Botany picture #194 Wahlenbergia gloriosa

On the weekend we made a little trip to Mount Franklin Road in the Brindabella Mountains, and for the first time I saw the 'royal bluebell' Wahlenbergia gloriosa (Campanulaceae) in flower. It is the floral emblem of the Australian Capital Territory, and it has been chosen as the logo of the upcoming Australasian Systematic Botany Society conference that my institution is hosting.

Stemmy large-evolutionary changes (that special issue)

(The following is the ninth part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

The final contribution to the special issue advocating paraphyletic taxa is Richard Zander's Support measures for caulistic macroevolutionary transformations in evolutionary trees. There are two ways of addressing it, and with previous papers in this issue I have sometimes taken one and sometimes the other: Either one can go through the paper bit by, carefully analyse the argumentation, rebut one claim here but concede another there, and so on; or one can take a step back, point at the fundamental assumption underlying the whole line of argumentation, and explain in a few words why one considers it to be wrong.

Because I am tired and have much else to do, I will mostly use the second approach and then spend just a bit more time addressing other random aspects of the paper that stick out to me.

Really it is very simple: Richard Zander sees groups of organisms that exist today as the ancestors of other groups of organisms that exist today. I, and with me presumably most systematists and evolutionary biologists, believe that a group of organisms that exists today cannot possibly be the ancestor of another group of organisms that exists today.

Unless one were to push them forcibly into a working time machine, today's chimpanzees are not going to become our ancestors, today's fish are not going to become the ancestors of the land animals, and today's ferns are not going to become the ancestors of the flowering plants. Instead, these groups have common ancestors in the past, and thus, no matter how much Zander ridicules the concept, “unknown hypothetical ancestor → (one extant group, another extant group)” remains the most appropriate way of describing evolutionary history. As a group of individuals in a time slice, the ancestral taxon is separate from all of its descendants, and as an evolutionary lineage through time it is identical to all of them, but it does not make sense to equate it with only some.

So again, I do not accept the premise that would enable us to even start thinking in terms of what Zander calls “caulistic macroevolutionary* transformations”, and thus for me the entire argumentation of this paper never even gets onto its feet. Conversely, Richard Zander does not accept the premise that ancestors should actually be ancestral to their descendants, and so nothing I can write would ever convince him. Agree to disagree and all that, I guess.

Dated phylogenies: My experience using r8s

In the spirit of my previous posts on species tree software and fastStructure, the following post is to summarise my experience trying to use the software r8s, again so that somebody who also tries to use it for the first time may have the chance of finding these remarks and thus avoid some of the frustrations I had.

First, what is this about? It can do more, but for my present purposes Mike Sanderson's r8s (~rates) is a program that takes a phylogenetic tree and at least one fossil calibration point provided by the user and then dates the other nodes of the tree.

Imagine you have a phylogeny of a group of plants - a tree of their evolutionary relationships, produced with molecular data and using one of the standard phylogenetic software tools, TNT, RAxML or MrBayes perhaps - and you want to know when some of the subgroups evolved. For example because you want to know whether a given climatic or geological event is associated with the diversification of one of the subgroups.

You need some kind of information that allows you to calibrate the phylogeny somewhere; either you know mutation rates in the molecular data you are using, or you have fossils that you can use to assign minimum ages to the groups they belong to (the group can be older but not younger than the fossil), or, weakest of all perhaps, you believe other people's dated phylogenies and use some of their results as calibration points. You also need to assume that branch lengths in your phylogenetic tree - mutations along the branches - have at least some kind of rough relationship with the age of that branch.

Clearly there are a lot of assumptions entering into this kind of analysis, and there are scientists who are highly sceptical of these kinds of methods. Still, the assumptions that a group is at least as old as its oldest fossil and that groups accumulate more differences the longer they are apart are surely reasonable, and so as long as we take precise ages in the results with a bucket of salt we can at least use the broad strokes to address some questions. Conversely, if we get an age of more than a billion years for a group of flowering plants we know that something must be amiss.

r8s is one of the two principal tools for doing dated analyses; the other one is the Bayesian software package BEAST. Many people, especially religious Bayesians, would probably say that r8s has been made redundant by BEAST. But as I have written here before, all of these methods have their own advantages and disadvantages. One of the major disadvantages of Bayesian phylogenetics is that it rests on an even greater number of assumptions and, specifically, priors than simpler methods. Add to that the often ridiculously long computing time especially for larger datasets or the problems BEAST often has with missing data and it should become clear that there will always be a comfortable niche for other approaches.

With this, we finally arrive at the program r8s itself, which I have tried out over the past few days. The manual does a good job of explaining its functionality and how to set up an analysis, so I will not deal with that here. Rather, I want to focus on the practical details that one usually has to find out the hard way:

Botany picture #193: Adoxa moschata

Adoxa moschata (Adoxaceae), Germany, 2008. Australia has many weird little ephemeral plants in the arid zone; often closely related to larger and longer lived species, they have evolved to quickly grow and seed after only a few weeks, often self-pollinating in the process, because they are living in a habitat with very unpredictable rainfall. This European herb does not have the same excuse. It is a fairly close relative of several groups of shrubs that used to be in the Caprifoliaceae but for some reason it has evolved to be so tiny that it is easily overlooked on the forest floor.

Alter Wein in neuen Schläuchen

It often seems to me as if the milieu or class of technology-savvy and allegedly, according to themselves at least, "rational" people who amalgamate around institutions such as MIRI and Less Wrong and around futurism gurus such as Nick Bostrom, Ray Kurzweil and Eliezer Yudkowsky believe pretty much the same things as people they would, as alleged rationalists in the computer age, most likely consider hopelessly backwards. The difference is that they cleverly tacked a 21st century terminology onto the same beliefs:

Botany picture #192: Craspedia leucantha

Today we can celebrate the successful completion of our ten week summer student projects and of the various events that we had this week, in particular the summer student symposium on Thursday. It seems fitting to post a botany picture of the genus that the project I supervised was about: Craspedia, in this case C. leucantha (Asteraceae).

This particular species is endemic to Kosciuszko National Park in New South Wales. Although it flourishes in dense lumps in rocky seepages the alpine zone, it is extremely hard to maintain in cultivation. It is one of only two mainland Australian Craspedias with white flowers. Bizarrely, it was the only mainland species of Craspedia in the current, stricter sense that was described before 1992; all other species published before that year are Tasmanian or New Zealandese.

Singularitarians once more

Browsing through the web I have just come across the current "Edge Question" and Sam Harris' answer to it. The question is, what do you think about machines that think? And Harris' answer shows that he is, or has gone, full bore Singularitarian. He argues that one of the greatest risks humanity faces is the construction of a hostile artificial super-intelligence, and that the construction of a benevolent artificial super-intelligence should be a high priority because it may solve all other major problems.

I can kind of understand why Singularitarians believe what they believe, in the same sense that I can understand why people right after the discovery of radioactivity believed that in the near future everything would be nuclear, including the living room heating. When something is all the rage, and in the current age it is computers, critical thinking can be overwhelmed by unwarranted enthusiasm.

After all, every saturation curve starts out like an exponential curve, and thus the rapid early advances are often happily extrapolated into the future. But I would have thought that Harris, who is, after all, a scientist and otherwise a sceptic, would have been more critical of the idea of an intelligence explosion.