Monday, June 29, 2015

Panbiogeography once more: relatedness between biota, parsimony of dispersal events, and the garden of Eden

For some reason, the first author of Nelson & Ladiges (2001), Gondwana, vicariance biogeography and the New York School revisited, recently sent me that paper with the comment "an item of possible interest". I can only assume that this is because I was anti-convinced that panbiogeography makes sense by the recent contributions of Michael Heads to Australian Systematic Botany.

(Anti-convinced meaning here that not only did they fail to convince me of the virtues of the approach, but the circularity of the first paper's example analysis actually pushed me further towards considering panbiogeography to be unscientific than I was before reading it.)

I always find it interesting to consider arguments challenging my position, but I am not entirely sure how Nelson & Ladiges (2001) is relevant to Heads (2015). The logic of the 2001 paper is rather different from Heads' recent argumentation, and its methodology is rather different from his demonstrative example of a panbiogeographic analysis, so even if I would say "hey, makes sense" after reading it that would still not help the circularity of Heads' analytic approach.

Still, reading it was very insightful; I only now fully appreciate that certain schools of thought appear to be interested not primarily in reconstructing the ancestral areas and movements of lineages (as Heads seemed to be in his recent papers) or in bioregionalisation, but in reconstructing relationships between biota. They try to arrive at something like a phylogenetic tree of biota, where one can say, for example, that the "boreal" region is the sister of the "austral" region.

I find this very remarkable, for several unrelated reasons.

Saturday, June 27, 2015

Science spam the umpteenth

Just when I thought spam mails from for-profit "journals" had gotten a bit more professional looking lately, I get this:

If trying to look like a serious scientific publication is here, then the above spam message is... somewhere outside the local group of galaxies, I think?

As for the claim that indexed journals are often considered to be higher quality than non-indexed ones, that is true as far as it goes. Unfortunately, Google Scholar is not really a selective indexing service but a search engine, and I have never heard of any of the others.

Wednesday, June 24, 2015

Fun with scientific plant names

Long time no blog; not enough ideas what to write, too much else to do.

Just went through a big dataset of Asteraceae (daisy or sunflower family, also known as Compositae), and I realised how many silly scientific genus names there are. Some of the highlights:

Pseudobahia, Pseudoclappia, Pseudoconyza, Pseudohandelia, Pseudonoseris, and Pseudostifftia are, of course, all based on similarity to genera with exactly the same names only without the Pseudo-.

Similarly, I feel that Senecio, Dendrosenecio, Nemosenecio, Parasenecio and Sinosenecio betray a certain, let us say, lack of imagination in naming members of the Senecioneae tribe.

Erato sounds odd but was apparently one of the Ancient Greek Muses. No idea whether the genus Oblivia has a similarly defensible etymology though.

Damnxanthodium is perhaps the best. Xantho- means yellow, and as can be imagined 'damn' is neither Ancient Greek nor Latin. It is an obvious reference to the American abbreviation DYC, which stands for Damn Yellow Composite, in other words the complaint about so many of them looking pretty much alike. A zoologist counterpart is apparently LBB for Little Brown Bird.

Friday, June 19, 2015

Botany picture #204: Cassinia arcuata

Admittedly Cassinia arcuata (Asteraceae) cannot be counted among the prettiest members of the sunflower family, and despite being native to Australia it is actually a declared noxious weed in the state of New South Wales. Still, it is an interesting plant. As a shrub with large numbers of brownish, few-flowered flower-heads - I can only assume it is wind-pollinated? - and apparently able to quickly come up after fires it has an interesting ecology. It is also strongly aromatic.

The specimen in the picture is part of plantings in the Southern Tablelands Ecosystems Park at the National Arboretum here in Canberra.

Monday, June 15, 2015

Peer review and competing schools of thought

Peer review in science works quite well, I think, if everybody is agreed on the fundamental assumptions and the proper methodology of the field. If somebody gives me a bog standard phylogenetic or taxonomic study to review, I know what to look for, I know what should be there, and it is easy to write a report.

The problem is when the paper is from one side in a heated controversy. In my field of work, generously circumscribed as ranging from systematics across biogeography to evolutionary biology, the following come to mind:
These are not all comparable, by the way. In some cases, the truth is likely somewhere in the middle, but in others only one side can be right.

Anyway, assume you are an entirely neutral journal editor and you need to get reviewers' reports for a paper from one of those sides, let us say from a panbiogeographer doing a panbiogeographic analysis. Who do you send it to?

If you send it to a mainstream biogeographer, you already know that they are going to recommend rejection because they consider the entire methodology and its assumptions to be unscientific. The same if the roles are reversed; a colleague had a paper rejected because he found evidence for long distance dispersal and ran into a reviewer (and an editor) who don't believe that it is possible. Send it to somebody who isn't on either side? Well, they are likely not qualified to review in the first place, otherwise they would already have picked a side.

So how does such a conflict ever get resolved? Keep the two parties carefully separated and hope that one of them dies out? That is also a form of post-publication review I guess.

My perspective is currently that of having been asked to review a paper from a representative of a school of thought that looks to me kind of like this:

What to do? I informed the editor that I should be considered biased, but he wanted my opinion anyway. Having an editor who listens to both sides, takes their respective views with a grain of salt, and then makes up their own mind is probably the best one can hope for. But pre-publication peer review is still a very imperfect tool in such a situation.

Thursday, June 11, 2015

Botany picture #203: Passiflora spec

Long time no botany picture, although I guess the lichens and mosses from Monga could count somewhat towards that quota.

I recently loaded the pictures from my field trip to Latin America in 2007 onto our current computer, so it is a good time to show one of them. Sadly I rarely know the names of the plants I was not specifically collecting for my project at the time, and such is the case with the passionflower shown above (Passiflora spec., Passifloraceae). It was growing a bit to the west of Santa Cruz in eastern Bolivia. Although not as spectacular as and much smaller than the better known ornamental passionflowers it shows the same intricate flower structure.

Tuesday, June 9, 2015

Religious instruction

A few days ago we got a form to fill out if we want our daughter to participate in upcoming religious instruction classes. They are generically Christian, on the lines of "learn about the kind of God Christians believe in"; that is, they leave open for the moment whether that god is an ill-defined feeling that everything will turn out alright or the kind that boils you in a lake of molten sulphur for having had impure thoughts.

Anyway, it is interesting to consider the different approaches taken by various countries. Despite being the most religious Western country, the USA are famously officially secular, and so there is no religious instruction in public schools.

In my native Germany, however, there are pretty much official state religions - Lutheranism in the north, Catholicism in the south. Not only does the government collect church taxes from all Lutherans and Catholics, but public schools everywhere except in the state of Berlin offer classes in their locally dominant religion as the default option, with atheists having to actively opt out. At least that is how it was when I grew up, but to the best of my knowledge the only thing that has changed is that some areas have become more open about offering an Islamic option.

Australia, or the Australian Capital Territory at any rate, sits kind of in the middle. As indicated above, there are generically Christian classes on offer in public schools. On the plus side, they appear to be opt-in instead of opt-out and they are run by volunteers, which means that apart from overheads like providing a room etc. no taxpayer money is wasted on sectarian beliefs.

However, this comes with a downside: the classes are run by volunteers. Although I am happy to be corrected I assume that they are unlikely to all have the same standards and pedagogical expertise as trained and certified teachers. Perhaps worse, in contrast to a professional teacher who is paid to do their job, unpaid volunteers are more likely to be motivated entirely by missionary zeal; it is at least conceivable that this self-selection effect will have what I will diplomatically call interesting consequences. And indeed one hears stories...

As should have become obvious, I am in two minds about whether the German professional system or the Australian voluntarist system is better. I am, however, quite positive that of all three I personally would prefer the American one: Just keep religion out of public schools and let the various sects organise religious instruction in their own time.

And what to make of the openly sectarian private schools supported by hundreds of millions of tax dollars is yet another issue.

Sunday, June 7, 2015

Monga National Park

Today we made a family trip to Monga National Park. Sadly the sun never came out, and consequently the weather was a bit chilly, and it was hard to get decent pictures under those light conditions.

Our main objective was to visit Penance Grove, depicted above. It is quite beautiful but has been the site of severe ecological vandalism in the past. Some complete @#$%^ went there and chopped off dozens of tree ferns. Their sad, dead stumps can be seen between the surviving ones, because tree ferns generally don't re-sprout. It is also strongly to be assumed that the pieces the vandal harvested died as well; one just wonders if they did so before he sold them or after. Anyway, depressing sight, but happily there are a lot of living tree ferns too.

Apart from its general beauty, we wanted to visit the grove because it is a place where Dawsonia superba (Polytrichaceae), the largest moss in the world, can be found in the wild. This is a clump of it above. Apart from producing spores the plant spreads via a rhizome-like stem system in the ground.

The above picture shows how large an individual stem and its leaves are. This is something quite different from other mosses, and many people mistake it for a vascular plant.

Apart from lots of ferns and mosses there are also many lichens. The one above makes a rotting tree stump look like a miniature alien landscape.

Finally, the Mongarlowe river near Dasyurus Picnic Area. Along the riverbanks the local Waratah species Telopea mongaensis (Proteaceae) can be seen flowering in October to December. Perhaps a reason to visit again.

Saturday, June 6, 2015

Will you only believe that the sky is blue if a recent peer-reviewed paper says so?

The usual disclaimer: The following is my personal opinion. It is not my professional opinion and much less necessarily the opinion of any other person or any institution associated with me in any way.

Sometimes I see the kind of discussion where one person will claim that science has refuted the existence of gods, and then somebody else will offer a challenge on the following lines:
If you are going to respond that that's because "science" has decided that there is no God, surely you can point me to a number of high profile papers in Nature or Science that clearly shows how such a conclusion was arrived at, scientifically.
Even if one is convinced that science has not and cannot disprove the existence of gods this argument seems very weak.

Monday, June 1, 2015

Scientific fraud doesn't make sense to me

Having just read about an alleged data manipulation scandal in political science in the USA, I wonder once more why people are committing scientific fraud. I get plagiarism in the humanities, although of course the risk of getting caught is growing ever greater considering the ease with which text searches can be conducted these days. Still, I realise why people might be tempted into doing it, especially if they are not pursuing a career in scholarship, just want a few extra letters to appear on their business card, and are unwilling or unable to make the necessary effort. Inventing or manipulating empirical data as a career scientist, however, I don't really understand.