure XML makes life easier for the end user because please insert reasons here.

Next, imagine writing a program that should be able to read a phylogeny. If you want it to read a Newick tree, you merely need to parse nested brackets, recognise taxon names, and deal with branch length and support value annotations; this is relatively straightforward. If you want it to be able to read NeXML trees, on the other hand, it needs to be able to handle a large number of possible tags in varying order, plus various parameters in each tag that can appear in varying order (<node id="ne16" otu="ou27" label="Senecio_vulgaris"/> could just as well be <node otu="ou27" label="Senecio_vulgaris" id="ne16"/>, for example). This makes life easier for programmers because I'm sorry I really have no idea. But I mean, the nexml.org website says that this format is "more easily validated and processed", so that must be true, right? Otherwise they wouldn't claim so, would they?

While on the topic of phylogenetics software, to the best of my knowledge none of the programs that I currently use or have seriously used in the past can read or write phylogenies in XML format. BEAST, PAUP, and MrBayes produce Nexus files, TNT exports its own idiosyncratic format or Nexus, and RAxML produces Newick files. (BEAST uses famously convoluted XML input files, but even here the assumption is that most users import Nexus data matrices into the GUI BEAUTi. At any rate it does not save its output as NeXML.) Mesquite, which uses Nexus as its default format, is supposed to be able to export into NeXML format once we install a certain add-on library, but when I tried to do such a conversion I merely got an incomprehensible crash report.

Perhaps more to the point, if NeXML phylogenies produced by some obscure phylogenetics software that I never employ myself are supposed to be of use they have to be displayed, so how are we doing for tree viewers? The very popular cross-platform software FigTree expects Nexus or Newick phylogenies, and as far as I know the same is true for TreeView. DendroScope claims to read NeXML files but then only gave me an error message when I tried to import the simple example phylogeny after conversion by the official nexml.org website. To quote from that same website, "the future data exchange standard is here!"

While on that topic, standardisation is one of the main benefits claimed by NeXML or by XML more generally. As Simon St. Laurent wrote already in 1998:

XML allows developers to set standards defining the information that should appear in a document, and in what sequence. XML, in combination with other standards, makes it possible to define the content of a document separately from its formatting, making it easy to reuse that content in other applications or for other presentation environments. Most important, XML provides a basic syntax that can be used to share information between different kinds of computers, different applications, and different organizations without needing to pass through many layers of conversion.

I guess at this stage it should come as no surprise at all that there are already at least two different XML standards for phylogenetic trees, which is another way of saying that there is no XML standard for phylogenetic trees. In addition to NeXML, which I have discussed in detail above, there is phyloXML. Where NeXML describes trees using lists of nodes and edges phyloXML uses nested clade tags, which I find more intuitive and useful because it allows easier parsing and easier manual editing, and which is also more similar in spirit to Newick and Nexus and would thus be more deserving of a name like NeXML than NeXML. Otherwise it appears to be just as inefficient and convoluted though.

So concerning standardisation I guess the reality is that XML is flexible enough that anybody could come up with a new, XML-based standard. Just think of a few words, put is-smaller-than and is-larger-than signs around them, convince a handful of colleagues to adopt this standard, and off you go. Yes, if it is so easy to do then everybody will do it, and then we achieve the exact opposite of standardisation, but I guess that is where XML proponents can switch to touting its "flexibility". Heads XML wins, tails all other data standards lose.

As far as I can see Newick and Nexus work just fine. Compared to XML phylogenies they are easier to parse, are already standardised, are accepted by virtually every phylogenetics software and tree viewer, and take up a fraction of the disk space. Why fix what isn't broken?

The joys of single-character taxonomy

Time for a little rant. Two days ago I tried to identify an Australian native Asteraceae. I already knew that it had to belong to one of two genera, and had always wondered why those two genera were recognised as distinct in the first place. If you put a randomly chosen species from the first next to one from the second you will be hard pressed to see any difference beyond hair cover or suchlike.

I assumed there would be some fruit character, for example feathery versus smooth pappus bristles. That would be bad enough because it would probably still mean that one genus is phylogenetically nested within the other, as is usually the case when there is only a difference in one trait. This is because then one genus is defined by having the trait and the other merely by lacking it; in systematics, we call that an 'apomorphic segregate'. But okay, such a fruit character, even if evolutionarily irrelevant and phylogenetically uninformative, is at least user-friendly. You can look at the pappus (or beak, or whatever) and quickly conclude: ah yes, it must be this genus.

What was the difference in the present case? "Florets homogamous" or "florets heterogamous". Before we consider the trait itself, hands up everybody who knows what that means! Yes, that's what I thought. The identification key in question was apparently written for an end user group of about half a dozen fellow taxonomists in Australia or so, but certainly not for conservation managers, community ecologists, or plant-enthusiastic non-scientists.

Now the trait itself. It means whether the flowers in the daisy flower-head are all of the same type or if there are different types present; and here we are not talking about the presence or absence of petal-like ray florets or anything easy to see like that. We are talking about one of the two genera sometimes having a few female flowers at the edge of the flower-head in addition to the normal, bisexual flowers. In other words, get out the anatomy grade tweezers and a dissecting microscope!

And as expected we are dealing with a single character difference. It is extremely unlikely that the two genera are reciprocally monophyletic, so they probably don't make sense in modern systematics. But even from a so-called 'evolutionary' taxonomy perspective this is weird. Again, you place species from the two genera next to each other, you will not see any significant difference; and surely having or not having a few female flowers in the head is not going to put a species into a different 'adaptive zone' or something. So what is the idea?

What is weirder is that this criterion is not even applied consistently. Another closely related genus has got several homogamous and one heterogamous species.

Of course this is not the first time I have seen a situation like that. The genus I did my honours on was Suessenguthia (Acanthaceae), a group of (now) six species with four fertile stamens and little hooks on the anthers. Some of its species are pretty similar to those of the larger genus Sanchezia except that the latter has only two fertile stamens. In addition, there is a monotypic genus Trichosanchezia that looks exactly like certain hairy, northern Peruvian Sanchezias but has four fertile stamens without the little hooks. Even better, there was once a likewise monotypic genus called Steirosanchezia characterised by two fertile stamens without hooks; that one, however, has already been put out of its misery and sunk back into Sanchezia.

So once there were four genera based merely on minutiae of the androecium, for species that are so similar that they constantly get misidentified to each other's genera, and obviously all forming one tight natural group. How is that helpful? How did that ever make sense even before Phylogenetic Systematics, even before the Theory of Evolution?

Believe me, you wouldn't want your five year old to breathe this either

Trick question: what is this haze covering our suburb?

(a) Fog.
(b) Chemical warfare.
(c) The toxic fumes resulting from a successful attempt to make it into the Guinness Book of World Records in the category of Pointless Waste of Perfectly Good Car Tyres and Petrol?

Hint: it smells like (b).

A metric of Twitter and blog hits for scientific articles

On this blog I have sometimes mentioned, and complained about, the influence that the obsession with article citations and journal impact factors (IF) has on scientific publishing, scientific careers, and the hiring choices of scientific institutions.

In short, instead of actually reading and understanding scientific papers, many people 'assess' their value by looking at how often they have been cited. Instead of reading and understanding their work, many people, even members of search committees or advisors of funding agencies, 'assess' scientists by looking at how often their papers have been cited. And instead of reading and understanding the articles published in them, many people 'assess' scientific journals by looking at how often their average article is cited within the first two years after publication.

And as mentioned before, this approach systematically favours areas of science that have a quick turn-around and lots of practitioners able to cite each other whereas it systematically disadvantages areas of science where many publications are written for long term use, published in books as opposed to journals, and while very useful to many people may not even be meant to be cited. Such as the floras and monographs produced by taxonomists, for example.

But of course, once you think you know what bad looks like somebody will introduce you to something worse.