Currently, it's the time of year spent indoors, reading, writing, thinking and identifying last summer's collections. We entomologists anticipate the first days where we can once again enter the field and observe insects.
From the Victorian days when entomology was a gentleman's hobby, insects continue to garner enthusiasts other than professionals. There are myriad guides on the market for butterflies and dragonflies, for tiger beetles, and even smaller taxa such as ant genera. These are most often the charismatic groups, those which have easy identifications, bright coloring, large body sizes or have been championed by workers who go beyond simply being taxonomists. In North America, there are even regional guides for different states.
In between the general field guides (including those for charismatic species) and the specialist lab manuals (like the Manual of the Neartic Diptera or various revisions of genera and families), there is a void of intermediate literature and field guides. We have multiple field guides to Lepidoptera, but what about parasitoid Hymenoptera? What about Diptera families? Clearly there is a need for such literature, as there is little time in the field to pull out a large hardbound key and microscope. This is especially true when the objects of study are still living, and /killing/ them would end any interesting behaviors you may be observing. A relative identification in the field can help put things in perspective later reading your notes, and that is where field guides serve best. Cries of "it's simply too difficult" are not sufficient when the same have been covered nicely in other regions (see the many British and European field guides).
True flies, for example, have a very nice, yet somewhat outdated, manual to all the North American families and genera, and there are many revisions of individual families and genera, but there is no adequate field guide for North America. The closest thing is the Diptera chapter from Peterson Field Guide to the Insects, which is very out of date and not nearly as user friendly as I would like.
Perhaps the only viable option is to champion the cause and write it.
Saturday, December 25, 2010
A preoccupation with phylograms.
Systematists and comparative biologists like, among other things, making trees. A tree (phylogram, cladogram, dendrogram, whatever other names you might want to call it) is a nice summary of relationships (nodes) between lineages (branches). We take great joy in constructing these drawings, find them aesthetically pleasing, use them to store information.
You might even say we like them too much.
The problem with "making trees" is that these phylograms (or cladograms or dendrograms) are not endpoints, but starting points. Even when we are talking about something other than the black box analyses of molecular systematics, this summary is not meant as a be all end all to our research. Even if we had the perfect summary tree of all extant life, our work would not be done, it would be just beginning.
There is this preoccupation with tree making to the exclusion of the potent question: why do we make trees? Yes, of course, to summarize, but that is only the start! Comparative biology is reciprocal illumination, whereby each new piece of evidence is fitted into the whole and shuffled back through an endlessly tightening spiral of work.
My first thought upon viewing a dendrogram (after the obvious "does this make sense?") is: how does this inform me of everything else? What hypotheses about genetics, physiology, morphology, ecology and behavior does this suggest? What further description in what areas will allow me to refine and test our understanding?
I mean, take this recent paper on Arthropod sysematics. What does a taxon Pancrustacea really mean? And I'm not meaning "this taxon includes so and so taxa", I'm asking those above questions. What hypotheses about morphology would Pancrustacea imply? What more can we learn about the Cephalocardia and Remipedia that would enhance our understanding of the relationships? Or this paper: What sort of interesting biological traits does this hypothesized "Simulioidea" have? What can it inform us of the biology of the included families?
A friend of mine said, "A conclusion is simply where you stop thinking." It seems trees in biology can be the same, which is missing the point. One of the other things biologists enjoy making is lists, which are always seen as simple summaries and never conclusions. How is it that trees are any different?
You might even say we like them too much.
The problem with "making trees" is that these phylograms (or cladograms or dendrograms) are not endpoints, but starting points. Even when we are talking about something other than the black box analyses of molecular systematics, this summary is not meant as a be all end all to our research. Even if we had the perfect summary tree of all extant life, our work would not be done, it would be just beginning.
There is this preoccupation with tree making to the exclusion of the potent question: why do we make trees? Yes, of course, to summarize, but that is only the start! Comparative biology is reciprocal illumination, whereby each new piece of evidence is fitted into the whole and shuffled back through an endlessly tightening spiral of work.
My first thought upon viewing a dendrogram (after the obvious "does this make sense?") is: how does this inform me of everything else? What hypotheses about genetics, physiology, morphology, ecology and behavior does this suggest? What further description in what areas will allow me to refine and test our understanding?
I mean, take this recent paper on Arthropod sysematics. What does a taxon Pancrustacea really mean? And I'm not meaning "this taxon includes so and so taxa", I'm asking those above questions. What hypotheses about morphology would Pancrustacea imply? What more can we learn about the Cephalocardia and Remipedia that would enhance our understanding of the relationships? Or this paper: What sort of interesting biological traits does this hypothesized "Simulioidea" have? What can it inform us of the biology of the included families?
A friend of mine said, "A conclusion is simply where you stop thinking." It seems trees in biology can be the same, which is missing the point. One of the other things biologists enjoy making is lists, which are always seen as simple summaries and never conclusions. How is it that trees are any different?
Thursday, December 9, 2010
All Species: The biggest task of Systematics.
A question: What is the most efficient way to go about finishing that task that started even before Carl von Linne, the description of all species on the planet?
I've been critical of the Encyclopedia of Life project in the past, but that pertains more to their timeline and setup than their goal. The ultimate goal of alpha systematics is the description of all species on the planet, and the Biodiversity Crisis is working against that goal. What is really needed right now is efficiency. Unfortunately, new species descriptions are painfully inefficient.
Dr. Neal Evanhuis describes some problems and solutions for efficiency by outlining what he calls "The Eight Steps to Enlightenment and Taxonomic Nirvana". His thesis is that the efficiency by which species are described depends on the efficiency (and joy in) each of the steps. Obviously the exact techniques vary between groups, but overall, successful species description requires the above steps, including field work and collection, sorting and identifying of samples, literature searching and resources, writing of publications and illustrating, and communicating discoveries to the public. I'm not going to address discovery through sequence data because mostly these are used to resolve species complexes and are inefficient by any means, and new species still require morphological descriptions for identification and validity, lest they become nomena dubia.
So, I would like to address efficiency in each of the steps, and what might be done to increase this.
1. Enjoyment of Nature. This, for most biologists, should not be a hard sell. Often we become interested in our field as children, playing in the outdoors. However, some of us, myself included, have changed into indoor creatures as we age. While I'm not advocating we all live without roofs there is certainly something to be said about spending time just observing nature firsthand, and locally, since local is where we are the majority of the time.
Solutions: Partaking in weekly (or daily) nature walks, local surveys and inventories of biota, and inclusion of friends and family with these delights can increase the enjoyment and therefore the want to get away from the computer and outside. Keeping a field journal (more on that below) can increase this even further, as your observations and thoughts will stay in mind longer.
2. Enjoyment of Collecting Specimens. While there are often ethical concerns about taking life for reasons other than survival and nourishment, most organisms require collecting and dispatching for proper identification and cataloging. One of the issues that I find myself having is that, while I am particularly good in the lab, I am a poor field biologist and not a very good "hunter". I'm sure there are others who do not have the same abilities yet excel in identifying.
The obvious solution is to use traps (or other passive collecting methods) so that the organisms come to you and not the other way around. There is still the obvious issue of when and where to place the traps, but that goes hand in hand with satisfying Step 1. A second issue is that collecting often takes volume but not diversity, therefore, the type and placement of trap should be linked to something I call novel catch efficiency (NCE). NCE is an relative character of a trapping method for the person using it and the particular taxon of interest, and is calculated as the average novel catch per unit time of effort. A trap that will collect an average of 3 species you've never found before per week of trapping is much more efficient in surveying diversity than a trap that only collects one group in large numbers. Collecting methods with higher NCE should be favored over those with lower NCE for the purposes of taxonomic surveys. For example, different sorts of flight intercept traps will be differentially suited to collecting a diversity of different groups of insects.
One of the most important parts of collecting (or field biology in general) is keeping a record of what where and when. The best method I know is called the Grinnel Journal System, which consists of a field notebook, a field journal, species accounts, and a catalog of collections. More information on this system can be found here and in Judith Winston's excellent book Describing Species. I've adapted the system as follows: I use a rite-in-the-rain notebook and pencil for taking notes in the field, a soft bound Moleskine lined journal as my Field Journal, a standard three ring binder with looseleaf for the species accounts, and a hardbound Moleskine squared notebook for my catalog. I also have several other notebooks I use to keep track of my laboratory activities, and synthesize information. All of these items will keep you from forgetting important information when it comes time to produce publications, and will provide observational notes on distribution and ecology which will help in writing.
Solutions: Use collection techniques suited to your taxon and personal abilities, including traps with high NCE; Keep a system of journals which track your collections and other field activities; choosing areas of high diversity, local or distant, from which to collect (or perhaps, more fundamentally, choosing a taxon which is poorly known so your efforts bring success no matter where you go).
3. Enjoyment of Sorting. While some people find this a joy, other people can find the task of sorting specimens to be extremely tedious. And, depending on one's group, this may be just so. However, it is impossible to find new species while samples go unsorted, or incompletely so.
Solution: The most efficient way to sort insects is to have something akin to the following system. The sample is laid out before you in a white tray or on a flat surface, with adequate lighting. The specimens are then taken out individually and put in containers or vials sorted roughly to order. If you are only collecting for one portion of the samples, and know of no other people who would be interested in picking through, the loess can be discarded. It helps if you have a desk or workbench set up for only this task. Once the rough sorting is complete, groups can individually be separated further for preservation. It is unefficient to identify specimens at the same time as sorting. What usually ends up happening is the researcher (and I am guilty of this) will find an interesting specimen and spend several hours pouring over it, while the sample sits aside, unfinished. Instead, samples should be sorted first and identified later. Rough sorted portions of a sample (e.g. a vial full of Diptera) can be set aside with the unique collection numerical identifier which corresponds to a single sample entered in your Catalog, and you will easily know what to do with it later.
4. Enjoyment of Discovery. This step encompasses identification. Species identification is the only type that will lead to discovery of new species, and most groups are very poorly known with dispersed literature. A continued problem is identification of part of a sample, then quickly forgetting about it, thus reversing hours of work.
Solution: The most important thing for this step is to be well versed in identification of a particular group, and have all the necessary literature on hand (see Step 5). Such skills come with time and practice, and require particular equipment and techniques such as microscopes and slide mounts. The second most important thing is to identify and immediately label specimens, lest you later forget what they were. It is good to make a list of all the species collected in a sample along with numbers and enter it into your catalog, and species accounts as needed. These can then be easily integrated into master distribution lists later.
5. Enjoyment of Researching Taxonomic Literature. This is a necessary step for every successful taxonomist. My mentors have pointed out on several occasions that the primary step towards taxonomic expertise is gathering a database of literature about a group. The difficulty arises with the amount; there is so much information available, where do I start?
Solution: The obvious way to approach this is to work from the general to the specific. Start with literature and keys for higher taxa, and work downwards to species level. Keep your resources for the higher taxa broad and the lower taxa narrow. In other words, it's foolish to start by trying to collect all the type descriptions and species keys for all Hymenoptera. Instead, start by finding a good family key to Hymenoptera, then genera keys for groups of interest, and then pick several genera of interest as focus and expand slowly from those into adjacent genera. Online literature databases such as Zoological Records and various group specialized sites are excellent resources and makes this task much easier, as does the uploading of various articles and books as PDF files. For groups you specialize in, it may be best to keep both an electronic and physical copy of publications, especially of keys and atlases.
Part of the task of becoming well versed in a group is creating checklists and atlases, both personal and for publication. Most groups are poorly studied and do not have regional resources, so you must build your own. The most simple form of checklist is with only species names organized by genus and family. The best is annotated with synonymy, distribution summaries, and lists of publications that mention the taxon with notes about their content. An atlas is a summarized key for entire group in a particular region, and often consists only of illustrations used for identification. Such a resource can be invaluable as a quick reference.
6. Enjoyment of Describing. This step encompases describing and illustrating a new species. Most taxonomists are not particularly good writers or illustrators, so this task can be the hardest of them all.
Solution: Fortunately, most taxonomic papers have a standard format that can be copied and altered as needed. A short introduction and methods section, then straight into the description, which starts with the new name, a diagnosis which is a short statement of how to tell the species from others in it's group, a full description which is just a logical progression starting from one end and moving to the other, material examined, and remarks on ecology, biology or other interesting notes. Illustration methods vary from group to group; for insects, most often one can use a dissecting scope with a gridded eyepiece, or if you are a truly horrible artist, a camera lucida may work better. For larger animals (ie vertebrates) a photograph may suffice. In either case, there are various image manipulation programs that can alter and augment your abilities. This whole task should be as reasonably quick and painless as possible; it should not take weeks to write a species description by the above method.
7. Enjoyment of Submitting your Manuscript for Publication. Once the publication is complete, some people waffle at actually publishing it. This has been due to money, or no proper journal for such a thing, or failure to properly complete the above steps.
Solution: For zoologists, the journal of choice is Zootaxa. This online peer reviewed journal has no cost for non-open access articles and can expedite articles to within a month of submission. For animal species, there is no contest this is the best route.
I would like to note that, in addition to primary descriptions there are many other things taxonomists should be publishing, including their personal checklists, atlases, and many many notes about distribution and ecology. There is so much information which would be useful but goes unpublished, possibly because the biologist in question suspects it has been previously published. These too are part of Step 7. Checklists and atlases may be best published online these days, while short articles on observations and new records can be nicely published in journals such as Entomological Notes.
8. Enjoyment of Educating Others. Outreach to the public increases efficiency of new species description by relating your discoveries, and getting people interested in doing the same. The solution is to be interested, and therefore to be interesting. Public speaking isn't easy but with enthusiasm for the subject matter it is not important to be perfect. Your enthusiasm is shared with your audience. Free availability of information makes our work easier, therefore, making your publications freely available may be the most important part of this step. [Ed: Blogging seems to be an excellent way of communicating publications; see here for more information]
Overall, if the above solutions were used, taxonomists would not have any trouble publishing their discoveries, or finding discoveries in the first place. The efficiency of alpha systematics would be increased 100 fold.
I've been critical of the Encyclopedia of Life project in the past, but that pertains more to their timeline and setup than their goal. The ultimate goal of alpha systematics is the description of all species on the planet, and the Biodiversity Crisis is working against that goal. What is really needed right now is efficiency. Unfortunately, new species descriptions are painfully inefficient.
Dr. Neal Evanhuis describes some problems and solutions for efficiency by outlining what he calls "The Eight Steps to Enlightenment and Taxonomic Nirvana". His thesis is that the efficiency by which species are described depends on the efficiency (and joy in) each of the steps. Obviously the exact techniques vary between groups, but overall, successful species description requires the above steps, including field work and collection, sorting and identifying of samples, literature searching and resources, writing of publications and illustrating, and communicating discoveries to the public. I'm not going to address discovery through sequence data because mostly these are used to resolve species complexes and are inefficient by any means, and new species still require morphological descriptions for identification and validity, lest they become nomena dubia.
So, I would like to address efficiency in each of the steps, and what might be done to increase this.
1. Enjoyment of Nature. This, for most biologists, should not be a hard sell. Often we become interested in our field as children, playing in the outdoors. However, some of us, myself included, have changed into indoor creatures as we age. While I'm not advocating we all live without roofs there is certainly something to be said about spending time just observing nature firsthand, and locally, since local is where we are the majority of the time.
Solutions: Partaking in weekly (or daily) nature walks, local surveys and inventories of biota, and inclusion of friends and family with these delights can increase the enjoyment and therefore the want to get away from the computer and outside. Keeping a field journal (more on that below) can increase this even further, as your observations and thoughts will stay in mind longer.
2. Enjoyment of Collecting Specimens. While there are often ethical concerns about taking life for reasons other than survival and nourishment, most organisms require collecting and dispatching for proper identification and cataloging. One of the issues that I find myself having is that, while I am particularly good in the lab, I am a poor field biologist and not a very good "hunter". I'm sure there are others who do not have the same abilities yet excel in identifying.
The obvious solution is to use traps (or other passive collecting methods) so that the organisms come to you and not the other way around. There is still the obvious issue of when and where to place the traps, but that goes hand in hand with satisfying Step 1. A second issue is that collecting often takes volume but not diversity, therefore, the type and placement of trap should be linked to something I call novel catch efficiency (NCE). NCE is an relative character of a trapping method for the person using it and the particular taxon of interest, and is calculated as the average novel catch per unit time of effort. A trap that will collect an average of 3 species you've never found before per week of trapping is much more efficient in surveying diversity than a trap that only collects one group in large numbers. Collecting methods with higher NCE should be favored over those with lower NCE for the purposes of taxonomic surveys. For example, different sorts of flight intercept traps will be differentially suited to collecting a diversity of different groups of insects.
One of the most important parts of collecting (or field biology in general) is keeping a record of what where and when. The best method I know is called the Grinnel Journal System, which consists of a field notebook, a field journal, species accounts, and a catalog of collections. More information on this system can be found here and in Judith Winston's excellent book Describing Species. I've adapted the system as follows: I use a rite-in-the-rain notebook and pencil for taking notes in the field, a soft bound Moleskine lined journal as my Field Journal, a standard three ring binder with looseleaf for the species accounts, and a hardbound Moleskine squared notebook for my catalog. I also have several other notebooks I use to keep track of my laboratory activities, and synthesize information. All of these items will keep you from forgetting important information when it comes time to produce publications, and will provide observational notes on distribution and ecology which will help in writing.
Solutions: Use collection techniques suited to your taxon and personal abilities, including traps with high NCE; Keep a system of journals which track your collections and other field activities; choosing areas of high diversity, local or distant, from which to collect (or perhaps, more fundamentally, choosing a taxon which is poorly known so your efforts bring success no matter where you go).
3. Enjoyment of Sorting. While some people find this a joy, other people can find the task of sorting specimens to be extremely tedious. And, depending on one's group, this may be just so. However, it is impossible to find new species while samples go unsorted, or incompletely so.
Solution: The most efficient way to sort insects is to have something akin to the following system. The sample is laid out before you in a white tray or on a flat surface, with adequate lighting. The specimens are then taken out individually and put in containers or vials sorted roughly to order. If you are only collecting for one portion of the samples, and know of no other people who would be interested in picking through, the loess can be discarded. It helps if you have a desk or workbench set up for only this task. Once the rough sorting is complete, groups can individually be separated further for preservation. It is unefficient to identify specimens at the same time as sorting. What usually ends up happening is the researcher (and I am guilty of this) will find an interesting specimen and spend several hours pouring over it, while the sample sits aside, unfinished. Instead, samples should be sorted first and identified later. Rough sorted portions of a sample (e.g. a vial full of Diptera) can be set aside with the unique collection numerical identifier which corresponds to a single sample entered in your Catalog, and you will easily know what to do with it later.
4. Enjoyment of Discovery. This step encompasses identification. Species identification is the only type that will lead to discovery of new species, and most groups are very poorly known with dispersed literature. A continued problem is identification of part of a sample, then quickly forgetting about it, thus reversing hours of work.
Solution: The most important thing for this step is to be well versed in identification of a particular group, and have all the necessary literature on hand (see Step 5). Such skills come with time and practice, and require particular equipment and techniques such as microscopes and slide mounts. The second most important thing is to identify and immediately label specimens, lest you later forget what they were. It is good to make a list of all the species collected in a sample along with numbers and enter it into your catalog, and species accounts as needed. These can then be easily integrated into master distribution lists later.
5. Enjoyment of Researching Taxonomic Literature. This is a necessary step for every successful taxonomist. My mentors have pointed out on several occasions that the primary step towards taxonomic expertise is gathering a database of literature about a group. The difficulty arises with the amount; there is so much information available, where do I start?
Solution: The obvious way to approach this is to work from the general to the specific. Start with literature and keys for higher taxa, and work downwards to species level. Keep your resources for the higher taxa broad and the lower taxa narrow. In other words, it's foolish to start by trying to collect all the type descriptions and species keys for all Hymenoptera. Instead, start by finding a good family key to Hymenoptera, then genera keys for groups of interest, and then pick several genera of interest as focus and expand slowly from those into adjacent genera. Online literature databases such as Zoological Records and various group specialized sites are excellent resources and makes this task much easier, as does the uploading of various articles and books as PDF files. For groups you specialize in, it may be best to keep both an electronic and physical copy of publications, especially of keys and atlases.
Part of the task of becoming well versed in a group is creating checklists and atlases, both personal and for publication. Most groups are poorly studied and do not have regional resources, so you must build your own. The most simple form of checklist is with only species names organized by genus and family. The best is annotated with synonymy, distribution summaries, and lists of publications that mention the taxon with notes about their content. An atlas is a summarized key for entire group in a particular region, and often consists only of illustrations used for identification. Such a resource can be invaluable as a quick reference.
6. Enjoyment of Describing. This step encompases describing and illustrating a new species. Most taxonomists are not particularly good writers or illustrators, so this task can be the hardest of them all.
Solution: Fortunately, most taxonomic papers have a standard format that can be copied and altered as needed. A short introduction and methods section, then straight into the description, which starts with the new name, a diagnosis which is a short statement of how to tell the species from others in it's group, a full description which is just a logical progression starting from one end and moving to the other, material examined, and remarks on ecology, biology or other interesting notes. Illustration methods vary from group to group; for insects, most often one can use a dissecting scope with a gridded eyepiece, or if you are a truly horrible artist, a camera lucida may work better. For larger animals (ie vertebrates) a photograph may suffice. In either case, there are various image manipulation programs that can alter and augment your abilities. This whole task should be as reasonably quick and painless as possible; it should not take weeks to write a species description by the above method.
7. Enjoyment of Submitting your Manuscript for Publication. Once the publication is complete, some people waffle at actually publishing it. This has been due to money, or no proper journal for such a thing, or failure to properly complete the above steps.
Solution: For zoologists, the journal of choice is Zootaxa. This online peer reviewed journal has no cost for non-open access articles and can expedite articles to within a month of submission. For animal species, there is no contest this is the best route.
I would like to note that, in addition to primary descriptions there are many other things taxonomists should be publishing, including their personal checklists, atlases, and many many notes about distribution and ecology. There is so much information which would be useful but goes unpublished, possibly because the biologist in question suspects it has been previously published. These too are part of Step 7. Checklists and atlases may be best published online these days, while short articles on observations and new records can be nicely published in journals such as Entomological Notes.
8. Enjoyment of Educating Others. Outreach to the public increases efficiency of new species description by relating your discoveries, and getting people interested in doing the same. The solution is to be interested, and therefore to be interesting. Public speaking isn't easy but with enthusiasm for the subject matter it is not important to be perfect. Your enthusiasm is shared with your audience. Free availability of information makes our work easier, therefore, making your publications freely available may be the most important part of this step. [Ed: Blogging seems to be an excellent way of communicating publications; see here for more information]
Overall, if the above solutions were used, taxonomists would not have any trouble publishing their discoveries, or finding discoveries in the first place. The efficiency of alpha systematics would be increased 100 fold.
Monday, December 6, 2010
The Six Principles of the ICZN: Priority
In the 18th and 19th centuries, species description was like a gold rush. Paleontologists, botanists and other naturalists were moving as quickly as possible to make a name for themselves in the field, a name above all other workers. Incidentally, this caused the near simultaneous publication of many species and subsequent arguments about who was first, and whether that mattered. With the ICZN, this problem is solved by the following:
The Principle of Priority affects all aspects of the Code, including validity of synonyms (different names for the same species), homonyms (same name for different species), correct spellings, and the validity of a publication. It means that to be valid, a name must be the first published and available. Any synonyms or homonyms made available after the first are considered junior to the earlier senior homonym or synonym. It also means that when a taxon is formed by combining two or more different taxa, it takes the name of the first described.
While this solves most problems as far as which name can be considered valid, there are still issues that can arise. The most frequent is when long since unused names are discovered for well known taxa. Normally, the junior synonyms would have to be replaced with the earlier senior synonym, but the stability of zoological nomenclature would be widely affected by such an action. Therefore, the International Commission of Zoological Nomenclature can vote to partially suppress (the name is treated as published and available except for the purposes of priority) or completely suppress (the name and/or nomenclatural act are treated as unavailable, as if they had never been published) the offending senior synonym if such a case is brought to them. A good example of this use of plenary power is the suppression of a work by J. W. Meigen (1800) which included many family and genus names which he subsequently changed in his 1804 work. Both sets of names were in use well into the 20th century, but the later names were used more often so the commission ruled against the senior synonyms and suppressed the whole publication as well as several junior homonyms that would be made valid by the suppression (ICZN 1963).
Aside from the above situations, Principle of Priority generally leads to great stability in zoological nomenclature, and while it can be misused (for example, stealing work and publishing first) it easily solves many arguments that may arise due to all other aspects of the Code.
Works Cited
International Commission on Zoological Nomenclature. 1963. Opinion 678. The suppression under the plenary powers of the pamphlet published by Meigen, 1800. Bulletin of Zoological Nomenclature 20: 339–342. [21 October]
Meigen, J. W. 1800. Nouvelle classification des mouches à deux ailes (Diptera L.) d’après un plan tout nouveau. Par J.G. Meigen. “An VIII (1800 v.s.)”. J.J. Fuchs, Paris. 40 p. [before 22 September]
Meigen, J. W. 1804. Klassifikazion und Beschreibung der europäischen zweiflügligen Insekten. (Diptera Linn.). Erster Band. Abt. I. K. Reichard, Braunschweig [= Brunswick]. xxviii + 152 p. [5 November]
"The valid name of a taxon is the oldest available name applied to it, unless that name has been invalidated or another name is given precedence by any provision of the Code or by any ruling of the commission."
The Principle of Priority affects all aspects of the Code, including validity of synonyms (different names for the same species), homonyms (same name for different species), correct spellings, and the validity of a publication. It means that to be valid, a name must be the first published and available. Any synonyms or homonyms made available after the first are considered junior to the earlier senior homonym or synonym. It also means that when a taxon is formed by combining two or more different taxa, it takes the name of the first described.
While this solves most problems as far as which name can be considered valid, there are still issues that can arise. The most frequent is when long since unused names are discovered for well known taxa. Normally, the junior synonyms would have to be replaced with the earlier senior synonym, but the stability of zoological nomenclature would be widely affected by such an action. Therefore, the International Commission of Zoological Nomenclature can vote to partially suppress (the name is treated as published and available except for the purposes of priority) or completely suppress (the name and/or nomenclatural act are treated as unavailable, as if they had never been published) the offending senior synonym if such a case is brought to them. A good example of this use of plenary power is the suppression of a work by J. W. Meigen (1800) which included many family and genus names which he subsequently changed in his 1804 work. Both sets of names were in use well into the 20th century, but the later names were used more often so the commission ruled against the senior synonyms and suppressed the whole publication as well as several junior homonyms that would be made valid by the suppression (ICZN 1963).
Aside from the above situations, Principle of Priority generally leads to great stability in zoological nomenclature, and while it can be misused (for example, stealing work and publishing first) it easily solves many arguments that may arise due to all other aspects of the Code.
Works Cited
International Commission on Zoological Nomenclature. 1963. Opinion 678. The suppression under the plenary powers of the pamphlet published by Meigen, 1800. Bulletin of Zoological Nomenclature 20: 339–342. [21 October]
Meigen, J. W. 1800. Nouvelle classification des mouches à deux ailes (Diptera L.) d’après un plan tout nouveau. Par J.G. Meigen. “An VIII (1800 v.s.)”. J.J. Fuchs, Paris. 40 p. [before 22 September]
Meigen, J. W. 1804. Klassifikazion und Beschreibung der europäischen zweiflügligen Insekten. (Diptera Linn.). Erster Band. Abt. I. K. Reichard, Braunschweig [= Brunswick]. xxviii + 152 p. [5 November]
Monday, November 29, 2010
The Six Principles of the ICZN: Binomial nomenclature.
Before Linnaeus, the scientific naming of species was very messy. There was no standard way of going about it. Names were often long descriptive phrases in Latin (which was the standard scholarly language of the time). For example, a species of Geranium was written like the following:
GERANIUM pedunculis bifloris, calycibus pyramidatis angulatis rugosis, foliis quinquelobis rotundatis.
Needless to say, if names are to act as a reference system the above is extremely cumbersome. At the time of Linnaeus, an unimaginable amount of species were being discovered over a relatively short period of time. A simpler system was badly needed, and binomial nomenclature filled this need. Linnaeus consistently used binomial nomenclature for his Systema Naturae and it was popularized further by like minded workers of the day in Zoology and Botany. When the first code of zoological nomenclature came into use, the Strickland Code (1845), the use of binomial nomenclature was made a rule, and has been retained through the subsequent codes, up to today's 4th edition of the ICZN.
It is stated thus -
The Principle of Binomial Nomenclature provides for a stable and easily recognizable scientific species name. Only a species name is made of two names, the first capitalized and the second lowercase. The Code gives further corollary statements on subspecies trinomens, higher ranks than species being of only one word, but this follows the general statement of the principle above. Its our starting point in zoology. With a two word name where no other names are two words, there's no room for ambiguity.
With the possible ease of a 1 word system, a person may wonder why Linnaeus didn't just use that? The answer is, in a monomial system one would quickly run out of names for all the animals. With a binomial system, the number of combinations is nearly infinite (when I try to calculate it, my graphing calculator gives me an overflow error for n=1 million; it gives me overflow for 10,000 for that matter).
GERANIUM pedunculis bifloris, calycibus pyramidatis angulatis rugosis, foliis quinquelobis rotundatis.
Needless to say, if names are to act as a reference system the above is extremely cumbersome. At the time of Linnaeus, an unimaginable amount of species were being discovered over a relatively short period of time. A simpler system was badly needed, and binomial nomenclature filled this need. Linnaeus consistently used binomial nomenclature for his Systema Naturae and it was popularized further by like minded workers of the day in Zoology and Botany. When the first code of zoological nomenclature came into use, the Strickland Code (1845), the use of binomial nomenclature was made a rule, and has been retained through the subsequent codes, up to today's 4th edition of the ICZN.
It is stated thus -
The scientific name of a species, and not of a taxon of any other rank, is a combination of two names (a binomen), the first being the generic name and the second being the specific name. The generic name must begin with an upper-case letter and the specific name must begin with a lower-case letter.(From ICZN, Article 5)
The Principle of Binomial Nomenclature provides for a stable and easily recognizable scientific species name. Only a species name is made of two names, the first capitalized and the second lowercase. The Code gives further corollary statements on subspecies trinomens, higher ranks than species being of only one word, but this follows the general statement of the principle above. Its our starting point in zoology. With a two word name where no other names are two words, there's no room for ambiguity.
With the possible ease of a 1 word system, a person may wonder why Linnaeus didn't just use that? The answer is, in a monomial system one would quickly run out of names for all the animals. With a binomial system, the number of combinations is nearly infinite (when I try to calculate it, my graphing calculator gives me an overflow error for n=1 million; it gives me overflow for 10,000 for that matter).
Sunday, November 28, 2010
Book Review: Darwin and the Barnacle.
Several years ago I attended a discussion class reading On the Origin of Species, first edition. Like most biologists, I had never read the book (though thankfully more biologists have read it than the ICZN), and it was very enlightening to study the entire document as a group, chapter by chapter, and discuss the contents both in relation to science in the mid 1800s and today.
One of the little tidbits I learned about Charles during that class was his years of work on barnacles. He spent ten years of his life, prior to the publication of On the Origin of Species, studying barnacles just so he could place a single strange species into context. And at the time this seemed quite incredible, much like being told that George Washington cut down the cherry tree or Kerry Mullis discovered PCR during an acid trip. It was a historical myth, maybe true, a little factoid, a morsel, etc.
Rebecca Stott takes this morsel and explodes it into a full blown thanksgiving feast with a 20 lb. turkey and loads of mashed potatoes. She begins with Darwn's childhood experiences with marine invertebrates and works her way up to the discovery of what he called "Mr. Arthrobalanus" on a beach in Chile. What started as a 6 month project became a 10 year task, during which he published 4 large volumes on all known extinct and extant barnacles. Stott serves this through the gravy of interpretive biography, and while she is not a biologist she handles the biology quite nicely. Most people who try to tackle writing about Darwin screw it up by completely misunderstanding On the Origin, littering the text with references to "survival of the fittest", and other spoonfuls much like finding your piece of turkey is nothing but boney bits, or your cranberry sauce is full of seeds. Thankfully she had a full team of Darwin specialists aiding her research. There was only once I felt she mishandled the theory, and it was quickly forgotten with the tastiness of the rest.
Darwin and the Barnacle had me sitting up in bed late at night to finish it. This is the tale of what Darwin did BEFORE he published his main course. It is not dry in the least. It's the moist bird you had the pleasure of sharing with family last Thursday (I hope).
http://www.amazon.com/Darwin-Barnacle-Spectacular-Scientific-Breakthrough/dp/0393057453
Also, I'm all out of Thanksgiving puns.
One of the little tidbits I learned about Charles during that class was his years of work on barnacles. He spent ten years of his life, prior to the publication of On the Origin of Species, studying barnacles just so he could place a single strange species into context. And at the time this seemed quite incredible, much like being told that George Washington cut down the cherry tree or Kerry Mullis discovered PCR during an acid trip. It was a historical myth, maybe true, a little factoid, a morsel, etc.
Rebecca Stott takes this morsel and explodes it into a full blown thanksgiving feast with a 20 lb. turkey and loads of mashed potatoes. She begins with Darwn's childhood experiences with marine invertebrates and works her way up to the discovery of what he called "Mr. Arthrobalanus" on a beach in Chile. What started as a 6 month project became a 10 year task, during which he published 4 large volumes on all known extinct and extant barnacles. Stott serves this through the gravy of interpretive biography, and while she is not a biologist she handles the biology quite nicely. Most people who try to tackle writing about Darwin screw it up by completely misunderstanding On the Origin, littering the text with references to "survival of the fittest", and other spoonfuls much like finding your piece of turkey is nothing but boney bits, or your cranberry sauce is full of seeds. Thankfully she had a full team of Darwin specialists aiding her research. There was only once I felt she mishandled the theory, and it was quickly forgotten with the tastiness of the rest.
Darwin and the Barnacle had me sitting up in bed late at night to finish it. This is the tale of what Darwin did BEFORE he published his main course. It is not dry in the least. It's the moist bird you had the pleasure of sharing with family last Thursday (I hope).
http://www.amazon.com/Darwin-Barnacle-Spectacular-Scientific-Breakthrough/dp/0393057453
Also, I'm all out of Thanksgiving puns.
Saturday, November 27, 2010
The Six Principles of the ICZN: Intro
Recently, I read the International Code of Zoological Nomenclature (ICZN) in it's entirety. The Code is sometimes considered to be the constitution or rulebook of zoology. It defines how new species names and other taxa can be created and then later revised. The Code provides the ground for all other work in zoology, because if we couldn't somehow classify and summarize the units of life in some meaningful and standard way, the whole of biology would be a disordered mess.
Unfortunately, very few biologists have actually read The Code (or for non zoologists, the comparable documents, the International Code of Botanical Nomenclature, and the International Code for the Nomenclature of Bacteria), and because of this there is very little understanding of WHY we have the Code and why it is ultimately responsible for stability in biology as a whole.
Over the next several weeks I will be reviewing The Code through the six principles that are the main guideposts in zoological nomenclature, why they are important, and how to interpret and use them.
Unfortunately, very few biologists have actually read The Code (or for non zoologists, the comparable documents, the International Code of Botanical Nomenclature, and the International Code for the Nomenclature of Bacteria), and because of this there is very little understanding of WHY we have the Code and why it is ultimately responsible for stability in biology as a whole.
Over the next several weeks I will be reviewing The Code through the six principles that are the main guideposts in zoological nomenclature, why they are important, and how to interpret and use them.
Species concepts.
After reviewing the arguments of species as real entities vs. species as made up configurations for the past several hours, I remain a pluralist on the topic of species concepts.
The Biological Species concept by Ernst Mayr (members of metapopulations that actually or potentially interbreed) works quite well for large animals that undergo only sexual reproduction. Such organisms can be easily observed for discrete interbreeding over time. But what about those populations that show discrete yet sympatric behaviors and habits in the field yet interbreed easily in the laboratory. Would these be considered species? Do these actually offer discrete units? Under the Ecological Species concept (isolated phenetic clusters of individuals sharing a particular niche) they would.
This is all well and good for laboratory animals. But how about those organisms that don't easily take well to experimentation? How about asexual animals, where breeding doesn't occur, or those organisms (like plants) that easily hybridize? Do we once again scrap "species"?
And yet, there are other concepts we can use (a good list is in the book Speciation - Coyn and Orr) that do not rely on a strict and exacting understanding of the direct mechanisms or processes to obtain understanding. In systematics, we aim to describe and understand biodiversity. The title "species" is used in multiple ways to best describe different organisms. Of course we would love to test the biology and ecology of every candidate species on this planet; almost always this is currently impossible or unfeasible. Unless we are to simply give up on describing and understanding biodiversity, there needs to be some way to separate and describe units we believe are candidates species. With the biodiversity crisis, we cannot wait for every or even most units to be verified. Operational concepts provide a framework for describing species that the Biological Species concept could not. Homeostatic Property Cluster theory provides basis for species in asexual organisms like Eubacteria and Archaea.
So I remain a pluralist. A scientific method should make the world LESS confusing and not more so. Rejecting the reality of species or retaining only one species concept means that only very little of the diversity on this planet will make sense. And even if species are just arbitrary human conceptualizations making discrete compartmentalizations of continuous diversity, well, how else would you suggest making any sense of it? A good scientist knows that the best way to tackle a problem is to break it down into workable pieces.
The Biological Species concept by Ernst Mayr (members of metapopulations that actually or potentially interbreed) works quite well for large animals that undergo only sexual reproduction. Such organisms can be easily observed for discrete interbreeding over time. But what about those populations that show discrete yet sympatric behaviors and habits in the field yet interbreed easily in the laboratory. Would these be considered species? Do these actually offer discrete units? Under the Ecological Species concept (isolated phenetic clusters of individuals sharing a particular niche) they would.
This is all well and good for laboratory animals. But how about those organisms that don't easily take well to experimentation? How about asexual animals, where breeding doesn't occur, or those organisms (like plants) that easily hybridize? Do we once again scrap "species"?
And yet, there are other concepts we can use (a good list is in the book Speciation - Coyn and Orr) that do not rely on a strict and exacting understanding of the direct mechanisms or processes to obtain understanding. In systematics, we aim to describe and understand biodiversity. The title "species" is used in multiple ways to best describe different organisms. Of course we would love to test the biology and ecology of every candidate species on this planet; almost always this is currently impossible or unfeasible. Unless we are to simply give up on describing and understanding biodiversity, there needs to be some way to separate and describe units we believe are candidates species. With the biodiversity crisis, we cannot wait for every or even most units to be verified. Operational concepts provide a framework for describing species that the Biological Species concept could not. Homeostatic Property Cluster theory provides basis for species in asexual organisms like Eubacteria and Archaea.
So I remain a pluralist. A scientific method should make the world LESS confusing and not more so. Rejecting the reality of species or retaining only one species concept means that only very little of the diversity on this planet will make sense. And even if species are just arbitrary human conceptualizations making discrete compartmentalizations of continuous diversity, well, how else would you suggest making any sense of it? A good scientist knows that the best way to tackle a problem is to break it down into workable pieces.
Friday, November 19, 2010
A question pertaining to selection vs. inheritance.
Hypothetical situation:
If there was a community of organisms which for all purposes had infinite longevity (ie they would not die of old age), and zero reproduction (ie no new cohorts), would selection still occur?
If there was a community of organisms which for all purposes had infinite longevity (ie they would not die of old age), and zero reproduction (ie no new cohorts), would selection still occur?
Wednesday, November 17, 2010
Clearing insects: Lactic Acid vs. KOH
Using Google searches, I have found little information on clearing of insects to observe their structure. What information that is available does not relate the benefits and detriments of various clearing agents. Here I will summarize these issues, especially to show the benefit of using lactic acid contrasted with hydroxides.
Potassium hydroxide (KOH: also known as caustic potash or lye) is a strongly basic chemical that has historically been most often used for insect clearing. It is stored as a solid and dissolved in distilled water for use, usually as a 10% solution. When heated, soft tissue is quickly destroyed as well as lightly sclerotized cuticle. Continued exposure to KOH will cause the chitonous matrix of cuticle to become sticky and soft, and a specimen left in KOH for extended periods will become clear and dissolve into invisibility. The destructive process can be slowed down by clearing in room temperature solution rather than heated, but a specimen exposed to KOH cannot ever be neutralized completely. Many old slides of specimens, including holotypes, today seem to contain nothing due to the long term caustic action of this chemical. In addition, once a specimen is placed in glycerin for viewing, it cannot be returned to KOH for more clearing.
Sodium hydroxide (NaOH) has similarly been used in clearing. It has the same properties of KOH, except it is reported that it is less caustic on weakly sclerotized tissue and membrane (Gurney et al. 1964).
Lactic acid (2-hydroxypropanoic acid) is a weakly acidic chemical now coming into favor as a clearing agent. It is stored as a fluid, usually at 80% concentration, and can be used directly. Unlike the previous hydroxides, lactic acid will not indefinitely clear material, even when heated. Membraneous and weakly sclerotized structures are retained while muscle and fat are dissolved. Lactic acid also will cause membraneous structures to expand under heat, which can make the treatment useful for eversing an aedeagus stuck within a phallocrypt. In addition, the specimen can be passed through glycerin and returned to the clearing solution if needed.
I have begun using lactic acid for all my clearing. The benefits are obvious, with some precautions. First, since heating causes expansion of tissue, sometimes specimens will explode. Therefore, only low circulating heat rather than boiling should be used. Second, while weakly sclerotized structures will be retained, intersegmental membrane is more likely to be broken over time. Gentle care when using probes and forceps will insure the parts stay connected.
Reference:
Gurney, A. B.; Kramer, J. P.; Steyskal, G. C. 1964. Some techniques for the
preparation, study, and storage in microvials of insect genitalia. Annals of the
Entomological Society of America 57:240-242.
Potassium hydroxide (KOH: also known as caustic potash or lye) is a strongly basic chemical that has historically been most often used for insect clearing. It is stored as a solid and dissolved in distilled water for use, usually as a 10% solution. When heated, soft tissue is quickly destroyed as well as lightly sclerotized cuticle. Continued exposure to KOH will cause the chitonous matrix of cuticle to become sticky and soft, and a specimen left in KOH for extended periods will become clear and dissolve into invisibility. The destructive process can be slowed down by clearing in room temperature solution rather than heated, but a specimen exposed to KOH cannot ever be neutralized completely. Many old slides of specimens, including holotypes, today seem to contain nothing due to the long term caustic action of this chemical. In addition, once a specimen is placed in glycerin for viewing, it cannot be returned to KOH for more clearing.
Sodium hydroxide (NaOH) has similarly been used in clearing. It has the same properties of KOH, except it is reported that it is less caustic on weakly sclerotized tissue and membrane (Gurney et al. 1964).
Lactic acid (2-hydroxypropanoic acid) is a weakly acidic chemical now coming into favor as a clearing agent. It is stored as a fluid, usually at 80% concentration, and can be used directly. Unlike the previous hydroxides, lactic acid will not indefinitely clear material, even when heated. Membraneous and weakly sclerotized structures are retained while muscle and fat are dissolved. Lactic acid also will cause membraneous structures to expand under heat, which can make the treatment useful for eversing an aedeagus stuck within a phallocrypt. In addition, the specimen can be passed through glycerin and returned to the clearing solution if needed.
I have begun using lactic acid for all my clearing. The benefits are obvious, with some precautions. First, since heating causes expansion of tissue, sometimes specimens will explode. Therefore, only low circulating heat rather than boiling should be used. Second, while weakly sclerotized structures will be retained, intersegmental membrane is more likely to be broken over time. Gentle care when using probes and forceps will insure the parts stay connected.
Reference:
Gurney, A. B.; Kramer, J. P.; Steyskal, G. C. 1964. Some techniques for the
preparation, study, and storage in microvials of insect genitalia. Annals of the
Entomological Society of America 57:240-242.
Tuesday, November 16, 2010
Criticisms of Encyclopedia of Life.
When I first heard E.O. Wilson's TED prize wish (see: http://www.youtube.com/watch?v=e-txR1WSPBs) I too applauded the endevour to create an online "encyclopedia" with a webpage for every species, where research could be uploaded and shared openly with the world. Such a resource would be to the benefit of every person. As a comparative biologist I appreciate synthetic resources of information on life, whereas most species descriptions now are spread far and wide in the literature.
However, after two years the Encyclopedia of Life database is no closer to it's ten year goal. If there are 1.8 described species, then contributors must write 500 species pages a day! This is hardly occurring. Even the so called exemplar pages have little information, mostly taken from other web pages such as Wikipedia. It seems the database is mostly a vehicular framework for flicker photos of wildlife, from what little is available. And even that, the mere task of uploading photographs, is difficult and requires a Flicker account.
It is not only that there are few people uploading information, it's also that each piece requires curation from an "expert", meaning it takes even longer for a page to be complete.
I cannot help but be cynical, even with Wilson giving his full support. People just don't have the time to provide to such a project to make it useful. I hope I am wrong.
However, after two years the Encyclopedia of Life database is no closer to it's ten year goal. If there are 1.8 described species, then contributors must write 500 species pages a day! This is hardly occurring. Even the so called exemplar pages have little information, mostly taken from other web pages such as Wikipedia. It seems the database is mostly a vehicular framework for flicker photos of wildlife, from what little is available. And even that, the mere task of uploading photographs, is difficult and requires a Flicker account.
It is not only that there are few people uploading information, it's also that each piece requires curation from an "expert", meaning it takes even longer for a page to be complete.
I cannot help but be cynical, even with Wilson giving his full support. People just don't have the time to provide to such a project to make it useful. I hope I am wrong.
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