The Quest for Phaeocollybia

part 4

 

On to Nomenclature: Print vs Online

Leon Shernoff: I’m going to try and make a segue here.

Lorelei Norvell: Good! (laughing)

LS: A transition. And maybe we can use your book as an example of this. You’ve been involved in the committees and the nomenclature groups…

LN: The International Botanical Congress Permanent Committee for Fungal Nomenclature, yeah.

LS: which has recently done a lot of loosening of the rules for publishing

LN: Right, yes.

LS: So, if your book were published today, could you for instance have published it online, and just released it as a pdf?

11 This is an article in Mycotaxon where Lorelei explained the rule changes. You can download it at http://www.ingentaconnect.com/content/mtax/mt/2011/00000116/00000001/art00056.

LN: Yes, as long as you have… you have to have an ISBN number. I’ve written a paper on the changes in the new Melbourne code11 (ironically now my most-cited paper) which sets forth exactly the requirements for publishing a name. You can’t just put a new species name online in a self-standing pdf file without meeting certain requirements.

Usually, scientists publish papers in a journal, now often online, where there is no page limit. Finally, you may legally propose species online. For that matter, if I wanted to publish a new name I could do so quite quickly via Paul Kirk’s Index Fungorum. But such one-line proposals are best used for what I call bookkeeping name changes and are not at all helpful for field mycologists. It’s for people who want to get new combinations12 out there in a sort of a one-click effort. The single-page paper is published immediately online, but contains very little taxonomic or biological information.

12 A new combination is a new name for an existing species. For example, when new genus Parasola was created, a number of existing species were transferred into that genus – for example, Coprinus plicatilis became Parasola plicatilis – then this new name is called a new combination. New combinations are also created when you raise a variety to the status of a species.

Obviously as editor of Mycotaxon, I have a rather strong feeling that when you decide to move a species from one genus to another, you should explain why that decision has been made. Although we also publish what we call ‘bookkeeping papers.’ When somebody has established a new genus, they will transfer existing species into it but may not name all species that belong. So someone comes along later doing the ‘tidying-up thing.’ They know that such-and-such species really belongs in this new genus. In such cases, all you need do is publish a paper with the new name and provide the basionym (the first genus + species name for that fungus) and the paper where the species epithet was first proposed (citing author, date, reference, & page).

Such bookkeeping papers can be published without any explanation. But most field mycologists really want to know “Well, what makes you say that they go in that genus?” So Mycotaxon encourages authors to offer at least a brief explanation: “These species have these characters, and therefore they belong in this genus.”

Regarding the move to electronic publication of names. Some botanists have been trying for a while, but it had been resoundingly defeated, particularly in Vienna – I mean, it just really never got out of the starting gate, and that was in 2005. But the sub-committee for 2011 Melbourne Botanical Congress that was in charge of investigating whether to go electronic really did excellent work. And in the meantime, the internet had finally grown up so that most Congress delegates agreed that it is stupid to have to depend upon the printed version of nomenclatural proposals at this point.

The current Code stipulates that the published papers must always be available and accessible online, so you’re not going to lose them – and that is a problem with electronic media. You always wonder because text is too easily changed and websites are too easily lost. There’s also a lot of competition on the internet and you have to be extremely sophisticated to ferret out what is true and what is sheer hyperbole or a blog, or what is something that is not, um, based in fact. You know from dealing with Mushroom the Journal that it’s a hard go, publishing a hard-copy print medium! It’s extremely difficult, and people seem more comfortable nowadays with iPads and Kindles.

I was raised old school, and I like reading paper. So it was very difficult when Mycotaxon decided that we were going to go completely online. It was motivated by economics: we simply could not afford to send out those heavy volumes anymore. But the competition right now between online journals is rife and some are kind of unreliable: there are good ones, and there are bad ones. It gets difficult, because you wonder, “Well, this sounds like a good paper,” but unless you know the actual focus or specialty, you can be fooled. I mean, I as an editor have been!

Running Mycotaxon

When I first started editing Mycotaxon, I knew… what all about anamorphic species. But I began to notice certain problems with some papers. It was sort of like there were student factories with professors who decreed, “Okay, it’s the time of day to write up a new species paper.” So I started clamping down on the restrictions real fast. If I felt there was anything that was a problem, I would send it out to external specialists and say “Is this… is this anywhere within the realm? Is this just… (starts laughing) Is this a real species or are they just whistling Dixie?” One review I got back from Keith Seifert was prefaced with “Great howling lizards!” was his remark. The incomprehensible text turned out to be also scientifically just horrible.

13 Articles in scientific journals go through a process called peer review, where other scientists in the field vet the articles before they are accepted for publication. Traditionally, the journal selects the reviewers and actually hides their identity from the author of the article, so the author can’t try to influence them. But in mycology (as in many fields, actually) there are usually so few specialists in any given area that the author would know who they are anyway. So some mycological journals choose not to maintain the pretense of anonymity; but it’s still a big break with the traditional way of handling peer review.

But one of the nice things about nomenclature – getting back to your original segue – is that there are rules that must be followed, and once we instituted the nomenclature editor position which was in 2005 with Shaun Pennycook, it has made things surprisingly restful, and we’ve become a reassuringly rigorous journal. We do permit the authors to select their own peer reviewers, however, and there’s a lot of controversy about that.13

My feeling is that taxonomy is inherently user-focused: the reader public will determine whether or not a species concept is going to stand the test of time. There are plenty of names out there that people have made that no other mycologist has ever picked up and used. So the problem limits itself. So taxonomy lends itself better than most – definitely better than what I would call a hard-science journal – to having peer reviewers that are selected by the author.

But I did have to clamp down. I made sure that I received those reviews directly from the experts(instead of having the authors forward them with their final submissions) because some authors (laughing) were actually rerunning forms that and I began to notice seemed a little ‘familiar!’ They no longer bothered to ask the reviewers, whom I would contact and get, “What do you mean? I’ve never reviewed this!” So now I make certain that the reviewers are always thanked and mentioned in the acknowledgements and when I have a final submission the reviewers are always incorporated in it, so when I send it back and say “This isn’t good enough; you’ve got to consult your reviewers” I copy the experts as well. And I’m really trying hard to make sure that that foreign authors use at least one reviewer expert in English, because I’m really tired of rewriting paper after paper. It’s an issue.

But back to nomenclature itself… you have a code. And once the code changes, it covers everything forward from the date that it becomes effective. Electronic publications was well done. There are now rules for things like “When is it a final copy?” so you know what date to cite. And it’s ironic because Mycotaxon uses Ingenta as a host server, which is (sighs) notoriously slow and it takes them forever to process, which I never understood, because I prepare all the final pdfs that readers see, so everything’s ready to go when I send it in. And still, it can still take two, three, four weeks! Whereas with the Lulu hard copy, I say “Well, the journal has been uploaded” and Noni (our webmaster) immediately forwards it to both Ingenta and Lulu at the same time. Usually within about five days, I have a hard copy on my shelf. Yet we must wait for sometimes over a month until it is published online and all the author names, titles, and dates display properly

Nomenclaturally, the date of publication of a name is critical; the date itself is determined from the date that the journal is out. The postmark on the editorial hard copy tells me exactly the date that Lulu sent it to me. For hard copy, then, the date is the first date that the publication is mailed to its subscribers. For an online publication, it would be the date that the switch is flipped. But the difficulty with determining the online dating is that the papers have to be paginated and in final form. There are an awful lot of online prepublications that are visible online before they’re actually published; sometimes these are still in double-lined author-typed copy and lack the final pagination. That’s a problem – you must have that page number as required by the botanical code: you must write the date where the name is introduced, accompanied by the protologue. All of this determines how you cite something to make a nomenclaturally valid publication.

So the date is very important, because surprisingly enough there will be the same species named with two different names – sometimes not close to the same day, but definitely in the same year. So that’s where the date of publication becomes really important.

LS: Wow. So… you think that the possibility of electronic publication is a big improvement.

Lorelei (very carefully): At the present time, we’re in transition, and therefore it’s difficult. But I think it was… it’s pragmatic, and it was going to happen, and the internet is not going to go away. I wouldn’t call it an improvement. I just think its time had come. And I like the fact that they set up in the code that whichever name is published first determines the date of priority, because for Mycotaxon the earlier date coincides with the hardcopy mailings. Because although we don’t have to, we still mail hardcopy copies to several libraries.

The earlier code specified that you should have several copies in different localities (such as libraries). You couldn’t just ‘publish a new name in a church bulletin’ as I used to phrase it. We kind of fine-tuned how many copies should be shared in Vienna, when we decided not to go with electronic publication.

Now it is left to the discretion of each journal as to whether or not they want to pay to send out library copies. Mycotaxon sends copies to the Centralbureau voor Schimmelcultures in Amsterdam, Kew (in the UK), Harvard, Beijing, and several others. Basically, it is comforting to have the hardcopy; and obviously since I have a library of thousands of books, I like hardcopy. So: improvement? No. But it’s… a logical consequence of the current era.

Nomenclature: Latin vs English

Leon: And how do you feel about not requiring a Latin description anymore?

Lorelei: There also, I felt the time had come. It was very easy. When we were in Edinburgh at the International Mycological Congress in 2010, there were three nomenclature sessions held at the same time as the poster sessions. They went surprisingly well. David Hawksworth distributed nomenclatural questionnaires to everyone at the start of the Congress. And when we collected and counted those ballots, we found hands-down that voting mycologists wanted English descriptions. The time for Latin had passed by.

It was amazing how quickly English was approved in Melbourne. It wasn’t a problem. They still permit Latin for those people who are more comfortable with Latin, and that seemed to take care of it. Oh, there was a political moment in Melbourne where everybody tried to include their particular language, but people just weren’t interested in making things more complicated.

What you need in a description

Now, at Mycotaxon – there, again, I keep going back to Mycotaxon, but that’s what I do full-time – we require a diagnosis (in either English or Latin) in addition to what I call a technical description. The diagnosis differs from a description in that it tells you precisely how a proposed new taxon differs from its perceived closest known relative. A diagnosis should be very short, and if you have ever looked at any of Singer’s diagnoses, you know how short diagnoses can be. You simply mention a previously named taxon, so that readers know “Well, this is the one that you’re likely to confuse it with, and it differs in this detail.”

That is extremely handy, and that’s the first thing we place after the proposed name (after the Mycobank or Index Fungorum fungal name code). I had always found if you’re using a monograph, well…. you have a tendency to look at the pictures. We all look at the pictures. We may say we don’t, but we do! And thennnn we skip all the way down and we go to the comments, because usually in the comments it tells you how it differs from other species and what’s alike; and then finally, if you’re really truly desperate, you will go up and wade through the technical description, which of course includes everything, and so there’s so much detail you’re confused by the time you get to the end of it.

Joe used to say in his lab, “You know, it’s the darnedest thing: you sit there, and you’re holding this mushroom in your hand and you’re reading the technical description and you’ll go “Yeah, yeah, yeah,’ and then you’ll turn to the picture and it’s just nothing like it!” You just sit there and kind of blink. Well, with us the diagnosis is up at the very top, and it says, “Well, if you know this particular species, which we think it’s closest to, it’s different here.” And that just makes things a lot more restful.

Leon: I’m very happy to find I’m not the only person who immediately skips to the notes.

Lorelei: Oh, goodness. That’s the only way you can do it! (laughs) I’m serious! And it’s not easy to write them, either! When I came into Joe’s lab in 1990 I was a thoroughly entrenched field mycologist, field guides for years, and the first thing he does is sit me down to write a description. It turns out it was the mushroom that we ended up transferring to Chrysomphalina, which was at that time was Omphalina wynneae, which now is Chrysomphalina grossula – we won’t even go there! Writing a species description was… not… easy.. to learn… to do. But you have a certain way to do it, and once you’ve learned how to write the bloody things, it’s a little easier to wade through and read them.

14 Ridgway and Munsell are color charts that are used for putting names on colors. Ridgway’s book has emerged as the version of choice, which led to its price reaching several hundred dollars a few years back. New editions of the book in 2011 and again in 2014 have shown that there’s still a demand for it, and have also dropped the price by a factor of 25 or so. But at the time Lorelei’s talking about, the Munsell chart was much more available.

But you can really get lost. There’s all of these dimensions, there’s all of these colors, and of course mine are kind of the worst – where you want every color in the rainbow. I spent I don’t know how many months working from Bill Cibula’s color guide – he made a wonderful thing where he had taken the Ridgway colors and compared them to the Munsell chart14 using all this high-powered NASA equipment15 so I was making a translator, and I spent all of this time making overlays on my Munsell, because I used the Ridgway, which has nice little color names, you know, like glaucous gull blue or what have you. I was doing my descriptions of Phaeocollybia, which are essentially either rust-colored or green, and you get into the little nuances, you know, and the “this eventually turns this color… or maybe that one!”

15 Bill Cibula was the mycological consultant for NASA, so he had access to all sorts of fancy machines.

So I spent all this time and then I thought “Well, let’s analyze this with multi-variant analysis and see whether all these fancy colors fall out into distinct species.” Well, no, they didn’t. So I spent all of this time and then I realized: you know what tells you something? You have eight basic colors, and it’s either red, or green, or brown, and that’ll do it! Spending all of this time going into the fine shades of the edge of the cap doesn’t mean diddly-squat because you get that from the environment: if it’s very dry then it’s lighter, and if it’s moist it’s darker… you have “hygrophanous” in there, and nobody really understands what that means, but everybody uses it, and so here you are!

So after spending all of this time on this beautiful, beautiful chart, I found it doesn’t make a difference! You want to know what general color is the cap; what general color are the gills? Are they the same color or are they different? That’s the information that actually makes a difference. You need to put all that extra stuff in the technical description; you really do! But it’s not helpful to someone who wants to know what a mushroom is in a quick way.

Leon: What’s next on the nomenclature front?

Nomenclature: The Next Generation

Lorelei: I have resigned as secretary. I’m staying on the Committee for Fungi, but we can’t seem to find a replacement for me yet. Theoretically, I’m supposed to serve through the next congress: a total of twelve years. But given the unpredictable state of my health, and the fact that I’m sort of having to pick and choose where I want to spend my energy these days, I told Scott “I think I had better resign.” So now I’m tidying up things.

The Committee has not done much, because of my health, for about a year and a half; and at this point I’m getting ready to rev up again and assemble all of the things and send out the proposals. What the committee has to do now, however, is get into gear. There are nomenclatural sessions – and they are important nomenclatural sessions! – in Bangkok at the next International Mycological Congress, in August. But the Committee needs to have considered and have assembled the decisions that are a direct result of the fallout of the deletion of Article 59.

The article is still in the Code as a place marker to let folks know it once existed, but there is no longer any dual nomenclature.16 And of course there has been quite a fallout due… let’s say things like Aspergillus moving to one name, because it used to be that you had to use the name that was based on the teleomorph (which a lot of people ignored or did not know). With DNA, this is changing. Fungi developed Article 59 to deal with life stages that looked completely different and were thought to represent different organisms.

16 Many fungi have separate body forms that look very different for sexual and asexual reproduction, and over the years some of these have received different scientific names because the connection between the two sexual phases was not known.
Theoretically, the name for the sexual phase (the teleomorph) was supposed to be the proper name for both phases; however, some of the sexual phases were extremely rare and many teleomorphs looked very, very different from the anamorph (asexual phase). So if people had already been using an anamorph name for hundreds of years and would freak out if they had to change to the teleomorph, Article 59 said you could do that.
The new version of Article 59 says that only one name is permissible for both forms; but it also gives the anamorph’s name equal footing with the name of the teleomorph, so if the anamorph’s name is older, that becomes the official name.
There is a tremendous amount of sorting-out to do. For one thing, anamorphic fungi are as likely as any other two have been thrown together in a group because they look similar, without any close evolutionary relationship. So, for example, http://www.aspergilluspenicillium.org, the website of the International Commission of Penicillium and Aspergillus, lists 16 different genera of fungi that have Aspergillus anamorphs. Which of these gets to keep the name Aspergillus? There are also huge potential benefits: keeping the name Penicillium for only those fungi closely related to P. chrysogenum could save researchers from wasting time trying to find penicillin in the unrelated species that have been included in the genus.
If you’d like to learn more about the issue, I recommend Susan Milius’s article in Science News: https://www.sciencenews.org/article/name-fungus, which is also listed at the end of this article.

To some extent algae faced similar problems (but never permitted dual nomenclature). Fossils DID have several names based on body parts; but since Melbourne there’s only going to be one name permitted for plant fossil species.17

17 Because you can’t grow a fossil and watch it change as it matures, quite a few fossils have received different names for their different phases of development.

But now we must determine not only which specific name to accept, but there’s also the generic shakeout: do you go with Trichoderma or do you go with Hypomyces? This is going to have some impact on field mycology, but not as much as for people who work with things in dishes. It has been somewhat acrimonious, but not as bad as we feared. Which is good because the most major nomenclatural shock to mycologists at Melbourne was when 59 went down – and it went down rapidly! The aftershock pretty much kicked us in the teeth. The shakeout is still happening, but there are now committees to vote on nomenclature in the important groups, and Trichoderma is one.

There are two major committees; one is the International Commission for Fungal Taxonomy, which is headed by Keith Seifert; and then there is our (the International Botanical Congress) committee, of which Scott’s chair of and I’m secretary. Secretaries usually run the nomenclature committees, historically; and Scott’s had to move and become far more active, simply because he wanted to oversee the Article 59 fallout. It’s a complicated thing. We have not done our work, because of my health. But we need someone new, because we have to get back on track and… (laughs) I’m telling you, it’s a hard job! It’s just inherently dull. And whenever you’re not working on nomenclature, you can so easily think, “Oh, I need to get to that… maybe tomorrow!”

You know, David Hawksworth, just eats, breathes nomenclature – and of course he’s highly energetic – but a lot of the rest of us have to think “Well, okay, time to rev up!” And then once you get revved up, you have to have Asperger’s to really home in, and then you have personalities to deal with, and… you kind of have to… urge the committee along… somewhat subtly, and so there’s just all sorts of requirements at finding somebody to take over. But it’s a time sink of the first water, and finding somebody who has the time to devote to that is our biggest issue right now.

Leon: As far as I know, we’ve covered the big changes there – that I know of, that you’ve been involved with. Is there anything else that you want to let people know about?

Lorelei: Well, we were extremely delighted about the change in the name of the code, because it has always been the International Code of Botanical Nomenclature, which is a bit dismissive of mycology. There was a concerted movement afoot… I don’t know if you know David Minter, but he is a bit of a gadfly, and he is the president of the International Society for Fungal Conservation. He felt very strongly that because we were being taken care of under the <quote> botanical code <end quote> fungi were regarded as very poor stepchildren and essentially ignored – and we are especially ignored in any sort of funding, and environmental conservation considerations. He’s kind of assumed this one-man battle to get mycology some respect and is making progress.

Anyway, there was a group of mycologists including David M who felt that the only way to effect an awareness that fungi are not plants was to start an international code of mycological nomenclature, just for fungi. Those of us who are involved, (laughs) with the current code felt that this was a decided step in the wrong direction, because we’re moving towards a united nomenclature. I mean, the zoologists and bacteriologists have had their own codes for quite a while, but the sensible thing is to have one code govern all… biological nomenclature. This business of moving and fragmenting did not strike us as the way to go.

18 The phylocode movement peaked about ten years ago, when DNA sequencing was just coming of age and its proponents were really feeling their oats. The idea was to do away with verbal taxonomy altogether and give each organism a number based on its DNA sequence, without any reference to the actual features of the organism. Some people were very adamant about this at the time, but it has since faded away.

Anyone who’s ever worked with designing bylaws, codes, laws, any sort of legalistic thing, realizes that the bulk of the work is in setting things up. You cannot borrow little bits from other codes wholesale and expect a code to work. You have to make it a coherent whole. That means you need you need people who want to deal with fine semantics and who understand how to write the rules so that nothing is left out. We watched with a certain amount of bemusement the ramping up of the phylocode where everything was going to be identified by numbers, and this, that, and the other, and all based on the genes and the sequences18 and it just didn’t take hold, although I don’t know what its current status is. Basically, scientists want to be scientists, and they don’t want to spend time being accountants or lawyers, which is what you have to be when you set up a code.

We don’t want separate codes. What we want is recognition within one code. Working with the code itself has not a problem: pretty much anything we want, the botanists give us. This is not an issue. But the point is, we were poor stepchildren, particularly to the outside world, because they were not really aware of our existence. We realize that’s not the only issue, but we said “Change it to the code of botanical and mycological nomenclature, and that’ll take care of the rest!” (laughing) And of course, David Minter said “You need to mention fungi first!” And then the phycologists – well, there was only one in attendance in Melbourne – said “We should also include algae!” Because, let’s face it, they have it even worse than we do. So they said “and phycological” so you had this… horrendous name.

Well, IAPT president Vicki Funk asked that I, as secretary of the fungal committee, cosponsor a change in our already approved proposal. Thus Funk & Norvell proposed to get rid of the ‘–ologicals’ in favor of the more easily understood unions of fungi, plants, and algae. As we organized the unions alphabetically, fungi ended up before plants, which satisfied David Minter; and algae were even more happy because they were first. So now it’s the International Code of Nomenclature for algae, fungi, and plants (ICN), and most of us are a lot happier.