Sometimes, the politics of science can get ugly, and they don’t get much uglier than this ghastly mess going on among paleontologists. I’ve read a couple of accounts of this story so far, and it sounds to this outsider like a few senior scientists riding roughshod over their junior colleagues and students and appropriating as their own the interpretations and details of others’ explanations. There seem to be shenanigans all over the place, and it seems to be in the interests of all parties involved to resolve the issues.
The sensible thing to do would be to have an impartial review of both sides of the story by neutral but knowledgeable observers — as a non-paleontologist, someone like me would certainly defer to the judgment of such a panel. Well, the New Mexico Museum of Natural History and Science put together a review, supposedly, and did so in such a bumbling, biased, and stupid way that although they decided there was no wrongdoing, I’m persuaded otherwise. Why else make such an effort to assemble a kangaroo court?
Spencer Lucas and his colleagues at the NMMNHS were accused of using the work of William Parker, Jerzy Dzik, and Jeff Martz without proper attribution. To judge this accusation, the NMMNHS put together a committee of external experts that consisted of people who had published with Lucas, one of whom declared his summary judgment before the hearings were held.
Unbelievable.
They’re accused of a serious impropriety, so they blatantly fix the review, packing the jury and even declaring innocence before the trial? That’s compounding a major ethical lapse on top of an accusation of an ethical lapse, and only makes the problem worse. What were they thinking?
A lot of servers seem to be down today. These links get errors, abd Randi’s forum is also down.
NMMNHS? Who thought that acronym up?
I get so busy mocking fundamentalists, sometimes I forget that science is also run by human beings, and therefore also subject to instances of teh stupid.
Fortunately, it’s not a mandated or institutionalized stupid, so self-correction should kick in sooner or later, and hopefully some of the worst perpetrators will be kicked out.
Please oh please oh please can everybody stop using “-gate” as a lazy way of saying “something scandalous”?
C’mon, folks, how about we all see if we can come up with something original?
>A lot of servers seem to be down today. These links get errors, abd Randi’s forum is also down.
A lot of site were hit by ThePlanet datacenter outage: http://tech.slashdot.org/article.pl?sid=08/06/01/1715247
There’s an easy way to check where a site is hosted, just use NetCraft. For example: http://toolbar.netcraft.com/site_report?url=http://www.cectic.com
Interesting that the links were all to other blogs. This little story has been covered elsewhere in a more objective and perhaps informative fashion. And there are much more entertaining stories of scandal regularly in things like the Newsletter for NIH’s Office of Research Integrity and Science and Nature.
The problem, in my opinion, is paleontologists’ antiquated honor system that credits new species naming rights to the person who publishes first. Back in the old days, when people traditionally took years to write stuff up and journals took months or maybe a year to get stuff into print, this approach might have seemed workable and fair. But nowadays, when journals compete for fastest publication rates and online journals can have a paper ‘published’ within days of initial receipt, it’s a whole new ballgame. Add to that the fact that the villian in this case edits his own parochial journal, and you’re all set up for abuses. The ‘scooped’ authors should simply go ahead and publish their own undoubtedly more careful and complete descriptions of the samples and name them whatever they want. They can add a note that their samples ‘probably correspond to the same species as described by…’ and see if the reviewers and editors let it go (I would). Then, eventually, the field can refer to the species any way they feel it most appropriate. In molecular biology, we run into this all the time with regard to the naming of genes & proteins, etc. Genes and proteins often have multiple alternate names for years, until a favorite name arises by consensus or a new nomenclature system takes over. No big deal. People certainly don’t have fights and science doesn’t break down. We just deal with it like grownups, and the jerks get a reputation as jerks.
Upon reading about these shady tactics, I kept waiting to come across something about the Disco-Institute.
Oh man. It’s Bubble Fusion all over again! The Purdue Review board for Dr. Taleyarkhan was pretty heinously bad. So bad, the Office of Naval Research made them do it again. They’ve finally wrapped it and are waiting on the ONR response.
I am always tempted to use this kind of woo with my patients… to get them to feel better whichever way it happens (including placebo effect.) I kind of do this regardless by ‘selling’ a drug as effective and safe.
I wish there was a way I could be totally honest, but I feel like if i do, they will more often have no good effect and have adverse effects. So it is amoral quandary because of how effective the power of suggestion is.
“Please oh please oh please can everybody stop using “-gate” as a lazy way of saying “something scandalous”?”
You’re just saying that because you got caught in “Chili Peppergate.”
Seriously though, point taken, and…suggestions, anyone?
The NMMNHS Affair doesn’t have quite the right ring to it, especially as saying it aloud makes it sound like you are ball-gagged.
Dave #6, I agree wholeheartedly. Let them publish and name it as they wish. The jerks will get theirs and the authors will be vindicated. Sounds like professional jealousy to me and a couple of “old folks” feeling a little paranoid about the “upstarts” and that’s from an “old folk” here. I say let the “young bucks & does” have their place in the sun.
You’re kind of late to the party here, guys!
#6 and #11 read here:
http://www.miketaylor.org.uk/dino/nm/
Re: #6 and #11. . .the rules for naming new species don’t work that way, even if it isn’t fair sometimes. First publisher of a species (or genus), regardless of what the rest of the community thinks, gets to name the thing (under rules called the “International Code for Zoological Nomenclature”). That’s why we have Apatosaurus instead of Brontosaurus (and it has created a few uncomfortable, and sometimes quite accidental, situations for various workers).
Speaking as a taxonomist, you simply can’t skirt the naming rules. Even in cases of fraud.
The rules aren’t arbitrary, but are drawn instead from a couple hundred years’ of experience about what works and what doesn’t. The codes emerged as the consensus opinion about what leads to the most stable and most useful classification over the long term.Chief among what doesn’t work is the use of subjective criteria (i.e., thoroughness of the work) to set priority. Publication date is objective, and as such it leads to the most stable classification.
JF: Fortunately, it’s not a mandated or institutionalized stupid, so self-correction should kick in sooner or later, and hopefully some of the worst perpetrators will be kicked out.
I hate that “self-correction” meme. These kind of things are not “self-corrected” by impersonal processes – they are corrected by people screaming about them, humiliating the wrong-doers, and/or finding some way to punish them. There’s no “self” at all in there.
Second, it is institutionalized wrong-doing – that’s the whole point, that people leverage their institutional power to steal from folks lower on the pecking order. You’re right that it’s not mandated, but that’s distinct from institutionalized. Sometimes these things are never fixed (I’ve heard of credit thieveries that have become permanent). Fortunately, it is also not necessary to the function of science, so in the long term credit stealing stays fairly small — but not insignificant.
Sorry, Chili Pepper @ #4. The “gate” suffix is Nixon’s legacy to the English language and has stood the test of time. It’s not going away.
Technically it’s even NMMNH&S — New Mexico Museum of Natural History and Science.
Way too late. It has crept into a lot of other languages, even Arabic.
#13, 14: I understand that rules are rules (is this starting to sound like the Clinton-Obama delegate fight?). But my point is that maybe the Hallowed Rules are not serving the paleontology community as well as they once did. By tradition, genes & proteins are also named by the discoverer. But in practice, genes and proteins are rarely referred to by the ‘discoverers’ names. This is not because molecular biologists are particularly rude people; rather it’s that many times it’s (for example) not clear that a protein identified by lab #1 is the same as the one encoded by the gene studied in lab #2, until years later. Typically, the community settles on the most widely used name, or the name that makes the most sense given names of related proteins. Sometimes this is the original name proposed by the discoverer, oftentimes it is not. And when more complete and comparative analyses are done, it often becomes clear that the old naming system needs to be revised in a way that makes sense. In which case all the history is simply swept away. Readers familiar with the history of ion channel and enzyme names will be familiar with this. I personally have ‘renamed’ proteins, not to steal credit, but so that the scientific community would be better served. I have also initially named proteins, and had that name subsequently changed. I don’t get upset; in most cases the renaming by others was a good idea. Personally, I think it totally retarded that paleontologists presume that any sort of permanent naming scheme is even possible, given the incomplete phylogeny of most ‘discoveries’ and the fact that new species are typically identified based on very incomplete or questionably preserved samples. Remember that a species name in paleontology is an *inference*, based on sample analysis. And that conclusion can (and often should, and does) change. Species names are not immutable Truth. (Heck, people on this board should know better than others that even the concept of a species is pretty fluid.) It is not the 18th century. Linnaeus’ taxonomic cataloging of God’s Great Scheme is not the backbone of biology anymore, and your local Natural History Museum is no longer a serious authority on Life.
“Please oh please oh please can everybody stop using “-gate” as a lazy way of saying “something scandalous”?”
I don’t know. I think this is how words generally come into existence. They provide a concise way of conveying an idea or concept. It was taken from Watergate and now has become a very convenient short hand to describe a situation with unethical behavior followed by a cover up.
HOW does it work in Arabic? Do they actually use the “-gate” SOUND, or do they append the Arabic word for “gate”, or what? Enquiring minds and all that.
You don’t read much Tetrapod Zoology, do you?
I’m not seeing any of this. Journals only compete for impact factors, if at all, in paleontology. The Journal of Systematic Palaeontology, where Parker published, took a whole year from acceptance — not first reception, but final acceptance! — to publication (during which Lucas et al. submitted and published), and I know a case where the Journal of Paleontology took even longer, without any fault of any of the authors.
To some extent that’s a matter of financing. I’m told the Journal of Vertebrate Paleontology, a quarterly, gets enough good submissions that it could be turned into a monthly if only the Society for Vertebrate Paleontology were rich enough. The Journal of Systematic Palaeontology, on the other hand, is outrageously expensive.
By being enshrined in the International Code of Zoological Nomenclature, the International Code of Botanical Nomenclature, and the International Code of the Nomenclature of Bacteria, it is common to all biologists, not just the paleontologists.
Not so. Peer-review always takes months, and validly publishing a new name requires 100 “identical and durable” copies of the paper in some kind of tangible form. Palaeontologia Electronica does that by depositing CDs in libraries, but I’m not aware of any other journal that does that.
Impossible. It is the same, and only known, specimen.
Also, proposing a name conditionally is not allowed. You must be serious about it, says the ICZN.
Names for an organism are like Highlanders: there can only be one.
———————-
Very well said.
So have I.
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The Codes are much wider in scope than just paleontology. They apply to all of life.
All that can be done in the present cases is appealing to the International Committee for Zoological Nomenclature for suppressing Rioarribasuchus and conserving Heliocanthus, and at least in the absence of outright proof I can’t imagine this would go through. And, yes, even this would only fix one of the cases.
In the other two naming isn’t even at issue. What is at issue is that scientists in many countries, USA included, live off citations. We are judged by our impact factor. If plagiarism happens, the plagiator is cited instead of the victim… if the victim is at the start of their career, this can be a pretty crippling blow.
——————
BTW, the Republican scandal (but I repeat myself) Watergategate, which came to light in May 2006, gets 3,660 Google hits. Full grammaticalization in 30 years.
Yes. Don’t forget to read the comments, too.
@#21:
Yes, yes, I get it that there is an all-powerful rules committee with apparently God-like powers, before which everyone bows and scrapes. So what. Committees are made of people, who can change their minds and change the rules. Maybe they should do so.
Let be more blunt: I think the rigidity and authority with which paleontologists and other systematists treat naming reflects a retarded 18th century mentality. The assumption that each and every sample can be unambiguously and forever classified taxonomically ignores the fact that organisms evolve and assumes there will never be a conceptual reorganization of the presumed lineages. Species designations are, as I said, always tentative conclusions based on analysis of typically incomplete samples in the case of paleontology or selective analyses in the case of modern systamatists using, for example, genomic sequence comparisons. Species classifications are not insights into the mind of God. That view went out — or should have — 150 years ago. Why do systematists pretend that errors are never made or that reclassification never happens? What happened to all those citations to ‘brontosaurus’? What happens when enough ‘transitional’ fossils are discovered in China to warrant merging of more now-separate groups? What happens when the genome of coelocanth is sequenced? What about when more T. Rex protein is sequenced and collagen is isolated from other large fossils?
So I say that if people want to call the damn thing Heliocanthus, they should just do so. And cite whomever they want. I mean, seriously, when people are naming things based on their favorite uncle or rock stars or fictional characters, or the latin/greek translation of ‘bumpy-headed whatchacallit’ anyway, what’s really at stake? As I said, the molecular community deals with alternate names all the time, despite ‘rules’ which don’t really work in practice, and science hasn’t broken down there.
And in any case, 10 years from now the whole thing will probably look silly when someone discovers that heliocanthus/Rioarribasuchus is actually a juvenile/malformed something else.
“The assumption that each and every sample can be unambiguously and forever classified taxonomically ignores the fact that organisms evolve and assumes there will never be a conceptual reorganization of the presumed lineages.”
Not so. For instance the various species of Iguanodon have recently been reorganised into several different genera. Taxonomy is fluid, and names change and species are shuffled, split and lumped together regularly. The only way to maintain any kind of control over which names are valid and which are not is to use priority. Exceptions are made for names that are published and then forgotten (nomen oblitum), and names erected without sufficient descriptions (nomen nudum). Appeals to the ICZN can be made if the name that has priority is rarely used, but a junior synonym has appeared in hundreds of papers.
If you read a paper dealing with the taxonomy of groups you will often find a long list of various names that have been assigned to the specimens over the years. The lists can take up more space in the paper than the description of the animal.
The rules of nomenclature are important because names are attached to individual specimens. When that specimen is moved from species to species the name goes with it.
Its also important to make sure that the name you give an organism hasn’t been used elsewhere. While much of the time people won’t confuse Meteoraspis the fish with Meteoraspis the trilobite it could happen- especially when trying to track faunal changes through time.
When it was first found the Coelacanth was placed into two genera and species Latimeria chalumnae and Malania anjouanae (it turned out M. anjouanae was merely an individual with a missing dorsal fin, and the species sunk.) If future genome work indicates that the two current species should be further separated than they are now then they will be split. L. chalumnae will remain in Latimeria as it is the type species, while L. menadoensis will become the type species for a new genus. Alternatively L. chalumnae may need to be split, and, depending on which specimens belong in which new species L. anjouanae might be resurrected.
DaveGodfrey,
Wouldn’t a simpler system be a pronounceable random sequence of characters? The specimen could be identified by a sequence number, the name already is meaningless but would be explicitly meaningless, everyone would be happy and all requirements would be fulfilled without any claims of priority. Revision tracking of specimen/species relinking would be much easier.
It seems like the current system was an excellent solution for the 19th and early twentieth centuries. But today, if all you want is a unique identifier, put it in a database! No need for this complexity and renaming, no need for this fakey latin. The goal of the system appears to be what I suggest, but designed for the days of mailed paper.
Sadly Frog, I can’t see that working for the simple reason that names are the sort of thing that people have to remember. For many organisms there are lots of very interested laypeople. Its very hard to get excited about the difference between BMNH R 9951 and BNMH R 7995, but if I tell you that one is the type of Baryonyx walkeri, and the other of Dynamosaurus imperiosus (a synonym of T. rex) then things become far more interesting to people.
The idea that you can attack palaeontologists for using inference, shows an increadible blindness to the process of all science. Science can only be a process of inductive reasosning. Frankly, if you are a serious research scientist I would have expected better than ridiculas name calling. I have alot of repect for my forefathers in the field of Paleontology and the work they accomplished so early with so little, and thus I take offence at nothing but your ignorant attack on them.
In the end the behaviour of scientists is governed not by rules or restrictions by by norms and an honour code. For those of us who respect of the code, and who want to maintain the Mertonian norms of science, it is there is no problem, but for those who see science as nothing but a job, a source of income, and have no pride in the greater achievents of their field, self interest governs behaviour.
DG: You missed my point about pronouncable — I wasn’t suggesting protein-style names like BMNH R 9951.
I don’t think lay people would care whether it is T. Rex or Crexlorf — either one would be cool to most people who aren’t steeped in Latinate science. It would be a little less memorable to scientists who actually know the etymology — but aren’t most names nowadays meaningless to anyone but the identifiers and a few buddies?
Watch the Mighty Crexlorf tear Michael Crichton’s head off! See! Just as entertaining as D. imperiosus.
The difficulty of producing random names that are pronounceable in as many languages as the latinate ones shouldn’t be very difficult (since I’m sure many of the names are unpronounceable already outside of the IE language group).
We would on the other hand lose dung beetles name Bushei… a sad loss in the name of simplicity.
We would on the other hand lose dung beetles name Bushei… a sad loss in the name of simplicity.
but… dung beetles actually work to rid the world of shit, while Bush adds to it.
It would have to be some organism that actually produces much more feces by weight than it takes in as food.
some cyanobacterium, maybe?
I would suggest that publishing in a journal that you edit not count as a refereed publication for this purpose. I presume a refereed publication is required, not just a letter to the local newspaper.
“The idea that you can attack palaeontologists for using inference, shows an increadible blindness to the process of all science.”
————
I am not attacking anyone for using inference. Inference is a fine thing. I am simply pointing out that taxonomic classification is an inference based on analysis of inevitably incomplete information. Taxonomic classification is not a ‘discovery’. No reasonable person would argue anymore that scientific conclusions are set in stone, or that the information scientists have about the world is complete. Yet the priority system at the center of the trouble described in PZ’s original blog entry, to my mind, still assumes otherwise.
So useful as ‘tags’ may be, taxonomy as a ‘scientific’ endeavor seems to me to really be a somewhat outmoded product of a 200 year old mindset. As such, the whole fuss seemed a bit silly. As I said, in my field people would just ignore the jerk’s ‘priority’ and there never really would have been a problem.
Dave, So useful as ‘tags’ may be, taxonomy as a ‘scientific’ endeavor seems to me to really be a somewhat outmoded product of a 200 year old mindset.
I think you’re assuming too much thought in the process of taxonomy. From the outside, it’s a databasing problem linking articles, specimens and genetic relationship, and has been from the beginning. But the rules of this database where created under conditions of slow paper publishing, a much higher tendency to lose or degrade information (papers were literally lost), and an inability to sync different parts of the database. On top of it, there was no theory for databasing when the system was built, so they had to go by intuition and trial and error.
For that problem under those conditions, the species naming system by priority is an admirable solution. Unfortunately, these systems have an inertia well beyond their usefulness – some will rationalize this inertia, but in the end it’s simply too expensive to re-design the system (even with my tongue-in-cheek suggestion). It would take the co-ordinated action of too many actors to occur, short of a change in scientific language or writing system — it’s the same reason we’re stuck with this stupid Babylonian system for geometric measuremets.
They were thinking that they didn’t want to run the risk of sharing the glory like Darwin did. Once again, modern man is put to shame by the politeness of 19th century Brits. Tsk, tsk.
It’s amazing that professional researchers appear–according to the initial post–to have gotten away with academic crimes that would result in immediate expulsion if they had been committed by students.
Do as I say, not as I do?
I fear that the creos and other anti-sci types will opportunistically pounce on this and say, “See? I told you science is bad!” People like the ones involved in this scandal only add to the harm of the image of science.
I’m going to use Heliocanthus just ‘cos it’s easier to say.
Or maybe Crexlorf.
I can’t speak to paleontology, but when I worked at the NIH, we used to code our experiments in the incubator and take our codes home with us. This was to prevent stealage of the experiments.
Also, many times I’d come into work in the AM to find all my cultures taken out of the incubator and left on the counter. It seemed that someone of higher rank needed the space!
SG
“I hate that “self-correction” meme. These kind of things are not “self-corrected” by impersonal processes – they are corrected by people screaming about them, humiliating the wrong-doers, and/or finding some way to punish them. There’s no “self” at all in there.”
Piss-y.
I guess that instead of whipping off posts when I’m near a wireless internet source, I’ll copy everything here, go home, write a 5-10 page comment that covers any possible misunderstanding you could try your best to have about it, run in past 10 friends, and 5 professors, then come back to teh internets and post.
“These kind of things are not “self-corrected” by impersonal processes”
Who said they were impersonal forces?
“they are corrected by people screaming about them, humiliating the wrong-doers, and/or finding some way to punish them.”
That’s what I meant, and these people are usually professional peers, in same field, hence the “self.”
Geez. Just go scream in a cup, or at least find someone who actually disagrees with you to berate. I’m not your fcking whipping boy.
JF: Geez. Just go scream in a cup, or at least find someone who actually disagrees with you to berate. I’m not your fcking whipping boy.
You seem to have volunteered for the job. It doesn’t pay well, but it’s quite productive.
“These kind of things are not “self-corrected” by impersonal processes”
Who said they were impersonal forces?
That’s what fckin’ “self-correcting” means! That a feedback loop at a higher scale than the individual components do the “correction” instead of the components themselves as conscious entity — for example, markets instead of legal systems. God-damn it, if you’re going to use ideologically loaded terms, learn what they mean. Otherwise, you are such askin’ for a whoopin’.
I can see that appropriateness is very useful for naming genes and proteins, because when you find one you don’t necessarily know what else it does, what its sequence is (and hence which family of proteins it falls into). I can see that consistency is important for naming chemicals, and that as more work is done you probably won’t cite the first reports of a protein/gene’s existence very often.
It doesn’t work like that in taxonomy, simply because we keep going back to the descriptions written anything up to 200 years ago. We need to answer questions like “which specimens was he looking at?”, “What characters did he think were important?”, “How did he justify his decision?”, etc.
Dave,
I’m not sure where you’ve gotten your ideas about paleontology, but the field is not as backward as you think it is. No one is under the impression that species names are “immutable Truth” or “insights into the mind of God.” If you’ve found an interesting fossil and want to get it into the literature, you have to start somewhere, which is why taxonomic writeups on new fossils are important. But no one thinks that “each and every sample can be unambiguously and forever classified taxonomically,” and no one pretends that reclassification never happens. Quite the opposite, systematists these days spend a great deal of time evaluating different phylogenetic hypotheses for their study groups, and they’re always looking for new fossils that will shed further light on those relationships.
There has to be a system for organizing information about specimens and expressing hypotheses of relationship, just so that everyone can be on the same page, and so that there can be a jumping-off point for discussion of broader questions in evolution and ecology. The Linnaean system is convenient in many ways, so it’s what most of us use, but most paleontologists are well aware of its limitations (and alternatives have been proposed–Phylocode, for instance). The paleo literature includes endless discussions of species concepts, the limitations of our knowledge, the reality (or lack thereof) of higher taxa, and so on. Linnaean taxonomy may have implied “insights into the mind of God” once upon a time, but no one sees it that way anymore.
Incidentally, it’s not necessarily true that “new species are typically identified based on very incomplete or questionably preserved samples.” Perhaps dinosaur workers often face that problem, but if you’re dealing with smaller, more common fossils–microfossils, conodonts, trilobites, brachiopods, etc.–sample sizes may be up in the hundreds if not thousands of specimens per “species.” That’s enough to spot some clear morphological discontinuities between groups of organisms. Statistical studies and modern analogues provide some support for the idea that these groups are something akin to biological species. It’s certainly not a perfect system but it’s not quite as arbitrary as you’re implying.
It doesn’t work like that in taxonomy, simply because we keep going back to the descriptions written anything up to 200 years ago. We need to answer questions like “which specimens was he looking at?”, “What characters did he think were important?”, “How did he justify his decision?”, etc.
Dave, do you know anything at all about taxonomy? All of those questions do get answered, in the inital description in which the species is named, because without all of that the name is invalid. Sheesh, I’ve read everything you’ve written in this thread, and you seem to think that naming is something that scientists do over a beer at the pub on the weekend and put no thought into it, then wonder why things get messy later on. Do you honestly think taxonomists and systematists have no idea what they’re doing? There are rules. Lots and lots and lots of rules. They all have to be followed to have a valid name. Peer reviewers and editors check papers to be sure they followed the rules. There are reasons for the rules. Those rules get revised and revisited every 4 years by international committees.
Consistency is one of the cornerstones of those rules; you have to know what they are, how to follow them, and how to properly change a name when needed. Please, if you want to critique a field, know what you’re talking about first.
I have no doubt that taxonomists put lots of thought into what they do. And it’s obvious that there are lots of rules about how to do it. My original point was that perhaps some of the thought, and more importantly the angst in situations like those described in the original blog entry, might be avoided if the hallowed rules were bent or even avoided. Every field of science goes through a taxonomic phase. Physicists had to name and classify different motions and forces before they could figure out the relationships among them. Chemists had to name and classify elements before they could understand chemical compositions and transformations between them. Biologists had to identify and differentiate species and tissues and organs before they could understand how species and tissues and organs arise and evolve. We take a lot of this for granted, but it was a big conceptual leap at some point for a person to recognize/decide that an acorn and oak tree, or maggot and fly, or egg and bird, are the same ‘thing’. Humans could just as well have classified all life by age or color or size or ecological niche instead of genetic lineage, as we do now. Probably we have an inherent interest in human reproduction and early rise of agriculture to thank for biology as we know it.
Regardless, I still believe that the taxonomy phase of biology — while important — is waning. Cataloguing crap is fine but real 21st century biology is all about understanding the relationships and transformations between forms of life.
In this thread, I have noted how geneticists & molecular biologists are doing fine without worrying so much about the rules. Yet they are engaged in taxonomic endeavors as much (if not more than) paleontologists. What was the genome project if not a straightforward taxonomic task — How many genes? What do they look like? Can we lump them into categories? Who cares? The point is to understand what those genes do, how they work together, how their configurations arose evolutionarily, etc. Geneticists and molecular biologists know that. That’s why they don’t sweat the taxonomy, which is just a prerequisite for the interesting stuff.
Now, I am not saying that paleontologists have a lack of imagination. They are figuring out all sorts of interesting stuff about evolution and distribution of organisms across climates and through time, and the extent to which nature has tried all sorts of morphological possibilities that may or may not be represented among currently living species. That’s cool. But none of that cool stuff has to do with naming crap and the rules which the people described in the original blog entry are arguing about. In my opinion (and please — this is just my opinion, though obviously it’s why I’m not a taxonomist), the crap described in the original blog entry represents not just the worst of humanity, but also some of the most antiquated aspects of biology.
Of course, some people reading this may not agree with my opinion that naming new piles of rock is the opposite of exciting modern biology. And that arguing about naming new piles of rock is even more stupid. And that’s fine. Pretty much every time I’ve posted to PZ’s blog I’ve managed to piss people off*. So this is nothing new. But let’s not have a double standard. If people here have a right to laugh at theists with a 2000 year old understanding of nature who consistently misinterpret and get worked up over faults in a 150 year old book, then I am allowed to chuckle at taxonomists getting worked up over abuses of their sacred rules.
*In general, this may because I only post when I disagree with the prevailing sentiment. I see no need to clog up the boards with vacuous agreement. If you like, you can imagine the infinite number of my nonexistent posts as support for anything.
That might explain why GenBank is full of poorly identified crap and we geneticists sometimes can’t be sure about the data we need for doing the interesting stuff, because the taxonomy wasn’t done properly BEFOREhand.
This affair has certainly ballooned since I first read about it. A quick impression is that the community has had some ups (explicit rules) and downs (kicking young researchers and their modes of communication). So it has some importance.
Oh, and I learned from Janet Stemwedel’s excellent articles that plagiarism doesn’t require clear intent.
Sure, if those names were immortal.
But Dave raises an interesting point. Why can it be “only” one from the beginning; have anyone tried differently lately? All the presented reasons would presumable be valid for biomolecules as well (except uniqueness in many cases). IIRC some taxonomists claim that any naming system is flawed due to all the changes.
Maybe the most immediate reason is that biomolecules are actually accessed by database already.
Or, if this system is supposed to be a given due to demonstrated efficacy, that this system doesn’t take the current competitive atmosphere under consideration. Plagiarism should be cause for revocation, and the complications arising should be manageable:
“The only way to maintain any kind of control over which names are valid and which are not is to use priority. Exceptions are made for names that are published and then forgotten (nomen oblitum), and names erected without sufficient descriptions (nomen nudum). Appeals to the ICZN can be made if the name that has priority is rarely used, but a junior synonym has appeared in hundreds of papers.”
But in all fairness, people do care about taxonomy when they want to preserve species diversity.
I dunno if the same issues will ever arise with genes and alleles, but I’m sure they can be handled by the current system. In the same way that taxonomists current system is important for them.
Torbjorn and DG: The only way to maintain any kind of control over which names are valid and which are not is to use priority. Exceptions are made for names that are published and then forgotten (nomen oblitum), and names erected without sufficient descriptions (nomen nudum). Appeals to the ICZN can be made if the name that has priority is rarely used, but a junior synonym has appeared in hundreds of papers.
It still seems that the whole problem stems from the quoted belief. The only way to maintain any kind of control was priority. I’m sure, given the radical changes in technology in the last 30 years, that better solutions could be developed today (Crexlorf might be a non-starter, but then I’m not a taxonomist).
Additionally, going to the drawing board and really thinking the issue out from current technology could deal with numerous other issues — such as the slant of the system towards western languages. Might it not be time for the taxonomical community to really sit down, drop all preconceptions and time-honored tradition, bring in the database and information theories guys, and explicitly develop a system that works better, and yet is still compatible for transition purposes with the old system? Isn’t the very fact that Latinate rule names like nomen nudum are still in use enough to cause suspicion that the system is riding on inertia?
The system appears to have what is called in CS bit-rot and legacy demands. You become committed to an interface because of current requirements — as time goes on, the commitments to requirements from earlier eras become internal requirements for consistency long after the real requirements go away. Some rules even degrade and become destructive.
Has there been some kind of grand committee on taxonomy during the current generation?
Yes. There has to be some way to “tag” specimens of whole organisms, be it Linnaean name or something else.
What do they look like? Can we lump them into categories? Who cares? The point is to understand what those genes do, how they work together, how their configurations arose evolutionarily, etc.
And HOW THE HELL will you even talk about what they do and how they work together if you don’t have something to call them? Do you just say “that one over there” and “this one over here”??? That’s been one of the biggest goals of taxonomy, to make the names reflect what they are and how they work together and how they’re related to each other. That’s why organisms sometimes change names; oh, turns out it’s related to this and not that, so let’s make sure the name reflects that so that when I say “Brassica”, we’re talking about a group of things that share a common genetic and evolutionary history. Those ‘categories’ that you spit out with disdain are not just bins separated by color, they are constantly massaged to reflect reality of descent as much as is possible to discern. Yes, the relationships between the organisms is the major goal, because you can’t even BEGIN to discuss how their features arose evolutionarily and what that means until you know how gene flow happened between them.
Now, if your real point was to say that priority shouldn’t be such a big deal to the authors, then that’s another point entirely. In that case, you can attack the emphasis on publication and priority that have made it such a high and institutionalized currency within the field. But that’s another thing altogether – what you did was to say that taxonomy itself isn’t at all important and doesn’t address important questions.
Might it not be time for the taxonomical community to really sit down, drop all preconceptions and time-honored tradition, bring in the database and information theories guys, and explicitly develop a system that works better, and yet is still compatible for transition purposes with the old system?
That’s been tried, and is hashed out every time they get within shouting distance of each other. The problems are that different fields use taxonomy in different ways, and not all types of organisms can use the same type of taxon definitions. Wander into a systematic convention and yell “How do you define a species?” and watch the blood flow. What works for defining bacterial strains does NOT work for defining bird species does NOT work for defining aster hybrids does NOT work for defining dinosaur fossils. Different criteria are used for each, since dinosaur fossils don’t have genes (mostly) and bacteria don’t have sex to reproduce and plants have sex with anything remotely related to them etc. etc. Throw in gene trees that don’t actually track with the phylogenies of the organisms that own them, and it’s a right old mess. The reason there isn’t a Unified Theory of Everything in taxonomy is that there are so many different types of questions and ways to answer them. Efforts like the Tree of Life are trying to integrate as much as possible, but there’s only so much that can be done.
Carlie: Those ‘categories’ that you spit out with disdain are not just bins separated by color, they are constantly massaged to reflect reality of descent as much as is possible to discern.
Then the question, as an outsider, is why?. Naming and categorizing, in general, are two orthogonal functions. Names are just, in theory, arbitrary labels to identify a set. The relationship among those sets is a data structure which normally references those sets.
I see why historically naming and categorization were linked together — it was the only way to do it 200 years ago, or 50 years ago. Otherwise, you would have spent endless time trying to lookup the linkages. But technology has changed, so are there practical reasons today for your database indexes to be identical with your table links, in database language? Is there a reason why names should contain within them their location within the hierarchy? For very good reasons in other fields from physics to computer science, such names structures are intentionally avoided and kept distinct from the grouping of names. Often, arbitrary and humorous names are used to make this clear.
Carlie: The problems are that different fields use taxonomy in different ways, and not all types of organisms can use the same type of taxon definitions. Wander into a systematic convention and yell “How do you define a species?” and watch the blood flow.
But doesn’t that suggest what I just said above? That the naming scheme, and the system of taxons, should be distinct. Across fields you want unique and memorable identifiers — that’s one problem. But each field has a distinct taxonomic scheme related to the reproductive strategies of the organisms — a different problem.
Solve them separately and you avoid creating the illusion for the neophytes and the laymen that there is some kind of universal taxonomy, and additionally you can deal with subsidiary problems like priority in naming (which should be a non-issue at this point, like in proteins), and cultural bias (maybe that’s been solved — I don’t know).
Then the databasing scheme becomes a simpler problem — an incredibly difficult problem, yet still one set of variables smaller, which makes it easier to see the underlying issues.
>“It doesn’t work like that in taxonomy, simply because we keep going back to the descriptions
>written anything up to 200 years ago. We need to answer questions like “which specimens was he
>looking at?”, “What characters did he think were important?”, “How did he justify his decision?”,
>etc.”
Dave, do you know anything at all about taxonomy? All of those questions do get answered, in the inital description in which the species is named, because without all of that the name is invalid. ”
Carlie, I think you’re getting me (Dave Godfrey) and “Dave” confused. I’m not the one critiquing the field. I brought up old descriptions because they’re still considered important, and if you’re reviewing the taxonomy of a group then you’ll go back to the original descriptions and ask the questions I mentioned so that you can work out whether the diagnosis needs improving, if new names are needed, etc. I’m well aware of the rules that taxonomists follow.
For instance I’m currently working on a project to illustrate the type specimens in a museum collection, and a major part of this has been going through the literature digging out the relevant descriptions, and tracking the changes in nomenclature, emendations to species diagnoses, etc, over the past 160 years.
Oh. Um. As Emily Litella would say, never mind. I’m in large part a taxonomist as well, so when I started seeing red the names all smeared together. Mea culpa.
‘s okay, no harm done.
Ahhh, well then. The next time I am in the middle of the desert, without power or internet on a dig, I will take pleasure in knowing all the information is stored neatly on a database 2 months away.
We dont all work in wifi equipt, climate controlled labs hey?
You might like your technocentrism, but alot of paleo isnt happening in the well equipt western world.
If you manage to convince the editorial board of a journal to not follow the Rules, more power to you…
The beetles named after Bush, Cheney & Rumsfeld are not dung beetles. They eat slime molds.
That’s the specimen number (British Museum for Natural History).
No, peer-reviewed publication is not required.
Unfortunately.
Indeed not, but we’re not talking about taxonomy here. We’re talking about nomenclature.
Who will pay that?
There has never been such a committee. Nomenclature is a bandwagon phenomenon.
Just for the record, I agree entirely with comment 51 that it was, in retrospect, a stupid idea to make genus names an obligatory part of species names. Phylogenetic nomenclature might fix that one day, but not anytime soon.
DM:
Might it not be time for the taxonomical community to really sit down, drop all preconceptions and time-honored tradition, bring in the database and information theories guys, and explicitly develop a system that works better, and yet is still compatible for transition purposes with the old system?
Who will pay that?
Has there been some kind of grand committee on taxonomy during the current generation?
There has never been such a committee. Nomenclature is a bandwagon phenomenon.
If the latter is true, then why is the former a problem? You just solve the problem like in any field — someone throws together a series of conferences, which are paid for by redirection of grant funds, and you get a critical mass going.
I think your argument assumes that the taxonomists don’t really give a rat’s ass about this problem — they’re comfortable with the current situation as is, and really don’t feel a burning desire to put any significant effort to updating the system. So, for the next millenia we have the taxonomical equivalent of Babylonian angular measurements, and measuring planetary orbital foci relative to a long dead king’s foot.
Fair enough. Maybe the problems aren’t significant enough to make any effort over – that’s often the case. From time to time we lose space craft due to it (in the US), but at the end of the day that cost is insignificant compared to the cost of convincing the people of Indiana that meters aren’t a Bolshevik conspiracy.
Thanks for answers and other comments, very clarifying.
Please oh please oh please can everybody stop using “-gate” as a lazy way of saying “something scandalous”?
C’mon, folks, how about we all see if we can come up with something original?
I see quite a few familiar well-used words and idioms here. Does that mean you’re lazy … or stupid?
Seriously though, point taken, and…suggestions, anyone?
Don’t take the point; it’s moronic, as moronic as complaining about using “point taken” because it’s not original.