Saturday, June 20, 2020

Did Edward Gibbon blame Christianity for the decline of the Roman Empire?

I have now finally read Edward Gibbon's classic History of the Decline and Fall of the Roman Empire. Although certainly opinionated in a way that one might not consider up to the standards of historical research today, it is considered to be a ground-breaking work for its time (1776-1788) in the way that it used primary sources to tell its story.

But the most important reason I became interested in it is the pejorative way in which Gibbon is referred to in critiques of New Atheism. There is a general impression that Gibbon laid the blame for the collapse of the Roman Empire and the loss of its technology and learning at the feet of Christianity. In some circles, "Gibbonian fantasy" or "Gibbonian fiction" seems to be a short-hand for the belief that Christianity is singularly responsible for retarding scientific progress and causing the Dark Ages.

Having now read the book I have absolutely no idea where this is coming from. Maybe this idea is more clearly developed in some other work by the same author, but in the Decline and Fall I search for it in vain.

Don't get me wrong - it is clear that Gibbon had no love for Christianity. He argued in at least two sections of his book that early Christianity was more intolerant than the paganism that preceded it, and that Christianity wasted resources on piety that could have been better used for other, more practical purposes. (Nobody can seriously doubt the first claim, but the second seems a bit silly. Wasting resources on piety is not a Christian characteristic, it is a religious one; every pagan priest offering sacrifices to the gods and every Vestal Virgin performing a pointless ceremony could have more been more productively employed as an engineer, scholar, teacher, navigator, trader, or a variety of other professions.)

Due to his visible aversion to religion it is unsurprising that Christian apologists don't like Gibbon and want to cast aspersions on his work. But that does not mean that he actually made the argument that Christianity brought down the Roman empire and destroyed ancient learning. I really don't see where he did.

Even the Wikipedia page on the book as of today 20 June 2020 quotes a section that makes clear that despite Gibbon's dislike of Christianity he did not see it as a decisive factor: "if superstition had not afforded a decent retreat, the same vices would have tempted the unworthy Romans to desert, from baser motives, the standard of the republic" - in other words, the same decline would have taken place without Christianisation.

To any open-minded reader of his book it should become clear that his main culprit is an institutional process that can perhaps be usefully summarised as follows:

(1) As the republic expanded, the military was professionalised to increase its efficiency and flexibility of operation. What used to be a citizen army made up of free men expected to serve to defend the republic turned into an army of professional soldiers rewarded with property after a period of service.

(2) One of the consequences was that the average Roman citizen did not need, and ultimately did not want, to risk his life fighting to defend the republic. As the republic became an empire and grew even further, more and more of the armed forces were recruited from non-citizens, increasingly barbarian mercenaries or foederati, foreign tribes bribed to defend the empire from other, closely related tribes. It should be immediately obvious that these kinds of soldiers have considerably less loyalty to Rome than Roman citizen soldiers, and that mercenaries are only useful to you as long as you can guarantee their pay and nobody out-bids you. That alone could have been the empire's death knell, but...

(3) In addition, the empire had a severe institutional weakness in that there was never a clear rule of succession. There were phases where the next emperor was the previous emperor's son, whatever his ability, and others where the previous emperor would adopt a successor to ensure that the empire would be left in competent hands. But what if the emperor was a tyrant and got assassinated, with either no successor in place or his plan for succession as discredited as he was? Although technically an emperor needed to be recognised by the senate, imperator was a military title, and at any rate having control of a lot of swords is more of a, shall we say, practical argument than being endorsed by a bunch of elderly guys in togas. In practice the senate did not want those swords to be turned against themselves. It thus happened more and more that the next emperor was selected by the army and merely ratified by the senate. This again had two important consequences.

(4) First, the way for an ambitious officer to be elected emperor by the army was obviously to promise his fellow mercenaries a lot of money. In several parts of his book Gibbon is quite explicit about this tendency: the constant need to bribe the army to either get elected or to tolerate an emperor that the soldiers had not elected themselves drained the tax payers. Gibbon claims it also weakened the military vigour of the soldiers, who were at times living the good life spending their bribes while neglecting their training and insisting they shouldn't have to carry heavy armour.

(5) Second, frequently different parts of the army would elect different officers to be the new emperor. If both of them felt strong enough to give it a serious try, the empire would immediately be plunged into another short civil war. Just to decide whether the guy nominated by the Gaulish legions or the guy nominated by the Syrian legions gets to be the new ruler, they wasted the lives of thousands of soldiers who might more productively have been used to keep barbarian invaders or the Sassanian empire at bay.

So there we have it: the two key problems were the decreasing loyalty and increasing corruption of the armed forces and the institutional weakness of the republic. And both of them were probably entirely unavoidable. You cannot conquer and control an empire with an army made up of free farmers who have to travel back to northern Italy to bring in the harvest just when the enemy attacks in Mesopotamia, so you need a professional army. And even if you have very nice institutional arrangements they won't be of any use against a large army that has no loyalty to those institutions. The only alternative would have been not to have an empire in the first place.

I am not a historian. I do not know if this is accurate in all details. I do not know if this is really why the Roman empire declined, and I understand at least that plagues may have been another factor. The point is: this is Gibbon's argument, not that Christianity caused the decline.

Sunday, February 2, 2020


Recently the famous primatologist Jane Goodall attracted criticism for saying that environmental issues "wouldn't be a problem" if our numbers were at the levels they were 500 years ago. I assume what she meant is that they would be much more manageable, not absent, as even mere hundreds of millions of people would produce waste, use non-renewing resources, etc., but the point is that whenever somebody brings up population pressures, the immediate reaction in much of the social media that I frequent is an evidence-free rejection of the idea combined with personal attacks on the person who made the statement. The same happened in this case.

I am really quite puzzled by this. While a discussion could be had about whether the planet is overpopulated or not, depending on what resource constraints we assume, Goodall's statement is irrefutable. Of course 500 million people would have less of an environmental footprint than seven billion. One could just as well try to reject the idea that four people will have it easier to fit into a car than twelve.

Consequently I was quite interested to see an article in The Conversation titled "why we should be wary of blaming 'overpopulation' for the climate crisis". It was written by an academic and of some length, so the argument can be expected to have been developed more clearly than in a rage-tweet. After citing Goodall the author, Heather Alberro, begins her argumentation as follows:
This might seem fairly innocuous, but its an argument that has grim implications and is based on a misreading of the underlying causes of the current crises. As these escalate, people must be prepared to challenge and reject the overpopulation argument.
So we are promised here two different arguments:

First, nobody should say that the planet is overpopulated because it has "grim implications". This is not about whether a statement is wrong, it is about whether somebody else could misunderstand or deliberately exploit the statement to justify something terrible.

I am always uncomfortable with this stance, because the logical end-point is that nobody should be allowed to state a demonstrable fact if there is an interest group that will use this fact to promote a harmful agenda - and there will always be such a group if a topic is controversial at all. Or in other words, the logical end-point of this stance is to restrict your ability to use evidence in decision making towards your own, hopefully benevolent agenda, which means that your decisions will be ill-informed and less likely to solve the problem you are dealing with.

Therefore any argument along those lines must, in my eyes, meet a fairly high standard. It cannot simply be, "you aren't allowed to state this fact because somebody somewhere could do something bad". It would have to provide a clear, convincing causal chain from stating the fact to the probable occurrence of a harm that would be significantly less likely to happen if the fact were kept confidential. A causal chain like:
Somebody says the world is overpopulated -> ???? -> genocide
What needs to be in the middle of this chain to make genocide plausible?

Second, Alberro also argues that the world is not in fact overpopulated, that this would be a "misreading" of the situation. This claim is what I find particularly interesting, because as mentioned in the beginning the relevant conversation on social media can be comfortably summarised as "everybody who says there is overpopulation wants to commit genocide against the developing world", in other words the previous argument plus character assassination. I have yet to see anybody addressing the question whether the world is, actually, overpopulated; it simply gets ignored.

I will therefore start with the examination of this factual argument, which also makes up the majority of the article.
In reality, the global human population is not increasing exponentially, but is in fact slowing and predicted to stabilise at around 11 billion by 2100.
I do not quite understand what it means that "population is slowing". I assume what is meant is that population growth is slowing. That is great... but. First, it is like wanting praise for promising to only stuff eleven people into your five seater car, instead of infinity people. Yes, okay, but you already have seven people in there right now, and even that is not safe. So will you please stop putting the eighth in there, like, right now please, instead of ignoring the problem? Second, slowing growth is clearly irrelevant to Goodall's statement, which implied that we are already too many.
More importantly, focusing on human numbers obscures the true driver of many of our ecological woes. That is, the waste and inequality generated by modern capitalism and its focus on endless growth and profit accumulation.
This is the key argument of this article, which is subsequently detailed in various ways: inequality is the problem, not number of people. Now in what way would ending inequality solve ecological woes? First we need to consider how it would be ended, as there are at least two ways to do so.

First, raise the living standards of the poor. This would be the humane approach, but I do not see how it helps with carbon levels in the atmosphere, waste, soil erosion, groundwater overuse, whatever. It would only make things worse. Second, reduce the living standards of everybody to that of the poorest people on the planet. That would help reduce emissions etc., but spelling it out like this should reveal the obvious problem: nobody is going to accept this immiseration, neither the wealthiest nor the poorest, who desperately want a better life too.

Now one could reply to this that we could all live sustainably in equality if we just made our economy carbon-neutral. That is correct, but the whole controversy is about whether we turn the population-growth dial or the economic equality dial. (Why we should only do one of those is left unexplained.) Goodall said that we would have less of a problem if there were less people using fossil fuels, and Alberro (somehow) tries to argue that this specific statement is false, that we should not turn that dial but only the other. The third dial, carbon-neutrality, is orthogonal to this discussion.
The industrial revolution that first married economic growth with burning fossil fuels occurred in 18th-century Britain. The explosion of economic activity that marked the post-war period known as the "Great Acceleration" caused emissions to soar, and it largely took place in the Global North. That's why richer countries such as the US and UK, which industrialised earlier, bear a bigger burden of responsibility for historical emissions.
That is true and an important point but also completely irrelevant for the question of whether the planet is overpopulated. "Yes, I am trying to stuff eleven people into my five-seater, but that is totally safe because last week that other guy was speeding."
In 2018 the planet's top emitters - North America and China - accounted for nearly half of global CO2 emissions. In fact, the comparatively high rates of consumption in these regions generate so much more CO2 than their counterparts in low-income countries that an additional three to four billion people in the latter would hardly make a dent on global emissions.
Well, clearly adding more people will not make a dent in emissions, it would increase them, but I get what is meant here: adding more poor people to the planet will have less of an impact than the rich increasing their consumption even further. I find it ironic, however, that China is mentioned as one of the two worst offenders, because if we should be worried about how racists spin concerns about overpopulation then we should also be worried about somebody concluding "see, it is China's fault, so we Europeans don't need to do anything".

Consumption levels in China have risen, of course, but they are still much lower per person than in the USA. A key reason why China rivals North America in emissions is that it accounts for about one fifth of the world population all by itself. And we are back at Goodall's point, which applies across all consumption levels.
There's also the disproportionate impact of corporations to consider. It is suggested that just 20 fossil fuel companies have contributed to one-third of all modern CO2 emissions, despite industry executives knowing about the science of climate change as early as 1977.
This is another argument that frequently comes up on social media, very often citing the number twenty, so that meme must all go back to one statistic somewhere. Now I will agree immediately that more powerful people bear more moral responsibility, because a CEO has more influence than a single supermarket customer or a single assembly line worker.

But still, what rarely seems to be considered is that these corporations produce the emissions to offer products and services that we seven billion humans buy and consume. It is not the case that these industry executives run polluting factories and refineries at a loss and for the giggles because they like pollution, like some cartoon villain. It is not the case that they are doing their thing over there, and we normal people are doing our entirely unrelated thing here. They run their factories because we buy stuff, and they run them unsustainably because many of us insist on buying stuff as cheaply as possible. Conversely, that also means that if there were only one billion of us these corporations would produce only one seventh of the emissions that they are producing now.
Inequalities in power, wealth and access to resources - not mere numbers - are key drivers of environmental degradation. The consumption of the world's wealthiest 10% produces up to 50% of the planet's consumption-based CO2 emissions, while the poorest half of humanity contributes only 10%.
I have already mentioned how likely the poorer half are to accept that they should never see the wealth of the wealthier half themselves (i.e. not very likely), but let's assume that we reduce everybody's standards of living to those of the poorer half: even those who are currently billionaires will live in crowded little, non-AC'd apartments with only a bicycle and the bus as transport options. I am a frugal person myself, so I could happily live with that. But what exactly does that for us, carbon-wise? According to the numbers cited above, it would logically reduce "consumption-based" emissions to a fifth of what they currently are.

Now it is a bit unclear, at least to me, what exactly is meant with "consumption-based". Googling for some guidance I find that, according to the EPA, US greenhouse gas emissions in 2017 were distributed as follows: transportation 29%, electricity 28%, industry 22%, commercial & residential 12%, agriculture 9%. What is consumption? I assume all of agriculture and at least part of industry, so at a minimum perhaps 20%. The rest is less easy - is electricity consumption in Alberro's sense? Maybe yes, maybe no, but transport probably not.

So we are talking about reducing to a fifth what may now be somewhere between 20% and 50% of the total emissions. That means tackling inequality by impoverishing everybody would reduce our overall emissions by 16-40%, or to 60-84% of what they currently are. That is hardly going to stave ecological and societal collapse off by many years, much less solve the problem. Reducing inequality by the more desirable approach of lifting everybody out of poverty or an approach in the middle between those extremes would, of course, have the opposite effect.
With a mere 26 billionaires now in possession of more wealth than half the world, this trend is likely to continue.
I do not like inequality either because of how unfair it is and how it distorts democracy, and I certainly do not believe anybody morally deserves to have a billion dollars, but purely in terms of greenhouse gases I doubt that somebody with a hundred thousand times my money contributes a hundred thousand times the emissions that I do. There are only so many private jets or yachts any single billionaire can use at a time and only so much a single person can "consume". Much of their wealth is invested or used for gambling at the stock exchange as opposed to buying a hundred thousand people's worth of food, for example.
Developing regions in Africa, Asia and Latin America often bear the brunt of climate and ecological catastrophes, despite having contributed the least to them.
Again true but again does not contradict Goodall's statement that environmental problems would be less pressing if there were less humans.
The problem is extreme inequality, the excessive consumption of the world's ultra-rich, and a system that prioritises profits over social and ecological well-being. This is where where we should be devoting our attention.
See above. Again, I would prefer a much more equal distribution of wealth. But that does not mean that overpopulation is not an issue. It is simply an undeniable fact that all else being equal, reducing our numbers by half reduces our ecological impact by half. Just as it is a fact that all else being equal, reducing our consumption would also reduce our ecological impact. There is no either-or, and we can devote attention to several problems at the same time.

Coming now to the political or strategic argument:
The idea that there were simply too many people being born - most of them in the developing world where population growth rates had started to take off - filtered into the arguments of radical environmental groups such as Earth First! Certain factions within the group became notorious for remarks about extreme hunger in regions with burgeoning populations such as Africa - which, though regrettable, could confer environmental benefits through a reduction in human numbers.
Here the implied causal chain is: Somebody says the world is overpopulated -> fringe group without any political influence whatsoever thinks that famine is beneficial -> genocide. Not sure I am convinced. Then towards the end of the text:
Issues of ecological and social justice cannot be separated from one another. Blaming human population growth - often in poorer regions - risks fuelling a racist backlash...
Somebody says the world is overpopulated -> racist backlash -> genocide. There might be a few steps missing here. Also, see above regarding the backlash that could result from blaming China for half the problem even from an inequality angle.
...and displaces blame from the powerful industries that continue to pollute the atmosphere.
Somebody says the world is overpopulated -> fossil fuel industries can claim it isn't their fault. I do not see this logic at all, sorry. They still sell the fossil fuels, and the only difference is that they sell them to even more people.

Is it really that difficult to keep three factors in one's head at the same time? Imagine a three-dimensional graph, a cube. In one corner are very few humans, all getting along with very little, and what little they need is produced using renewable energies. In the opposite corner are billions of humans, each of them consuming massive amounts of throw-away goods, and these goods are produced burning the dirtiest coal you can imagine. To change the emissions we produce we can move along all three axes of this graph, along all three edges of the cube.

Not only is entirely unclear to me how the idea that we would have less emissions if we moved down on the population-axis is refuted by arguing that we should move down on the consumption per person axis; it is not even clear whether Alberro even argues for that, because again, inequality could also be resolved by moving up that axis, making our ecological impact worse.

So in summary, I do not see how this article refutes Goodall, and nor could it have, because the relationship between population size and ecological footprint is obvious. It does not appear to make an argument that the planet is not overpopulated either - as always the question is merely deflected. And finally, it does not even provide a plausible causal chain leading from the discussion of this question to "grim implications", leaving the intermediate steps up to the imagination of the reader, who, however, could just as well say, "what is so terrible about empowering people to be able to do family planning?"

Saturday, October 19, 2019

Arguments for paraphyletic taxa, part 543,997 or so

Although having largely moved on from blogging, I found myself writing another post on the most frequent topic of this blog, arguments for the acceptance of paraphyletic taxa and whether they make sense. A paper has recently appeared that describes a new species of flowering plants (Carnicero et al 2019, Bot J Linn Soc: boz052). The first paragraph of its introduction argues for paraphyletic taxa as follows:
From a cladistic perspective, monophyly of taxa is desirable, but important evolutionary processes such as hybridization, anagenetic and anacladogenetic speciation (budding sensu Mayr & Bock, 2002) unavoidably result in non-dichotomous branching patterns (Hörandl, 2006; Hörandl & Stuessy, 2010).
I am afraid I already find this first bit confused in several details. First, from a cladistic perspective, monophyly is not merely desirable but required. That is the entire point of cladism.

Second, non-dichotomous branching patters are polytomies, meaning the branch splits into more than two sub-branches. Polytomies are no problem for making supraspecific taxa monophyletic, so on the face of it, it is not clear what the argument is. But none of the mentioned processes necessarily produce polytomies anyway, and some of them do not even produce any branching at all.

Hybridisation - presumably the authors mean hybridogenic speciation, e.g. by allopolyploidy, and not actually hybridisation per se, which is usually a dead end - is not branching, it is the opposite. The problem for the argument here is that reticulation does not just mean there is no monophyly, it also means there no is paraphyly either, as there is no phyletic (tree-like) structure. It makes no sense to argue for paraphyly in a situation where there is no paraphyly. (More on that below.)

'Budding' speciation is dichotomous, just like any other lineage split, unless an ancestral species fractures into three or more descendant species at the exact same moment, just like could happen with a non-'budding' lineage split. It is no problem whatsoever for making supraspecific taxa monophyletic.

Third, anagenetic means that something happens along a lineage without a lineage split, so it is again odd to speak of a "non-dichotomous" branching pattern. If anagenesis is happening there is by definition no branching pattern, dichotomous or otherwise. Nor is there any problem for making supraspecific taxa monophyletic. So yes, the observation that there is no dichotomy is correct, but merely in the same trivial sense as the observation that a book isn't a car. You can go around saying that, but book authors or publishers will simply say, "we know, so what?" Cladists likewise when told that anagenesis happens.
Anacladogenesis is a case of peripatric speciation, in which a population or a group of populations from a species diverge, resulting in a derivative monophyletic species (Stuessy, Crawford & Marticorena, 1990). Unlike in cladogenetic processes, the ancestral species remains essentially unchanged and often becomes paraphyletic (Mayr & Bock, 2002; Crawford, 2010).
With this the two closely related misconceptions at the heart of the paper's argumentation become clear. The first is that the cladist approach requires making species monophyletic. It doesn't. The second is that it makes sense to call species monophyletic or paraphyletic in the first place. It doesn't. (Although this is a very, very common and widespread misconception.)

As already indicated above, the concepts ending in -phyly apply in tree-like structures, such as the tree of life. The individuals of sexually reproducing species, however, do not form a tree-like but instead a net-like structure. Consequently, -phyly does not apply inside sexually reproducing species. Another attempt at an analogy: I can be asleep, but the molecules I consist of do not sleep. The concept "asleep or awake" does not apply to individual molecules, just as monophyly does not apply to individuals of the same sexually reproducing species. Fallacy of division is the keyword here.

This is not a new idea that cladists came up with only as a rearguard action, as frequently claimed by paraphyletists. We can go back all the way to the inventor of cladism, Willi Hennig. The central and best known figure in his book illustrates the different relationships that species, individuals, and life stages have to each other. Phylogenetic systematics ('cladism') is the approach to take when classifying species into supraspecific taxa, but not when classifying individuals into species. The claim that a species is monophyletic or paraphyletic is a category error.
Over time, the ancestral species may converge to monophyly through gene flow and lineage sorting (Baum & Shaw, 1995).
Same as above, but in addition it has to be unclear what is meant with 'gene flow', as on the face of it such flow would work against lineage sorting. It is possible that the authors meant to say 'restriction of gene flow'.

This sentence also makes clear where the conceptual error is located that leads a surprising number of people to the idea that species can be something or other-phyletic. Lineage sorting happens to alleles, and yes, the alleles of a gene occurring inside a sexually reproducing species can be paraphyletic to the alleles occurring inside a different sexually reproducing species. But taxonomists do not classify alleles into species, they classify individuals into species, so this would be another category error.
Far from an exception, anacladogenetic speciation has been considered to be of main importance in plant evolution (Rieseberg & Brouillet, 1994; Anacker & Strauss, 2014). As integrative taxonomy advocates that taxa should reflect evolutionary processes (Stuessy, 2009; Schlick-Steiner et al., 2010), it may be necessary to recognize certain paraphyletic entities.
The argument that Integrative Taxonomy requires paraphyly was not familiar to me. My understanding has always been that Integrative Taxonomy is about combining diverse kinds of evidence to support taxonomic decisions in species delimitation, e.g. a combination of ecological niche, population genetics, and morphology. The seminal Schlick-Steiner paper, for example, was clearly about alpha taxonomy, i.e. species delimitation. Searching it for the snippet "paraph" brings up only one entry in its reference list. (Stuessy is a different story, as he is one of the two or three most vociferous botanists still arguing for paraphyletic taxa; but then again he is not to my understanding a founding figure of Integrative Taxonomy.)

Again the central problem is, however, not what Schlick-Steiner et al may have thought about paraphyletic taxa, but that Integrative Taxonomy is about species delimitation, where paraphyly applies just as much as decibels apply to colours, and not about supraspecific taxa, where there concept properly applies.

The paragraph ends with something like an argumentum ad populum.
Indeed, examples of recognized paraphyletic taxa exist at various taxonomic levels (e.g. class Reptilia: Mayr & Bock, 2002; Pozoa coriacea Lag.: López et al., 2012; Helichrysum Mill.: Galbany- Casals et al., 2014; Plethodon wehrlei Fowler & Dunn: Kuchta, Brown & Highton, 2018; Columnea strigosa Benth.: Smith, Ooi & Clark, 2018).
The individual species used as examples are irrelevant for the reasons outlined above, because unless they are reproducing clonally, in which case they should have been circumscribed to be monophyletic, they are not paraphyletic but instead tokogenetic (net-like), and cladism does not apply inside tokogenetic structures. That leaves two supraspecific taxa that the taxonomic community has long recognised as ill-circumscribed due to their paraphyly: reptilia and Helichrysum.

One might point out that Mayr, for example, remained opposed to phylogenetic classification even as he saw it being adopted by the scientific community around him, and that recognition of reptilia as a paraphyletic taxon is not state of the art in zoology today. The vast majority of animal systematists today classify animals consistently by relatedness.

But more importantly, there is no way to base the acceptance of paraphyletic reptilia or Helichrysum on the argumentation presented in this paper, which argues entirely from the existence of hybridogenic and 'budding' speciation. This illustrates an extremely common pattern in papers arguing for paraphyletic taxa: an argument is made that applies inside a species (although even that only if we misconstrue the conceptual basis and actual practice of phylogenetic systematics), and then the entirely unwarranted jump is made to the conclusion that paraphyly should be accepted at a much higher level of classification, where the argument would not apply even if it were correct.

Thursday, September 26, 2019

Incongruence Length Difference test in TNT

Because I am fed up with figuring it out anew every time I need to use the Incongruence Length Difference (ILD) test (Farris et al., 1994) in TNT, I will post it once and for all here:

Download TNT and the script "" from PhyloWiki. In the script, you may have to replace all instances of "numreps" with "num_reps" to make it functional. I at least get the error "numreps is a reserved expression", suggesting that the programmer should not have used that as a variable name.

Open TNT, increase memory, and set data to DNA and treating gaps as missing data. Then load your data matrix, which should of course be in TNT format:

mxram 200 ;
nstates DNA ;
nstates NOGAPS ;
proc (your_alignment_file_name) ;

Look up how many characters your first partition has, then run the test with:

run (length_of_first_partition) (replicates) ;

There is an alternative script for doing the test called, but I have so far failed to set the number of user variables high enough to accommodate my datasets. They seem to be limited to 1,000?

Perhaps this guide will also be useful to somebody besides me.


Farris JS, Källersjö M, Kluge AG, Bult C, 1994. Testing significance of incongruence. Cladistics 10: 315-319.

Friday, April 5, 2019

Still not convinced by Vicariance Biogeography

When reading recent methodological papers, review articles, or publications on my study group I sometimes add to the mix the odd paper that is not directly relevant for my work and maybe not even very recent but which is relevant to my broader interests. In this case I decided to take a look at Heads 2009, Inferring biogeographic history from molecular phylogenies, Biol J Linn Soc 98: 757-774.

Michael Heads is perhaps the most published proponent of Vicariance Biogeography, the school of biogeography that rejects speciation following long-distance dispersal (LDD) because... and that is where it gets interesting, because I still find that rejection puzzling. To the best of my understanding at least some vicariance biogeographers consider the conclusion of LDD to be unscientific because they believe it can explain any possible contemporary range, on the lines of 'if your hypothesis can explain every observation it explains nothing'. This does not make sense to me, because LDD would still be more or less plausible depending on the dating of cladogenesis events relative to tektonic events or island ages, prevailing wind and water currents, dispersal ecology, and many other factors. It also seems rather more unscientific to reject a possible explanation a priori, regardless of any evidence in its favour. But to get a better understanding of the arguments of vicariance biogeographers is precisely my reason for picking up this paper. So, on with it.

In a section titled "critique of founder dispersal in population genetic studies", Heads first describes the concept as "the founder individual has been isolated from its parent population by dispersing over a barrier (an apparent contradiction)". Right out of the gate this seems odd. I may be missing something, but it appears as if Heads would accept only extremes: either there is a barrier, meaning zero dispersal, or there is none, meaning panmixis. I have previously observed similar arguments in other papers from the vicariance school.

Assume I have a garden with a fence around it, and then one day a cat jumps over it. Does this mean I have no barrier around the garden? Of course not, it may still have kept various stray dogs and neighbours' children out. On the other hand, it was never a barrier to birds or insects. The same in biogeography. No barrier on this planet is absolute, and each barrier has a different force for different groups of organisms. A channel that is near-insurmountable to a monkey may be crossed by insects if blown over by a strong enough storm, and it may be no barrier at all to fern spores. Perhaps even more importantly, dispersal is a stochastic process. The Atlantic Ocean did not keep all cacti from crossing (Rhipsalis made it over to Africa), but it kept the seeds of >99.9% of them away, so it is still a barrier even if not an absolute one.

Beyond that the argument of the section relies on citing five papers that "failed to corroborate predictions of founder effect speciation", of which one is missing from the reference list. I checked three of the remaining four papers, and in all cases they are experiments on fruit flies limited to time frames on the order of ten years and designed to test the very narrow question whether severe population bottlenecks will cause pre-mating isolation. Now I may completely have misunderstood the claim made by mainstream biogeographers regarding founder speciation, but I believe it was not "ten years after an organism has dispersed to an island it will have achieved biological pre-mating isolation". The way I understand it the claim is more on the lines of the large distance from the parental population producing geographic pre-mating isolation, which enables speciation to take place subsequently. The point is not the speed with which the new population evolves (although that is an exciting research question in itself) but rather that it has become geographically isolated.

The argument consequently seems to miss the point. If there is a problem for founder speciation then it would be whether a single pregnant female or a single seed can establish a viable population. Potential problems are inbreeding and, in plants that have such features, self-incompatibility systems that cause failure to set seed. But if a population establishes, helped perhaps by herbivore release and lack of competition, subsequent speciation is not an extraordinary claim. It really does not matter if isolation has been achieved by vicariance or by LDD, the subsequent process of divergence is the same except the latter will also cause a genetic bottleneck.

The section "critique of founder dispersal in biogeographic studies" points out that there is good evidence for similar vicariance patters in many taxa. I am unaware of anybody who denies that vicariance is an important process - but it does not logically follow that LDD is therefor implausible. I can agree that a lot of white swans exist without therefore having to believe that black ones cannot possibly exist.

This is followed by "founder dispersal and new ideas on rift tectonics", where the idea seems to be that seemingly young oceanic islands do not require LDD to be colonised because they kind of have always been there. It is not entirely clear to me if the claim is that the individual islands are all much older than the oldest still observable lava flows or if, as implied by the reference to "seamounts", the local species would have constantly hopped from one short-lived and now submerged island to the next. If the first, it seems rather ad-hoc; if the second, one wonders why species that can so easily jump ten times from one disappearing island to the next island in the chain cannot simply jump a single time from continent to island. What is the more parsimonious conclusion here?

Next, molecular clocks and time calibration of phylogenies are rejected. All inferences, be it from fossils but in particular from geological events such as the formation of the isthmus of Panama, are dismissed as unreliable, but apparently present distributions are reliable evidence of ancestral distributions. Unfortunately I remain anti-convinced.

To quote the following paragraph in full:

"In Ronquist's (1997) method of dispersal-vicariance analysis, inferences of dispersal events are minimized as they attract a 'cost'. Extinction also attracts a cost but vicariance does not. It was not explained why this approach was taken and it appears to be based on a confusion of the two different concepts of 'dispersal'. Ecological dispersal in the sense of ordinary movement should not attract any cost in any model; founder dispersal would attract no cost in a traditional dispersalist model, but, in a vicariance model of speciation or evolution, it is rejected a priori."

What Heads does here is reject a formal parsimony-based inference of ancestral ranges in favour of, to judge from the second half of the paper, an informal, intuitive, pencil-on-a-map deduction process. What does he not like about Dispersal-Vicariance Analysis (DIVA)? Apparently primarily that dispersal events have a parsimony cost. It may be that he did not contemplate how such an analysis would work or if it could even work at all, if the only process having a cost would be extinction - of course it would mean that dispersal would be much too 'cheap', and every single ancestral species would always be inferred to have occupied the union of the ranges of its two descendants.

The great irony here is that even with a dispersal cost DIVA is well known for mercilessly (and implausibly) favouring vicariance as a process. I ran that analysis on two or three data sets a few years ago, and unless one restricts the maximum range size of ancestral species to something biologically plausible one pretty much always ends up with the vicariance biogeographers' preferred conclusion: the ancestor of the study group was already everywhere where any of its descendants occur today.

The second part of the paper is taken up by a large number of case studies, taxa which have sometimes been suggested to have undergone LDD but for which Heads presents a vicariance explanation instead. Some of these I find more plausible than others, but I do not want to go into each of them in detail. Instead, it seems more efficient to discuss what I see as three problems running through the entire argumentation:

First, there seems to be a lot of ad-hoccery going on. Where necessary to arrive at the conclusion of vicariance, for example to explain the overlapping distributions of African Arctotideae, 'normal ecological' range expansion is invoked as common and easy. But where necessary to arrive at the conclusion of vicariance, for example when distantly related subclades of a taxon occur right next to each other in Tasmania or New Zealand (suggesting relatively recent LDD from elsewhere), they are assumed to have been sitting in these narrow localities for tens of millions of years, apparently unable to move at all, so that a very ancient vicariance event can have taken place between their present ranges. Is that not rather convenient?

Which brings me to the second point. The text presenting the case studies certainly uses words like "may" and "might" a lot. To be honest, I sometimes found myself reminded of Erich von Daniken, whose style was to the effect of "the traditional explanation is that the pyramids were build by the ancient Egyptians - but could it not have been extra-terrestrials?" Yes, in each of these cases vicariance (or extra-terrestrials) could be the explanation. But mere possibility is a low hurdle to clear; the real question is, is that the most plausible explanation?

Third, as always with vicariance- or panbiogeography the problem is that dispersal is still required. Somehow this taxon here must have reached this volcanic island, somehow that taxon there must have spread all over the world. How does the vicariance biogeographer arrive at contemporary ranges without invoking jumps across oceans? Partly by hiding the dispersal away before the start of the analysis. To quote the present paper, "assuming a worldwide ancestor..." Well, if we can just assume that at our leisure it becomes easy to conclude few dispersal events, long distance or otherwise.

Now quite apart from the question whether a single species occurring worldwide is biologically realistic for all groups of organisms (I'd say it isn't), the problem remains that we have a lot of nested groups that would all have to have been ancestrally cosmopolitan, requiring several global range expansions in between. The daisy family is an excellent example. With reference to them, Heads writes that "through the history of the family as a whole, only a small number of widespread ancestors may have existed (groups such as Senecioneae and Astereae each require their own global ancestor)." I think that is a wee bit of an underestimate.

To walk through just one example in order of containing taxon to subordinate taxon: The Asteraceae family is cosmopolitan. The Asteroideae subfamily is cosmopolitan. The Astereae tribe is cosmopolitan. And the genus Conyza is cosmopolitan. If vicariance is the explanation for all speciation events we still need at least four consecutive cases of spreading across all continents. The same applies to a large number of the other tribes in the family: yes, that includes the aforementioned Senecioneae, but also Gnaphalieae, Anthemideae, Heliantheae, Cichorieae, Cardueae, Inuleae, and Vernonieae. And several of these include genera occurring across several continents or even (as with Senecio) all of them except Antarctica.

There is certainly a lot of dispersal required to explain that even in a vicariance approach, and unless we assume that most speciation in these groups took place before the breakup of Pangaea 175 million years ago (meaning the early dinosaurs would have known many of the same daisies as we do now, tens of millions of years before the oldest estimates for the origin of the daisy family) we will have to assume that some of that dispersal was long-distance.

Why not simply accept that organisms can sometimes, rarely but often enough to matter, cross an ocean and establish on the other side, followed by speciation? What is is so extraordinary about that conclusion, really? What is so different about it compared to being separated by vicariance, followed by speciation? I am still puzzled.

Wednesday, February 20, 2019

Review of the Aachen Memorandum

I picked this book up at a book fair after having read that it was a satire on bureaucracy and 'political correctness'. Although I am not the kind of person who believes that not being able to use sexist and racist insults is the end of the world and thus unlikely to agree with the author politically I nonetheless thought I might still find this kind of book interesting. I can, for example, read the original Conan novels through to the end without believing myself, as their author did, that all civilisation is corrupt and deserves to be destroyed.

Unfortunately, Robert E. Howard was a master of wit and subtlety compared to Andrew Roberts, and I only made it halfway through the Aachen Memorandum before giving up. Roberts took everything he dislikes - immigration, high taxes on the rich, animal protection, weed, speed limits, feminism, anti-racism, grade inflation, concern for healthy nutrition, and so much more, stuffed it all into one pot and then scrawled 'Europe' onto it.

The results are, unfortunately, not even intellectually coherent. The book has all European nations dissolved into a Euro-superstate, but somehow France is still able to buy the Channel Islands off England. The dominant culture is depicted as a caricature of feminist prudery, while the protagonist is constantly lecherous and voyeuristic, but he also complains that advertisements are all using sex to sell products. Europe is a total dictatorship with complete surveillance of communications, no free press, and continental armies stationed in England to forcefully squash nationalist protests, but (what follows is the only minor spoiler here) somehow the entire edifice collapses the moment somebody finds evidence that a referendum a generation ago was manipulated. The ruling ideology is clearly supposed to be left-wing and cosmopolitan, but at the same time Adolf Hitler is venerated in the schools.

How does that any of that even start to make sense? It seems as if the author believed that everybody who is not part of his own political sect is interchangeable and in cahoots with each other.

Underneath the visceral hatred of everybody outside of Britain oozing from the pages it is just about possible to see the outline of a potentially amusing thriller, but the problem is that I cannot maintain willing suspension of disbelief. Yes, the reader will soon understand that the author despises the European Union in general and Germany and Polish taxi drivers in particular, so well done communicating that, but novels also need an at least somewhat plausible and logically coherent setting, otherwise they don't work. And that is before even mentioning how blatant a wish-fulfillment self-insert the protagonist is.

I assume there was, and still is, a very particular audience for this book in one particular country, but at least in my eyes everybody else would be better served by doing something more entertaining than reading it, such as watching paint dry or counting how many grains there are in one kg of sugar.

Friday, June 29, 2018

TreeBASE and Dryad

It is now generally expected that scientists, unless working on commercial or otherwise confidential projects, make the data underlying their scientific publications freely and publicly available, so that the studies can be replicated if necessary and so that others can use the data for further research.

Sometimes the data are submitted as supplementary material to be published on the journal website, together with the article itself. Some research organisations have their own data repositories. In many cases, however specialised databases are used. GenBank, for example, is a repository of DNA sequence data. Further down the analysis pipeline, I have in the past used TreeBASE to make available sequence alignment matrices and phylogenetic trees, and in one case I have reanalysed other people's data after obtaining them from there.

Recently I had reason to submit another such set of data matrices and phylogenetic trees to a database, and I thought I would go back to TreeBASE. Somehow it did not work out as well as it did a few years ago.

I was able to log in, I created a new submission, I submitted my files, and I described our analysis. The latter process is rather clunky, but okay, it works. Then it turned out that we needed to redo one of the phylogenetic analyses minus one sequence, so I had to delete one of the matrices and one of the trees and replace them with updated versions. That is when the fun started.

Although googling around a bit suggests that other people can do so, I find it impossible to delete anything in TreeBASE. There is no delete button next to anything except co-authors and submissions (i.e. the entire studies). Being unable to change data in a submission, I decided to delete the entire submission and start from scratch. That is surely not how it is meant to work, and it is a lot of extra effort, but what can I do?

As it turns out, not even that. When I ask that a submission be deleted, the web interface thinks for a bit an then throws a Java error at me. I now have three submissions under identical names and cannot delete the first two. Hurray.

At some point I thought I could maybe try out the alternative data repository Dryad.  Perhaps that would work more reliably? At least I have seen it used in several publications lately. I have now twice submitted my eMail address on their 'sign up for a new account' form, been told twice that a confirmation eMail has been sent, and days later neither I nor my spam folder have received any such message.

Perhaps the journal will accept our manuscript without us having the matrix and trees in a public repository? This process is becoming somewhat off-putting.

Update: After a mere four days I have now finally been sent a confirmation link by Dryad. Will see how that repository works.