Overly honest methods

Just got sent a link by a colleague. It's hilarious, check it out. The one with "reviewer 1" might be my favorite, as you can imagine.

No True Scotsman, No True Christian, No True Rationalist

My long text-post a few days ago got me thinking, for some reason, about the No True Scotsman fallacy and its application to belief systems. In case it is not common knowledge, the name comes from a hypothetical conversation that does something like this:

A: No Scotsman drinks his tea with sugar.
B: That cannot be true. I know a Scotsman who does.
A: Then he is not a true Scotsman, because no Scotsman drinks his tea with sugar.

The problem is, of course, that whether one drinks tea with sugar or not is not really part of the definition of "Scotsman". Instead the concept is based on ancestry, place of residence, integration into a community of other Scots, etc. A is simply wrong unless he unilaterally redefines the word. Sometimes disagreements between two people are due to at least one side being wrong on the facts, sometimes they are due to different definitions of a relevant term (consciously or unconsciously), and sometimes one side is simply irrational and tries to twist the definition of a term to win by default. The latter two scenarios are the ones where the No True Scotsman becomes relevant.

The relevance for religions or other belief systems is pretty obvious - many of us will have had a conversation like the following:

C: Christians are more moral than atheists / Without religion there is no moral guidance, and terrible things will happen.
D: Not so fast. What about the inquisition? They did terrible things to innocent people in the name of Christianity. And mind you, Adolf Hitler was a Catholic.
C: Well, none of them were true Christians. If they had really been Christians, they would not have done these things.

As in the case of the Scotsman, it is now important to have a clear definition of "a real Christian". Unfortunately, that is where it gets difficult.

Botany picture #79: Lathraea squamaria

Lathraea squamaria (Orobanchaceae), Germany, 2009. When I went to university, the Rhinanthoideae were still, for some bizarre reason, part of the Scrophulariaceae although it was a complete no-brainer that they were more closely related to Orobanche than to other Scrophulariaceae. About the only rationale one could perhaps perceive in the classification that was accepted then was that the Orobanchaceae were holoparasitic, that is they do not have chlorophyll and steal everything they need from a host plant, and the Rhinanthoideae were hemiparasitic, that is they steal water and nutrients but still conduct their own photosynthesis to produce complex organic molecules. Lathraea, however, used to be in the Scrophulariaceae despite also being holoparasitic, making that classification even less defensible. Another example where the new phylogenetic classification makes more sense.

The inflorescence in the above picture is all that ever shows above ground, and there are no green leaves. There is another species that has even less above ground parts but unfortunately I do not have an image of it.

Do as I say, don't do as I do

Lately awareness seems to be rising that impact factor mania has reached ridiculous proportions, and interestingly it appears as if one of the highest impact scientific journals is trying to hop onto the train. The American Association for the Advancement of Science, the publisher of the journal Science, is one of the signatories of the San Francisco Declaration on Research Assessment that quite sensibly urges researchers and their institutions to stop judging fellow researchers by the impact factor of the journals they publish in.

Perhaps to promote the declaration, the editor-in-chief of Science followed up with an editorial making the same argument, explaining how destructive the obsession with impact factors is and that they were never meant to evaluate people. Now another editorial has been published in Science bemoaning the emphasis on impact on a more general level, such as the increased push for applied as opposed to fundamental research, and the short-term-ism and risk avoidance that come with such a focus.

Basically I wholeheartedly agree with all of this. But here is the thing: I take issue with being lectured about impact mania from the pages of a journal that embodies all that those complaints are about. It's about the messenger, not the message. This is a journal that is well known for accepting publications not primarily on quality but on expected impact, and for rejecting everything out of hand that is unlikely to be a big thing over the next few years.

Don't get me wrong - I am not saying they don't have a generally good peer review, or that they publish more bad papers than would be expected from rare and unavoidable failures of the review process as they can happen anywhere. No, what I mean are those many, many papers, probably the majority of the submissions, that are never even reviewed because some managing editor turned them down on sight. Does anybody really assume they do that because they can immediately see that the paper is poor quality, or that the analyses are wrong? No, they do that because the topic is not sparkly enough, because if they published high quality papers that aren't sparkly enough then their rank as one of the two or three highest impact journals might suffer. Just you try submitting the most excellent taxonomic revision or seed germination experiment you have ever seen to Science, and see how it fares against cancer research, the discovery of a new exoplanet or even just the discovery of a new hominid bone fragment. Go on, I dare you. That is the name of the game.

And so it is rather galling to read these editorials in, of all places, Science, because to me they sound like "do as I say, don't do as I do". And honestly, gems like this, where the editorial argues against impact factor mania with the observation:

And it wastes the time of scientists by overloading highly cited journals such as Science with inappropriate submissions from researchers who are desperate to gain points from their evaluations.

Cry me a river. A journal that advertises itself with a tag line as nauseating as "The World's Leading Journal of Original Scientific Research, Global News, and Commentary" on its website does not really get to complain if people consider it a feather in their cap to get an article in there.

Botany picture #78: Corydalis ochroleuca

Corydalis ochroleuca (Papaveraceae/Fumariaceae), Botanic Garden of Halle, 2008. Traditionally treated as their own family, the Fumariaceae are today usually included in the poppy family Papaveraceae. Essentially, they are poppies that have evolved highly specialized, zygomorphic flowers. However, if I understand the situation correctly, the two groups may be reciprocally monophyletic, so in this case it is purely a matter of personal preference whether to treat them as separate or not.

Asynchronous species concepts: internodal and composite

As indicated before in this series about species concepts, most of them apply only to contemporary organisms or more generally to those existing in the same time slice. That becomes clear quite quickly if we try to apply them in an asynchronous fashion, i.e. through time.

The Biological Species Concept (BSC), for example, sees species as breeding groups. Because we humans do not interbreed with desert oaks, and indeed would find it hard to do so, we are clearly separate species. If we let our gaze drift over all of evolutionary history, however, it becomes clear that there must have been an unbroken chain of individuals connecting me, the desert oak I photographed on the Great Central Road in 2010, and some common ancestor the two of us had sometime a few hundred million years ago. In other words, seen through deep time all of life on earth is a breeding community, and thus the BSC would fail to cleave the diversity of life into species.

As another example, the Genotypic Cluster Species Concept (GCSC) identifies species as clusters of individuals in some morphological or genetic analysis that have no or few intermediates with other such clusters in the same analysis. Again, because all organisms on the planet appear to be parts of the same great tree of life, and because evolutionary change happens gradually through the change of allele frequencies in populations, there just is no place along the branches of the tree of life where there are "no or few intermediates". Just as the BSC, the GCSC would not work.

Of course, if you see species as breeding groups, you might immediately conclude that applying species concepts through time must be absurd. Still, there are those who have tried to formulate ideas on how to make the word "species" work in this context. There aren't many, and one of them I have already discussed before is Willi Hennig's Internodal Species Concept, so I will keep it short on that one. A few more words are then needed for the newer alternative.

Botany picture #77: Pimelea linifolia

Pimelea linifolia (Thymelaeaceae), New South Wales, 2011.

Systematists and taxonomists have their favorite groups, and it is usually hard to say why they like this one better than another. I, for example, am particularly fond of the asterids, the large subclade of the eudicots that has evolved fused petals (the other large subclade, the rosids, has free petals). This group includes plant families such as the Lamiaceae and Acanthaceae, on which I have conducted research before I came to Australia, and the Asteraceae, which I am studying now.

In general I am not overly fond of most rosids or monocots. There are, however, non-asterid groups that I also like very much, and the Thymelaeaceae are one of them although they belong to the rosids. I have no clear explanation but it is interesting to note that they have gone out of their way to pretend that they have fused petals like the asterids - the picture above sure gives the impression that we are dealing with a long, narrow corolla tube and four corolla lobes. But what really happened in the evolution of the family is something different: the tube is a hypanthium, a floral cup that merely pretends to be a corolla tube. What looks like petals are the sepals, and the real petals are lost (although in other members of the family they can still be seen as small scales at the flower orifice).

Pimelea is by far the largest genus of the Thymelaeaceae in Australia. The species are generally small to medium sized shrubs and have only two stamens per flower. The genus is easily recognized but it is harder to determine the species.