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.

Just grumbling a bit about a few things

Yes, I am aware that the following is nothing of importance, but there are a few things in science that have annoyed me recently.

1. People constantly writing things like "X has got 250 papers, several of them in Science or Nature" or "Y has an h-index of 18 despite his young age". Yeah, sure. But quite apart from the fact that throwing around numbers does not, on its own, prove anything whatsoever, just look at the publication lists in question. Did X write those 250 papers on her own? Does Y have that h-index based on single-author papers? Of course not. We are talking papers with >20 authors in many cases, especially in the high impact ones. So how about we divide the number of papers and the citations per paper by the number of co-authors? Does it still look that impressive compared to others in the same area who have a seemingly less copious output because they don't get to undeservedly tack their name onto papers to which they contributed perhaps 4% of the work? Thought so.

2. It seems to get ever more difficult to submit DNA sequences to Genbank (which we have to do so that they are publicly available, so that our studies are reproducible). Years ago they accepted nearly everything, today it is standard procedure to engage in a long e-mail conversation with their staff complaining that you haven't annotated the sequences correctly. See, as phylogeneticists we are often using intergenic spacer regions for our analyses, and the sequences we generate may have a few bases of coding region on their left and on their right, which are completely irrelevant for our purposes, but Genbank wants them correctly annotated. A noble goal, and so far so good.

The problem is that I do not have the foggiest idea how I can really be sure, just from my PCR products, where exactly that intergenic spacer starts and the coding region ends, and vice versa at the other end. (And again, I don't really care about those ca. twenty base pairs anyway, not least because as coding regions they are usually so conservative that they don't contain any phylogenetically useful information, but they are also too short a fragment to be useful to anybody who would want to do something with the gene.) What resources do I have to find out? The only guide I have are annotations of the same regions previously submitted to Genbank by other researchers.

Now, remember the sentence above, the one with "years ago they accepted nearly everything"? So I look up how others have annotated their DNA before, all of which was accepted by Genbank, and they have genes not starting with start-codons, or not ending with stop-codons, or three different submitters have annotated the end of the same gene to be in three different places. The only people I can rely on were as clueless as me. Yippee.

3. Over the last few years, an increasing number of buildings, research groups and even faculty positions seems to be named after people, generally famous scientists of the past although I assume that the odd sponsor may also be among them. At the same time, research groups are more and more named after the professor leading them instead of after what they actually do. Now I see how that may flatter the people these things are named after, but practical it isn't.

How about "Institute of Microbiology" instead of "Eliza Helms Institute"? How about writing "Research Group for Applied Genomics" on a door instead of merely "Smith lab"? The first of these would actually, you know, provide some useful clue as to what these institutions are actually for. Can't have that, I guess. And seriously, is an official job title like "Edward and Regina Whittaker Assistant Professor of Ecology and Evolutionary Biology" supposed to look good on a business card, as opposed to conceited? What are the people thinking who come up with these?

(The specific names were chosen arbitrarily and do not refer to real names that I would be aware of. Any similarity to existing institutions is purely accidental.)

Botany picture #76: Gazania rigens

Gazania rigens (Asteraceae), on the way to the playground last weekend. This daisy native to South Africa has been introduced to Australia as an ornamental and has sometimes escaped into the bush, especially in coastal areas.

A somewhat unusual example of the corrosive effect of the promotion of faith on intellectual consistency

Some months ago, I discovered the blog of John Michael Greer, who calls himself the "Grand Archdruid of the Ancient Order of Druids in America and the author of more than twenty books on a wide range of subjects". Despite this pompous introduction, the main topic of his blog is really peak oil, the fairly obvious but often willfully ignored fact that oil is limited, that we have already passed the point where growing demand for oil outpaces the development of new sources, and that we will have to live with decreasing amounts of ever more expensive oil in the decades to come.

As mentioned, so far so obvious. JMG further belongs to those who argue that this will mean the end of industrial civilization because there are no real alternatives to the cheap fossil fuels we have come to rely on, both in terms of return on energy invested and in terms of energy density and transportability. He locates himself in the reasonable middle (isn't that true of everybody?) between, in this case, those he considers to adhere to the "religion of progress" on the one side and the those believing in an apocalyptic collapse of society and the possible extinction of humanity on the other side. His own prognosis is that of what he calls a "long descent", a future of slowly decreasing standards of living and a drawn-out falling apart of our current industrial civilization.

Although one should always be careful about making predictions, I should stress that I mostly agree with him on the crux of the matter. Unless somebody invents fusion power really quite soon, it turns out to be really affordable as an investment, and somebody else invents really really damn good rechargeables so that a harvesting machine, airplane or truck can be powered by them, all of which I consider to be highly unlikely, our current automobile and globalization way of living will come crashing down in the foreseeable future. That being said, it is not a pleasant experience to read JMG's blog, although that is not even the main point I want to make here.

Botany picture #75: Red eucalypt

I do not know the name of this species of Eucalyptus (Myrtaceae) growing in our suburb, but this is a very instructive picture. It shows all the stages from buds at the top over flowers casting off the lid and unfolding the stamens to full bloom at the bottom. The lid is, of course, the apical portion of the entirely fused calyx.

Botany picture #74: Solanum sturtianum

Solanum sturtianum (Solanaceae), Australian National Botanic Garden, 2013. The genus Solanum is best known for the potato and the deadly nightshade. Here in Australia, the fruits of several arid zone species are apparently edible and there are even a few fairly pretty species. Others are poisonous and terribly spiny - I once collected one of them on a field trip and it was a very unpleasant experience. The present species is a shrub without spines.

Authorship of scientific papers

One topic that comes up among scientists ever so often is that of paper authorship. There are several issues here but clearly they all revolve around the underlying question of what it means to deserve a co-authorship. First, the situation.

Botany picture #73: lichen growing on wire

Another lichen from last weekend, this one from our Sunday trip. These fruticose lichens are growing on wire fence (!) in the Sanctuary of Tidbinbilla. Tough little chimeras, they need nothing but a foothold, everything else they get from the air and rain.

Update on species tree methods

I have updated my earlier post on species tree methods to include three methods made available on a very useful server and to reflect what I have recently learned about PhyloNet, STEM-hy and the speed (or rather, lack thereof) of Mesquite when trying to find MDC species trees for larger datasets. I have also promoted the post to appear among the links on the right.

Schneiderberg

Today we went for a walk in Mt Taylor Nature Reserve in the southern half of Canberra. A very nice day for it, and the summit offers a fantastic view over the city.

This is Mt Taylor as seen from below.

The view from the summit. The great mass of houses in the middle is the centre of Woden. In the background are, from left to right, Black Mountain with Telstra Tower, Lake Burley Griffin, the city centre, and a chain of hills the highest of which is Mt Majura. We live just to the left of Mt Majura. Most of Canberra is remarkably inconspicuous because there are so many trees that you can hardly see the houses. It is a very green city.

Eastern grey kangaroos grazing under the setting sun.

View from Mt Taylor towards the mountains of Namadgi National Park right after sunset.

This being early winter, there is not much in the way of flowers. Instead, enjoy these colourful crustose lichens! I don't know their systematics at all, unfortunately, but I like lichens, not least because they can look so alien.

Botany picture #72: Euphorbia amygdaloides

Euphorbia amygdaloides (Euphorbiaceae), Germany, 2005. Euphorbia is one of the largest plant genera and usually easily recognized by the highly modified inflorescences. The flowers are arranged in a structure called a cyathium which consists of a central female flower reduced only to its reproductive organ, several male flowers reduced only to its reproductive organ, and a ring of glands (in this case they are the half-moon shaped, yellowish structures). Cyathia are then arranged in cymes. This particular species is a typical part of the spring flower carpets in Germany.

Paley's watch

Over the last few days a creationist has been commenting on the Sandwalk blog linked to from my blogroll bar. Mostly he (?) has been rude and childish, but he also made a wearily familiar argument:

John Harsh-manure
What should be the reward for misplacing one's logic or brain?
I will give you an example, that Larry can understand. So, I would like to build a doghouse. I already have all the materials and tools to speed-up the self-shiting process. I have the power and all the materials. How long would it take for evolution=accidents to build this pretty simple structure? My Italian neighbor says it would take him 45 minutes. How about the mathematically calculated shit-ific calcu-shitions?
Would 4.2 billion yours suffice or you need a new brain to evolve to think straight? Well, no shit-ist can think like that so you may need some help...hihihi

To the degree that this is coherent (and admittedly that degree is not high), this is basically the argument from design, well known from William Paley's watchmaker analogy:

In crossing a heath, suppose I pitched my foot against a stone, and were asked how the stone came to be there; I might possibly answer, that, for anything I knew to the contrary, it had lain there forever: nor would it perhaps be very easy to show the absurdity of this answer. But suppose I had found a watch upon the ground, and it should be inquired how the watch happened to be in that place; I should hardly think of the answer I had before given, that for anything I knew, the watch might have always been there. (...) There must have existed, at some time, and at some place or other, an artificer or artificers, who formed [the watch] for the purpose which we find it actually to answer; who comprehended its construction, and designed its use. (...) Every indication of contrivance, every manifestation of design, which existed in the watch, exists in the works of nature; with the difference, on the side of nature, of being greater or more, and that in a degree which exceeds all computation.

(Update: I should mention that I copied this quotation from Wikipedia, ellipses and all, because I do not have the book.) Really the only differences are that the watch is exchanged for a doghouse and that Paley was a better writer. And in fact all creationism or "intelligent design" ultimately reduces to this argument.

The problem is, of course, that the argument is a false analogy, a fact that would have been painfully clear even when Paley advanced it (and others even before him). But while it is immediately clear to most observers that that is so, it is often less easy to articulate the precise problem, which is why I write this. There are at least two very important differences between the analogy and the structures the creationist considers it analogous to, i.e. living organisms:

1. In the case of a watch or doghouse, we know the creator, or if not the specific individual then at least we know that such creators exist as a class of beings. We know from experience that there are other humans and that they sometimes develop the desire to construct a watch or, for that matter, a doghouse, and that they have the capabilities to act on this desire. In the case of life, we do not know that such a creator exists. In fact the argument from design is meant to demonstrate the existence of the creator, making it a case of begging the question or circular reasoning. (Because, in case clarification is necessary, the analogy only becomes valid if what it is supposed to demonstrate, the existence of a creator, is smuggled into it from the start.)
2. In the case of the watch or doghouse, we know the process by which they were created by their creators. Again, this is not so for life. Depending on the superstition one is thinking of, the best suggestions for a creator's mechanism of action are somewhere between "the ways of the LORD are mysterious" and "the gods shaped some clay and breathed life into it". That is why engineering is a science and creationism is not*.

Finally, yes, if piles of wood and nails would reproduce with slightly modified offspring, and if that offspring had a higher likelihood of surviving to produce more offspring if it looked more like a doghouse, then a couple of million years would certainly result in the evolution of doghouses. Again, a failed analogy, but only because piles of wood and nails do not actually reproduce and because this specific selective pressure does not appear to exist.

Footnotes

*) Admittedly I am more generous in this regard than others. I can imagine intelligent design with an unspecified, mysterious creator to be a reasonable scientific conclusion under certain circumstances. Imagine we found an extraterrestrial planet with complex life where there was no fossil record until 500,000 years ago, no phylogenetic or biogeographic structure to the organisms, and population genetics indicate that all organisms apparently started to evolve** around 500,000 years ago with remarkable genetic uniformity but no deleterious alleles. Under those circumstances, terraforming and subsequent bioengineering of life forms by an unknown extraterrestrial intelligence would constitute a valid preliminary scientific conclusion. Clearly that extraterrestrial intelligence would still have been the product of evolution itself, skyhooks vs. cranes and all that, but that is not the point here.

**) Of course, once you have things that mutate and reproduce evolution is not a question of evidence any more but one of logical necessity, but that is not what creationists are really concerned about.

Six birds on my way to work

Did I mention lately how awesome the biodiversity is in this country? These are some birds that I photographed on my way to work one day last week.

Top left: Galahs (Eolophus roseicapilla) are seriously cute, especially because they are mostly seen in pairs and are very gentle with each other. They make nice little chirping sounds which one does not immediately associate with a parrot.

Top right: The Australian Magpie (Cracticus tibicen) is not closely related to real magpies but, well, colonists never were the most imaginative bunch - just look at city names. This is one of the best known and most popular Australian birds but also well respected for the males' tendency to attack passers-by in the vicinity of their nests during the breeding season. Their songs are strangely melodious in a very alien-sounding way.

Middle left: Speaking of birds for which the colonists did not come up with original names, this is a magpie lark (Grallina cyanoleuca). Its alternative name is peewee, after its call. There is also a magpie goose in Australia. Guess what colours it is!

Middle right: Male wood ducks (Chenonetta jubata). This species of ducks is one of the three most frequent here in Canberra, the other two being black ducks and the beautiful hardheads. Wood ducks appear to forage more on the dry land than the other species, especially while raising their young.

Bottom left: The sulfur-crested cockatoo (Cacatua galerita) has featured on this blog before. They are large, highly intelligent, playful, boisterous, destructive, and loud. Their call is an annoying screech which they love to produce while stretching their wings after a night's rest or after a long day's searching for food. Preferably in front of your bedroom window or above your head, of course. But they can also be terribly cute.

Bottom right: Corellas (Cacatua sanguinea) are smaller than the sulfur-crested cockatoos and give more pleasant calls. Unfortunately, they are also shyer and thus harder to get a good picture of. These two apparently felt safe from me on top of this lamp.

Botany picture #71: Calotis glandulosa

Calotis glandulosa (Asteraceae), Australian National Botanic Garden, 2013. The genus Calotis has very characteristic spiny and/or winged fruits which provide the major characters for identification. The spinier species are known as "bindi", and it is very unpleasant to step on them or to get them into your boots during field work, as I know from experience. Unfortunately, many of them are very hard to tell apart without the fruits. This is one of the prettier species and also fairly easy to recognize due to its strikingly glandular indumentum. Others often have smaller flowerheads, either also in purple or often in yellow.

Fundamental and realized niche

A short follow-up on the previous post mentioning the Ecological Species Concept: As discussed, ecological niches are not entirely unproblematic. It sounds like a useful mental model to view each species as "fulfilling a role" in its community but reality is more complex.

To mention just one issue, there is a difference between fundamental niches and realized niches. What does that mean? Well, it could be that a plant, for example, could happily grow under wet, mesic and dry conditions if it were the only plant around. However, there is another plant that can also grow under mesic conditions but it is much more competitive than the first plant. That means that if they occur in different areas, the first plant will grow in all three habitats and the second one only in the mesic habitat, but if they happen to occur in the same area, you will find the first species in wet and dry places and the second one in the mesic places where it excludes the first.

For illustration, this is how well both species do along a moisture gradient, which we could call their fundamental niches:

And this is how many individuals of each species you would really be able to find along the moisture gradient if they both occur together, which would show their realized niches:

What this shows is first that no organism should be expected to come with a clearly defined role but that it has to settle into one depending on what other organisms are around. Also, which of these two is the niche relevant for the Ecological Species Concept?

If we go with the realized niche, for example because we have so far only observed the species together in nature and don't realize that the orange species would feel even happier under mesic conditions than where it is actually forced to live, we would probably intuit that the orange populations in dry and the wet habitats are two Ecospecies. Perhaps there is a bit of circular reasoning involved on my part (i.e. I may be smuggling the criteria of the Biological Species Concept into my argument), but this seems plainly absurd to me. But if we take the fundamental niche as a guide, what use is that if it may never be realized in nature?