Thursday, November 28, 2013

Beating the dead horse Paraphyly.

I know I said I was going to cut back on the ICZNerdery. But this letter by Jaroslav Flegr to Zootaxa this week was too weird to pass up. Morgan Jackson summed it up nicely:

Summary (tl;dr): There is not one shred of anything new here. There's not even anything nomeclature related. The author is using Zootaxa to opine about paraphyletic inclusive classification, that is it, there's nothing else to this "paper" if it could even be called that. (Though, note: the link above only contains the first page and references if you don't have a subscription.)

The title, "Why Drosophila is not Drosophila anymore, why it will be worse and what can be done about it?", suggests this is going to be about the Drosophila melanogaster ICZN case last year. I never wrote a proper post about it, and given the complicated nature of the case I'd prefer not to repeat it here. So check out Kim Van Der Lin's summary in the link if you need a reminder. 

But the title is deceptive. Flegr starts off discussing the case, and he gets one thing wrong immediately. Molecular taxonomic studies have not shown that "the correct name of this species should be Sophophora melanogaster". What they have shown is that Drosophila as it stands now is a paraphyletic taxon. The actual raising of the subgenera to genus level is something that has yet to happen. And when, inevitably, someone revises the genus and raises them, the rest of us can dispute that action. That's right, you heard me correctly. Changing a taxon's rank, changing it's genus, etcetera, are subjective decisions, and unlike the fixation of types are not regulated under the Code. Someone else can come along later and challenge it without getting the Commission involved. D. melanogaster is also not "the fly that eats their fruit". Though they are often called "fruit flies", the common name is "vinegar flies" because they feed on fermenting fluids.

The rest of the "paper" is devoted to supporting a paraphyly friendly classification system, something that seems quite strange to the Cladist majority of taxonomists. Now, mind you, there's nothing in the Code prohibiting paraphyly, but the majority reject it because we've become devoted to a classification system that is descriptive, predictive, and explanatory. We've discovered that when our biological classification is based upon evolutionary descent, and in particular on monophyletic groups (groups that contain a common ancestor and all of it's descendants), it is a powerful general reference system. And when that system includes paraphyletic groups (which contain a common ancestor and only some of it's descendants), it looses predictive and explanatory power.

Flegr moves to his point in a roundabout manner, first starting with an utterly confusing explanation of paraphyly. (Note: Taxonomists are overwhelmingly visual. Reading a long list of possible relationships between Taxon A and Taxon B is about like trying to decipher one of my grandfather's differential equations.) Fer Linneaus sake, use a real life example!  He blames molecular systematics for the multiplication of paraphyletic taxa in recent years, which is a common enough theme in the literature that I don't pay it much attention. All it tells us is that the author is a traditional taxonomist who probably uses physical structures of the organism exclusively.

His statements about "inner and outer similarity" reflect a real problem in systematics, sometimes called the phenotype/genotype conflict. When we infer evolutionary relationships, often times the physical and DNA characters deliver us a differently shaped tree, and we're unable to tell whether one or either of these reflects reality better. But calling it a "conflict" is a misnomer. As one of my committee members recently told me, there is no real conflict between between the morphological and molecular characters. The conflict is in the methodology, and how we analyze the data. Flegr writes "nothing might be possible to guess from a system that would not reflect the inner similarity of the species", as if morphology is doomed to forever represent convergence and DNA is innately neutral to selection. Neither of these are right. 

The deep and real problem that he is reaching for but missing, is that many traditional classifications are based upon obvious physical characters rather than evolutionarily meaningful ones. There are, for example, many characters that place birds as a therapod lineage. But since these are not as obvious as "has feathers" and "is warm blooded", and since this uniqueness is part of a traditional classification, people continue to place them in a separate lineage from other archaeosaurs. Why? Because tradition, because, as Flegr puts it, "secondary school biology teachers are far much more numerous than theoretical taxonomists."

I'll refrain from commenting upon this except to say that allowing high school biology teachers to dictate how we should classify organisms is ridiculous.

Flegr's solution is to allow paraphyletic groups to stand. Of course. What better way to solve a problem than to ignore that it exists? Then you don't have to go through the messy route of educating people. And while we're at it, why don't we just throw out this whole evolution thing? It's so much easier to classify organisms based on obvious characters like, for example, lacking wings. The insect order "Aptera" worked out so well.

There are also some fairly ugly diagrams which are not at all convincing. 

Throughout, Flegr tries to make his case using the prevalence of punctuated equilibrium in major radiations rather than gradual change. Somehow this is evidence for rejecting reciprocal monophyly. I don't see it. There's also the opinion that these phylogenies will make our classification system inherently unstable. To which I reply: They are unstable now. Classifications that are based upon obvious similarities rather than evolutionarily relevant characters will forever be subject to the whims of authority opinions. What Flegr wants is to go back to the days of evolutionary taxonomy, where if Dr. Smith was the expert on so and so group, then whatever he said goes. NOPE NOPE NOPE. 

This is all very much a Dubois-ism, in the spirit of the last paper I wrote about. He concludes,

It is, of course, probable that most of the current theoretical taxonomists, who spent a large part of their active professional life fighting the fuzzy eclectic phylogenetics and taxonomy, would not be very enthusiastic about the recurrent more and more urgent suggestions of rehabilitating the paraphyletic taxa (Hörandl, 2006; Hörandl & Stuessy, 2010; Podani, 2010a; Zander, 2010). The change, fuelled by practical taxonomists who mostly use a ‘wrong’ eclectic taxonomy in their everyday practice anyway, will be probably slow and painful. It is, however, necessary to start the change as soon as possible. Otherwise, we might soon have to say farewell not only to drosophilas but to the whole taxonomic system.
I suspect these authors he cites are all in the same boat, a bunch of "taxonomic reactionaries" who can't cope with their authority being overturned and their traditional taxa being reshaped by evolutionary understanding. They call it "practical taxonomy"; I call it the easy way out. Flegr also shows himself to be a doomsayer by the last line. It's the end of the world as we know it, apparently.

In closing, no, wait. I don't think this mess merits a wrap up. Flegr leaves us one last gift, a tagline. 

"Australopithecus sapiens, possibly Reptilia, Pisces"
  1. Australopithecus does not have priority over Homo
  2. Reptilia is a paraphyletic group.
  3. So is Pisces.

Friday, November 22, 2013

Important kernels lost in the chaff.

There are clear, concise collections of criticism. And then there's this paper. At 94 pages, it's not a short read, so I don't blame you for skimming. It's already received a lot of flack. In short summary, Alain Dubois and 18 other authors published an almost op-ed style article on problems existing in zoological nomenclature, particularly in reference to electronic publication of names and nomenclatural acts. The above links already have eviscerated it.  By that standard, I shouldn't even bother. But wait, what's this?

Given the demands on their time, the ICZN members could probably do without a reprisal of the online versus print naming debate — a debate, remember, that saw the farcical printing to paper of hard copies of online-only papers, which were then handed to libraries to fulfil the exact wording of the code. The Zootaxa authors seem unwilling, or unable, to move on. They have a semantic bee in their bonnet over the code’s requirement that species descriptions must be always “available”. When the online publishers they contacted explained that, no, they did not routinely supply paper versions of the files on the journal’s websites, the authors, rather uncharitably, deemed the information unavailable to them. ---the Nature editorial
Uhhhh.....cue Indigo Montoya. "Availability" does not mean "I can pick it up at the library" under the Code. To be available is to satisfy all criteria within the Code necessary to be considered for validity, priority, and other things. It is a whole lot more than the location of the published work. For example, a nomina novum, or 'new name', is not available unless the type specimen(s) are referenced explicitly, as well as the location where the types are to be deposited. You forgot to do this? Sorry! Your new name might as well have never been put in the literature for all it means to the Code. Refining the articles on availability means that species descriptions have higher standards, which is considered good by anyone who's tried to wade through the old literature.

Given that Nature failed to understand that, a basic and important concept in the Code, I wondered how much more they were flubbing about the article. So I read it. All 94 pages.

What I discovered was, well, a mess. Oodles of footnotes, most of them irrelevant to the paper. CamelCase, really? Symbols in journal names? Philosophizing about supplementary materials? It doesn't matter if I agree with them or not, this is supposed to be a paper about problems with electronic publication of new names. Then there's the intentional emotive, non-academic language. See the footnote on page 29 for an example. And in all things there's this sort of ivory tower dictatorial outlook, as if their opinions are final. Maybe from the authors' point of view they are. The majority of the authors hail from old European natural history institutions. And there's the fact that Dubois cited himself 38 times in the references. 

It's unfortunate that within all this there are some actual relevant criticisms, some of which were not covered in electronic vs. paper debates before the 2012 amendment. For example, some journals mistook the allowance for optical disk deposition (sometimes called the "5-copy rule") to extend to all electronic publications, including PDFs. Which means there are a whole bunch of names between 1999 and 2012 which are not available due to poor reading of the Code. This does not include mixed-model journals like Zootaxa, which publish both an electronic and a printed version with separate identification numbers. In those cases, the printed versions satisfy the Code. The rest, not so much. 

There's also criticisms of pre-publication editions (which make establishing date of publication more difficult), publishing of new names in electronic supporting information (which does not fulfill the criteria of availability, even under the 2012 amendment), and the treatment of online checklists as authoritative. All of these are useful criticisms, as is the main (lost) point of the appendixes, namely, that authors and journals don't understand the changes in the 2012 amendment very well. BioMed Central has responded to the authors' complaints, which is understandable as they took the brunt of the criticism. They reference their editorial policies on describing new taxa, which is available for all to see. They also reference the "5-copy rule", saying they followed the Code. (Note: there is no 5-copy rule in the code anymore. Even if this prior rule could have been interpreted to include deposition not in the form of optical disks, all electronic-only publications before 2012 are considered unavailable.) All of this is irrelevant, as they are still publishing unavailable names even now, after the 2012 amendment. Again, I don't blame them for being upset. The Dubois et al. paper was purposefully inflammatory and should be derided as such.

In summary, there are still problems with electronic publishing of names. But this paper will not be remembered for valid criticisms. Instead, it will be another sign that taxonomy has lost sight of the times. As the Nature editorial pointed out, all the recent ICZN news seems to be bad press. Taxonomists look as if we are a bunch of doryphores, interested more in trivial piddly lawyerisms than solving actual problems. Spend some time on the listservs, for example, or read this paper, it's the same. Without change we'll be irrelevant.

Tuesday, November 19, 2013

ICZN funded...for now.

Earlier this year, we received word that the International Commission of Zoological Nomenclature was broke. As you might imagine, I was and still am concerned.

But there is a temporary reprieve. The National University of Singapore will fund the ICZN secretariat for the next three years. In other words, they will pay for the ~$80,000 in costs it takes to run the basic "government" body of the commission. This includes Zoobank, the zoological name registry, which takes the majority of those funds to upkeep.

But this is all temporary. When the funding runs out in three years, will another organization step forward to help out? The ICZN isn't the Olympics here, nations aren't lining up to back the Commission. About the only thing any individual institution gets out of funding the ICZN is the associated prestige, which doesn't go far in this modernist world where value equals direct monetary gain or less cost.

So now there will be the inevitable talk about "business models", which works fine for a natural history museum but horribly for a multinational consortium. There's no ICZN giftshop where we can buy nomenclature themed t-shirts saying things like "Deus creavit, Linnaeus disposuit" and "Save the ICZN!" with a picture of Hugh Strickland. (Though, that's not a bad idea. Hipsters might be good for something after all. Hmm....)

Usually in these situations you have member states or institutions contributing to the total cost, e.g. UNESCO. Or, like the International Union of Biological Sciences (IUBS), there are membership fees. Or, like the International Botanical Congress (IBC), there is a meeting that coincides with the arbitration.

But the Commission is a small body of 26 people, and their respective institutions do not provide funding. Nor are there membership fees, or a large meeting associated with arbitration.

One way to fund it may be to enlarge the membership, make it the entirety of the International Congress of Zoology, and increase the membership fees to coincide with voting rights. Then amending the Code is something everyone at the ICZ can take part in, just as it is at the IBC. But the Code itself is written to be arbitrated by a limited commission, not a large governing body, so the change in itself would require an amendment. With 15,000 new names a year, a number which grows yearly, maybe it's time for a change. There were 36 cases (or at least that many decisions) this year. Can the Commission keep up?

In any case, this problem isn't going away. And where is IUBS in all this? They're the mandating body, they're the organization from which new commissioners are chosen. Three years will speed past. Now is the time to find a solution.

Monday, November 18, 2013

Smart Phone Etiquette

We now have tricorders.

Back in the day (or more recently), did you watch the original Star Trek series? Remember those communicators everyone carried around, the ones that could record and transfer data? They were called tricorders, and we have those. People have in their pockets, a camera, video camera, global positioning system, Internet interface, data recorder, communication device, music player, and a whole lot more in a package no bigger than a deck of cards. Not just a few people, but a whole LOT of people. Yes, true, there are a few things smartphones can't do, like take lifeform readings, but apparently there are people working on that.

I'm what you might call a "late adopter" or "laggard" when it comes to new technology. Some might even say "neophobe", since I tend to be dragged into the New kicking and screaming. 30 years from now when everyone has moved on to the next interface I'll be still using the old laptops. I'll complain that the new tech feels insubstantial (because it practically is), and that a good computer is weighty and takes up more space than a sheet of paper. How can I even type anything worth reading without the physical clicky-clack of a keyboard?

But, staring down at my 2007 Nokia Tracfone, so old that I have to go to tech support every time I want to add minutes, and looking at the new technology and all it can do, I wonder if it's time. How incredibly useful would it be to have a combination camera/GPS/phone with me every time I go in the field? Or, at professional meetings, I could join in all the community building on Twitter and tweet about talks. Some of my colleagues have designed apps which allow the recording of behavioral observations in the click of a button, and then upload the data to the cloud. No need for a clipboard checklist and stopwatch.

At the same time there's so much that disgusts me about smart phone use, and cell phone use in general. This video pretty much sums it up. It's become a huge distraction that keeps us from interacting with one another. This is because there's no standard etiquette for smart phone use. We've finally gotten to the point as a society when cell phone use in each other's company is shamed. The same does not apply to smart phones, since they aren't so much a phone as they are a tiny computer interface. The standard rules of "turn your phone off in a meeting" do not apply anymore, because most of the use isn't making phone calls.

I'm afraid that when I take the leap, I'll be tempted to use this wondrous tech to distraction. Which is why I'm proposing in advance some basic etiquette rules for smart phone use. And I'd like to hold everyone else to the same standard because that's just the world I want to live in.

The first and foremost rule in smartphone use is the Rule of Engagement, which is:

Your present company is who you should be engaged with.

By company, I mean "anyone who is either with you or currently holds your attention." And it really cuts to the heart of when and why smart phone and indeed, all cell phone use is rude. It's taking us away from engagement with whatever is happening around us. Including, but not limited to, the people we are presently with.

Why I'm using the Rule of Engagement as prime is because there are many instances where using a smartphone while with company can add to engagement. You may, for example, be viewing a talk at a professional meeting and wish to right then and there share what you are learning on Twitter. This is not only engagement, this is hyper-engagement. What the speaker is telling you excites you so much that you feel impelled to share their conversation with everyone else by using the hashtag for the meeting. There is absolutely no shame to this, in fact, it should be encouraged. Last week, tweeting at the 2013 Entomological Society of America meeting (#EntSoc13) allowed me and other people who were not able to attend to actually feel involved and learn and build community. Tweeting the talks as they were actually proceeding was outreach! Other cases where smartphone use doesn't limit engagement is when you can provide a piece of information to move a discussion forward (e.g. by a simple Google search).

In these cases there are still limits. In addition to the Rule of Engagement I have a few more.

1. All the old cell phone rules still apply. If you're in public and with company, using your smart phone for calling is still discouraged. And this is equally true with company in private. In other words, talking on the phone or texting in the company of others is rude. You are telling that other person or people that you don't value their time or presence, that they are boring or at least less interesting than the person you are talking to or texting on your phone. Since these classic examples violate the Rule of Engagement, they are still rude and should be avoided.

2. Other smart phone applications should be used sparingly in company. By which I mean, don't use your phone without a legimate reason. This is not the time to go link jumping on TV tropes, or check your email, or Facebook, or do /anything/ that takes more than a few seconds. Whatever you /do/ use it for should be relevant to the circumstances, like the examples I gave above. It's a tool, not a distraction device.

3. Approved smart phone use in company should be discrete and efficient. In and out, and as little of a distraction for everyone around you as possible. In a dark room, this might include dimming the screen so it isn't as bright. The point is not to be bothersome, and to cut away from it as quickly as possible so as not to disengage your company.

4. If use is extended, you should excuse yourself from present company.
This was true for phone calls, and it's true for apps. You may find it inconvenient, but frankly is so freaking rude to sit with me and stare at your smartphone for five minutes as I try to have a conversation with you. If you have to do that, I'd rather you go elsewhere and indicate you need that privacy.

Now, I've made some of these mistakes in the past. Not with a smartphone, but with my laptop. Even with a 10 inch screen and keyboard on my lap it's so easy to disengage from physical reality and forget my surroundings. We need to treat these tools as what they are, tools, not as entertainment units to distract ourselves from being truly present with others. And when used legitimately we still need to be considerate of others.

The ultimate goal is more engagement. Smartphones can help with that, but they can also harm. We should be aware of their consequences and use them wisely.

Thursday, November 14, 2013

Caddisfly weirdos.

Previously on Trichopterology...about 5 years previously, I talked about some very cool caddisflies that live in tide pools. These marine caddisflies feed on soft corals, and also use it to construct their cases. And the females of at least one species, Philanisus plebeius, oviposit into the body cavity of sea stars. Now, I'm not quite sure you'd call this relationship parasitic, because I don't know if the sea stars are harmed at all by the oviposition or the eggs. As soon as the larvae hatch, they leave the sea star through its stomach and out its mouth, and start munching on coral. They seem to be more of a commensalist incubation chamber than a host in a parasitic relationship. It's unfortunate that there hasn't been any more recent research in the literature, nor photographs because I would really love to show you all one of their cases.

Out of the three main indicator aquatic insect groups (caddisflies, mayflies, and stoneflies or EPTs), Trichoptera seem to have the widest range of niche. They range from free moving predators to plant shredders, to filter feeders, to scrapers and grazers. You can find them in tiny spring seeps and large rivers, in temporary pools and the wind swept shores of the Great lakes, and in aquatic habitats ranging from fully freshwater to marine. This diversity of habitats and feeding guilds is a testament to their wondrous use of silk, building cases out of practically every kind of material that can be found in aquatic habitats, or spinning silk into webs and nets.

Marine caddisflies are pretty weird, they have a semi-parasitic lifestyle and they live in habitats that are avoided by all other insects. But, there are other weirdos.

I've talked previously about the tethered casemakers, Limnocentropodidae, which connect their cases to the substrate with a sturdy silk stalk, sometimes tethering to other cases in long aggregations during pupation.

Then there's the Atriplectidae, which really deserve a blog post of their own. They're sometimes called the 'vulture caddis' due to their specialized telescoping head. Much like a vulture, they feed on carrion, but in this case it's other arthropods. The long 'neck' allows them to stay outside the corpse and insert only their head for feeding.

There are several species of caddisflies which spend most of their lives out of the water, in moist habitats. This includes the Platte River caddisfly, Ironoquia plattensis, which undergoes a terrestrial estivation period as larvae during the summer. There's also a British species, Enoicyla pusilla the land caddis, which feeds on dead oak leaves in humid forests and spends most of it's lifecycle out of water. A stranger habit is that of the retreat maker Xiphocentron sturmi. Typical of it's family, it makes a network of tubes appressed to a substrate, in this case rotting wood. What's not so typical is the tunnels are out of water, and weirder yet is it's "chrysalis". When X. sturmi finish larval development, they build a hanging structure that looks sort of like a tiny lemon on a rope, and pupate inside of it.

But really, these are all sideshows compared to the main attractions, a caddisfly-sponge mutualism and an honest-to-god caddisfly parasitoid.

Ceraclea is a genus of caddisflies in the family Leptoceridae, the long horned caddisflies. As the name implies, most leptocerids have long antennae in both adults and larvae. Ceraclea is unusually for a number of reasons, first of which is that their antennae are much shorter than other leptocerids. Another reason is that several species feed on freshwater sponges. I wouldn't suggest trying sponge for yourself, though. It would be like eating fiberglass, since the sponge skeleton is made of tiny glass bars called spicules. These sponge feeding caddisflies are able to ingest both the soft tissues and the spicules without damaging their guts because they have a super tough midgut. They're really feeding on the zooanthellae, endosymbiotic algae that live within the sponge tissue.

The sponge outwardly seems to be the host in a parasitic relationship, since the caddis feeds on and damages host tissue but doesn't consume the whole colony. But according to research from 2003, the sponge benefits as well. Electron micrographs of Ceraclea fulva cases showed that they are composed of a tightly bound series of silk bridges attached to sponge spicules. Furthermore, pieces of living sponge attach to the cases, especially in the late larval instars. Since sponges often spread by fragmentation, the combination of larval integration of living sponge fragments into its case as well as fragmentation during feeding means that the sponge can spread to new habitats with help from the caddisfly larva. Mutualisms are rare enough in aquatic insects that this is the only example I know where both species benefit. There are other aquatic insects that feed on sponges, the spongillaflies for example. But these are parasites, and are not dispersal agents for the sponge like Ceraclea cases.

Case of C. fulva; 'S' indicates living sponge tissue (Corallini & Gaino 2003)

At the other end of the spectrum from mutualism, you have parasitoids. This life history includes many groups of terrestrial insects, like the tachinid flies on which I am currently working. Most aquatic parasitoids are not truly aquatic, since they have no special adaptations for the aquatic environment. There is at least one species of truly aquatic chironomid midge which is an ectoparasitoid of caddisfly pupae. And, there are at least a few species of microcaddisflies that do the same.

Orthotrichia species, like all members of the family Hydroptilidae (microcaddisflies), spend 4 out of five of their larval molts as free living. In the final instar, hydroptilid larvae undergo hypermetamorphosis, greatly inflating their abdomens and building a portable case. This is believed to be an evolutionary link between the free living habit and the true casemaking habit, not quite a casemaker but not completely free living either. Orthotrichia in particular builds a tiny purse shaped case out of sand grains. The case is open at both ends and unlike true casemakers can be used bidirectionally.

Orthotrichia spp. larvae; 1. in pillbox case; 2 & 3. with host pupae; note distended abdomen (Wells 2005)

In a few unusual Australian Orthotrichia, the initial case is much smaller and pillbox like. The larvae are swept by the current into the nets of filter feeding caddisflies, which they somehow escape and get enclosed within the pupal case of their host. From there, these Orthotrichia construct their normal case, and begin feeding on the caddisfly pupa. This continues until the Orthotrichia abdomen is big and swollen, and the host is no more than a pupal husk. Having taken over it's host's pupal case, the Orthotrichia larva spins it's own cocoon and pupates. The adults are apparently larger than non-parasitic Orthotrichia, which could be in part due to the easy and massive food supply provided by a net spinning caddisfly pupa.

Even the sea star ovipositing marine caddisflies don't seem too bizarre when I consider all the other Trichoptera oddities. Parasitoids bring to mind tachinid flies and brachonid wasps, not aquatic insects. But I guess that caddisflies prove once again that if there's an aquatic habit, they'll find some way of making it work.

Wait...who am I kidding? Marine insects, feeding on soft corals, ovipositing into sea star incubation chambers? Nothing can beat that level of weird.