The taxonomic impediment and DNA barcoding

Further to yesterday's conference, there was also a talk about DNA barcoding. First, what is that?

Some time ago I did a post on the taxonomic impediment, the problem that the number of taxonomists worldwide is too small (and, due to short-sighted funding policies, shrinking) to deal with the massive amount of biodiversity still to be described and classified, a situation that impedes downstream studies in ecology, evolutionary biology, conservation management etc relying on an accurate description and classification of life.

The idea behind DNA barcoding is to allow an easier determination of species by sequencing a few carefully chosen gene regions for as many species as possible and depositing that information in a searchable database. So if you found, for example, a plant in a rainforest plot and you needed to know what it is, you don't collect a specimen any more and send it to a botanist for determination, but instead you extract DNA, sequence the right gene regions, and then use the database to find out, say, that there is an 98.9% likelihood that the plant you are dealing with is Ruellia brevifolia.

Optimists could say that this is a good solution to take superfluous work off the shoulders of overtaxed taxonomists so that they can get on with describing new species. Cynics might think that the idea is ultimately to de-fund taxonomic research and to replace taxonomists with shiny DNA sequencers.

There are good reasons to believe that barcoding cannot work in principle, at least not at the species level. (Hint: the most important one starts with "i" and ends with "ncomplete lineage sorting".) But the talk I heard yesterday raised a different issue.

You see, the colleague who presented it had earlier been at a different conference dedicated specifically to barcoding, and one of the things she learned there was that the vast majority of barcode reference sequences in Genbank are what is called "level 0", meaning that nobody knows what species they are from because the people who produced them were unable to find a taxonomist who could confidently determine the specimen they got the DNA out of.

Is that not just awesome? Of course barcoding, even discounting other technical problems, can only work if there is a high quality, reliable reference database. Maybe at a minimum one should have waited with starving taxonomic expertise to death until such a high quality database was in place.

Bush Blitz Symposium 2013

All day today I was participating in the Bush Blitz Symposium 2013, a one day meeting here in Canberra at Old Parliament House.

What is Bush Blitz? In the words of the eponymous website:

Bush Blitz is Australia’s largest nature discovery project - a three-year multimillion dollar partnership to document the plants and animals in hundreds of properties across Australia’s National Reserve System. Since the program began in 2010 Bush Blitz has discovered about 600 new and undescribed species and has added thousands of species to what is already known - providing baseline scientific data that will help us protect our biodiversity for generations to come.

Perhaps most importantly, the initiative organizes targeted surveys to document all species of certain focus groups (one of them being vascular plants) in defined areas, often properties that are being transformed into nature reserves. In every case, botanists and zoologists with different specialties are brought together for one or two weeks to inventory the biodiversity of the place, with all the logistics provided by the Bush Blitz team. The scientists collect samples, process them in the base camp, determine them to species and ultimately compose species lists. The Bush Blitz team then writes a report on the survey summarizing the results.

I was lucky enough to participate in two Bush Blitz surveys, one in New South Wales and one in central Tasmania. While I did my part to document the local plant diversity, both field trips also allowed me to obtain samples for my research and to learn more about the Australian flora. One of the most interesting aspects of those surveys is the close interaction with biologists studying other groups of organisms.

In addition to the surveys, the initiative also provides grant money for taxonomic research resulting from the survey work. The symposium today presented results from the activities conducted so far and additional talks on topics relevant to the Bush Blitz project. Topics of the talks were extremely diverse, including teaching and outreach, collaboration with the traditional custodians of the land, hard scientific analyses as well examples of species discovered as new to science, and conservation planning. (I presented a talk on collecting biases - field botanists collect mostly close to where they are and along roads, and they under-sample spiny, very small, ugly and non-native plants. Bush Blitz addresses all these issues by targeting neglected areas and by inventorying all species of a group, not only the conspicuous ones.) The talks were very interesting and the speakers were really enthusiastic about biodiversity. All in all a great meeting.

In summary, the Bush Blitz is a fantastic and globally unique institution; if you want to learn more, you could do worse than reading through their website.

Moral philosophy and personal maturity

A few more remarks on morality. Often when people disagree they ask themselves whether the other side is stupid or evil (or, if you want to be more charitable, uninformed or dishonest). But that clearly does not exhaust the possibilities. Many controversies, especially in economics and politics, simply do not allow for a rational resolution because they are questions of values instead of questions of fact. In those cases, the two sides might merely have different economic interests and/or different value systems, and the solution cannot be a clear decision on who is right but only a compromise.

Another option might be insanity of one side in a controversy although that will not be a problem so terribly often, one would hope. Finally, one possibility that I think is under-appreciated is different levels of maturity. For example, it is a sign of immaturity to prefer immediate gratification over greater deferred gains, so a conflict over two possible courses of action could be simply based on one person being more mature than the other.

Although I do believe that there is no objectively, universally deducible system of morals, I also think that we humans share many of the same instincts and interests and could potentially agree on more ethical questions than we generally manage to do, and that the problem has its roots at least partly in different levels of maturity. It seems fairly clear that there are different stages of moral development that a person can go through as they mature:

1. They are completely self-interested and lack empathy. Rules are only followed because of the fear of some form of punishment (ranging from the mild disapproval of authority figures to severer penalties). It is perhaps an oversimplification to assign this state to babies and very young toddlers but not by much. It is certainly also the stage at which most house cats appear to be stuck: once you turn your back, they do what they see fit.
2. They know that there are rules and that one should follow the rules, and that is it. In hindsight it was fairly clear when my daughter had reached that stage of her personal development.
3. They understand that rules exist for a reason, and that what really counts is whether the intention behind the rules is being achieved. Some rules may be in conflict with each other, and knowing what they were written to achieve allows you to figure out which of them to break in such a case. In fact some rules are silly and can be ignored while others are crucial. A clear example would be rules whose real purpose is to minimize harm to people; if you can minimize that harm better by exceptionally breaking one of the rules, so be it.
4. Finally, they start to question how the intention behind the rules can actually be justified. Who says that achieving accident-free traffic flow, minimizing harm or suchlike are actually the things we should care about? Can we justify them from first principles? Some people might fear the collapse into nihilism here but really this stage of moral development is both necessary and liberating. Leave nothing unexamined. (And yes, ultimately we make our own rules, but that is how it has to be because they are for us and about us and by us. Pretending that the rules came from the gods, for example, is merely a self-serving lie because they were really created by humans. If we all acknowledge that we have a better basis to improve them.)

The point is now that different people have gotten stuck on different of these developmental stages. A small minority even of adults never makes it past the first, and they are often called psychopaths.

Many more are stuck at the second stage, the one of blindly following rules. This is behaviour often associated with bureaucrats although that is perhaps unfair as administrations are built precisely to foster it. More importantly, it is obviously what we might generously call the moral philosophy of religious fundamentalists: X is bad because God says so, look it's here in my holy book. Ah, but X does not actually hurt anybody, so who cares? Doesn't matter, God says X is bad, that settles it. The same is true for many very conservative people who value stability over all and fear that not following the traditional mores of society will result in whole-scale societal collapse (instead of merely a similarly stable and healthy society with different mores).

It is because large numbers of people are stuck at stage 2 in their moral development and many others have advanced to stage 3 that moral controversies (the "culture wars" in American terminology) are so intractable. If one side thinks that rules are rules are rules, and that is it, and the other side thinks that rules are only tools that need to be changed if they don't achieve some more transcendental goal, then it is hard to ever reach an agreement.

Botany picture #89: Hydrocotyle laxiflora

Hydrocotyle laxiflora (Apiaceae), Australian Capital Territory, 2010. In central Europe, nearly all members of the carrot family Apiaceae look very similar: medium sized herbs with double umbels of small usually white or rarely yellow flowers and deeply divided leaves. Easy to recognize as a family but hard to determine to species or even only genus, especially for a beginner and especially if you have a specimen without fruits. Towards the Mediterranean, it gets morphologically more diverse with increasing representation of interesting genera such as Bupleurum or Eryngium. Here in Australia, there are also quite a few unique looking Apiaceae, and it is sometimes even harder to figure out that you are dealing with an Apiaceae than to determine the species once you have done so. Admittedly the genus Hydrocotyle is fairly easily recognizable as a member of its family but it is still interesting to somebody who is used to the Apiaceae of northern Germany. It is well represented in the flora with both native and introduced species.

Objective versus arbitrary morality, and aliens

Jerry Coyne recently wrote a post on his website expressing his conviction that there is no objectively deducible and universally valid morality or ethics comparable with the objectivity and universality that one would find in empirical science, abstract logic or mathematics.

I would argue the same. There simply does not appear to be a way to bridge the famous is-ought gap. Claims such as the one that morality is ultimately about the well-being of sentient creatures are really just begging the question. Why should (mostly) human welfare be the yardstick of moral decisions? Ultimately only because we humans say so. And really, that is okay - who else except humans should decide what human morality has to look like? But let us not pretend that such a decision is universally and rationally justifiable.

And let's not get started on other proposed solutions such as divine command theory, which collapsed under the weight of its intellectual incoherence more than two thousand years ago. Even if there were a cosmic tyrant, why should it be moral to follow their arbitrary orders?

No, a more interesting set of questions than whether we can rationally deduce a single set of objectively and universally true norms would be where our actual norms in fact do come from, and how much of them is contingent versus a necessary development. As we will see, the second of these questions is somewhat related to that of arbitrary versus objective morals, only  without the claim of a rational derivation.

Botany picture #88: Wahlenbergia graniticola

Wahlenbergia graniticola (Campanulaceae), Australian Capital Territory, 2010. Well, I am not entirely sure I got the species right, I find Wahlenbergias rather hard to determine to species. This genus of bellflowers is nearly cosmopolitan but could be seen as the southern hemisphere counterpart to northern hemisphere Campanula. The major difference between the two is apparently the opening of the capsule, but apart from that they are fairly similar. The state flower of the ACT is also a Wahlenbergia but not this particular species.

An analogy that might help to clarify some issues with cladism

An extended discussion I am currently having with a colleague and tangentially related observations on a discussion over at Larry Moran's Sandwalk blog have made it clearer to me why some people reject phylogenetic systematics, or cladism. Because there are events of lateral gene transfer, introgression, endosymbiosis, chloroplast capture and suchlike, all processes that transfer genetic information between different species or lineages, they see life as having a fundamentally net-like or tokogenetic instead of a tree-like or phylogenetic structure. They consequently reject phylogenetic systematics because you cannot have clades in a non-phylogenetic structure.

That conclusion follows from the premises, but unfortunately one of the premises of the argument is seriously flawed, and it is the premise that life does not show a phylogenetic structure. There are different levels at which evolutionary processes take place, and to really understand what is going on we need to ask ourselves two questions: What are the items that need to form a phylogenetic structure? And what do I see if I zoom in or out while looking at evolutionary history?

As for the fist of these, let us be clear that there are, at a minimum, the following items to be considered: Individual gene copies evolving within organisms and forming gene families which may be mostly tree-like but also potentially net-like through recombination; mitochondria and chloroplasts, both of which are endosymbiontic bacteria inside of Eukaryote cells, and which fairly clearly evolve in a tree-like relationship; individual organisms which stand in a net-like relationships with conspecific organisms if they are sexually reproducing and in a tree-like relationship if they are asexually reproducing; and finally lineages or biological species of organisms.

The claim here is now that evolutionary relationships of species are net-like because the relationships of individual organisms are often net-like. That, however, would mean succumbing to the fallacy of composition, assuming that what is true of the parts must also be true of the whole. A more familiar example would be to claim that an airplane cannot possibly fly because any single part it is constructed from cannot fly, and that claim is obviously wrong. Similarly, biological species can be in a tree-like relationship with each other although there are net-like relationships of individuals within the species.

However, the problems people see with cladism are not all as easily addressed as this. As pointed out in the first paragraph, there are also processes that transfer genes between species. Does that turn everything into a big net, making cladism impossible because we do not have a phylogenetic tree any more?

And this is where I would like to introduce an analogy that might help to visualize a few concepts and clarify why that argument does not really show all that it is supposed to show. That analogy is a river system. Rivers are familiar and they also have generally tree-shaped structure, with the major difference that the directionality is exactly opposite: where life diversifies into more and more branches, a river system starts out as many small branches that ultimately unite into one river and flow into the ocean. Still, the similarities are instructive.